CaFE: a tool for binding affinity prediction using end-point free energy methods.

PubMed

Liu, Hui; Hou, Tingjun

2016-07-15

Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. tingjunhou@zju.edu.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of an affinity binding model.

PubMed

Zhang, Lin; Sun, Yan

2014-04-29

Platelet adhesion on a collagen surface through integrin α2β1 has been proven to be significant for the formation of arterial thrombus. However, the molecular determinants mediating the integrin-collagen complex remain unclear. In the present study, the dynamics of integrin-collagen binding and molecular interactions were investigated using molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis. Hydrophobic interaction is identified as the major driving force for the formation of the integrin-collagen complex. On the basis of the MD simulation and MM-PBSA results, an affinity binding model (ABM) of integrin for collagen is constructed; it is composed of five residues, including Y157, N154, S155, R288, and L220. The ABM has been proven to capture the major binding motif contributing 84.8% of the total binding free energy. On the basis of the ABM, we expect to establish a biomimetic design strategy of platelet adhesion inhibitors, which would be beneficial for the development of potent peptide-based drugs for thrombotic diseases.

Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β.

PubMed

Kumar, Akhil; Srivastava, Gaurava; Negi, Arvind S; Sharma, Ashok

2018-01-19

BACE-1 and GSK-3β both are potential therapeutic drug targets for Alzheimer's disease. Recently, both these targets received attention for designing dual inhibitors. Till now only two scaffolds (triazinone and curcumin) derivatives have been reported as BACE-1 and GSK-3β dual inhibitors. In our previous work, we have reported first in class dual inhibitor for BACE-1 and GSK-3β. In this study, we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3β through docking, molecular dynamics, binding energy (MM-PBSA). These computational methods were performed to estimate the binding affinity of naphthofuran derivatives towards the BACE-1 and GSK-3β. In the docking results, two derivatives (NS7 and NS9) showed better binding affinity as compared to previously reported inhibitors. Hydrogen bond occupancy of NS7 and NS9 generated from MD trajectories showed good interaction with the flap residues Gln73, Thr72 of BACE-1 and Arg141, Thr138 residues of GSK-3β. MM-PBSA and energy decomposition per residue revealed different components of binding energy and relative importance of amino acid involved in binding. The results showed that the binding of inhibitors was majorly governed by the hydrophobic interactions and suggesting that hydrophobic interactions might be the key to design dual inhibitors for BACE1-1 and GSK-3β. Distance between important pair of amino acid residues indicated that BACE-1 and GSK-3β adopt closed conformation and become inactive after ligand binding. The results suggested that naphthofuran derivatives might act as dual inhibitor against BACE-1 and GSK-3β.

The protein-protein interactions between SMPI and thermolysin studied by molecular dynamics and MM/PBSA calculations.

PubMed

Adekoya, Olayiwola A; Willassen, Nils-Peder; Sylte, Ingebrigt

2005-04-01

Thermolysin is a zinc-metalloendopeptidase secreted by the gram-positive thermophilic bacterium Bacillus thermoproteolyticus. Thermolysin belongs to the gluzinicin family of enzymes, which is selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI). Very little is known about the interaction between SMPI and thermolysin. Knowledge about the protein-protein interactions is very important for designing new thermolysin inhibitors with possible industrial or pharmaceutical applications. In the present study, two binding modes between SMPI and thermolysin were studied by 2300 picoseconds (ps) of comparative molecular dynamics (MD) simulations and calculation of the free energy of binding using the molecular mechanics-Poisson-Boltmann surface area (MM/PBSA) method. One of the positions, the 'horizontal arrow head docking' (HAHD) was similar to the previously proposed binding mode by Tate et al. (Tate, S., Ohno, A., Seeram, S. S., Hiraga, K., Oda, K., and Kainosho, M. J. Mol. Biol. 282, 435-446 (1998)). The other position, the 'vertical arrow head docking' (VAHD) was obtained by a manual docking guided by the shape and charge distribution of SMPI and the binding pocket of thermolysin. The calculations showed that SMPI had stronger interactions with thermolysin in the VAHD than in the HAHD complex, and the VAHD complex was considered more realistic than the HAHD complex. SMPI interacted with thermolysin not only at the active site but had auxiliary binding sites contributing to proper interactions. The VAHD complex can be used for designing small molecule inhibitors mimicking the SMPI-thermolysin binding interfaces.

Statistical analysis of EGFR structures' performance in virtual screening

NASA Astrophysics Data System (ADS)

Li, Yan; Li, Xiang; Dong, Zigang

2015-11-01

In this work the ability of EGFR structures to distinguish true inhibitors from decoys in docking and MM-PBSA is assessed by statistical procedures. The docking performance depends critically on the receptor conformation and bound state. The enrichment of known inhibitors is well correlated with the difference between EGFR structures rather than the bound-ligand property. The optimal structures for virtual screening can be selected based purely on the complex information. And the mixed combination of distinct EGFR conformations is recommended for ensemble docking. In MM-PBSA, a variety of EGFR structures have identically good performance in the scoring and ranking of known inhibitors, indicating that the choice of the receptor structure has little effect on the screening.

Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N.

PubMed

Vorontsov, Ivan I; Miyashita, Osamu

2011-04-30

Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods. Copyright © 2010 Wiley Periodicals, Inc.

Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis.

PubMed

Sang, Peng; Xie, Yue-Hui; Li, Lin-Hua; Ye, Yu-Jia; Hu, Wei; Wang, Jing; Wan, Wen; Li, Rui; Li, Long-Jun; Ma, Lin-Ling; Li, Zhi; Liu, Shu-Qun; Meng, Zhao-Hui

2017-04-01

Pyrroline-5-carboxylate reductase (P5CR), an enzyme with conserved housekeeping roles, is involved in the etiology of cutis laxa. While previous work has shown that the R119G point mutation in the P5CR protein is involved, the structural mechanism behind the pathology remains to be elucidated. In order to probe the role of the R119G mutation in cutis laxa, we performed molecular dynamics (MD) simulations, essential dynamics (ED) analysis, and Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on wild type (WT) and mutant P5CR-NAD complex. These MD simulations and ED analyses suggest that the R119G mutation decreases the flexibility of P5CR, specifically in the substrate binding pocket, which could decrease the kinetics of the cofactor entrance and egress. Furthermore, the MM-PBSA calculations suggest the R119G mutant has a lower cofactor binding affinity for NAD than WT. Our study provides insight into the possible role of the R119G mutation during interactions between P5CR and NAD, thus bettering our understanding of how the mutation promotes cutis laxa. Copyright © 2017 Elsevier Ltd. All rights reserved.

Poly(lactide)-g-poly(butylene succinate-co-adipate) with High Crystallization Capacity and Migration Resistance

PubMed Central

Yang, Xi; Xu, Huan; Odelius, Karin; Hakkarainen, Minna

2016-01-01

Plasticized polylactide (PLA) with increased crystallization ability and prolonged life-span in practical applications due to the minimal plasticizer migration was prepared. Branched plasticized PLA was successfully obtained by coupling poly(butylene succinate-co-adipate) (PBSA) to crotonic acid (CA) functionalized PLA. The plasticization behavior of PBSA coupled PLA (PLA-CA-PBSA) and its counterpart PBSA blended PLA (PLA/PBSA) were fully elucidated. For both PLA-CA-PBSA and PLA/PBSA, a decrease of Tg to around room temperature and an increase in the elongation at break of PLA from 14% to 165% and 460%, respectively, were determined. The crystallinity was increased from 2.1% to 8.4% for PLA/PBSA and even more, to 10.6%, for PLA-CA-PBSA. Due to the inherent poor miscibility between the PBSA and PLA, phase separation occurred in the blend, while PLA-CA-PBSA showed no phase separation which, together with the higher crystallinity, led to better oxygen barrier properties compared to neat PLA and PLA/PBSA. A higher resistance to migration during hydrolytic degradation for the PLA-CA-PBSA compared to the PLA/PBSA indicated that the plasticization effect of PBSA in the coupled material would be retained for a longer time period. PMID:28773437

Identification of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations

PubMed Central

Liu, Jianling; Liu, Mengmeng; Yao, Yao; Wang, Jinan; Li, Yan; Li, Guohui; Wang, Yonghua

2012-01-01

Chitinolytic β-N-acetyl-d-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-d-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 106 compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand–receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and π–π stacking interactions with the ligands. Finally, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides. PMID:22605995

GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanning

NASA Astrophysics Data System (ADS)

Paissoni, C.; Spiliotopoulos, D.; Musco, G.; Spitaleri, A.

2014-11-01

GMXPBSA 2.0 is a user-friendly suite of Bash/Perl scripts for streamlining MM/PBSA calculations on structural ensembles derived from GROMACS trajectories, to automatically calculate binding free energies for protein-protein or ligand-protein complexes. GMXPBSA 2.0 is flexible and can easily be customized to specific needs. Additionally, it performs computational alanine scanning (CAS) to study the effects of ligand and/or receptor alanine mutations on the free energy of binding. Calculations require only for protein-protein or protein-ligand MD simulations. GMXPBSA 2.0 performs different comparative analysis, including a posteriori generation of alanine mutants of the wild-type complex, calculation of the binding free energy values of the mutant complexes and comparison of the results with the wild-type system. Moreover, it compares the binding free energy of different complexes trajectories, allowing the study the effects of non-alanine mutations, post-translational modifications or unnatural amino acids on the binding free energy of the system under investigation. Finally, it can calculate and rank relative affinity to the same receptor utilizing MD simulations of proteins in complex with different ligands. In order to dissect the different MM/PBSA energy contributions, including molecular mechanic (MM), electrostatic contribution to solvation (PB) and nonpolar contribution to solvation (SA), the tool combines two freely available programs: the MD simulations software GROMACS and the Poisson-Boltzmann equation solver APBS. All the calculations can be performed in single or distributed automatic fashion on a cluster facility in order to increase the calculation by dividing frames across the available processors. The program is freely available under the GPL license.

Calculation of protein-ligand binding affinities.

PubMed

Gilson, Michael K; Zhou, Huan-Xiang

2007-01-01

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.

Degradation and mineralization of organic UV absorber compound 2-phenylbenzimidazole-5-sulfonic acid (PBSA) using UV-254nm/H2O2.

PubMed

Abdelraheem, Wael H M; He, Xuexiang; Duan, Xiaodi; Dionysiou, Dionysios D

2015-01-23

Various studies have revealed the non-biodegradable and endocrine disrupting properties of sulfonated organic UV absorbers, directing people's attention toward their risks on ecological and human health and hence their removal from water. In this study, UV-254nm/H2O2 advanced oxidation process (AOP) was investigated for degrading a model UV absorber compound 2-phenylbenzimidazole-5-sulfonic acid (PBSA) and a structurally similar compound 1H-benzimidazole-2-sulfonic acid (BSA), with a specific focus on their mineralization. At 4.0mM [H2O2]0, a complete removal of 40.0μM parent PBSA and 25% decrease in TOC were achieved with 190min of UV irradiation; SO4(2-) was formed and reached its maximum level while the release of nitrogen as NH4(+) was much lower (around 50%) at 190min. Sulfate removal was strongly enhanced by increasing [H2O2]0 in the range of 0-4.0mM, with slight inhibition in 4.0-12.0mM. Faster and earlier ammonia formation was observed at higher [H2O2]0. The presence of Br(-) slowed down the degradation and mineralization of both compounds while a negligible effect on the degradation was observed in the presence of Cl(-). Our study provides important technical and fundamental results on the HO based degradation and mineralization of SO3H and N-containing UV absorber compounds. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular insight into γ-γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC)

NASA Astrophysics Data System (ADS)

Suri, Charu; Hendrickson, Triscia W.; Joshi, Harish C.; Naik, Pradeep Kumar

2014-09-01

γ-tubulin is essential for the nucleation and organization of mitotic microtubules in dividing cells. It is localized at the microtubule organizing centers and mitotic spindle fibres. The most well accepted hypothesis for the initiation of microtubule polymerization is that α/β-tubulin dimers add onto a γ-tubulin ring complex (γTuRC), in which adjacent γ-tubulin subunits bind to the underlying non-tubulin components of the γTuRC. This template thus determines the resulting microtubule lattice. In this study we use molecular modelling and molecular dynamics simulations, combined with computational MM-PBSA/MM-GBSA methods, to determine the extent of the lateral atomic interaction between two adjacent γ-tubulins within the γTuRC. To do this we simulated a γ-γ homodimer for 10 ns and calculated the ensemble average of binding free energies of -107.76 kcal/mol by the MM-PBSA method and of -87.12 kcal/mol by the MM-GBSA method. These highly favourable binding free energy values imply robust lateral interactions between adjacent γ-tubulin subunits in addition to their end-interactions longitudinally with other proteins of γTuRC. Although the functional reconstitution of γ-TuRC subunits and their stepwise in vitro assembly from purified components is not yet feasible, we nevertheless wanted to recognize hotspot amino acids responsible for key γ-γ interactions. Our free energy decomposition data from converting a compendium of amino acid residues identified an array of hotspot amino acids. A subset of such mutants can be expressed in vivo in living yeast. Because γTuRC is important for the growth of yeast, we could test whether this subset of the hotspot mutations support growth of yeast. Consistent with our model, γ-tubulin mutants that fall into our identified hotspot do not support yeast growth.

Controlling the biodegradability of poly(butylene succinate-co-butylene adipate) (PBSA) by solvents used in the dried-gel process

NASA Astrophysics Data System (ADS)

Yamazaki, Hana; Kamitabira, Saya; Maeda, Tomoki; Hotta, Atsushi

Considering an environmentally friendly material, poly(butylene succinate-co-butylene adipate)(PBSA) is one of the attractive biodegradable plastics that can be eventually degraded into H2O and CO2 by neighboring water molecules and microorganisms after the disposal. In order to expand the application of PBSA, the precise control of the biodegradability of PBSA is necessary. In this study, the dried-gel process was introduced to control the biodegradability of PBSA. The dried PBSA gels were prepared by using three different solvents (toluene, cyclohexanone, and o-dichlorobenzene). The scanning electron microscopy (SEM) micrographs revealed that the PBSA prepared by toluene had smaller spherocrystals than the other PBSA dried-gels prepared by cyclohexanone or o-dichlorobenzene. The biodegradability testing by immersing the three types of PBSA in NaOH aq. showed that the percentage of the weight loss of the PBSA produced by toluene was the highest. The results indicated that the microstructures of PBSA could be controlled by changing solvents during the gel preparations, and that the biodegradability of PBSA could therefore be efficiently modified by changing solvents. This work was supported by a Grant-in-Aid for Scientific Research (A) (No. 15H02298 to A.H.) and a Grant-in-Aid for Research Activity Start-up (No.15H06586 to T.M.) from JSPS: KAKENHI\\x9D.

Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations.

PubMed

Hu, Guodong; Ma, Aijing; Wang, Jihua

2017-04-24

Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches. The snapshots used in MM-PBSA calculation were extracted from ten 50 ns MD simulation trajectories for each complex. These free energy results are in consistent with the experimental data and rationalize the selectivity of the riboswitches for different ligands. In particular, it is found that the loss in binding free energy upon mutation is mainly electrostatic in guanine (GUA) and riboswitch complex. Furthermore, new hydrogen bonds are found in mutated complexes. To reveal the conformational properties of guanine riboswitch, we performed a total of 6 μs MD simulations in both the presence and the absence of the ligand GUA. The MD simulations suggest that the conformation of guanine riboswitch depends on the distance of two groups in the binding pocket of ligand. The conformation is in a close conformation when U51-A52 is close to C74-U75.

Biodegradability of poly(butylene succinate-co-butylene adipate) (PBSA) controlled by temperature during the dried-gel process

NASA Astrophysics Data System (ADS)

Yamazaki, Hana; Maeda, Tomoki; Hotta, Atsushi

Currently there is a growing interest in biodegradable plastics that can be readily degraded into H2O and CO2. Among them, poly(butylene succinate-co-butylene adipate)(PBSA) is one of the mechanically attractive materials that can be biodegraded by surrounding water molecules and microorganisms after the disposal of the plastics. In order to expand the use of PBSA, the proper and effective control of the biodegradability of PBSA should be realized. In this work, the dried-gel process of the PBSA was carefully studied considering the temperature of the process. Three different types of dried PBSA gels were prepared at three different gel-process temperatures. From the biodegradability testing by immersing the PBSA samples in NaOH aq., it was found that the percentage of the weight loss of the PBSA was increased, indicating that the biodegradability was enhanced as the gel preparation temperature became lower. In fact, smaller spherocrystals were observed in PBSA dried at cooler temperature, studied by the scanning electron microscopy (SEM). It was therefore concluded that the microstructures of PBSA could be well controlled by changing the gel preparation temperatures for the precise control of the biodegradability of PBSA. This work was supported by a Grant-in-Aid for Scientific Research (A) (No. 15H02298 to A.H.) and a Grant-in-Aid for Research Activity Start-up (No.15H06586 to T.M.) from JSPS: KAKENHI\\x9D.

Contribution of soil esterase to biodegradation of aliphatic polyester agricultural mulch film in cultivated soils.

PubMed

Yamamoto-Tamura, Kimiko; Hiradate, Syuntaro; Watanabe, Takashi; Koitabashi, Motoo; Sameshima-Yamashita, Yuka; Yarimizu, Tohru; Kitamoto, Hiroko

2015-01-01

The relationship between degradation speed of soil-buried biodegradable polyester film in a farmland and the characteristics of the predominant polyester-degrading soil microorganisms and enzymes were investigated to determine the BP-degrading ability of cultivated soils through characterization of the basal microbial activities and their transition in soils during BP film degradation. Degradation of poly(butylene succinate-co-adipate) (PBSA) film was evaluated in soil samples from different cultivated fields in Japan for 4 weeks. Both the degradation speed of the PBSA film and the esterase activity were found to be correlated with the ratio of colonies that produced clear zone on fungal minimum medium-agarose plate with emulsified PBSA to the total number colonies counted. Time-dependent change in viable counts of the PBSA-degrading fungi and esterase activities were monitored in soils where buried films showed the most and the least degree of degradation. During the degradation of PBSA film, the viable counts of the PBSA-degrading fungi and the esterase activities in soils, which adhered to the PBSA film, increased with time. The soil, where the film was degraded the fastest, recorded large PBSA-degrading fungal population and showed high esterase activity compared with the other soil samples throughout the incubation period. Meanwhile, esterase activity and viable counts of PBSA-degrading fungi were found to be stable in soils without PBSA film. These results suggest that the higher the distribution ratio of native PBSA-degrading fungi in the soil, the faster the film degradation is. This could be due to the rapid accumulation of secreted esterases in these soils.

Inhibition of Mammalian 15-Lipoxygenase by Three Ebselen-like Drugs. A QM/MM and MM/PBSA Comparative Study.

PubMed

Cebrián-Prats, Anna; Rovira, Tiffani; Saura, Patricia; González-Lafont, Àngels; Lluch, José M

2017-12-28

Ebselen is a potent competitive inhibitor of the active form of rabbit 15-lipoxygenase, an enzyme involved in many inflammatory diseases. Light-induced Z-to-E isomerization of the ebselen-like 2-(3-benzylidene)-3-oxo-2,3-dihydrobenzo[b]thiophene-7-carboxylic acid methyl ester (BODTCM) molecule was used to convert the weak (Z)-BOTDCM inhibitor into the (E)-isomer with much higher inhibitory capacity. In this study, the binding modes of ebselen, (E)-BOTDCM and (Z)-BOTDCM, have been analyzed to provide molecular insights on the inhibitory potency of ebselen and on the geometric-isomer specificity of (E)- and (Z)-BOTDCM inhibitors. The inhibitor-enzyme structures obtained from docking and molecular dynamics simulations as well as from QM/MM calculations show that the inhibitor molecules are not coordinated to the nonheme iron in the active site. Thermal motion allows ebselen and (E)-BOTDCM to visit a wide range of the configurational space competing with the polyunsaturated fatty acid for binding at the active site. Both molecules present similar MM/PBSA binding free energies. The energy penalty for the bigger geometric deformation undergone by (E)-BODTCM would explain its lower inhibitor potency. The (Z)-isomer is the weakest inhibitor because thermal motion moves it to a region very far from the first coordination sphere of Fe, where it could not compete with the fatty acid substrate.

Structure and Barrier Properties of Multinanolayered Biodegradable PLA/PBSA Films: Confinement Effect via Forced Assembly Coextrusion.

PubMed

Messin, Tiphaine; Follain, Nadège; Guinault, Alain; Sollogoub, Cyrille; Gaucher, Valérie; Delpouve, Nicolas; Marais, Stéphane

2017-08-30

Multilayer coextrusion processing was applied to produce 2049-layer film of poly(butylene succinate-co-butylene adipate) (PBSA) confined against poly(lactic acid) (PLA) using forced assembly, where the PBSA layer thickness was about 60 nm. This unique technology allowed to process semicrystalline PBSA as confined polymer and amorphous PLA as confining polymer in a continuous manner. The continuity of PBSA layers within the 80/20 wt % PLA/PBSA layered films was clearly evidenced by atomic force microscopy (AFM). Similar thermal events to the reference films were revealed by thermal studies; indicating no diffusion of polymers during the melt-processing. Mechanical properties were measured for the multilayer film and the obtained results were those expected considering the fraction of each polymer, revealing the absence of delamination in the PLA/PBSA multinanolayer film. The confinement effect induced by PLA led to a slight orientation of the crystals, an increase of the rigid amorphous fraction (RAF) in PBSA with a densification of this fraction without changing film crystallinity. These structural changes allowed to strongly improve the water vapor and gas barrier properties of the PBSA layer into the multilayer film up to two decades in the case of CO 2 gas. By confining the PBSA structure in very thin and continuous layers, it was then possible to improve the barrier performances of a biodegradable system and the resulting barrier properties were successfully correlated to the effect of confinement on the microstructure and the chain segment mobility of the amorphous phase. Such investigation on these multinanolayers of PLA/PBSA with the aim of evidencing relationships between microstructure implying RAF and barrier performances has never been performed yet. Besides, gas and water permeation results have shown that the barrier improvement obtained from the multilayer was mainly due to the reduction of solubility linked to the reduction of the free volume while the tortuosity effect, as usually expected, was not really observed. This work brings new insights in the field of physicochemical behaviors of new multilayer films made of biodegradable polyesters but also in interfacial processes due to the confinement effect induced in these multinanolayer structures obtained by the forced assembly coextrusion. This original coextrusion process was a very advantageous technique to produce eco-friendly materials with functional properties without the help of tie layer, additives, solvents, surface treatments, or inorganic fillers.

GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning

NASA Astrophysics Data System (ADS)

Paissoni, C.; Spiliotopoulos, D.; Musco, G.; Spitaleri, A.

2015-01-01

GMXPBSA 2.1 is a user-friendly suite of Bash/Perl scripts for streamlining MM/PBSA calculations on structural ensembles derived from GROMACS trajectories, to automatically calculate binding free energies for protein-protein or ligand-protein complexes [R.T. Bradshaw et al., Protein Eng. Des. Sel. 24 (2011) 197-207]. GMXPBSA 2.1 is flexible and can easily be customized to specific needs and it is an improvement of the previous GMXPBSA 2.0 [C. Paissoni et al., Comput. Phys. Commun. (2014), 185, 2920-2929]. Additionally, it performs computational alanine scanning (CAS) to study the effects of ligand and/or receptor alanine mutations on the free energy of binding. Calculations require only for protein-protein or protein-ligand MD simulations. GMXPBSA 2.1 performs different comparative analyses, including a posteriori generation of alanine mutants of the wild-type complex, calculation of the binding free energy values of the mutant complexes and comparison of the results with the wild-type system. Moreover, it compares the binding free energy of different complex trajectories, allowing the study of the effects of non-alanine mutations, post-translational modifications or unnatural amino acids on the binding free energy of the system under investigation. Finally, it can calculate and rank relative affinity to the same receptor utilizing MD simulations of proteins in complex with different ligands. In order to dissect the different MM/PBSA energy contributions, including molecular mechanic (MM), electrostatic contribution to solvation (PB) and nonpolar contribution to solvation (SA), the tool combines two freely available programs: the MD simulations software GROMACS [S. Pronk et al., Bioinformatics 29 (2013) 845-854] and the Poisson-Boltzmann equation solver APBS [N.A. Baker et al., Proc. Natl. Acad. Sci. U.S.A 98 (2001) 10037-10041]. All the calculations can be performed in single or distributed automatic fashion on a cluster facility in order to increase the calculation by dividing frames across the available processors. This new version with respect to our previously published GMXPBSA 2.0 fixes some problem and allows additional kind of calculations, such as CAS on single protein in order to individuate the hot-spots, more custom options to perform APBS calculations, improvements of speed calculation of APBS (precF set to 0), possibility to work with multichain systems (see Summary of revisions for more details). The program is freely available under the GPL license.

GPU-enabled molecular dynamics simulations of ankyrin kinase complex

NASA Astrophysics Data System (ADS)

Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

2014-10-01

The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach.

PubMed

Anbarasu, K; Jayanthi, S

2018-05-01

Human lemur tyrosine kinase-3 (LMTK3) is primarily involved in regulation of estrogen receptor-α (ERα) by phosphorylation activity. LMTK3 acts as key biomarker for ERα positive breast cancer and identified as novel drug target for breast cancer. Due to the absence of experimental reports, the computational approach has been followed to screen LMTK3 inhibitors from natural product curcumin derivatives based on rational inhibitor design. The initial virtual screening and re-docking resulted in identification of top three leads with favorable binding energy and strong interactions in critical residues of ATP-binding cavity. ADME prediction confirmed the pharmacological activity of the leads with various properties. The stability and binding affinity of leads were well refined in dynamic system from 25 ns MD simulations. The behavior of protein motion towards closure of ATP-binding cavity was evaluated based on eigenvectors by PCA. In addition, MM/PBSA calculations also confirmed the relative binding free energy of LMTK3-lead complexes in favor of the effective binding. From our study, novel LMTK3 inhibitors tetrahydrocurcumin, curcumin 4,4'-diacetate, and demethoxycurcumin have been proposed with inhibition mechanism. Further experimental evaluation on reported lead candidates might prove its role in breast cancer therapeutics.

Personal care products in surface, ground and wastewater of a complex aquifer system, a potential planning tool for contemporary urban settings.

PubMed

Palmiotto, Marinella; Castiglioni, Sara; Zuccato, Ettore; Manenti, Angela; Riva, Francesco; Davoli, Enrico

2018-05-15

The use and discharge of personal care products (PCPs) result in their presence in the aquatic environment. This study investigates the occurrence and fate of some PCPs in wastewater, surface and groundwater in an urbanized area in the North of Italy. We investigated four UV filters: phenylbenzimidazole sulfonic acid (PBSA), benzophenone-3 (BP3), benzophenone-4 (BP4) and 4 methyl-benzilidine-camphor (4-MBC), and two antibacterial agents: triclosan (TCS) and triclocarban (TCC). BP3, BP4 and PBSA were detected in all WWTPs and concentrations ranged 27-822 ng/L (BP4 > PBSA > BP3). TCS was the only disinfectant detected in wastewater and ranged from <0.2 to 1690 ng/L. Removal efficiencies in WWTPs were good for BP3 and TCS (80-100%), but were quite low for PBSA and BP4 (0-40%). Consequently, PBSA and BP4 were the most abundant substances in surface water, detected up to 560.4 ng/L. TCS was also found in surface water (<0.2-161.0 ng/L). Only PBSA and TCS were found in untreated groundwater, and levels were higher in wells close to rivers, suggesting the contribution of surface water to this contamination, but not from the catchment and the sewer networks. These PCPs were confirmed to be ubiquitous in all the aquifers sampled, being reliable descriptors of human presence. The use of these data as direct indicators of pollutant's loads for the aquifers deriving from human presence could provide early warnings on chemicals that are continuously introduced into surface waters, identifying dynamic urban trends and suggesting paths for the planning in urban regions and for appropriate investment and rehabilitation strategies of infrastructure. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nanophotonic biosensor for space exploration (PBSA instrument)

NASA Astrophysics Data System (ADS)

Pantoja, S.; Parro, V.; Nestler, J.; Geidel, S.; Martins, R.; Cuesta, F.; Elvira, J. G.; Sousa, A.

2017-11-01

One of the biggest challenges of Astrobiology is the search for clear signs of present or past life on other planetary bodies. Thus, this poster will describe the project "Photonic Biosensor for Space Application" (PBSA, www.pbsa-fp7.eu) founded by the Directorate-General for Enterprise and Industry (DG ENTR) within the European Commission and managed by the Unit S2 (Space Research) of the Research European Agency (REA).

Properties of a bacterium which degrades solid poly(tetramethylene succinate)-co-adipate, a biodegradable plastic.

PubMed

Uchida, H; Nakajima-Kambe, T; Shigeno-Akutsu, Y; Nomura, N; Tokiwa, Y; Nakahara, T

2000-08-01

Various microorganisms were screened for their ability to degrade poly(tetramethylene succinate)-co-(tetramethylene adipate) (PBSA). Strain BS-3, which was newly isolated from a soil sample, was selected as the best strain. From taxonomical studies, the strain was tentatively ascribed to belong to the genus Acidovorax, most probably to the species A. delafieldii. Strain BS-3 could degrade both solid and emulsified PBSA, and also emulsified poly(tetramethylene succinate). During the degradation, a lipase activity was observed in the culture broth. This lipase activity was induced more strongly by PBSA than by tributyrin or triolein which are typical substrates of lipase. These observations strongly suggest that this lipase was involved in the PBSA biodegradation in strain BS-3.

Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.

PubMed

Spiliotopoulos, Dimitrios; Spitaleri, Andrea; Musco, Giovanna

2012-01-01

PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0). As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1) in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations

NASA Astrophysics Data System (ADS)

Tzoupis, Haralambos; Leonis, Georgios; Durdagi, Serdar; Mouchlis, Varnavas; Mavromoustakos, Thomas; Papadopoulos, Manthos G.

2011-10-01

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein-ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling.

PubMed

Tan, Jianjun; Yuan, Hongling; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin

2016-04-01

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

FESetup: Automating Setup for Alchemical Free Energy Simulations.

PubMed

Loeffler, Hannes H; Michel, Julien; Woods, Christopher

2015-12-28

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

Deep insights into the mode of ATP-binding mechanism in Zebrafish cyclin-dependent protein kinase-like 1 (zCDKL1): A molecular dynamics approach.

PubMed

Rout, Ajaya Kumar; Dehury, Budheswar; Maharana, Jitendra; Nayak, Chirasmita; Baisvar, Vishwamitra Singh; Behera, Bijay Kumar; Das, Basanta Kumar

2018-05-01

In eukaryotes, the serine/threonine kinases (STKs) belonging to cyclin-dependent protein kinases (CDKs) play significant role in control of cell division and curb transcription in response to several extra and intra-cellular signals indispensable for enzymatic activity. The zebrafish cyclin-dependent protein kinase-like 1 protein (zCDKL1) shares a high degree of sequence and structural similarity with mammalian orthologs and express in brain, ovary, testis, and low levels in other tissues. Regardless of its importance in the developmental process, the structure, function and mode of ATP recognition have not been investigated yet due to lack of experimental data. Henceforth, to gain atomistic insights in to the structural dynamics and mode of ATP binding, a series of computational techniques involving theoretical modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energies were employed. The modeled bi-lobed zCDKL1 shares a high degree of secondary structure topology with human orthologs where ATP prefers to lie in the central cavity of the bi-lobed catalytic domain enclosed by strong hydrogen bonding, electrostatic and hydrophobic contacts. Long range MD simulation portrayed that catalytic domain of zCDKL1 to be highly rigid in nature as compared to the complex (zCDKL1-ATP) form. Comparative analysis with its orthologs revealed that conserved amino acids i.e., Ile10, Gly11, Glu12, Val18, Arg31, Phe80, Glu 130, Cys143 and Asp144 were crucial for ATP binding mechanism, which needs further investigation for legitimacy. MM/PBSA method revealed that van der Waals, electrostatic and polar solvation energy mostly contributes towards negative free energy. The implications of ATP binding mechanism inferred through these structural bioinformatics approaches will help in understanding the catalytic mechanisms of important STKs in eukaryotic system. Copyright © 2018. Published by Elsevier Inc.

Molecular Determinants of Epidermal Growth Factor Binding: A Molecular Dynamics Study

PubMed Central

Sanders, Jeffrey M.; Wampole, Matthew E.; Thakur, Mathew L.; Wickstrom, Eric

2013-01-01

The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF ligands or the receptor itself. PMID:23382875

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Promoting fertilizer use via controlled release of a bacteria-encapsulated film bag.

PubMed

Wu, Chin-San

2010-05-26

A phosphate-solubilizing bacterium ( Burkholderia cepacia isolate) encapsulated in maleic anhydride (MA) grafted onto poly(butylene succinate adipate) (PBSA) and then combined with starch as film bag material (PBSA-g-MA/starch) incubated in a saline solution required approximately 20 days to deplete the starch in the film bags. Thereafter, the cell concentration in the saline solution increased significantly because of the release of cells from the severely destroyed film bags and also their growth by use of depolymerized PBSA-g-MA fragments as a substrate. The incubation proceeded for 60 days, by which time the PBSA-g-MA/starch composite had suffered a >80% weight loss. For practical application, effectiveness of the above-mentioned film bags was demonstrated because it could improve the absorbability of a fertilizer for plants and promote the growth of plants. As a result, it can avoid the accumulation of the phosphate in excess fertilizer that lead to the phenomenon of poor soils. These results demonstrate that PBSA-g-MA/starch can be used to encapsulate cells of an indigenous phosphate-solubilizing bacterium ( B. cepacia isolate) to form a controlled release of bacteria-encapsulated film bag (BEFB). The B. cepacia isolate was able to degrade the film bags material, causing cell release. Biodegradability of the film bags depended upon the type of material used, because the PBSA film bags were also degraded but to a lesser degree. The addition of starch made the film bags more biodegradable. The decrease in intrinsic viscosity was also higher for the starch composite, suggesting a strong connection between the biodegradability and these characteristics. The results suggest that the release of fertilizer-promoted bacteria might be controllable via a suitable film bag material formulation. In addition, this work adopted live bacteria to promote the absorption of phosphate, which is superior to the phosphate used in the traditional way.

Computational search for aflatoxin binding proteins

NASA Astrophysics Data System (ADS)

Wang, Ying; Liu, Jinfeng; Zhang, Lujia; He, Xiao; Zhang, John Z. H.

2017-10-01

Aflatoxin is one of the mycotoxins that contaminate various food products. Among various aflatoxin types (B1, B2, G1, G2 and M1), aflatoxin B1 is the most important and the most toxic one. In this study, through computational screening, we found that several proteins may bind specifically with different type of aflatoxins. Combination of theoretical methods including target fishing, molecular docking, molecular dynamics (MD) simulation, MM/PBSA calculation were utilized to search for new aflatoxin B1 binding proteins. A recently developed method for calculating entropic contribution to binding free energy called interaction entropy (IE) was employed to compute the binding free energy between the protein and aflatoxin B1. Through comprehensive comparison, three proteins, namely, trihydroxynaphthalene reductase, GSK-3b, and Pim-1 were eventually selected as potent aflatoxin B1 binding proteins. GSK-3b and Pim-1 are drug targets of cancers or neurological diseases. GSK-3b is the strongest binder for aflatoxin B1.

Effects of the Hydroxyl Group on Phenyl Based Ligand/ERRγ Protein Binding

PubMed Central

2015-01-01

Bisphenol-A (4,4′-dihydroxy-2,2-diphenylpropane, BPA, or BPA-A) and its derivatives, when exposed to humans, may affect functions of multiple organs by specific binding to the human estrogen-related receptor γ (ERRγ). We carried out atomistic molecular dynamics (MD) simulations of three ligand compounds including BPA-A, 4-α-cumylphenol (BPA-C), and 2,2-diphenylpropane (BPA-D) binding to the ligand binding domain (LBD) of a human ERRγ to study the structures and energies associated with the binding. We used the implicit Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method to estimate the free energies of binding for the phenyl based compound/ERRγ systems. The addition of hydroxyl groups to the aromatic ring had only a minor effect on binding structures and a significant effect on ligand/protein binding energy in an aqueous solution. Free binding energies of BPA-D to the ERRγ were found to be considerably less than those of BPA-A and BPA-C to the ERRγ. These results are well correlated with those from experiments where no binding affinities were determined in the BPA-D/ERRγ complex. No conformational change was observed for the helix 12 (H-12) of ERRγ upon binding of these compounds preserving an active transcriptional conformation state. PMID:25098505

Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B).

PubMed

Nguyen, Hung; Do, Nhat; Phan, Tuyn; Pham, Tri

2018-02-01

The aim of this study is to use steered molecular dynamics to investigate the dissociation process between IRK and PTP1Bs for wild type and five mutants (consisting of p.D181E, p.D181A, p.Q262A, p.D181A-Y46F, and p.D181A-Q262A). The gained results are observed not only the unbinding mechanism of IRK-PTP1B complexes came from pulling force profile, number of hydrogen bonds, and interaction energy between IRK and PTP1Bs but also described PTP1B's point mutations could variably change its binding affinity towards IRK. Additionally, the binding free energy calculated by Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) is also revealed that electrostatic energy and polar solvation energy mainly made up the binding free energy of PTP1B-IRK complexes.

Insights into the structure-function relationship of brown plant hopper resistance protein, Bph14 of rice plant: a computational structural biology approach.

PubMed

Gupta, Manoj Kumar; Vadde, Ramakrishna; Donde, Ravindra; Gouda, Gayatri; Kumar, Jitendra; Nayak, Subhashree; Jena, Mayabini; Behera, Lambodar

2018-05-02

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.

Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps

NASA Astrophysics Data System (ADS)

Negri, Matthias; Recanatini, Maurizio; Hartmann, Rolf W.

2011-09-01

17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG'-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π-π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.

Studies of the mechanism of selectivity of protein tyrosine phosphatase 1B (PTP1B) bidentate inhibitors using molecular dynamics simulations and free energy calculations.

PubMed

Fang, Lei; Zhang, Huai; Cui, Wei; Ji, Mingjun

2008-10-01

Bidentate inhibitors of protein tyrosine phosphatase 1B (PTP1B) are considered as a group of ideal inhibitors with high binding potential and high selectivity in treating type II diabetes. In this paper, the binding models of five bidentate inhibitors to PTP1B, TCPTP, and SHP-2 were investigated and compared by using molecular dynamics (MD) simulations and free energy calculations. The binding free energies were computed using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology. The calculation results show that the predicted free energies of the complexes are well consistent with the experimental data. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicates that the residues ARG24, ARG254, and GLN262 in the second binding site of PTP1B are essential for the high selectivity of inhibitors. Furthermore, the residue PHE182 close to the active site is also important for the selectivity and the binding affinity of the inhibitors. According to our analysis, it can be concluded that in most cases the polarity of the portion of the inhibitor that binds to the second binding site of the protein is positive to the affinity of the inhibitors while negative to the selectivity of the inhibitors. We expect that the information we obtained here can help to develop potential PTP1B inhibitors with more promising specificity.

Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays

PubMed Central

Liu, Huimin; Chen, Liangcheng; Li, Quan; Zheng, Mingzhu; Liu, Jingsheng

2014-01-01

Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown. This study is the first one to build the 3D structure of zmCP1 by computer-assisted homology modeling. In order to determine the substrate specificity of zmCP1, docking study is used for rapid and convenient analysis of large populations of ligand–enzyme complexes. Docking results show that zmCP1 has preference for P1 position and P2 position for Arg and a large hydrophobic residue (such as Phe). Gly147, Gly191, Cys189, and Asp190 are predicted to function as active residues at the S1 subsite, and the S2 subsite contains Leu283, Leu193, Ala259, Met194, and Ala286. SIFt results indicate that Gly144, Arg268, Trp308, and Ser311 play important roles in substrate binding. Then Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) method was used to explain the substrate specificity for P1 position of zmCp1. This study provides insights into the molecular basis of zmCP1 activity and substrate specificity. PMID:24921705

Follicle-stimulating hormone encapsulation in the cholesterol-modified chitosan nanoparticles via molecular dynamics simulations and binding free energy calculations.

PubMed

Yahyaei, Mohammad; Mehrnejad, Faramarz; Naderi-Manesh, Hossein; Rezayan, Ali Hossein

2017-09-30

Follicle-stimulating hormone (FSH) is widely applied in the modern ovarian stimulation techniques. However, it must be administered daily because of its short half-life. Recently, the cholesterol (CS) modified chitosan (CTS) nanogels have attracted significant interest as promising controlled release protein delivery because of their ability to minimize the aggregation and irreversible denaturation of proteins. Herein, we report a molecular dynamics (MD) simulation investigation on the molecular mechanisms of FSH encapsulation in the CS-CTS nanogels. The MD simulations have been performed using the GROMACS software for up to 200ns simulation time. Furthermore, the binding free energy has been calculated by the molecular mechanics [MM] with Poisson-Boltzmann [PB] and surface area solvation (MM/PBSA) method by using the g_mmpbsa tool. Our findings suggest that the main driving force of the formation of the CS-CTS nanogels is the hydrophobic interactions between the CS-CS moieties in water. The results have also indicated that the CS-CTS nanogel formation can occur through the hydrogen bonding in addition to the hydrophobic interactions. The obtained data demonstrate that the FSH encapsulation into the CS-CTS nanogels is a gradual process driven by the hydrophobic interactions between the hydrophobic patch of FSH and the hydrophobic nanodomains of the nanogel. Our results also reveal that except in the hydrophobic patch region, the flexibility of FSH was reduced in the presence of the nanogel. This study provides the elucidation of the nanogel-FSH interactions at the molecular level and presents new perspective for the ideal design and applications of the CS-CTS nanogel in protein delivery. Copyright © 2017 Elsevier B.V. All rights reserved.

Increased Levels of Markers of Oxidative Stress and Inflammation in Patients with Rheumatic Mitral Stenosis Predispose to Left Atrial Thrombus Formation

PubMed Central

Pulimamidi, Vinay Kumar; Murugesan, Vengatesan; Rajappa, Medha; Satheesh, Santhosh; Harichandrakumar, Kottenyen Thazhath

2013-01-01

Background: Rheumatic mitral stenosis (MS) causes stagnation of blood flow, leading to thrombus formation in the left atrium (LA), which may lead to systemic thromboembolic complications. We compared alterations in circulating levels of pro-/anti–oxidants and markers of inflammation in patients of severe rheumatic MS with and without LA thrombus and studied their predictive power to detect the presence of LA thrombus in patients with rheumatic MS. Material and Methods: This is a cross-sectional study of 80 patients with rheumatic MS, evaluated for percutaneous mitral commisurotomy. Group 1 comprised of patients with rheumatic MS with LA thrombus (n=35) and Group 2 included patients with rheumatic MS without LA thrombus (n=45). The following oxidative stress markers-malondialdehyde (MDA), protein carbonyls, total oxidant status and total antioxidant status and inflammation markers-high sensitivity C-reactive protein (hs-CRP), total sialic acid (TSA) and protein-bound sialic acid (PBSA) were estimated in all study subjects. Results: Levels of plasma MDA, protein carbonyl and total oxidant status were significantly elevated, whilst the total antioxidant status levels were significantly lowered, in Group 1, as compared with Group 2. hs-CRP, TSA and PBSA levels showed a significant rise in Group 1 patients, as compared with Group 2. Conclusion: Our results suggest that circulating levels of MDA, protein carbonyl and PBSA were independent predictors of occurrence of LA thrombus in patients with rheumatic MS. PMID:24392368

KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832

Lead levels in blood and saliva in a low-income population of Detroit, Michigan

PubMed Central

Nriagu, Jerome; Burt, Brian; Linder, Aaron; Ismail, Amid; Sohn, Woosung

2006-01-01

The relationships between blood lead (PbB) and saliva lead (PbSa) concentrations and the determinants of PbB and PbSa status in 970 low-income adults in the city of Detroit, Michigan were explored. Average PbB and PbSa values in the sample population were found to be 2.7 ± 0.1 μg/dl and 2.4 ± 0.13 μg/l (equivalent to 0.24 ± 0.13 μg/dl), respectively, and a weak but statistically significant association was found between the lead levels in the two types of body fluid samples. The average PbB level for men (4.0 ± 0.56 μg/dl) was higher than that for women (2.7 ± 0.11 μg/dl); other significant predictors of PbB included age, level of education, being employed, income level, the presence of peeling paint on the wall at home and smoking. There was no gender- or age-dependent difference in blood saliva values but statistically significant correlations were found between PbSa and level of education, employment, income level and smoking. Dental caries was severe in this population. Only 0.5% of the participants had no clinical signs of caries, over 80% had cavitated carious lesions (i.e., lesions that had progressed into dentin), and the number of lost teeth and carious lesions averaged 3.4 and 30, respectively. Weak but significant associations were found between PbB as well as PbSa and measures of dental caries in the study population. The positive associations are believed to be a reflection of the fact that the risk factors for dental caries, especially in low-income populations of the US, overlap extensively with those of lead poisoning and may not have a causal significance. PMID:16443391

Carbohydrate recognition by the antiviral lectin cyanovirin-N

PubMed Central

Fujimoto, Yukiji K.; Green, David F.

2012-01-01

Cyanovirin-N is a cyanobacterial lectin with potent antiviral activity, and has been the focus of extensive pre-clinical investigation as a potential prophylactic for the prevention of the sexual transmission of the human immunodeficiency virus (HIV). Here we present a detailed analysis of carbohydrate recognition by this important protein, using a combination of computational methods, including extensive molecular dynamics simulations and Molecular-Mechanics/ Poisson–Boltzmann/Surface-Area (MM/PBSA) energetic analysis. The simulation results strongly suggest that the observed tendency of wildtype CVN to form domain-swapped dimers is the result of a previously unidentified cis-peptide bond present in the monomeric state. The energetic analysis additionally indicates that the highest-affinity ligand for CVN characterized to date (α-Man-(1,2)-α-Man-(1,2)-α-Man) is recognized asymmetrically by the two binding sites. Finally, we are able to provide a detailed map of the role of all binding site functional groups (both backbone and side chain) to various aspects of molecular recognition: general affinity for cognate ligands, specificity for distinct oligosaccharide targets and the asymmetric recognition of α-Man-(1,2)-α-Man-(1,2)-α-Man. Taken as a whole, these results complement past experimental characterization (both structural and thermodynamic) to provide the most complete understanding of carbohydrate recognition by CVN to date. The results also provide strong support for the application of similar approaches to the understanding of other protein–carbohydrate complexes. PMID:23057413

Identification of Novel Compounds against an R294K Substitution of Influenza A (H7N9) Virus Using Ensemble Based Drug Virtual Screening

PubMed Central

Tran, Nhut; Van, Thanh; Nguyen, Hieu; Le, Ly

2015-01-01

Influenza virus H7N9 foremost emerged in China in 2013 and killed hundreds of people in Asia since they possessed all mutations that enable them to resist to all existing influenza drugs, resulting in high mortality to human. In the effort to identify novel inhibitors combat resistant strains of influenza virus H7N9; we performed virtual screening targeting the Neuraminidase (NA) protein against natural compounds of traditional Chinese medicine database (TCM) and ZINC natural products. Compounds expressed high binding affinity to the target protein was then evaluated for molecular properties to determine drug-like molecules. 4 compounds showed their binding energy less than -11Kcal/mol were selected for molecular dynamics (MD) simulation to capture intermolecular interactions of ligand-protein complexes. The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method was utilized to estimate binding free energy of the complex. In term of stability, NA-7181 (IUPAC namely {9-Hydroxy-10-[3-(trifluoromrthyl) cyclohexyl]-4.8-diazatricyclo [6.4.0.02,6]dodec-4-yl}(perhydro-1H-inden-5-yl)formaldehyde) achieved stable conformation after 20ns and 27ns for ligand and protein root mean square deviation, respectively. In term of binding free energy, 7181 gave the negative value of -30.031 (KJ/mol) indicating the compound obtained a favourable state in the active site of the protein. PMID:25589893

Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.

PubMed

Du, Juan; Wang, Xue; Dong, Chun-Hai; Yang, Jian Ming; Yao, Xiao Jun

2016-01-01

Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1-actin complex, we constructed a homology model of the AtADF1-actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.

Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana

PubMed Central

Wang, Xue; Dong, Chun-Hai; Yang, Jian Ming; Yao, Xiao Jun

2016-01-01

Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1–actin complex, we constructed a homology model of the AtADF1–actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson–Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin. PMID:27414648

New insights into the molecular characteristics behind the function of Renilla luciferase.

PubMed

Fanaei-Kahrani, Zahra; Ganjalikhany, Mohamad Reza; Rasa, Seyed Mohammad Mahdi; Emamzadeh, Rahman

2018-02-01

Renilla Luciferase (RLuc) is a blue light emitter protein which can be applied as a valuable tool in medical diagnosis. But due to lack of the crystal structure of RLuc-ligand complex, the functional motions and catalytic mechanism of this enzyme remain largely unknown. In the present study, the active site properties and the ligand-receptor interactions of the native RLuc and its red-shifted light emitting variant (Super RLuc 8) were investigated using molecular docking approach, molecular dynamics (MD) analysis, and MM-PBSA method. The detailed analysis of the main clusters led to identifying a lid-like structure and its functional motions. Furthermore, an induced-fit mechanism is proposed where ligand-binding induces conformational changes of the active site. Our findings give an insight into the deeper understanding of RLuc conformational changes during binding steps and ligand-receptor pattern. Moreover, our work broaden our understanding of how active site geometry is adjusted to support the catalytic activity and red-shifted light emission in Super RLuc 8. © 2017 Wiley Periodicals, Inc.

Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case.

PubMed

Yasuo, Kazuya; Yamaotsu, Noriyuki; Gouda, Hiroaki; Tsujishita, Hideki; Hirono, Shuichi

2009-04-01

In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifications of the correct poses of each ligand by consensus scoring and MM-PBSA analysis, and a construction of a CoMFA model with the obtained poses to predict the affinity of the ligands. By using a crystal structure of CYP 2C9 and the twenty known CYP inhibitors as a test case, we obtained a CoMFA model with a good statistics, which suggested that the classification of the binding sites as well as the predicted bound poses of the ligands should be reasonable enough. The scheme described here would give a method to predict the affinity of small compounds with a reasonable accuracy, which is expected to heighten the value of computational chemistry in the drug design process.

Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors.

PubMed

Mitra, Sarmistha; Dash, Raju

2018-05-04

The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain. Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands. The results showed that both these derivatives made direct contacts with the important conserved residues of the active site, where propionylshikonin demonstrated stronger binding and stability than acetylshikonin, according to molecular dynamics simulation and binding free energy calculations. Further, QM/MM energy calculation was employed to study the chemical reactivity of the propionylshikonin and also to describe the mechanism of non bonded interactions between the propionylshikonin and CREBBP bromodomain. Though this study demands in vitro and in vivo experiments to evaluate the efficiency of the compound, these insights would assist to design more potent CREBBP bromodomain inhibitor, guiding the site of modification of propionylshikonin moiety for designing selective inhibitors. Copyright © 2018 Elsevier Inc. All rights reserved.

Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study

NASA Astrophysics Data System (ADS)

Phanich, Jiraphorn; Rungrotmongkol, Thanyada; Kungwan, Nawee; Hannongbua, Supot

2016-10-01

The H7N9 avian influenza virus is a novel re-assortment from at least four different strains of virus. Neuraminidase, which is a glycoprotein on the surface membrane, has been the target for drug treatment. However, some H7N9 strains that have been isolated from patient after drug treatment have a R292K mutation in neuraminidase. This substitution was found to facilitate drug resistance using protein- and virus- assays, in particular it gave a high resistance to the most commonly used drug, oseltamivir. The aim of this research is to understand the source of oseltamivir resistance using MD simulations and the MM/PB(GB)SA binding free energy approaches. Both methods can predict the reduced susceptibility of oseltamivir in good agreement to the IC 50 binding energy, although MM/GBSA underestimates this prediction compared to the MM/PBSA calculation. Electrostatic interaction is the main contribution for oseltamivir binding in terms of both interaction and solvation. We found that the source of the drug resistance is a decrease in the binding interaction combined with the reduction of the dehydration penalty. The smaller K292 mutated residue has a larger binding pocket cavity compared to the wild-type resulting in the loss of drug carboxylate-K292 hydrogen bonding and an increased accessibility for water molecules around the K292 mutated residue. In addition, oseltamivir does not bind well to the R292K mutant complex as shown by the high degree of fluctuation in ligand RMSD during the simulation and the change in angular distribution of bulky side chain groups.

Determination of the Bridging Ligand in the Active Site of Tyrosinase.

PubMed

Zou, Congming; Huang, Wei; Zhao, Gaokun; Wan, Xiao; Hu, Xiaodong; Jin, Yan; Li, Junying; Liu, Junjun

2017-10-28

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.

Analysis of the ionic interaction between the hydrophobin RodA and two cutinases of Aspergillus nidulans obtained via an Aspergillus oryzae expression system.

PubMed

Tanaka, Takumi; Nakayama, Mayumi; Takahashi, Toru; Nanatani, Kei; Yamagata, Youhei; Abe, Keietsu

2017-03-01

Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1. We also reported that hydrophobin RodA of the model fungus Aspergillus nidulans, which was obtained via an A. oryzae expression system, interacted via ionic interactions with CutL1. In the present study, phylogenetic and alignment analyses revealed that the N-terminal regions of several RolA orthologs contained positively charged residues and that the corresponding negatively charged residues on the surface of CutL1 that were essential for the RolA-CutL1 interaction were highly conserved in several CutL1 orthologs. A PBSA microparticle degradation assay, a pull-down assay using a dispersion of Teflon particles, and a kinetic analysis using a quartz crystal microbalance revealed that recombinant A. nidulans RodA interacted via ionic interactions with two recombinant A. nidulans cutinases. Together, these results imply that ionic interactions between hydrophobins and cutinases may be common among aspergilli and other filamentous fungi.

Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods.

PubMed

Chang, Shan; Zhang, Da-Wei; Xu, Lei; Wan, Hua; Hou, Ting-Jun; Kong, Ren

2016-11-01

RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.

Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

PubMed Central

Chang, Shan; Zhang, Da-Wei; Xu, Lei; Wan, Hua; Hou, Ting-Jun; Kong, Ren

2016-01-01

ABSTRACT RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain. PMID:27592836

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

NASA Technical Reports Server (NTRS)

Carra, Claudio; Cucinotta, Francis A.

2007-01-01

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

In silico structure prediction and inhibition mechanism studies of AtHDA14 as revealed by homology modeling, docking, molecular dynamics simulation.

PubMed

Zhao, Ming-Lang; Wang, Wang; Nie, Hu; Cao, Sha-Sha; Du, Lin-Fang

2018-05-06

Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots. We also performed virtual screening of AtHDA14 by docking with small molecule drugs and predicted their ADMET properties to select representative inhibitors. MD simulation for representative AtHDA14-ligand complexes was carried out to further research and reveal their stability and inhibition mechanism. Meanwhile, MM/PBSA method was utilized to obtain more valuable information about the residues energy contribution. Moreover, compared with four candidate inhibitors, we also found that compound 645533 and 6918837 might be a more potent AtHDA14 inhibitor than TSA (444732) and SAHA (5311). Therefore, compound 6445533 and 6918837 was anticipated to be a promising drug candidate for inhibition of AtHDA14. Copyright © 2018 Elsevier Ltd. All rights reserved.

Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays.

PubMed

Tzoupis, Haralambos; Leonis, Georgios; Avramopoulos, Aggelos; Reis, Heribert; Czyżnikowska, Żaneta; Zerva, Sofia; Vergadou, Niki; Peristeras, Loukas D; Papavasileiou, Konstantinos D; Alexis, Michael N; Mavromoustakos, Thomas; Papadopoulos, Manthos G

2015-11-01

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction. Copyright © 2015 Elsevier Inc. All rights reserved.

Degradation of biodegradable plastic mulch films in soil environment by phylloplane fungi isolated from gramineous plants.

PubMed

Koitabashi, Motoo; Noguchi, Masako T; Sameshima-Yamashita, Yuka; Hiradate, Syuntaro; Suzuki, Ken; Yoshida, Shigenobu; Watanabe, Takashi; Shinozaki, Yukiko; Tsushima, Seiya; Kitamoto, Hiroko K

2012-08-02

To improve the biodegradation of biodegradable plastic (BP) mulch films, 1227 fungal strains were isolated from plant surface (phylloplane) and evaluated for BP-degrading ability. Among them, B47-9 a strain isolated from the leaf surface of barley showed the strongest ability to degrade poly-(butylene succinate-co-butylene adipate) (PBSA) and poly-(butylene succinate) (PBS) films. The strain grew on the surface of soil-mounted BP films, produced breaks along the direction of hyphal growth indicated that it secreted a BP-degrading enzyme, and has directly contributing to accelerating the degradation of film. Treatment with the culture filtrate decomposed 91.2 wt%, 23.7 wt%, and 14.6 wt% of PBSA, PBS, and commercially available BP polymer blended mulch film, respectively, on unsterlized soil within 6 days. The PCR-DGGE analysis of the transition of soil microbial community during film degradation revealed that the process was accompanied with drastic changes in the population of soil fungi and Acantamoeba spp., as well as the growth of inoculated strain B47-9. It has a potential for application in the development of an effective method for accelerating degradation of used plastics under actual field conditions.

Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA.

PubMed

Terauchi, Yuki; Kim, Yoon-Kyung; Tanaka, Takumi; Nanatani, Kei; Takahashi, Toru; Abe, Keietsu

2017-07-01

Aspergillus oryzae hydrophobin RolA adheres to the biodegradable polyester polybutylene succinate-co-adipate (PBSA) and promotes PBSA degradation by interacting with A. oryzae polyesterase CutL1 and recruiting it to the PBSA surface. In our previous studies, we found that positively charged amino acid residues (H32, K34) of RolA and negatively charged residues (E31, D142, D171) of CutL1 are important for the cooperative ionic interaction between RolA and CutL1, but some other charged residues in the triple mutant CutL1-E31S/D142S/D171S are also involved. In the present study, on the basis of the 3D-structure of CutL1, we hypothesized that D30 is also involved in the CutL1-RolA interaction. We substituted D30 with serine and performed kinetic analysis of the interaction between wild-type RolA and the single mutant CutL1-D30S or quadruple mutant CutL1-D30S/E31S/D142S/D171S by using quartz crystal microbalance. Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1.

Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.

PubMed

Velazquez, Hector A; Riccardi, Demian; Xiao, Zhousheng; Quarles, Leigh Darryl; Yates, Charless Ryan; Baudry, Jerome; Smith, Jeremy C

2018-02-01

Ensemble docking is now commonly used in early-stage in silico drug discovery and can be used to attack difficult problems such as finding lead compounds which can disrupt protein-protein interactions. We give an example of this methodology here, as applied to fibroblast growth factor 23 (FGF23), a protein hormone that is responsible for regulating phosphate homeostasis. The first small-molecule antagonists of FGF23 were recently discovered by combining ensemble docking with extensive experimental target validation data (Science Signaling, 9, 2016, ra113). Here, we provide a detailed account of how ensemble-based high-throughput virtual screening was used to identify the antagonist compounds discovered in reference (Science Signaling, 9, 2016, ra113). Moreover, we perform further calculations, redocking those antagonist compounds identified in reference (Science Signaling, 9, 2016, ra113) that performed well on drug-likeness filters, to predict possible binding regions. These predicted binding modes are rescored with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) approach to calculate the most likely binding site. Our findings suggest that the antagonist compounds antagonize FGF23 through the disruption of protein-protein interactions between FGF23 and fibroblast growth factor receptor (FGFR). © 2017 John Wiley & Sons A/S.

Insights into the effects of mutations on Cren7-DNA binding using molecular dynamics simulations and free energy calculations.

PubMed

Chen, Lin; Zheng, Qing-Chuan; Zhang, Hong-Xing

2015-02-28

A novel, highly conserved chromatin protein, Cren7 is involved in regulating essential cellular processes such as transcription, replication and repair. Although mutations in the DNA-binding loop of Cren7 destabilize the structure and reduce DNA-binding activity, the details are not very clear. Focusing on the specific Cren7-dsDNA complex (PDB code ), we applied molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations to explore the structural and dynamic effects of W26A, L28A, and K53A mutations in comparison to the wild-type protein. The energetic analysis indicated that the intermolecular van der Waals interaction and nonpolar solvation energy play an important role in the binding process of Cren7 and dsDNA. Compared with the wild type Cren7, all the studied mutants W26A, L28A, and K53A have obviously reduced binding free energies with dsDNA in the reduction of the polar and/or nonpolar interactions. These results further elucidated the previous experiments to understand the Cren7-DNA interaction comprehensively. Our work also would provide support for an understanding of the interactions of proteins with nucleic acids.

Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: a therapeutic target for prostate cancer.

PubMed

Kumar, Rakesh; Maurya, Ranjana; Saran, Shweta

2018-02-23

Prostate cancer (PC) is one of the leading cancers in men, raising a serious health issue worldwide. Due to lack of suitable biomarker, their inhibitors and the platform for testing those inhibitors result in poor prognosis of PC. AMP-activated protein kinase (AMPK) is a highly conserved protein kinase found in eukaryotes that is involved in growth and development, and also acts as a therapeutic target for PC. The aim of the present study is to identify novel potent inhibitors of AMPK and propose a simple cellular model system for understanding its biology. Structural modelling and MD simulations were performed to construct and refine the 3D models of Dictyostelium and human AMPK. Binding mechanisms of different drug compounds were studied by performing molecular docking, molecular dynamics and MM-PBSA methods. Two novel drugs were isolated having higher binding affinity over the known drugs and hydrophobic forces that played a key role during protein-ligand interactions. The study also explored the simple cellular model system for drug screening and understanding the biology of a therapeutic target by performing in vitro experiments.

Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

PubMed

Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

2017-05-05

Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design. Copyright © 2017. Published by Elsevier Masson SAS.

KLK14 interactions with HAI-1 and HAI-2 serine protease inhibitors: A molecular dynamics and relative free-energy calculations study.

PubMed

Solís-Calero, Christian; Carvalho, Hernandes F

2017-11-01

Kallikrein 14 (KLK14) is a serine protease linked to several pathologies including prostate cancer and positively correlates with Gleason score. Though KLK14 functioning in cancer is poorly understood, it has been implicated in HGF/Met signaling, given that KLK14 proteolytically inhibits HGF activator-inhibitor 1 (HAI-1), which strongly inhibits pro-HGF activators, thereby contributing to tumor progression. In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA. KLK14 was successfully modeled. Calculated free energies suggested higher binding affinity for the KLK14/HAI-1 interaction than for KLK14/HAI-2. This difference in binding affinity is largely explained by the higher stability of the hydrogen-bond networks in KLK14/HAI-1 along the simulation trajectory. A key arginine residue in both HAI-1 and HAI-2 is responsible for their interaction with the S1 pocket in KLK14. Additionally, MM/GBSA free-energy decomposition postulates that KLK14 Asp174 and Trp196 are hotspots for binding HAI-1 and HAI-2. © 2017 International Federation for Cell Biology.

Conformational elasticity can facilitate TALE-DNA recognition

PubMed Central

Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P.; Segal, David J.; Duan, Yong

2015-01-01

Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo- and bound- conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann/surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. PMID:24629191

Conformational elasticity can facilitate TALE-DNA recognition.

PubMed

Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P; Segal, David J; Duan, Yong

2014-01-01

Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. © 2014 Elsevier Inc. All rights reserved.

Comparative modeling and molecular dynamics suggest high carboxylase activity of the Cyanobium sp. CACIAM14 RbcL protein.

PubMed

Siqueira, Andrei Santos; Lima, Alex Ranieri Jerônimo; Dall'Agnol, Leonardo Teixeira; de Azevedo, Juliana Simão Nina; da Silva Gonçalves Vianez, João Lídio; Gonçalves, Evonnildo Costa

2016-03-01

Rubisco catalyzes the first step reaction in the carbon fixation pathway, bonding atmospheric CO2/O2 to ribulose 1,5-bisphosphate; it is therefore considered one of the most important enzymes in the biosphere. Genetic modifications to increase the carboxylase activity of rubisco are a subject of great interest to agronomy and biotechnology, since this could increase the productivity of biomass in plants, algae and cyanobacteria and give better yields in crops and biofuel production. Thus, the aim of this study was to characterize in silico the catalytic domain of the rubisco large subunit (rbcL gene) of Cyanobium sp. CACIAM14, and identify target sites to improve enzyme affinity for ribulose 1,5-bisphosphate. A three-dimensional model was built using MODELLER 9.14, molecular dynamics was used to generate a 100 ns trajectory by AMBER12, and the binding free energy was calculated using MM-PBSA, MM-GBSA and SIE methods with alanine scanning. The model obtained showed characteristics of form-I rubisco, with 15 beta sheets and 19 alpha helices, and maintained the highly conserved catalytic site encompassing residues Lys175, Lys177, Lys201, Asp203, and Glu204. The binding free energy of the enzyme-substrate complexation of Cyanobium sp. CACIAM14 showed values around -10 kcal mol(-1) using the SIE method. The most important residues for the interaction with ribulose 1,5-bisphosphate were Arg295 followed by Lys334. The generated model was successfully validated, remaining stable during the whole simulation, and demonstrated characteristics of enzymes with high carboxylase activity. The binding analysis revealed candidates for directed mutagenesis sites to improve rubisco's affinity.

Epitope mapping of epidermal growth factor receptor (EGFR) monoclonal antibody and induction of growth-inhibitory polyclonal antibodies by vaccination with EGFR mimotope.

PubMed

Navari, Mohsen; Zare, Mehrak; Javanmardi, Masoud; Asadi-Ghalehni, Majid; Modjtahedi, Helmout; Rasaee, Mohammad Javed

2014-10-01

One of the proposed approaches in cancer therapy is to induce and direct the patient's own immune system against cancer cells. In this study, we determined the epitope mapping of the rat anti-human epidermal growth factor receptor (EGFR) monoclonal antibody ICR-62 using a phage display of random peptide library and identified a 12 amino acids peptide, which was recognized as a mimotope. The peptide was synthesized and conjugated to bovine serum albumin (BSA) as carrier protein (P-BSA). We have shown that ICR-62 can react specifically with P-BSA as well as native EGFR. Two rabbits were immunized either by BSA or P-BSA and the rabbits IgGs were purified and examined for binding to the antigens, mimotope and the EGFR protein purified from the EGFR overexpressing A431 cell line. We showed that the rabbit IgG generated against the mimotope is capable of inhibiting the growth of A431 cells by 15%, but does not have any effect on the growth of EGFR-negative MDA-MB-453 cell line in vitro. Our results support the need for further investigations on the potential of vaccination with either mimotope of the EGFR or epitope displayed on the surface of phage particles for use in active immunotherapy of cancer.

Degradation of biodegradable plastic mulch films in soil environment by phylloplane fungi isolated from gramineous plants

PubMed Central

2012-01-01

To improve the biodegradation of biodegradable plastic (BP) mulch films, 1227 fungal strains were isolated from plant surface (phylloplane) and evaluated for BP-degrading ability. Among them, B47-9 a strain isolated from the leaf surface of barley showed the strongest ability to degrade poly-(butylene succinate-co-butylene adipate) (PBSA) and poly-(butylene succinate) (PBS) films. The strain grew on the surface of soil-mounted BP films, produced breaks along the direction of hyphal growth indicated that it secreted a BP-degrading enzyme, and has directly contributing to accelerating the degradation of film. Treatment with the culture filtrate decomposed 91.2 wt%, 23.7 wt%, and 14.6 wt% of PBSA, PBS, and commercially available BP polymer blended mulch film, respectively, on unsterlized soil within 6 days. The PCR-DGGE analysis of the transition of soil microbial community during film degradation revealed that the process was accompanied with drastic changes in the population of soil fungi and Acantamoeba spp., as well as the growth of inoculated strain B47-9. It has a potential for application in the development of an effective method for accelerating degradation of used plastics under actual field conditions. PMID:22856640

Free energy calculations of glycosaminoglycan-protein interactions.

PubMed

Gandhi, Neha S; Mancera, Ricardo L

2009-10-01

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

PubMed

Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

2015-06-01

Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.

Computational investigation of fullerene-DNA interactions: Implications of fullerene's size and functionalization on DNA structure and binding energetics.

PubMed

Papavasileiou, Konstantinos D; Avramopoulos, Aggelos; Leonis, Georgios; Papadopoulos, Manthos G

2017-06-01

DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its central role in storing and transferring genetic information can be severely hindered by molecules with structure altering abilities. Fullerenes are nanoparticles that find a broad spectrum of uses, but their toxicological effects on living organisms upon exposure remain unclear. The present study examines the interactions of a diverse array of fullerenes with DNA, by means of Molecular Dynamics and MM-PBSA methodologies, with special focus on structural deformations that may hint toxicity implications. Our results show that pristine and hydroxylated fullerenes have no unwinding effects upon DNA structure, with the latter displaying binding preference to the DNA major groove, achieved by both direct formation of hydrogen bonds and water molecule mediation. Fluorinated derivatives are capable of penetrating DNA structure, forming intercalative complexes with high binding affinities. Copyright © 2017 Elsevier Inc. All rights reserved.

In Vitro Test for Potential Inhibitors of Plasmepsin II and IV as Anti-malarial Agents

NASA Astrophysics Data System (ADS)

Kang, Hee-Kyoung; Hwang, Soon-Wook; Kim, Do-Won; Breton, Vincent; Kim, Doman

Plasmepsins (PMs) are involved in the degradation of host cell hemoglobin during malaria infection. PM II and IV initiate the degradative process, and have been suggested as attractive targets for treatment of malaria. Previously, 30 compounds were identified by post-processing the results of a large docking screen of commercially available compounds using an automated procedure based on molecular dynamics refinement and binding free-energy estimation using MM-PBSA and MM-GBSA (Degliesposti et al., 2009). Presently, these were experimentally validated using an inhibition assay based on fluorescence resonance energy transfer (FRET) and hemoglobin substrate degradation. Remarkably, 26 of the 30 tested compounds were active as PM II inhibitors, with FRET IC50 values ranging from 4.3 nM to 1.8 μM. Also, IC50 value for PM IV inhibition ranged from 9.34 nM to 83 μM and the best inhibitor among the 30 compounds was compound 7. Hemoglobin degradation by recombinant PM II and IV was completely inhibited by 100 μM of compound 7. The newly identified compounds, and one in particular (compound 7), can inhibit PM II and IV activity and hemoglobin degradation in vitro. These experiments suggest an overall approach in the design of powerful and selective PM II and IV inhibitors.

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

PubMed

Zhou, Xinrui; Zheng, Jie; Ivan, Fransiskus Xaverius; Yin, Rui; Ranganathan, Shoba; Chow, Vincent T K; Kwoh, Chee-Keong

2018-05-09

Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses.

Design, synthesis and biological evaluation of novel hydroxy-phenyl-1H-benzimidazoles as radical scavengers and UV-protective agents.

PubMed

Bino, Alessia; Baldisserotto, Anna; Scalambra, Emanuela; Dissette, Valeria; Vedaldi, Daniela Ester; Salvador, Alessia; Durini, Elisa; Manfredini, Stefano; Vertuani, Silvia

2017-12-01

An ever-increasing incidence of skin neoplastic diseases is registered. Therefore, it is important to protect the skin from the UV radiation that reaches the epidermis and dermis but also to block ROS generated by them. Our attention was attracted in developing new compounds provided with both UV filtering and antioxidant capacities. To this end, 2-phenyl-1H-benzimidazole-5-sulfonic acid (PBSA), a known UV filter, was selected as lead compound for its lack of antioxidant activity, high water solubility and good safety profile. PBSA was sequentially modified introducing hydroxyls on the phenyl ring and also substituting the functional group in position 5 of the benzimidazole ring. At the end of the synthetic study, a new, very potent class of antioxidants has been obtained. Surprisingly some of the developed molecules, while devoid of significant UV-filtering activity was endowed with potent UV-filtering booster capability if associated with known commercial UVB and UVA filters.

Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening

NASA Astrophysics Data System (ADS)

Yu, Miao; Gu, Qiong; Xu, Jun

2018-02-01

PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.

Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.

PubMed

Dehury, Budheswar; Maharana, Jitendra; Sahoo, Bikash Ranjan; Sahu, Jagajjit; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

2015-04-01

The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein.

PubMed

Poongavanam, Vasanthanathan; Kongsted, Jacob; Wüstner, Daniel

2016-09-13

Transport of cholesterol derived from hydrolysis of lipoprotein associated cholesteryl esters out of late endosomes depends critically on the function of the Niemann Pick C1 (NPC1) and C2 (NPC2) proteins. Both proteins bind cholesterol but also various other sterols and both with strongly varying affinity. The molecular mechanisms underlying this multiligand specificity are not known. On the basis of the crystal structure of NPC2, we have here investigated structural details of NPC2-sterol interactions using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. We found that an aliphatic side chain in the sterol ligand results in strong binding to NPC2, while side-chain oxidized sterols gave weaker binding. Estradiol and the hydrophobic amine U18666A had the lowest affinity of all tested ligands and at the same time showed the highest flexibility within the NPC2 binding pocket. The binding affinity of all ligands correlated highly with their calculated partitioning coefficient (logP) between octanol/water phases and with the potential of sterols to stabilize the protein backbone. From molecular dynamics simulations, we suggest a general mechanism for NPC2 mediated sterol transfer, in which Phe66, Val96, and Tyr100 act as reversible gate keepers. These residues stabilize the sterol in the binding pose via π-π stacking but move transiently apart during sterol release. A computational mutation analysis revealed that the binding of various ligands depends critically on the same specific amino acid residues within the binding pocket providing shape complementary to sterols, but also on residues in distal regions of the protein.

Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein.

PubMed

Zhao, Run-Ning; Fan, Song; Han, Ju-Guang; Liu, Guang

2015-01-01

Mcl-1 has emerged as a potential therapeutic target in the treatment of several malignancies. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic Mcl-1 and this segment is responsible for modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-peptide interaction is required to develop potent inhibitors specific for Mcl-1. Molecular dynamics simulations were performed for Mcl-1 in complex with three different BH3 peptides derived from Mcl-1, Bax, and Bim. Accordingly, the calculated binding free energies using MM-PBSA method are obtained and comparison with the experimentally determined binding free energies is made. The interactions involving two conserved charged residues (Aspi, and Arg/Lysi-4) and three upstream conserved hydrophobic residues (Leui-5, Ile/Vali-2, and Glyi-1, respectively) of BH3 peptides play the important roles in the structural stability of the complexes. The calculated results exhibit that the interactions of Bim BH3 peptides to Mcl-1 is stronger than the complex with Bax 19BH3 peptides. The hydrophobic residues (position i - 9, i - 8 and i + 2) of BH3 peptides can be involved in their inhibitory specificity. The calculated results can be used for designing more effective MCL-1 inhibitors.

Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation.

PubMed

Chen, Kai; Duan, Wenxiu; Han, Qianqian; Sun, Xuan; Li, Wenqian; Hu, Shuangyun; Wan, Jiajia; Wu, Jiang; Ge, Yushu; Liu, Dan

2018-03-08

Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.

All-atomic Molecular Dynamic Studies of Human CDK8: Insight into the A-loop, Point Mutations and Binding with Its Partner CycC

PubMed Central

Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

2014-01-01

The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable ‘CDK8 submodule’ consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex. Taken together, these analyses will improve our understanding of the exact functions of CDK8 and the interaction with its partner CycC. PMID:24754906

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations.

PubMed

Shuaib, Suniba; Goyal, Bhupesh

2018-02-01

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β 42 (Aβ 42 ) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ 42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ 42 . MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ 42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ 42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ 42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ 42 .

Molecular modeling on porphyrin derivatives as β5 subunit inhibitor of 20S proteasome.

PubMed

Arba, Muhammad; Nur-Hidayat, Andry; Ruslin; Yusuf, Muhammad; Sumarlin; Hertadi, Rukman; Wahyudi, Setyanto Tri; Surantaadmaja, Slamet Ibrahim; Tjahjono, Daryono H

2018-06-01

The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors β5 subunit which is a crucial active site in proteolysis. Targeting proteasome β5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the β5 subunit of the proteasome by employing molecular docking and dynamics simulations. The molecular docking was performed with the help of AutoDock 4.2, while molecular dynamics simulation was done using AMBER 14. All compounds bound to the proteasome with similar binding modes, and each porphyrin-proteasome complex was stable during 30 ns MD simulation as indicated by root-mean-square-deviation (RMSD) value. An analysis on protein residue fluctuation of porphyrin binding demonstrates that in all complexes, porphyrin binding produces minor fluctuation on amino acid residues. The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation shows that the binding affinities of mono-H 2 PyP, bis-H 2 PzP, and tetra-H 2 PyP were comparable with that of the potential inhibitor, HU10. It is noted that the electrostatic interaction increases with the number of meso-substituents, which was favourable for porphyrin binding. The present study shows that both electrostatic and van der Waals interaction are the main force which controls the interaction of porphyrin compounds with the proteasome. Copyright © 2018 Elsevier Ltd. All rights reserved.

Molecular dynamics of zinc-finger ubiquitin binding domains: a comparative study of histone deacetylase 6 and ubiquitin-specific protease 5.

PubMed

Dos Santos Passos, Carolina; Simões-Pires, Claudia A; Carrupt, Pierre-Alain; Nurisso, Alessandra

2016-12-01

HDAC6 is a unique cytoplasmic histone deacetylase characterized by two deacetylase domains, and by a zinc-finger ubiquitin binding domain (ZnF-UBP) able to recognize ubiquitin (Ub). The latter has recently been demonstrated to be involved in the progression of neurodegenerative diseases and in mediating infection by the influenza A virus. Nowadays, understanding the dynamic and energetic features of HDAC6 ZnF-UBP-Ub recognition is considered as a crucial step for the conception of HDAC6 potential modulators. In this study, the atomic, solvent-related, and thermodynamic features behind HDAC6 ZnF-UBP-Ub recognition have been analyzed through molecular dynamics simulations. The behavior was then compared to the prototypical ZnF-UBP from ubiquitin-specific protease 5 (USP5) in order to spot relevant differences useful for selective drug design. Principal component analysis highlighted flapping motions of the L2A loop which were lowered down upon Ub binding in both systems. While polar and nonpolar interactions involving Ub G75 and G76 residues were also common features stabilizing both complexes, salt bridges showed a different pattern, more significant in HDAC6 ZnF-UBP-Ub, whose energetic contribution in USP5 ZnF-UBP-Ub was compensated by the presence of a more stable bridging water molecule. Whereas molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) free energies of binding were comparable for both systems, in agreement with experiments, computational alanine scanning and free energy decomposition data revealed that HDAC6 E1141 and D1178 are potential hotspots for the design of selective HDAC6 modulators.

Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors.

PubMed

Wang, Jinghui; Yang, Yinfeng; Li, Yan; Wang, Yonghua

2016-07-27

Bovine viral diarrhea virus (BVDV) infections are prevailing in cattle populations on a worldwide scale. The BVDV RNA-dependent RNA polymerase (RdRp), as a promising target for new anti-BVDV drug development, has attracted increasing attention. To explore the interaction mechanism of 65 benzimidazole scaffold-based derivatives as BVDV inhibitors, presently, a computational study was performed based on a combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations. The resultant optimum CoMFA and CoMSIA models present proper reliabilities and strong predictive abilities (with Q(2) = 0. 64, R(2)ncv = 0.93, R(2)pred = 0.80 and Q(2) = 0. 65, R(2)ncv = 0.98, R(2)pred = 0.86, respectively). In addition, there was good concordance between these models, molecular docking, and MD results. Moreover, the MM-PBSA energy analysis reveals that the major driving force for ligand binding is the polar solvation contribution term. Hopefully, these models and the obtained findings could offer better understanding of the interaction mechanism of BVDV inhibitors as well as benefit the new discovery of more potent BVDV inhibitors.

Exploring the interactions of EGFR with phosphorylated Mig6 by molecular dynamics simulations and MM-PBSA calculations.

PubMed

Zhang, Yue; Zheng, Qing-Chuan

2018-06-14

Mig6, a negative regulator, directly binds to epidermal growth factor receptor (EGFR), including Mig6-segment1 and Mig6-segment2. Mig6 requires phosphorylation of Y394 on Mig6-segment2 in order to inhibit EGFR. Two phosphorylation pathways for Y394 have been previously reported and the first way may phosphorylate Y394 primed by Y395 phosphorylation. Besides, the binding mechanism of phosphorylated Mig6-segment2 with EGFR has not been elucidated clearly. Focused on EGFR complex with phosphorylated Mig6-segment2, molecular dynamics (MD) simulations were performed to explore the interactions of Mig6-segment2 with EGFR. Our results indicate a probable phosphorylation pathway on Y394 and some key residues of EGFR play important roles in binding to phosphorylated Mig6-segment2. In addition, a special L-shaped structure was found to be possibly associated with irreversible inhibition of EGFR by Mig6. Our work can give meaningful information to better understand the phosphorylation pathways for Y394 and the interactions of EGFR binding to phosphorylated Mig6-segment2. Copyright © 2018 Elsevier Ltd. All rights reserved.

Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus.

PubMed

Ai, Haixin; Zhang, Li; Chang, Alan K; Wei, Hongyun; Che, Yuchen; Liu, Hongsheng

2014-03-01

Inhibition of CPSF30 function by the effector domain of influenza A virus of non-structural protein 1 (NS1A) protein plays a critical role in the suppression of host key antiviral response. The CPSF30-binding site of NS1A appears to be a very attractive target for the development of new drugs against influenza A virus. In this study, structure-based molecular docking was utilized to screen more than 30,000 compounds from a Traditional Chinese Medicine (TCM) database. Four drug-like compounds were selected as potential inhibitors for the CPSF30-binding site of NS1A. Docking conformation analysis results showed that these potential inhibitors could bind to the CPSF30-binding site with strong hydrophobic interactions and weak hydrogen bonds. Molecular dynamics simulations and MM-PBSA calculations suggested that two of the inhibitors, compounds 32056 and 31674, could stably bind to the CPSF30-binding site with high binding free energy. These two compounds could be modified to achieve higher binding affinity, so that they may be used as potential leads in the development of new anti-influenza drugs.

Unveiling the molecular mechanism of brassinosteroids: Insights from structure-based molecular modeling studies.

PubMed

Lei, Beilei; Liu, Jiyuan; Yao, Xiaojun

2015-12-01

Brassinosteroid (BR) phytohormones play indispensable roles in plant growth and development. Brassinolide (BL) and 24-epibrassinolide (24-epiBL) are the most active ones among the BRs reported thus far. Unfortunately, the extremely low natural content and intricate synthesis process limit their popularization in agricultural production. Earlier reports to discover alternative compounds have resulted in molecules with nearly same scaffold structure and without diversity in chemical space. In the present study, receptors structure based BRs regulation mechanism was analyzed. First, we examined the detailed binding interactions and their dynamic stability between BL and its receptor BRI1 and co-receptor BAK1. Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation. The obtained binding structures and energetic results provided vital insights into the structural factors affecting the activity from both receptors and BRs aspects. Subsequently, the obtained knowledge will serve as valuable guidance to build pharmacophore models for rational screening of new scaffold alternative BRs. Copyright © 2015 Elsevier Inc. All rights reserved.

Alternative dimerization interfaces in the glucocorticoid receptor-α ligand binding domain.

PubMed

Bianchetti, Laurent; Wassmer, Bianca; Defosset, Audrey; Smertina, Anna; Tiberti, Marion L; Stote, Roland H; Dejaegere, Annick

2018-04-30

Nuclear hormone receptors (NRs) constitute a large family of multi-domain ligand-activated transcription factors. Dimerization is essential for their regulation, and both DNA binding domain (DBD) and ligand binding domain (LBD) are implicated in dimerization. Intriguingly, the glucocorticoid receptor-α (GRα) presents a DBD dimeric architecture similar to that of the homologous estrogen receptor-α (ERα), but an atypical dimeric architecture for the LBD. The physiological relevance of the proposed GRα LBD dimer is a subject of debate. We analyzed all GRα LBD homodimers observed in crystals using an energetic analysis based on the PISA and on the MM/PBSA methods and a sequence conservation analysis, using the ERα LBD dimer as a reference point. Several dimeric assemblies were observed for GRα LBD. The assembly generally taken to be physiologically relevant showed weak binding free energy and no significant residue conservation at the contact interface, while an alternative homodimer mediated by both helix 9 and C-terminal residues showed significant binding free energy and residue conservation. However, none of the GRα LBD assemblies found in crystals are as stable or conserved as the canonical ERα LBD dimer. GRα C-terminal sequence (F-domain) forms a steric obstacle to the canonical dimer assembly in all available structures. Our analysis calls for a re-examination of the currently accepted GRα homodimer structure and experimental investigations of the alternative architectures. This work questions the validity of the currently accepted architecture. This has implications for interpreting physiological data and for therapeutic design pertaining to glucocorticoid research. Copyright © 2018. Published by Elsevier B.V.

Insight into the interaction mechanism of human SGLT2 with its inhibitors: 3D-QSAR studies, homology modeling, and molecular docking and molecular dynamics simulations.

PubMed

Dong, Lili; Feng, Ruirui; Bi, Jiawei; Shen, Shengqiang; Lu, Huizhe; Zhang, Jianjun

2018-03-06

Human sodium-dependent glucose co-transporter 2 (hSGLT2) is a crucial therapeutic target in the treatment of type 2 diabetes. In this study, both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to generate three-dimensional quantitative structure-activity relationship (3D-QSAR) models. In the most accurate CoMFA-based and CoMSIA-based QSAR models, the cross-validated coefficients (r 2 cv ) were 0.646 and 0.577, respectively, while the non-cross-validated coefficients (r 2 ) were 0.997 and 0.991, respectively, indicating that both models were reliable. In addition, we constructed a homology model of hSGLT2 in the absence of a crystal structure. Molecular docking was performed to explore the bonding mode of inhibitors to the active site of hSGLT2. Molecular dynamics (MD) simulations and binding free energy calculations using MM-PBSA and MM-GBSA were carried out to further elucidate the interaction mechanism. With regards to binding affinity, we found that hydrogen-bond interactions of Asn51 and Glu75, located in the active site of hSGLT2, with compound 40 were critical. Hydrophobic and electrostatic interactions were shown to enhance activity, in agreement with the results obtained from docking and 3D-QSAR analysis. Our study results shed light on the interaction mode between inhibitors and hSGLT2 and may aid in the development of C-aryl glucoside SGLT2 inhibitors.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

PubMed

Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza

2015-10-14

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis.

PubMed

Zúñiga, Matías A; Alderete, Joel B; Jaña, Gonzalo A; Jiménez, Verónica A

2017-07-01

Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis

NASA Astrophysics Data System (ADS)

Zúñiga, Matías A.; Alderete, Joel B.; Jaña, Gonzalo A.; Jiménez, Verónica A.

2017-07-01

Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

Performance-Based Service Acquisition (PBSA) Study and Graduate Level Course Material

DTIC Science & Technology

2005-12-01

Realizing Marketplace Potential, Acquisition Solutions, Inc (Advisory), February 2001 Dickson, Bob, March 10, 2003. Federal 7 Contract Law : Feds...Management and Policy Federal Contract Law : Feds should use market research to refine IT plans Session 4: The Performance Requirements and...March 10, 2003. Federal Contract Law : Feds should use market research to refine IT plans, Post-Newsweek Media, Inchttp://appserv.gcn.com/cgi- bin/udt

Novel biocomposite of carboxymethyl chitosan and pineapple peel carboxymethylcellulose as sunscreen carrier.

PubMed

Wongkom, Lucksanee; Jimtaisong, Ampa

2017-02-01

This study aims to prepare of biocomposite of carboxymethyl chitosan (CM-chitosan) and carboxymethylcellulose (CMC) from Ananas comosus (pineapple) peel for use as broad spectrum sunscreen carrier. Biocomposite was produced by using ferulic acid (FA), a plant extract, as crosslinker with the optimal ratio of CMC: CM-chitosan: FA at 1:2:4%w. FT-IR technique demonstrated that crosslinking may occur at amine group of CM-chitosan and carboxyl group of FA and hydrogen bonding between hydroxyl group of CMC and carboxyl group of FA. Biocomposite is pale yellow powder and present fibre bundle-like surface in the SEM image. DSC, TGA and XRD results indicated that new compound was formed. The particle size of biocomposite is 626nm determined by using Zetasizer. Hydrophilic TiO 2 and phenylbenzimidazole sulphonic acid (PBSA) were used as sunscreen agent at ratio of TiO 2 : PBSA at 2:1%w. The biocomposite sunscreen possesses the SPF value of 2.47 with boost star rating of 3 at 2% compound. The results obtained indicate that the biocomposite was successfully prepared from CM-chitosan and pineapple peel CMC and the system can be used as matrix delivery system for hydrophilic sunscreens. Copyright © 2016 Elsevier B.V. All rights reserved.

Using chloride and chlorine-36 as soil-water tracers to estimate deep percolation at selected locations on the U.S. Department of Energy Hanford site, Washington

USGS Publications Warehouse

Prych, Edmund A.

1995-01-01

Long-term average deep-percolation rates of water from precipitation on the U.S. Department of Energy Hanford Site in semiarid south-central Washington, as estimated by a chloride mass-balance method, range from 0.008 to 0.30 mm/yr (millimeters per year) at nine locations covered by a variety of fine-grain soils and vegetated with sagebrush and other deep-rooted plants plus sparse shallow-rooted grasses. Deep-percolation rates estimated using a chlorine-36 bomb-pulse method at three of the nine locations range from 2.1 to 3.4 mm/yr. Because the mass-balance method may underestimate percolation rates and the bomb-pulse method probably overestimates percolation rates, estimates by the two methods probably bracket actual rates. These estimates, as well as estimates by previous investigators who used different methods, are a small fraction of mean annual precipitation, which ranges from about 160 to 210 mm/yr at the different test locations. Estimates by the mass-balance method at four locations in an area that is vegetated only with sparse shallow-rooted grasses range from 0.39 to 2.0 mm/yr. Chlorine-36 data at one location in this area were sufficient only to determine that the upper limit of deep percolation is more than 5.1 mm/yr. Although estimates for locations in this area are larger than the estimates for locations with deep-rooted plants, they are at the lower end of the range of estimates for this area made by previous investigators.

Molecular modeling reveals binding interface of γ-tubulin with GCP4 and interactions with noscapinoids.

PubMed

Suri, Charu; Joshi, Harish C; Naik, Pradeep Kumar

2015-05-01

The initiation of microtubule assembly within cells is guided by a cone shaped multi-protein complex, γ-tubulin ring complex (γTuRC) containing γ-tubulin and atleast five other γ-tubulin-complex proteins (GCPs), i.e., GCP2, GCP3, GCP4, GCP5, and GCP6. The rim of γTuRC is a ring of γ-tubulin molecules that interacts, via one of its longitudinal interfaces, with GCP2, GCP3, or GCP4 and, via other interface, with α/β-tubulin dimers recruited for the microtubule lattice formation. These interactions however, are not well understood in the absence of crystal structure of functional reconstitution of γTuRC subunits. In this study, we elucidate the atomic interactions between γ-tubulin and GCP4 through computational techniques. We simulated two complexes of γ-tubulin-GCP4 complex (we called dimer1 and dimer2) for 25 ns to obtain a stable complex and calculated the ensemble average of binding free energies of -158.82 and -170.19 kcal/mol for dimer1 and -79.53 and -101.50 kcal/mol for dimer2 using MM-PBSA and MM-GBSA methods, respectively. These highly favourable binding free energy values points to very robust interactions between GCP4 and γ-tubulin. From the results of the free-energy decomposition and the computational alanine scanning calculation, we identified the amino acids crucial for the interaction of γ-tubulin with GCP4, called hotspots. Furthermore, in the endeavour to identify chemical leads that might interact at the interface of γ-tubulin-GCP4 complex; we found a class of compounds based on the plant alkaloid, noscapine that binds with high affinity in a cavity close to γ-tubulin-GCP4 interface compared with previously reported compounds. All noscapinoids displayed stable interaction throughout the simulation, however, most robust interaction was observed for bromo-noscapine followed by noscapine and amino-noscapine. This offers a novel chemical scaffold for γ-tubulin binding drugs near γ-tubulin-GCP4 interface. © 2015 Wiley Periodicals, Inc.

Measurement of intrahepatic pressure during radiofrequency ablation in porcine liver.

PubMed

Kawamoto, Chiaki; Yamauchi, Atsushi; Baba, Yoko; Kaneko, Keiko; Yakabi, Koji

2010-04-01

To identify the most effective procedures to avoid increased intrahepatic pressure during radiofrequency ablation, we evaluated different ablation methods. Laparotomy was performed in 19 pigs. Intrahepatic pressure was monitored using an invasive blood pressure monitor. Radiofrequency ablation was performed as follows: single-step standard ablation; single-step at 30 W; single-step at 70 W; 4-step at 30 W; 8-step at 30 W; 8-step at 70 W; and cooled-tip. The array was fully deployed in single-step methods. In the multi-step methods, the array was gradually deployed in four or eight steps. With the cooled-tip, ablation was performed by increasing output by 10 W/min, starting at 40 W. Intrahepatic pressure was as follows: single-step standard ablation, 154.5 +/- 30.9 mmHg; single-step at 30 W, 34.2 +/- 20.0 mmHg; single-step at 70 W, 46.7 +/- 24.3 mmHg; 4-step at 30 W, 42.3 +/- 17.9 mmHg; 8-step at 30 W, 24.1 +/- 18.2 mmHg; 8-step at 70 W, 47.5 +/- 31.5 mmHg; and cooled-tip, 114.5 +/- 16.6 mmHg. The radiofrequency ablation-induced area was spherical with single-step standard ablation, 4-step at 30 W, and 8-step at 30 W. Conversely, the ablated area was irregular with single-step at 30 W, single-step at 70 W, and 8-step at 70 W. The ablation time was significantly shorter for the multi-step method than for the single-step method. Increased intrahepatic pressure could be controlled using multi-step methods. From the shapes of the ablation area, 30-W 8-step expansions appear to be most suitable for radiofrequency ablation.

Measurement and analysis of a small nozzle plume in vacuum

NASA Technical Reports Server (NTRS)

Penko, P. F.; Boyd, I. D.; Meissner, D. L.; Dewitt, K. J.

1993-01-01

Pitot pressures and flow angles are measured in the plume of a nozzle flowing nitrogen and exhausting to a vacuum. Total pressures are measured with Pitot tubes sized for specific regions of the plume and flow angles measured with a conical probe. The measurement area for total pressure extends 480 mm (16 exit diameters) downstream of the nozzle exit plane and radially to 60 mm (1.9 exit diameters) off the plume axis. The measurement area for flow angle extends to 160 mm (5 exit diameters) downstream and radially to 60 mm. The measurements are compared to results from a numerical simulation of the flow that is based on kinetic theory and uses the direct-simulation Monte Carlo (DSMC) method. Comparisons of computed results from the DSMC method with measurements of flow angle display good agreement in the far-field of the plume and improve with increasing distance from the exit plane. Pitot pressures computed from the DSMC method are in reasonably good agreement with experimental results over the entire measurement area.

Computer-aided identification of potential TYK2 inhibitors from drug database

NASA Astrophysics Data System (ADS)

Zhang, Wei; Li, Jianzong; Huang, Zhixin; Wang, Haiyang; Luo, Hao; Wang, Xin; Zhou, Nan; Wu, Chuanfang; Bao, Jinku

2016-10-01

TYK2 is a member of JAKs family protein tyrosine kinase activated in response to various cytokines. It plays a crucial role in transducing signals downstream of various cytokine receptors, which are involved in proinflammatory responses associated with immunological diseases. Thus, the study of selective TYK2 inhibitors is one of the most popular fields in anti-inflammation drug development. Herein, we adopted molecular docking, molecular dynamics simulation and MM-PBSA binding free energy calculation to screen potential TYK2-selective inhibitors from ZINC Drug Database. Finally, three small molecule drugs ZINC12503271 (Gemifloxacin), ZINC05844792 (Nebivolol) and ZINC00537805 (Glyburide) were selected as potential TYK2-selective inhibitors. Compared to known inhibitor 2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide, these three candidates had better Grid score and Amber score from molecular docking and preferable results from binding free energy calculation as well. What's more, the ATP-binding site and A-loop motif had been identified to play key roles in TYK2-targeted inhibitor discovery. It is expected that our study will pave the way for the design of potent TYK2 inhibitors of new drugs to treat a wide variety of immunological diseases such as inflammatory diseases, multiple sclerosis, psoriasis inflammatory bowel disease (IBD) and so on.

Exploring the mechanism how AF9 recognizes and binds H3K9ac by molecular dynamics simulations and free energy calculations.

PubMed

Wang, Quan; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-11-01

Histone acetylation is a very important regulatory mechanism in gene expression in the chromatin context. A new protein family-YEATS domains have been found as a novel histone acetylation reader, which could specific recognize the histone lysine acetylation. AF9 is an important one in the YEATS family. Focused on the AF9-H3K9ac (K9 acetylation) complex (ALY) (PDB code: 4TMP) and a serials of mutants, MUT (the acetyllsine of H3K9ac was mutated to lysine), F59A, G77A, and D103A, we applied molecular dynamics simulation and molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculations to examine the role of AF9 protein in recognition interaction. The simulation results and analysis indicate that some residues of the protein have significant influence on recognition and binding to H3K9ac peptides and hydrophobic surface show the hydrophobic interactions play an important role in the binding. Our work can give important information to understand how the protein AF9 recognizes the peptides H3K9ac. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 779-786, 2016. © 2016 Wiley Periodicals, Inc.

Combined 3D-QSAR, molecular docking, molecular dynamics simulation, and binding free energy calculation studies on the 5-hydroxy-2H-pyridazin-3-one derivatives as HCV NS5B polymerase inhibitors.

PubMed

Yu, Haijing; Fang, Yu; Lu, Xia; Liu, Yongjuan; Zhang, Huabei

2014-01-01

The NS5B RNA-dependent RNA polymerase (RdRP) is a promising therapeutic target for developing novel anti-hepatitis C virus (HCV) drugs. In this work, a combined molecular modeling study was performed on a series of 193 5-hydroxy-2H-pyridazin-3-one derivatives as inhibitors of HCV NS5B Polymerase. The best 3D-QSAR models, including CoMFA and CoMSIA, are based on receptor (or docking). Furthermore, a 40-ns molecular dynamics (MD) simulation and binding free energy calculations using docked structures of NS5B with ten compounds, which have diverse structures and pIC50 values, were employed to determine the detailed binding process and to compare the binding modes of the inhibitors with different activities. On one side, the stability and rationality of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM-PBSA method gave a good correlation with the experimental biological activity. On the other side, by analyzing some differences between the molecular docking and the MD simulation results, we can find that the MD simulation could also remedy the defects of molecular docking. The analyses of the combined molecular modeling results have identified that Tyr448, Ser556, and Asp318 are the key amino acid residues in the NS5B binding pocket. The results from this study can provide some insights into the development of novel potent NS5B inhibitors. © 2013 John Wiley & Sons A/S.

Effects of the central potassium ions on the G-quadruplex and stabilizer binding.

PubMed

Wang, Zhiguo; Liu, Jun-Ping

2017-03-01

Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K + in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K + with the parallel G-quadruplex is a coordinated water directed step-wise process. The K + above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K + binding. Present molecular dynamics studies on the two most potent stabilizers RHPS4 and BRACO-19 reveal that the central K + has little influence on the binding conformations of the bound stabilizers. But without the central K + , either RHPS4 or BRACO-19 cannot stabilize the structure of G-quadruplex. The binding strength of stabilizers evaluated by the MM-PBSA method follows the order of BRACO-19> RHPS4, which agrees with the experimental results. The difference in binding affinities between RHPS4 and BRACO-19 is probably related to the ability to form intramolecular hydrogen bonds and favorable van del Waals interactions with G-quadruplex. In the models that have one central K + located at the upper/lower binding site, the corresponding top/bottom stacked stabilizers show more favorable binding affinities, indicating the apparent promoting effect of central K + on the stabilizer binding. Our findings provide further insights into the regulatory effect of K + on the G-quadruplex targeted binding, which is meaningful to the development of G-quadruplex stabilizers. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Dynamics Simulation of the Complex PBP-2x with Drug Cefuroxime to Explore the Drug Resistance Mechanism of Streptococcus suis R61

PubMed Central

Xia, Yingjie; Yang, Ming; Xiao, Jingfa; Yu, Jun

2012-01-01

Drug resistance of Streptococcus suis strains is a worldwide problem for both humans and pigs. Previous studies have noted that penicillin-binding protein (PBPs) mutation is one important cause of β-lactam antibiotic resistance. In this study, we used the molecular dynamics (MD) method to study the interaction differences between cefuroxime (CES) and PBP2x within two newly sequenced Streptococcus suis: drug-sensitive strain A7, and drug-resistant strain R61. The MM-PBSA results proved that the drug bound much more tightly to PBP2x in A7 (PBP2x-A7) than to PBP2x in R61 (PBP2x-R61). This is consistent with the evidently different resistances of the two strains to cefuroxime. Hydrogen bond analysis indicated that PBP2x-A7 preferred to bind to cefuroxime rather than to PBP2x-R61. Three stable hydrogen bonds were formed by the drug and PBP2x-A7, while only one unstable bond existed between the drug and PBP2x-R61. Further, we found that the Gln569, Tyr594, and Gly596 residues were the key mutant residues contributing directly to the different binding by pair wise energy decomposition comparison. By investigating the binding mode of the drug, we found that mutant residues Ala320, Gln553, and Thr595 indirectly affected the final phenomenon by topological conformation alteration. Above all, our results revealed some details about the specific interaction between the two PBP2x proteins and the drug cefuroxime. To some degree, this explained the drug resistance mechanism of Streptococcus suis and as a result could be helpful for further drug design or improvement. PMID:22563422

Molecular dynamics simulation of the complex PBP-2x with drug cefuroxime to explore the drug resistance mechanism of Streptococcus suis R61.

PubMed

Ge, Yan; Wu, Jiayan; Xia, Yingjie; Yang, Ming; Xiao, Jingfa; Yu, Jun

2012-01-01

Drug resistance of Streptococcus suis strains is a worldwide problem for both humans and pigs. Previous studies have noted that penicillin-binding protein (PBPs) mutation is one important cause of β-lactam antibiotic resistance. In this study, we used the molecular dynamics (MD) method to study the interaction differences between cefuroxime (CES) and PBP2x within two newly sequenced Streptococcus suis: drug-sensitive strain A7, and drug-resistant strain R61. The MM-PBSA results proved that the drug bound much more tightly to PBP2x in A7 (PBP2x-A7) than to PBP2x in R61 (PBP2x-R61). This is consistent with the evidently different resistances of the two strains to cefuroxime. Hydrogen bond analysis indicated that PBP2x-A7 preferred to bind to cefuroxime rather than to PBP2x-R61. Three stable hydrogen bonds were formed by the drug and PBP2x-A7, while only one unstable bond existed between the drug and PBP2x-R61. Further, we found that the Gln569, Tyr594, and Gly596 residues were the key mutant residues contributing directly to the different binding by pair wise energy decomposition comparison. By investigating the binding mode of the drug, we found that mutant residues Ala320, Gln553, and Thr595 indirectly affected the final phenomenon by topological conformation alteration. Above all, our results revealed some details about the specific interaction between the two PBP2x proteins and the drug cefuroxime. To some degree, this explained the drug resistance mechanism of Streptococcus suis and as a result could be helpful for further drug design or improvement.

A Computational Model for Docking of Noncompetitive Neuraminidase Inhibitors and Probing their Binding Interactions with Neuraminidase of Influenza Virus H5N1.

PubMed

Chintakrindi, Anand S; Martis, Elvis A F; Gohil, Devanshi J; Kothari, Sweta T; Chowdhary, Abhay S; Coutinho, Evans C; Kanyalkar, Meena A

2016-01-01

With cases of emergence of drug resistance to the current competitive inhibitors of neuraminidase (NA) such as oseltamivir and zanamavir, there is a present need for an alternative approach in the treatment of avian influenza. With this in view, some flavones and chalcones were designed based on quercetin, the most active naturally occurring noncompetitive inhibitor. We attempt to understand the binding of quercetin to H5N1-NA, and synthetic analogs of quercetin namely flavones and its precursors the chalcones using computational tools. Molecular docking was done using Libdock. Molecular dynamics (MD) simulations were performed using Amber14. We synthesized the two compounds; their structures were confirmed by infrared spectroscopy, 1H-NMR, and mass spectrometry. These molecules were then tested for H5N1-NA inhibition and kinetics of inhibition. Molecular docking studies yielded two compounds i.e., 4'-methoxyflavone and 2'-hydroxy-4-methoxychalcone, as promising leads which identified them as binders of the 150-cavity of NA. Furthermore, MD simulation studies revealed that quercetin and the two compounds bind and hold the 150 loop in its open conformation, which ultimately perturbs the binding of sialic acid in the catalytic site. Estimation of the free energy of binding by MM-PBSA portrays quercetin as more potent than chalcone and flavone. These molecules were then determined as non-competitive inhibitors from the Lineweaver-Burk plots rendered from the enzyme kinetic studies. We conclude that non-competitive type of inhibition, as shown in this study, can serve as an effective method to block NA and evade the currently seen drug resistance.

Characterization of Upper Eyelid Tarsus and Lid Wiper Dimensions.

PubMed

Navascues-Cornago, Maria; Maldonado-Codina, Carole; Gupta, Ruchi; Morgan, Philip B

2016-09-01

To measure various dimensions of the upper tarsal plate and the area of upper lid wiper staining. The repeatability of the method of measurement was investigated. Thirty-five healthy non-contact lens wearers were enrolled. The following parameters were measured from digital images of the upper eyelid captured with a slitlamp camera: length, height, and total area of the tarsal plate and area of lid wiper staining (lissamine green). Measurements were performed in a randomized and masked fashion on two separate occasions by the same investigator using ImageJ (National Institutes of Health). Coefficients of repeatability (COR) were calculated. The dimensions (mean±SD) of the tarsal plate were 20.6±1.9 mm length, 7.9±0.8 mm height, and 103.3±18.8 mm total area. The area of lid wiper staining was 2.7±2.0 mm. No association was found between tarsal dimensions and lid wiper staining (all P>0.05). Image analysis COR values were 0.6 mm tarsal length, 0.1 mm tarsal height, 1.2 mm tarsal area, and 0.4 mm lid wiper staining. There was no significant difference between repeated measurements for any parameter (all P>0.05). Limits of agreement were narrow for all parameters, indicating good agreement between repeated measurements. This work has demonstrated that there is a wide range in the dimensions of the upper tarsal plate in an urban UK population. No association was found between the upper tarsal dimensions and lid wiper staining. ImageJ was shown to be a repeatable method to measure the dimensions of the upper tarsal plate and upper lid wiper staining.

An Analysis of the Performance-Based Service Acquisition (PBSA) and Its Applicability to Hellenic Navy Service Acquisition Activities

DTIC Science & Technology

2012-12-01

potential offeror in response to its request must not be disclosed if doing so would reveal the potential offeror’s confidential business strategy...also the Navy Academy and the Navy hospital have and operate kitchen facilities. Ships have their own kitchen facilities too and dedicated personnel...abandoned. Now the HN dedicates personnel, has kitchen facilities to provide the food services and doing the whole process. The HN could outsource

Development of a biosensor for caffeine.

PubMed

Babu, V R Sarath; Patra, S; Karanth, N G; Kumar, M A; Thakur, M S

2007-01-23

We have utilized a microbe, which can degrade caffeine to develop an Amperometric biosensor for determination of caffeine in solutions. Whole cells of Pseudomonas alcaligenes MTCC 5264 having the capability to degrade caffeine were immobilized on a cellophane membrane with a molecular weight cut off (MWCO) of 3000-6000 by covalent crosslinking method using glutaraledhyde as the bifunctional crosslinking agent and gelatin as the protein based stabilizing agent (PBSA). The biosensor system was able to detect caffeine in solution over a concentration range of 0.1 to 1 mg mL(-1). With read-times as short as 3 min, this caffeine biosensor acts as a rapid analysis system for caffeine in solutions. Interestingly, successful isolation and immobilization of caffeine degrading bacteria for the analysis of caffeine described here was enabled by a novel selection strategy that incorporated isolation of caffeine degrading bacteria capable of utilizing caffeine as the sole source of carbon and nitrogen from soils and induction of caffeine degrading capacity in bacteria for the development of the biosensor. This biosensor is highly specific for caffeine and response to interfering compounds such as theophylline, theobromine, paraxanthine, other methyl xanthines and sugars was found to be negligible. Although a few biosensing methods for caffeine are reported, they have limitations in application for commercial samples. The development and application of new caffeine detection methods remains an active area of investigation, particularly in food and clinical chemistry. The optimum pH and temperature of measurement were 6.8 and 30+/-2 degrees C, respectively. Interference in analysis of caffeine due to different substrates was observed but was not considerable. Caffeine content of commercial samples of instant tea and coffee was analyzed by the biosensor and the results compared well with HPLC analysis.

5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

NASA Astrophysics Data System (ADS)

Jarmuła, Adam; Cieplak, Piotr; Montfort, William R.

2005-02-01

We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

[Drainage characteristic of the brain interstitial fluid detected by using fluorescence and magnetic tracer method].

PubMed

Zhao, Y; Li, Y Q; Li, H Y; Li, Y L; Liu, L X; Yuan, L; Zhang, S J; Han, H B

2017-04-18

Compare the results of molecular diffusion and mass flow in the interstitial space(ISS) displayed by using optical and magnetic probes and study partitioned drainage of the brain interstitial fluid (ISF). In the study, 36 male SD rats were randomly divided into fluorescent inspection group (18), magnetic tracer group (18). Then they were divided equally into caudate nucleus (Cn), thalamus (T) and substantia nigra (Sn) subgroup, 6 rats in each subgroup. Referencing the brain stereotaxic atlas, the coronal globus pallidus as center level, Cn, T or Sn were acted as puncture positioning target. A 10 μL microsyringe was stereotaxically positioned and the lucifer yellow (LY) solution of 2 μL 10 mmol/L was infused into centric position. The coronary slices undergo cardiac perfusion and fix respectively in time point Cn 3 h, T 2 h and Sn 1 h. The rat brain was placed in rat stainless steel brain matrices and cut backward along visual intersection. The injection point of coronal slice as the center level, take 3 slices in front of the center level and 2 slices behind of it. 1 mm for each slice and 6 slices in total. Then slices were detected by laser scanning confocal microscope (LSCM). Simultaneous, in the same coordinate brain regions of another three groups, a gadolinium-diethylene triamine pentaacetic acidm (Gd-DTPA) solution of 2 μL 10 mmol/L was infused into different injection and detected by MRI tracer-based method. Then the Radiant can be used to measure distribution area of Gd-DTPA. LY and Gd-DTPA have different distribution regions in Cn, T and Sn. After LY and Gd-DTPA were introduced into the Cn subgroup 3 h, compare the 1 to 6 levels distribution area of LY and Gd-DTPA as follows: (10.95±4.27) mm 2 vs. (8.33±2.25) mm 2 , (18.16±4.74) mm 2 vs. (16.42±2.88) mm 2 , (24.57±3.65) mm 2 vs. (20.75±2.29) mm 2 , (34.81±3.32) mm 2 vs. (28.88±1.51) mm 2 , (30.53±3.12) mm 2 vs. (20.92±2.75) mm 2 , (12.15±4.92) mm 2 vs. (10.00±1.89) mm 2 . The statistical analysis of every level was made by T test, and the difference of the distribution area between the two tracers were not statistically significant (t=0.940, P=0.400; t=0.546, P=0.614; t=1.534, P=0.200; t=2.809, P=0.480; t=2.693, P=0.055; t=0.707, P=0.518); After LY and Gd-DTPA were introduced into the T subgroup 2 h, compare the 1-6 levels distribution area of LY and Gd-DTPA as follows: (5.56±4.61) mm 2 vs. (3.33±2.25) mm 2 , (16.21±3.36) mm 2 vs. (11.42±2.88) mm 2 , (19.00±5.21) mm 2 vs. (15.75±2.29) mm 2 , (25.32±5.49) mm 2 vs. (22.33±3.25) mm 2 , (17.34±5.31) mm 2 vs. (15.92±2.75) mm 2 , (7.67±6.19) mm 2 vs. (5.00±1.89) mm 2 . The statistical analysis of every level was made by T test, and the difference of the distribution area between the two tracers were not statistically significant (t=0.753, P=0.493; t=1.875, P=0.134; t=0.990, P=0.378; t=0.810, P=0.464; t=0.413, P=0.701; t=0.716, P=0.514); After LY and Gd-DTPA were introduced into the Sn subgroup 1 h, compare the 1-6 levels distribution area of LY and Gd-DTPA as follows: (6.78±4.56) mm 2 vs. (4.75±2.00) mm 2 , (12.65±5.04) mm 2 vs. (10.44±1.13) mm 2 , (19.51±6.54) mm 2 vs. (17.55±0.30) mm 2 , (28.72±5.45) mm 2 vs. (24.48±1.32) mm 2 , (21.34±4.42) mm 2 vs. (17.72±0.25) mm 2 , (13.00±5.46) mm 2 vs. (12.00±2.88) mm 2 . The statistical analysis of every level was made by T test and the difference of the distribution area between the two tracers were not statistically significant (t=0.705, P=0.519; t=0.743, P=0.499; t=0.517, P=0.656; t=1.310, P=0.260; t=1.416, P=0.292; t=0.281, P=0.793), but the distribution area of LY is slightly more than Gd-DTPA. LSCM imaging technology confirmed partitioned drainage of the brain ISF found by MRI tracer-based method and provided technology and method validation for MRI tracer-based method. LSCM imaging technology with higher contrast and resolution, therefore more sophisticated partitioned drainage of the brain interstitial fluid were got.

Efficacy of contraceptive methods: a review of the literature.

PubMed

Mansour, Diana; Inki, Pirjo; Gemzell-Danielsson, Kristina

2010-12-01

To provide a comprehensive and objective summary of contraceptive failure rates for a variety of methods based on a systematic review of the literature. Medline and Embase were searched using the Ovid interface from January 1990 to February 2008, as well as the reference lists of published articles, to identify studies reporting contraceptive efficacy as a Pearl Index or life-table estimate. Reports that recruited less than 400 subjects per study group and those covering less than six cycles/six months were excluded. In addition, unlicensed products or those not internationally available, emergency contraception, and vasectomy studies were excluded. Information was identified and extracted from 139 studies. One-year Pearl Indices reported for short-acting user-dependent hormonal methods were generally less than 2.5. Gross life-table rates for long-acting hormonal methods (implants and the levonorgestrel releasing-intrauterine system [LNG-IUS]) generally ranged between 0-0.6 per 100 at one year, but wider ranges (0.1-1.5 per 100) were observed for the copper intrauterine devices (0.1-1.4 per 100 for Cu-UIDs with surface area ≥ 300 mm2 and 0.6-1.5 per 100 for those with surface area < 300 mm2). Barrier and natural methods were the least effective. Our review broadly confirms the hierarchy of contraceptive effectiveness in descending order as: (1) female sterilisation, long-acting hormonal contraceptives (LNG-IUS and implants); (2) Cu-IUDs with ≥ 300 mm2 surface area; (3) Cu-IUDs with < 300 mm2 surface area and short-acting hormonal contraceptives ( injectables, oral contraceptives, the patch and vaginal rings), (4) barrier methods and natural methods.

Efficacy of contraceptive methods: A review of the literature.

PubMed

Mansour, Diana; Inki, Pirjo; Gemzell-Danielsson, Kristina

2010-02-01

To provide a comprehensive and objective summary of contraceptive failure rates for a variety of methods based on a systematic review of the literature. Medline and Embase were searched using the Ovid interface from January 1990 to February 2008, as well as the reference lists of published articles, to identify studies reporting contraceptive efficacy as a Pearl Index or life-table estimate. Reports that recruited less than 400 subjects per study group and those covering less than six cycles/six months were excluded. In addition, unlicensed products or those not internationally available, emergency contraception, and vasectomy studies were excluded. Information was identified and extracted from 139 studies. One-year Pearl Indices reported for short-acting user-dependent hormonal methods were generally less than 2.5. Gross life-table rates for long-acting hormonal methods (implants and the levonorgestrel releasing-intrauterine system [LNG-IUS]) generally ranged between 0-0.6 per 100 at one year, but wider ranges (0.1-1.5 per 100) were observed for the copper intrauterine devices (0.1-1.4 per 100 for Cu-IUDs with surface area > or =300 mm( 2 ) and 0.6-1.5 per 100 for those with surface area <300 mm( 2 )). Barrier and natural methods were the least effective. Our review broadly confirms the hierarchy of contraceptive effectiveness in descending order as: (1) female sterilisation, long-acting hormonal contraceptives (LNG-IUS and implants); (2) Cu-IUDs with > or =300 mm( 2 ) surface area; (3) Cu-IUDs with <300 mm( 2 ) surface area and short-acting hormonal contraceptives (injectables, oral contraceptives, the patch and vaginal ring), and (4) barrier methods and natural methods.

In silico study of carvone derivatives as potential neuraminidase inhibitors.

PubMed

Jusoh, Noorakmar; Zainal, Hasanuddin; Abdul Hamid, Azzmer Azzar; Bunnori, Noraslinda M; Abd Halim, Khairul Bariyyah; Abd Hamid, Shafida

2018-03-15

Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites. Docking simulations revealed that ligand A18 has the lowest energy binding (∆G bind ) value of -8.30 kcal mol -1 , comparable to OTV with ∆G bind of -8.72 kcal mol -1 . A18 formed seven hydrogen bonds (H-bonds) at residues Arg292, Arg371, Asp151, Trp178, Glu227, and Tyr406, while eight H-bonds were formed by OTV with amino acids Arg118, Arg292, Arg371, Glu119, Asp151, and Arg152. Molecular dynamics (MD) simulation was conducted to compare the stability between ligand A18 and OTV with NA. Our simulation study showed that the A18-NA complex is as stable as the OTV-NA complex during the MD simulation of 50 ns through the analysis of RMSD, RMSF, total energy, hydrogen bonding, and MM/PBSA free energy calculations.

Homology modelling, molecular docking, and molecular dynamics simulations reveal the inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase enzyme by Withaferin-A.

PubMed

Vadloori, Bharadwaja; Sharath, A K; Prabhu, N Prakash; Maurya, Radheshyam

2018-04-16

Present in silico study was carried out to explore the mode of inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase (Ld DHFR-TS) enzyme by Withaferin-A, a withanolide isolated from Withania somnifera. Withaferin-A (WA) is known for its profound multifaceted properties, but its antileishmanial activity is not well understood. The parasite's DHFR-TS enzyme is diverse from its mammalian host and could be a potential drug target in parasites. A 3D model of Ld DHFR-TS enzyme was built and verified using Ramachandran plot and SAVES tools. The protein was docked with WA-the ligand, methotrexate (MTX)-competitive inhibitor of DHFR, and dihydrofolic acid (DHFA)-substrate for DHFR-TS. Molecular docking studies reveal that WA competes for active sites of both Hu DHFR and TS enzymes whereas it binds to a site other than active site in Ld DHFR-TS. Moreover, Lys 173 residue of DHFR-TS forms a H-bond with WA and has higher binding affinity to Ld DHFR-TS than Hu DHFR and Hu TS. The MD simulations confirmed the H-bonding interactions were stable. The binding energies of WA with Ld DHFR-TS were calculated using MM-PBSA. Homology modelling, molecular docking and MD simulations of Ld DHFR-TS revealed that WA could be a potential anti-leishmanial drug.

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scanning system for angle-resolved low-coherence interferometry.

PubMed

Steelman, Zachary A; Ho, Derek; Chu, Kengyeh K; Wax, Adam

2017-11-15

Angle-resolved low-coherence interferometry (a/LCI) detects precancer by enabling depth-resolved measurements of nuclear morphology in vivo. A significant limitation of a/LCI is the point-probe nature of the method, sampling <0.5  mm 2 before probe relocation is necessary. In this work, we demonstrate a scanning method capable of assessing an area >100  mm 2 without repositioning. By utilizing a reflection-only three-optic rotator prism and a two-axis scanning mirror, we demonstrate radial scans of a sample with a linear range of 12 mm and a full rotational range of 180°. Use of this design will improve the diagnostic utility of a/LCI for wide-area screening of tissue health.

A scanning system for angle-resolved low-coherence interferometry

PubMed Central

Steelman, Zachary A.; Ho, Derek; Chu, Kengyeh K.; Wax, Adam

2018-01-01

Angle-resolved low-coherence interferometry (a/LCI) detects precancer by enabling depth-resolved measurements of nuclear morphology in vivo. A significant limitation of a/LCI is the point-probe nature of the method, sampling <0.5 mm2 before probe relocation is necessary. In this work, we demonstrate a scanning method capable of assessing an area >100 mm2 without repositioning. By utilizing a reflection-only three-optic rotator (ROTOR) prism and two-axis scanning mirror, we demonstrate radial scans of a sample with a linear range of 12 mm and a full rotational range of 180°. Use of this design will improve the diagnostic utility of a/LCI for wide-area screening of tissue health. PMID:29140317

SU-F-T-272: Patient Specific Quality Assurance of Prostate VMAT Plans with Portal Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darko, J; Osei, E; University of Waterloo, Waterloo, ON

Purpose: To evaluate the effectiveness of using the Portal Dosimetry (PD) method for patient specific quality assurance of prostate VMAT plans. Methods: As per institutional protocol all VMAT plans were measured using the Varian Portal Dosimetry (PD) method. A gamma evaluation criterion of 3%-3mm with a minimum area gamma pass rate (gamma <1) of 95% is used clinically for all plans. We retrospectively evaluated the portal dosimetry results for 170 prostate patients treated with VMAT technique. Three sets of criterions were adopted for re-evaluating the measurements; 3%-3mm, 2%-2mm and 1%-1mm. For all criterions two areas, Field+1cm and MLC-CIAO were analysed.Tomore » ascertain the effectiveness of the portal dosimetry technique in determining the delivery accuracy of prostate VMAT plans, 10 patients previously measured with portal dosimetry, were randomly selected and their measurements repeated using the ArcCHECK method. The same criterion used in the analysis of PD was used for the ArcCHECK measurements. Results: All patient plans reviewed met the institutional criteria for Area Gamma pass rate. Overall, the gamma pass rate (gamma <1) decreases for 3%-3mm, 2%-2mm and 1%-1mm criterion. For each criterion the pass rate was significantly reduced when the MLC-CIAO was used instead of FIELD+1cm. There was noticeable change in sensitivity for MLC-CIAO with 2%-2mm criteria and much more significant reduction at 1%-1mm. Comparable results were obtained for the ArcCHECK measurements. Although differences were observed between the clockwise verses the counter clockwise plans in both the PD and ArcCHECK measurements, this was not deemed to be statistically significant. Conclusion: This work demonstrates that Portal Dosimetry technique can be effectively used for quality assurance of VMAT plans. Results obtained show similar sensitivity compared to ArcCheck. To reveal certain delivery inaccuracies, the use of a combination of criterions may provide an effective way in improving the overall sensitivity of PD. Funding provided in part by the Prostate Ride for Dad, Kitchener-Waterloo, Canada.« less

The Right Tool for the Job: Detection of Soil-Transmitted Helminths in Areas Co-endemic for Other Helminths

PubMed Central

Periago, Maria V.; Diniz, Renata C.; Pinto, Simone A.; Yakovleva, Anna; Correa-Oliveira, Rodrigo; Diemert, David J.; Bethony, Jeffrey M.

2015-01-01

Background Due to the recent increased use of the McMaster (MM) fecal egg counting method for assessing benzimidazole drug efficacy for treating soil-transmitted helminth (STH) infections, the aim of the current study was to determine the operational value of including the MM method alongside the Kato-Katz (KK) fecal thick smear to increase the diagnostic sensitivity when STHs are co-endemic with trematode helminths (e.g., Schistosoma mansoni). Methods A cross-sectional study was conducted in school-aged children aged 4-18 years in the northeastern region of the State of Minas Gerais (Brazil), where Necator americanus, Ascaris lumbricoides, Trichuris trichiura, and S. mansoni are co-endemic. One fecal sample from each participant was collected and transported to the field laboratory for analysis. Coprological diagnosis was performed on each fecal sample by three different methods: Formalin-Ether Sedimentation (FES), KK and the MM technique. The diagnostic sensitivity and negative predictive value (NPV) of each technique was calculated using the combination of all three techniques as the composite standard. In order to determine the agreement between the three techniques Fleiss´ kappa was used. Both the Cure Rate (CR) and the Fecal Egg Count Reduction (FECR) were calculated using the two quantification techniques (i.e., the MM and KK). Results Fecal samples from 1260 children were analyzed. The KK had higher diagnostic sensitivity than the MM for the detection of both A. lumbricoides (KK 97.3%, MM 69.5%) and hookworm (KK 95.1%, MM 80.8%). The CR of a single dose of mebendazole varied significantly between the KK and MM for both A. lumbricoides (p = 0.016) and hookworm (p = 0.000), with lower rates obtained with the KK. On the other hand, the FECR was very similar between both techniques for both A. lumbricoides and hookworm. Conclusion The MM did not add any diagnostic value over the KK in areas where both STHs and trematodes were co-endemic. The lower sensitivity of the MM would have an important impact on the administration of selective school-based treatment in this area since if only the MM were used, 36 (13.9%) children diagnosed with A. lumbricoides would have gone untreated. PMID:26241329

Development of a (147)Pm source for beta-backscatter thickness gauge applications.

PubMed

Kumar, Manoj; Udhayakumar, J; Nuwad, J; Shukla, Rakesh; Pillai, C G S; Dash, Ashutosh; Venkatesh, Meera

2011-03-01

This paper describes a method for the preparation of (147)Pm sources, utilized in the determination of graphite coating thickness on the inner surface of the zircaloy cladding tube of nuclear fuels. (147)Pm was adsorbed on a limited surface area [1.5mm (ϕ)×2mm (l)] of a cylindrical aluminum rod [1.5mm (ϕ)×10mm (l)]. In brief, the selected tip area [1.5mm (ϕ)×2mm (l)] was anodized at a current density of 15mA/cm(2) at 15°C in 3M·H(2)SO(4) for 2h followed by immersion of this area in 10μL of (147)Pm solution containing 37MBq (1mCi) of activity at pH 6.0 for 24h. The radioactive area was subsequently covered with a thin layer of Polymethyl Methacrylate (PMMA) to prevent leaching of (147)Pm from the source. The quantity of incorporated (147)Pm activity was assayed in a calibrated ion chamber. Quality control tests were carried out to ensure nonleachability, uniform distribution of activity and stability of the sources. Copyright © 2010 Elsevier Ltd. All rights reserved.

Sensitivity and specificity of a new MRI method evaluating temporo-mandibular joint disc-condyle relationships: an in vivo study.

PubMed

Benbelaïd, R; Fleiter, B

2006-03-01

The aim of this study was to evaluate sensitivity and specificity of a new method to locate temporo-mandibular joint (TMJ) disc using magnetic resonance imaging (MRI) and analyze disc-condyle relationships, in asymptomatic subjects and patients with disc displacement. Twenty-nine sagittal MRI of 16 subjects, 8 asymptomatic volunteers and 8 subjects with anterior disc displacement, were carried out during controlled opening from intercuspal position up to a 25 mm opening. Selected sections were analyzed with a graphic computerized system of coordinates. The total surface area (TS) of disc section was separated into anterior surface area (AS) and posterior surface area. Areas were determined by computer. Two trained examiners drew images at random. The reliability of AS/TS ratio index was evaluated in a previous study. AS/TS ratio sensitivity (Se) and specificity (Sp) were calculated closed mouth, 5 mm open and 25 mm open mouth. Best sensitivity (Se=0.63) and specificity (Sp=0.81) were obtained when MRI was realized with closed mouth and 25 mm open mouth. Lower sensitivity was observed when MRI was performed either with closed mouth (Se=0.54) or 25 mm open mouth (Se=0.18). Lower specificity was observed with 5 mm open mouth (Sp=0.68). In conclusion, it was confirmed as well that MRI of anterior disc displacement should be performed with closed mouth and opened mouth. Thus, further studies are required to assess disc displacement and mechanical alterations and to evaluate the risk of direct damage on TMJ tissues.

Research on Methods of High Coherent Target Extraction in Urban Area Based on Psinsar Technology

NASA Astrophysics Data System (ADS)

Li, N.; Wu, J.

2018-04-01

PSInSAR technology has been widely applied in ground deformation monitoring. Accurate identification of Persistent Scatterers (PS) is key to the success of PSInSAR data processing. In this paper, the theoretic models and specific algorithms of PS point extraction methods are summarized and the characteristics and applicable conditions of each method, such as Coherence Coefficient Threshold method, Amplitude Threshold method, Dispersion of Amplitude method, Dispersion of Intensity method, are analyzed. Based on the merits and demerits of different methods, an improved method for PS point extraction in urban area is proposed, that uses simultaneously backscattering characteristic, amplitude and phase stability to find PS point in all pixels. Shanghai city is chosen as an example area for checking the improvements of the new method. The results show that the PS points extracted by the new method have high quality, high stability and meet the strong scattering characteristics. Based on these high quality PS points, the deformation rate along the line-of-sight (LOS) in the central urban area of Shanghai is obtained by using 35 COSMO-SkyMed X-band SAR images acquired from 2008 to 2010 and it varies from -14.6 mm/year to 4.9 mm/year. There is a large sedimentation funnel in the cross boundary of Hongkou and Yangpu district with a maximum sedimentation rate of more than 14 mm per year. The obtained ground subsidence rates are also compared with the result of spirit leveling and show good consistent. Our new method for PS point extraction is more reasonable, and can improve the accuracy of the obtained deformation results.

Fabrication of a Horizontal and a Vertical Large Surface Area Nanogap Electrochemical Sensor

PubMed Central

Hammond, Jules L.; Rosamond, Mark C.; Sivaraya, Siva; Marken, Frank; Estrela, Pedro

2016-01-01

Nanogap sensors have a wide range of applications as they can provide accurate direct detection of biomolecules through impedimetric or amperometric signals. Signal response from nanogap sensors is dependent on both the electrode spacing and surface area. However, creating large surface area nanogap sensors presents several challenges during fabrication. We show two different approaches to achieve both horizontal and vertical coplanar nanogap geometries. In the first method we use electron-beam lithography (EBL) to pattern an 11 mm long serpentine nanogap (215 nm) between two electrodes. For the second method we use inductively-coupled plasma (ICP) reactive ion etching (RIE) to create a channel in a silicon substrate, optically pattern a buried 1.0 mm × 1.5 mm electrode before anodically bonding a second identical electrode, patterned on glass, directly above. The devices have a wide range of applicability in different sensing techniques with the large area nanogaps presenting advantages over other devices of the same family. As a case study we explore the detection of peptide nucleic acid (PNA)−DNA binding events using dielectric spectroscopy with the horizontal coplanar device. PMID:27983655

Pedicle distraction increases intervertebral and spinal canal area in a cadaver and bone model

PubMed Central

Hughes, Matthew; Papadakos, Nikolaos; Bishop, Tim; Bernard, Jason

2018-01-01

Introduction: Lumbar spinal stenosis is degenerative narrowing of the spinal canal and/or intervertebral foramen causing compression of the spinal cord and nerve roots. Traditional decompression techniques can often cause significant trauma and vertebral instability. This paper evaluates a method of increasing pedicle length to decompress the spinal and intervertebral foramen, which could be done minimally invasive. Methods: Three Sawbone (Sawbones Europe, Sweden) and 1 cadaveric lumbar spine underwent bilateral pedicle distraction at L4. A pedicle channel was drilled between the superior articular process and transverse process into the vertebral body. The pedicles underwent osteotomy at the midpoint. Screws were inserted bilaterally and fixated distraction of 0 mm, 2 mm, 4 mm and 6 mm. CT images were taken at each level of distraction. Foramen area was measured in the sagittal plane at L3/4. Spinal canal area was measured at L4 in the axial images. The cadaver was used to evaluate safety of osteotomy and soft tissue interactions preventing distraction. Statistical analysis was by student paired t-test and Pearson rank test. Results: Increasing distraction led to greater Spinal canal area. From 4.27 cm2 to 5.72 cm2 (p = 0.002) with 6 mm distraction. A Maximal increase of 34.1%. Vertebral foramen area also increased with increasing pedicle distraction. From 2.43 cm2 to 3.22 cm2 (p = 0.022) with 6 mm distraction. A maximal increase of 32.3%. The cadaver spinal canal increased in area by 21.7%. The vertebral foramen increased in area by 36.2% (left) and 22.6% (right). Discussion: For each increase in pedicle distraction the area of the spinal and vertebral foramen increases. Pedicle distraction could potentially be used to alleviate spinal stenosis and root impingement. A potential osteotomy plane could be at the midpoint of the pedicle with minimal risk to nerve roots and soft tissue restrictions to prevent distraction. PMID:29727270

Use of Persistent Scatterer Interferometry to Assess Land Deformation in the Nile Delta and its Controlling Factors

NASA Astrophysics Data System (ADS)

Gebremichael, E.; Sultan, M.; Becker, R.; Emil, M.; Ahmed, M.; Chouinard, K.

2015-12-01

We applied Persistent scatterer interferometry (PSInSAR) to assess land deformation (subsidence and uplift) across the entire Nile delta and its surroundings and to identify possible causes of the observed deformation. For the purpose of the present study, 100 Envisat Advanced Synthetic Aperture Radar (ASAR; level 0) scenes that were acquired along four tracks and covering a time span of seven years (2004 to 2010) were used. The scenes extend from the Mediterranean coast in the north to Cairo city in the south. These scenes were focused using Repeat Orbit Interferometry PACkage (ROI_PAC) software and the subsequent PSI processing was done using the Stanford Method for Persistent Scatterers (StaMPS) method. A low coherence threshold (0.2) was used to decrease the impact of vegetation-related poor coherence and decorrelation of the scenes over the investigated time span. Subsidence was observed over: (1) the Demietta Nile River branch (3 to 14 mm/yr) where it intersects the Mediterranean coastline, (2) thick (~ 40 m) Holocene sediments in lake Manzala (up to 9 mm/yr), (3) reclaimed desert areas (west of Nile Delta; up to 12 mm/yr) of high groundwater extraction, (4) along parts of a previously proposed flexure line (up to 10 mm/yr), and (5) along the eastern sections of the Mediterranean coastline (up to 15.7 mm/yr). The city of Alexandria (underlain by carbonate platform) and the terminus of the Rosetta branch of the Nile River seem to experience almost no ground movement (mean subsidence of 0.28 mm/yr and 0.74 mm/yr respectively) while the cities of Ras Elbar and Port Said (underlain by thick Holocene sediment) exhibit the highest subsidence values (up to 14 mm/yr and 8.5 mm/yr respectively). The city of Cairo has also experienced subsidence in limited areas of up to 7.8 mm/yr. High spatial correlation was also observed between the subsiding areas and the Abu Madi incised valley; the largest gas field in the Nile Delta. Most of the area undergoing subsidence in the Nile Delta is related to sediment compaction and/or groundwater extraction, with other factors such as gas extraction and tectonic drivers correlating with smaller areas.

COMPARISON OF MANUAL AND SEMIAUTOMATED FUNDUS AUTOFLUORESCENCE ANALYSIS OF MACULAR ATROPHY IN STARGARDT DISEASE PHENOTYPE.

PubMed

Kuehlewein, Laura; Hariri, Amir H; Ho, Alexander; Dustin, Laurie; Wolfson, Yulia; Strauss, Rupert W; Scholl, Hendrik P N; Sadda, SriniVas R

2016-06-01

To evaluate manual and semiautomated grading techniques for assessing decreased fundus autofluorescence (DAF) in patients with Stargardt disease phenotype. Certified reading center graders performed manual and semiautomated (region finder-based) grading of confocal scanning laser ophthalmoscopy (cSLO) fundus autofluorescence (FAF) images for 41 eyes of 22 patients. Lesion types were defined based on the black level and sharpness of the border: definite decreased autofluorescence (DDAF), well, and poorly demarcated questionably decreased autofluorescence (WDQDAF, PDQDAF). Agreement in grading between the two methods and inter- and intra-grader agreement was assessed by kappa coefficients (κ) and intraclass correlation coefficients (ICC). The mean ± standard deviation (SD) area was 3.07 ± 3.02 mm for DDAF (n = 31), 1.53 ± 1.52 mm for WDQDAF (n = 9), and 6.94 ± 10.06 mm for PDQDAF (n = 17). The mean ± SD absolute difference in area between manual and semiautomated grading was 0.26 ± 0.28 mm for DDAF, 0.20 ± 0.26 mm for WDQDAF, and 4.05 ± 8.32 mm for PDQDAF. The ICC (95% confidence interval) for method comparison was 0.992 (0.984-0.996) for DDAF, 0.976 (0.922-0.993) for WDQDAF, and 0.648 (0.306-0.842) for PDQDAF. Inter- and intra-grader agreement in manual and semiautomated quantitative grading was better for DDAF (0.981-0.996) and WDQDAF (0.995-0.999) than for PDQDAF (0.715-0.993). Manual and semiautomated grading methods showed similar levels of reproducibility for assessing areas of decreased autofluorescence in patients with Stargardt disease phenotype. Excellent agreement and reproducibility were observed for well demarcated lesions.

Characterization of the Correct Mandibular Premolar Region for Delayed Dental Implantation in Beagle Dogs.

PubMed

Xie, Chenxi; Fu, Xiaoming; Xu, Ling; Xu, Sheng

2018-05-01

For delayed dental implantation into the mandible, the implant size should be chosen according to the characteristics of that bone. This study investigated anatomic features of the mandible in beagle dogs, to develop recommendations regarding the correct implantation region and available bone area for delayed dental implantation surgery. We used 20 healthy male beagle dogs to create delayed dental implantation models. The dogs' mandibles underwent cone beam CT (CBCT) imaging; the locations of the middle mental foramen and canine root apex were measured on CBCT images. The dogs then were euthanized and their mandibles measured by using a digital vernier caliper. In addition, the correct implantation region and available bone areas were evaluated. The data obtained by using the 2 measuring methods were compared statistically. The results showed that the positions of the middle mental foramen and canine root apex were relatively fixed, with little variation. The implantation and available bone regions showed little variation among dogs and did not differ significantly between the 2 measuring methods. In conclusion, the correct implantation region (mean ± 1 SD) in the beagle mandible for delayed dental implantation surgery was 17.53 ± 0.46 mm in width. The recommended available bone areas (height × width) were 7.22 ± 0.68 mm × 5.32 ± 0.49 mm (P2), 8.21 ± 0.71 mm × 5.81 ± 0.56 mm (P3), and 9.17 ± 0.65 mm × 6.39 ± 0.56 mm (P4) in the premolar region.

Quantitative optical frequency domain imaging assessment of in-stent structures in patients with ST-segment elevation myocardial infarction: impact of imaging sampling rate.

PubMed

Muramatsu, Takashi; García-García, Hector M; Lee, Il Soo; Bruining, Nico; Onuma, Yoshinobu; Serruys, Patrick W

2012-01-01

The impact of the sampling rate (SR) of optical frequency domain imaging (OFDI) on quantitative assessment of in-stent structures (ISS) such as plaque prolapse and thrombus remains unexplored. OFDI after stenting was performed in ST-segment elevation myocardial infarction (STEMI) patients using a TERUMO OFDI system (Terumo Europe, Leuven, Belgium) with 160 frames/s and pullback speed of 20 mm/s. A total of 126 stented segments were analyzed. ISS were classified as either attached or non-attached to stent area boundaries. The volume, mean area and largest area of ISS were assessed according to 4 frequencies of SR, corresponding to distances between the analyzed frames of 0.125, 0.25, 0.50 and 1.0 mm. ISS volume was calculated by integrating cross-sectional ISS areas multiplied by each sampling distance using the disk summation method. The volume and mean area of ISS became significantly larger, while the largest area became significantly smaller as sampling distance became larger (1.11 mm(2) for 0.125 mm vs. 1.00 mm(2) for 1.0 mm, P for trend=0.036). In addition, variance of difference was positively associated with increasing width of sampling distance. Quantification of ISS is significantly influenced by the applied frequency of SR. This should be taken into account when designing future OFDI studies in which quantitative assessment of ISS is critical for the evaluation of STEMI patients.

Morphometric analysis of pulp size in maxillary permanent central incisors correlated with age: An indirect digital study

PubMed Central

Ravindra, S. V.; Mamatha, G. P.; Sunita, J. D.; Balappanavar, Aswini Y.; Sardana, Varun

2015-01-01

Context: Teeth are hardest part of the body and are least affected by the taphonomic process. They are considered as one of the reliable methods of identification of a person in forensic sciences. Aim: The aim of the following study is to establish morphometeric measurements by AutoCad 2009 (Autodesk, Inc) of permanent maxillary central incisors in different age groups of Udaipur population. Setting and Design: Hospital-based descriptive cross-sectional study carried out in Udaipur. Materials and Methods: A study was carried out on 308 subjects of both genders with the age range of 9-68 years. Standardized intra-oral radiographs were made by paralleling technique and processed. The radiographs were scanned and the obtained images were standardized to the actual size of radiographic film. This was followed by measuring them using software AutoCad 2009. Statistical Analysis Used: F-test, post-hoc test, Pearson's correlation test. Results: For left maxillary central incisor, the total pulp area was found to be of 38.41 ± 12.88 mm and 14.32 ± 7.04 mm respectively. For right maxillary central incisor, the total pulp size was 38.39 ± 14.95 mm and 12.35 ± 5 mm respectively. Males (32.50, 32.87 mm2) had more pulp area when compared with females (28.82, 30.05 mm2). Conclusion: There was a decrease in total pulp area with increasing age which may be attributed to secondary dentin formation. PMID:26816461

Quantitative Comparison of Retrosigmoid Intradural Suprameatal Approach and Retrosigmoid Transtentorial Approach: Implications for Tumors in the Petroclival Region

PubMed Central

Ambekar, Sudheer; Amene, Chiazo; Sonig, Ashish; Guthikonda, Bharat; Nanda, Anil

2013-01-01

Background Retrosigmoid transtentorial (RTT) and retrosigmoid intradural suprameatal (RISA) approaches have been used in the treatment of petroclival tumors. Objective To compare the area of exposure of brainstem and petroclival region obtained through RTT and RISA in cadaveric specimens. Methods Five cadaveric specimens with a total of 10 sides were analyzed. RTT and RISA were performed on five sides each. Brainstem and petroclival surface exposure were measured using both the approaches. These values were compared between the two approaches. Results Brainstem area exposure with RTT was 441 ± 63 mm2 and that with RISA was 311 ± 61 mm2. Student's t-test revealed that the difference was significant (p = 0.01). The area of petroclival exposure medial to the Meckel cave through RTT was 696 ± 57 mm2, and that through RISA was 716 ± 51 mm2 (p = 0.69). The area of brainstem exposure between V and VII-VII complex through RTT and RISA was 387 ± 86 mm2 and 378 ± 76 mm2 (p = 0.87). Conclusion The RTT approach is an excellent approach to ventrolateral brainstem and petroclival region. It provides greater superoventral exposure of the ventrolateral brainstem than RISA and provides similar petroclival exposure. PMID:24436928

Evidence that Chemical Chaperone 4-Phenylbutyric Acid Binds to Human Serum Albumin at Fatty Acid Binding Sites

PubMed Central

James, Joel; Shihabudeen, Mohamed Sham; Kulshrestha, Shweta; Goel, Varun; Thirumurugan, Kavitha

2015-01-01

Endoplasmic reticulum stress elicits unfolded protein response to counteract the accumulating unfolded protein load inside a cell. The chemical chaperone, 4-Phenylbutyric acid (4-PBA) is a FDA approved drug that alleviates endoplasmic reticulum stress by assisting protein folding. It is found efficacious to augment pathological conditions like type 2 diabetes, obesity and neurodegeneration. This study explores the binding nature of 4-PBA with human serum albumin (HSA) through spectroscopic and molecular dynamics approaches, and the results show that 4-PBA has high binding specificity to Sudlow Site II (Fatty acid binding site 3, subdomain IIIA). Ligand displacement studies, RMSD stabilization profiles and MM-PBSA binding free energy calculation confirm the same. The binding constant as calculated from fluorescence spectroscopic studies was found to be kPBA = 2.69 x 105 M-1. Like long chain fatty acids, 4-PBA induces conformational changes on HSA as shown by circular dichroism, and it elicits stable binding at Sudlow Site II (fatty acid binding site 3) by forming strong hydrogen bonding and a salt bridge between domain II and III of HSA. This minimizes the fluctuation of HSA backbone as shown by limited conformational space occupancy in the principal component analysis. The overall hydrophobicity of W214 pocket (located at subdomain IIA), increases upon occupancy of 4-PBA at any FA site. Descriptors of this pocket formed by residues from other subdomains largely play a role in compensating the dynamic movement of W214. PMID:26181488

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides.

PubMed

Bruce, Neil J; Chen, Deliang; Dastidar, Shubhra G; Marks, Gabriel E; Schein, Catherine H; Bryce, Richard A

2010-11-01

Accumulation and aggregation of the 42-residue amyloid-β (Aβ) protein fragment, which originates from the cleavage of amyloid precursor protein by β and γ secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the Aβ sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of Aβ and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LPFFD) and inactive (LHFFD) β-sheet breaker peptide with an Aβ fibril structure from solid-state NMR studies. We found that LHFFD had a weaker interaction with the fibril than the active peptide, LPFFD, from geometric and energetic considerations, as estimated by the MM/PBSA approach. Cluster analysis and computational alanine scanning identified important ligand-fibril contacts, including a possible difference in the effect of histidine on ligand-fibril π-stacking interactions, and the role of the proline residue in establishing contacts that compete with those essential for maintenance of the inter-monomer β-sheet structure of the fibril. Our results show that molecular dynamics simulations can be a useful way to classify the stability of docking sites. These mechanistic insights into the ability of LPFFD to reverse aggregation of toxic Aβ will guide the redesign of lead compounds, and aid in developing realistic therapies for AD and other diseases of protein aggregation. Copyright © 2010 Elsevier Inc. All rights reserved.

Synthesis, antiviral evaluation and molecular docking studies of N4-aryl substituted/unsubstituted thiosemicarbazones derived from 1-indanones as potent anti-bovine viral diarrhea virus agents.

PubMed

Soraires Santacruz, María C; Fabiani, Matías; Castro, Eliana F; Cavallaro, Lucía V; Finkielsztein, Liliana M

2017-08-01

A series of N 4 -arylsubstituted thiosemicarbazones derived from 1-indanones and a set of compounds lacking such substitution in the N 4 position of the thiosemicarbazone moiety were synthesized and evaluated for their anti-bovine viral diarrhea virus (BVDV) activity. Among these, derivatives 2 and 15 displayed high activity (EC 50 =2.7±0.4 and 0.7±0.1µM, respectively) as inhibitors of BVDV replication. Novel key structural features related to the anti-BVDV activity were identified by structure-activity relationship (SAR) analysis. In a previous study, the thiosemicarbazone of 5,6-dimethoxy-1-indanone (5,6-TSC) was characterized as a non-nucleoside inhibitor (NNI) of the BVDV RNA-dependent RNA polymerase. In the present work, cross-resistance assays were performed with the most active compounds. Such studies were carried out on 5,6-TSC resistant BVDV (BVDV-TSC r T1) carrying mutations in the viral polymerase. This BVDV mutant was also resistant to compound 15. Molecular docking studies and MM/PBSA calculations were performed to assess the most active derivatives at the 5,6-TSC viral polymerase binding site. The differences in the interaction pattern and the binding affinity of derivative 15 either to the wild type or BVDV-TSC r T1 polymerase were key factors to define the mode of action of this compound. Copyright © 2017 Elsevier Ltd. All rights reserved.

A fully automatic approach to register mobile mapping and airborne imagery to support the correction of platform trajectories in GNSS-denied urban areas

NASA Astrophysics Data System (ADS)

Jende, Phillipp; Nex, Francesco; Gerke, Markus; Vosselman, George

2018-07-01

Mobile Mapping (MM) solutions have become a significant extension to traditional data acquisition methods over the last years. Independently from the sensor carried by a platform, may it be laser scanners or cameras, high-resolution data postings are opposing a poor absolute localisation accuracy in urban areas due to GNSS occlusions and multipath effects. Potentially inaccurate position estimations are propagated by IMUs which are furthermore prone to drift effects. Thus, reliable and accurate absolute positioning on a par with MM's high-quality data remains an open issue. Multiple and diverse approaches have shown promising potential to mitigate GNSS errors in urban areas, but cannot achieve decimetre accuracy, require manual effort, or have limitations with respect to costs and availability. This paper presents a fully automatic approach to support the correction of MM imaging data based on correspondences with airborne nadir images. These correspondences can be employed to correct the MM platform's orientation by an adjustment solution. Unlike MM as such, aerial images do not suffer from GNSS occlusions, and their accuracy is usually verified by employing well-established methods using ground control points. However, a registration between MM and aerial images is a non-standard matching scenario, and requires several strategies to yield reliable and accurate correspondences. Scale, perspective and content strongly vary between both image sources, thus traditional feature matching methods may fail. To this end, the registration process is designed to focus on common and clearly distinguishable elements, such as road markings, manholes, or kerbstones. With a registration accuracy of about 98%, reliable tie information between MM and aerial data can be derived. Even though, the adjustment strategy is not covered in its entirety in this paper, accuracy results after adjustment will be presented. It will be shown that a decimetre accuracy is well achievable in a real data test scenario.

Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.

PubMed

Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

2013-05-16

Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here highlights that structural inspection alone is not sufficient for identifying the key contributions to binding affinities and affinity changes for the design of drugs but that solvation effects must be taken into account. A detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of new inhibitors against HIV-1 PR variants that are resistant against current drugs.

Optimal thresholds for the estimation of area rain-rate moments by the threshold method

NASA Technical Reports Server (NTRS)

Short, David A.; Shimizu, Kunio; Kedem, Benjamin

1993-01-01

Optimization of the threshold method, achieved by determination of the threshold that maximizes the correlation between an area-average rain-rate moment and the area coverage of rain rates exceeding the threshold, is demonstrated empirically and theoretically. Empirical results for a sequence of GATE radar snapshots show optimal thresholds of 5 and 27 mm/h for the first and second moments, respectively. Theoretical optimization of the threshold method by the maximum-likelihood approach of Kedem and Pavlopoulos (1991) predicts optimal thresholds near 5 and 26 mm/h for lognormally distributed rain rates with GATE-like parameters. The agreement between theory and observations suggests that the optimal threshold can be understood as arising due to sampling variations, from snapshot to snapshot, of a parent rain-rate distribution. Optimal thresholds for gamma and inverse Gaussian distributions are also derived and compared.

Validity and reliability of computerized measurement of lumbar intervertebral disc height and volume from magnetic resonance images.

PubMed

Neubert, Ales; Fripp, Jurgen; Engstrom, Craig; Gal, Yaniv; Crozier, Stuart; Kingsley, Michael I C

2014-11-01

Magnetic resonance (MR) examinations of morphologic characteristics of intervertebral discs (IVDs) have been used extensively for biomechanical studies and clinical investigations of the lumbar spine. Traditionally, the morphologic measurements have been performed using time- and expertise-intensive manual segmentation techniques not well suited for analyses of large-scale studies.. The purpose of this study is to introduce and validate a semiautomated method for measuring IVD height and mean sagittal area (and volume) from MR images to determine if it can replace the manual assessment and enable analyses of large MR cohorts. This study compares semiautomated and manual measurements and assesses their reliability and agreement using data from repeated MR examinations. Seven healthy asymptomatic males underwent 1.5-T MR examinations of the lumbar spine involving sagittal T2-weighted fast spin-echo images obtained at baseline, pre-exercise, and postexercise conditions. Measures of the mean height and the mean sagittal area of lumbar IVDs (L1-L2 to L4-L5) were compared for two segmentation approaches: a conventional manual method (10-15 minutes to process one IVD) and a specifically developed semiautomated method (requiring only a few mouse clicks to process each subject). Both methods showed strong test-retest reproducibility evaluated on baseline and pre-exercise examinations with strong intraclass correlations for the semiautomated and manual methods for mean IVD height (intraclass correlation coefficient [ICC]=0.99, 0.98) and mean IVD area (ICC=0.98, 0.99), respectively. A bias (average deviation) of 0.38 mm (4.1%, 95% confidence interval 0.18-0.59 mm) was observed between the manual and semiautomated methods for the IVD height, whereas there was no statistically significant difference for the mean IVD area (0.1%±3.5%). The semiautomated and manual methods both detected significant exercise-induced changes in IVD height (0.20 and 0.28 mm) and mean IVD area (5.7 and 8.3 mm(2)), respectively. The presented semiautomated method provides an alternative to time- and expertise-intensive manual procedures for analysis of larger, cross-sectional, interventional, and longitudinal MR studies for morphometric analyses of lumbar IVDs. Copyright © 2014 Elsevier Inc. All rights reserved.

Structure-function studies of BPP-BrachyNH2 and synthetic analogues thereof with Angiotensin I-Converting Enzyme.

PubMed

Arcanjo, Daniel D R; Vasconcelos, Andreanne G; Nascimento, Lucas A; Mafud, Ana Carolina; Plácido, Alexandra; Alves, Michel M M; Delerue-Matos, Cristina; Bemquerer, Marcelo P; Vale, Nuno; Gomes, Paula; Oliveira, Eduardo B; Lima, Francisco C A; Mascarenhas, Yvonne P; Carvalho, Fernando Aécio A; Simonsen, Ulf; Ramos, Ricardo M; Leite, José Roberto S A

2017-10-20

The vasoactive proline-rich oligopeptide termed BPP-BrachyNH 2 (H-WPPPKVSP-NH 2 ) induces in vitro inhibitory activity of angiotensin I-converting enzyme (ACE) in rat blood serum. In the present study, the removal of N-terminal tryptophan or C-terminal proline from BPP-BrachyNH 2 was investigated in order to predict which structural components are important or required for interaction with ACE. Furthermore, the toxicological profile was assessed by in silico prediction and in vitro MTT assay. Two BPP-BrachyNH 2 analogues (des-Trp 1 -BPP-BrachyNH 2 and des-Pro 8 -BPP-BrachyNH 2 ) were synthesized, and in vitro and in silico ACE inhibitory activity and toxicological profile were assessed. The des-Trp 1 -BPP-BrachyNH 2 and des-Pro 8 -BPP-BrachyNH 2 were respectively 3.2- and 29.5-fold less active than the BPP-BrachyNH 2 -induced ACE inhibitory activity. Molecular Dynamic and Molecular Mechanics Poisson-Boltzmann Surface Area simulations (MM-PBSA) demonstrated that the ACE/BBP-BrachyNH 2 complex showed lower binding and van der Wall energies than the ACE/des-Pro 8 -BPP-BrachyNH 2 complex, therefore having better stability. The removal of the N-terminal tryptophan increased the in silico predicted toxicological effects and cytotoxicity when compared with BPP-BrachyNH 2 or des-Pro 8 -BPP-BrachyNH 2 . Otherwise, des-Pro 8 -BPP-BrachyNH 2 was 190-fold less cytotoxic than BPP-BrachyNH 2 . Thus, the removal of C-terminal proline residue was able to markedly decrease both the BPP-BrachyNH 2 -induced ACE inhibitory and cytotoxic effects assessed by in vitro and in silico approaches. In conclusion, the aminoacid sequence of BPP-BrachyNH 2 is essential for its ACE inhibitory activity and associated with an acceptable toxicological profile. The perspective of the interactions of BPP-BrachyNH 2 with ACE found in the present study can be used for development of drugs with differential therapeutic profile than current ACE inhibitors. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Surgical treatment of glioblastoma multiforme localized in the motor area of the brain using the technique of cortical electrostimulation.

PubMed

Bogosavljevic, Vojislav; Tasic, Goran; Nestorovic, Branislav; Jovanovic, Vladimir; Rakic, Miodrag; Samardzic, Miroslav

2012-01-01

Glioblastoma multiforme in the motor area is the surgical challenge because of the need for more radical resection in order to extend the life of the patient, and the risk that radicalism could lead to additional neurological deficit. We present series of 26 patients with glioblastoma multiforme localized in and around the motor area, who were hospitalized from October 2004 to February 2009. During all operations, we conducted electrostimulation display area of the brain, to the anatomical location of M1 segment of the motor cortex. Distance of the central sulcus in relation to the coronary suture, measured by magnetic resonance imaging (MRI) was 18.38 mm ± 9.564 mm. The volume of electricity required for a motor response was mean 8.79 ± 1.484 mA, with increasing distance from the coronary suture the amperage required to explicit motor responses decreased. The difference (mm) between the distance from the coronary suture measured using MRI and distances measured electrostimulation smaller and power consumption was less (F = 13.285, p < 0.01). The method of cortical cerebral cortex electrostimulation is simple and safe method and a binding protocol to the patient safe operation glioblastoma multiforme localized in the motor area of the brain.

Heavy rain prediction using deterministic and probabilistic models - the flash flood cases of 11-13 October 2005 in Catalonia (NE Spain)

NASA Astrophysics Data System (ADS)

Barrera, A.; Altava-Ortiz, V.; Llasat, M. C.; Barnolas, M.

2007-09-01

Between the 11 and 13 October 2005 several flash floods were produced along the coast of Catalonia (NE Spain) due to a significant heavy rainfall event. Maximum rainfall achieved values up to 250 mm in 24 h. The total amount recorded during the event in some places was close to 350 mm. Barcelona city was also in the affected area where high rainfall intensities were registered, but just a few small floods occurred, thanks to the efficient urban drainage system of the city. Two forecasting methods have been applied in order to evaluate their capability of prediction regarding extreme events: the deterministic MM5 model and a probabilistic model based on the analogous method. The MM5 simulation allows analysing accurately the main meteorological features with a high spatial resolution (2 km), like the formation of some convergence lines over the region that partially explains the maximum precipitation location during the event. On the other hand, the analogous technique shows a good agreement among highest probability values and real affected areas, although a larger pluviometric rainfall database would be needed to improve the results. The comparison between the observed precipitation and from both QPF (quantitative precipitation forecast) methods shows that the analogous technique tends to underestimate the rainfall values and the MM5 simulation tends to overestimate them.

40 CFR 211.204-2 - Primary label size, print and color.

Code of Federal Regulations, 2013 CFR

2013-07-01

... each area shall be as follows, based upon a scale of 72 points=1 inch: (1) Area A—2.8 millimeters (mm) or 8 point. (2) Area B—7.6 mm or 22 point for the Rating;—1.7 mm or 5 point for -“Decibels”. (3) Area A-B—1.5 mm or 4 point. (4) Area C—1.5 mm or 4 point. (5) Area D—0.7 mm or 2 point. (6) Area E—0.7 mm...

40 CFR 211.204-2 - Primary label size, print and color.

Code of Federal Regulations, 2014 CFR

2014-07-01

... each area shall be as follows, based upon a scale of 72 points=1 inch: (1) Area A—2.8 millimeters (mm) or 8 point. (2) Area B—7.6 mm or 22 point for the Rating;—1.7 mm or 5 point for -“Decibels”. (3) Area A-B—1.5 mm or 4 point. (4) Area C—1.5 mm or 4 point. (5) Area D—0.7 mm or 2 point. (6) Area E—0.7 mm...

40 CFR 211.204-2 - Primary label size, print and color.

Code of Federal Regulations, 2012 CFR

2012-07-01

... each area shall be as follows, based upon a scale of 72 points=1 inch: (1) Area A—2.8 millimeters (mm) or 8 point. (2) Area B—7.6 mm or 22 point for the Rating;—1.7 mm or 5 point for -“Decibels”. (3) Area A-B—1.5 mm or 4 point. (4) Area C—1.5 mm or 4 point. (5) Area D—0.7 mm or 2 point. (6) Area E—0.7 mm...

Aluminum alloy material structure impact localization by using FBG sensors

NASA Astrophysics Data System (ADS)

Zhu, Xiubin

2014-12-01

The aluminum alloy structure impact localization system by using fiber Bragg grating (FBG) sensors and impact localization algorithm was investigated. A four-FBG sensing network was established. And the power intensity demodulation method was initialized employing the narrow-band tunable laser. The wavelet transform was used to weaken the impact signal noise. And the impact signal time difference was extracted to build the time difference localization algorithm. At last, a fiber Bragg grating impact localization system was established and experimentally verified. The experimental results showed that in the aluminum alloy plate with the 500 mm*500 mm*2 mm test area, the maximum and average impact abscissa localization errors were 11 mm and 6.25 mm, and the maximum and average impact ordinate localization errors were 9 mm and 4.25 mm, respectively. The fiber Bragg grating sensors and demodulation system are feasible to realize the aviation aluminum alloy material structure impact localization. The research results provide a reliable method for the aluminum alloy material structure impact localization.

Subject-Specific Finite Element Analysis of the Carpal Tunnel Cross-Sectional to Examine Tunnel Area Changes in Response to Carpal Arch Loading

PubMed Central

Walia, Piyush; Erdemir, Ahmet; Li, Zong-Ming

2017-01-01

Background Manipulating the carpal arch width (i.e. distance between hamate and trapezium bones) has been suggested as a means to increase carpal tunnel cross-sectional area and alleviate median nerve compression. The purpose of this study was to develop a finite element model of the carpal tunnel and to determine an optimal force direction to maximize area. Methods A planar geometric model of carpal bones at hamate level was reconstructed from MRI with inter-carpal joint spaces filled with a linear elastic surrogate tissue. Experimental data with discrete carpal tunnel pressures (50, 100, 150, and 200 mmHg) and corresponding carpal bone movements were used to obtain material property of surrogate tissue by inverse finite element analysis. The resulting model was used to simulate changes of carpal arch widths and areas with directional variations of a unit force applied at the hook of hamate. Findings Inverse finite element model predicted the experimental area data within 1.5% error. Simulation of force applications showed that carpal arch width and area were dependent on the direction of force application, and minimal arch width and maximal area occurred at 138° (i.e. volar-radial direction) with respect to the hamate-to-trapezium axis. At this force direction, the width changed to 24.4 mm from its initial 25.1 mm (3% decrease), and the area changed to 301.6 mm2 from 290.3 mm2 (4% increase). Interpretation The findings of the current study guide biomechanical manipulation to gain tunnel area increase, potentially helping reduce carpal tunnel pressure and relieve symptoms of compression median neuropathy. PMID:28073093

A comparison of groundwater recharge estimation methods in a semi-arid, coastal avocado and citrus orchard (Ventura County, California)

NASA Astrophysics Data System (ADS)

Grismer, Mark E.; Bachman, S.; Powers, T.

2000-10-01

We assess the relative merits of application of the most commonly used field methods (soil-water balance (SWB), chloride mass balance (CMB) and soil moisture monitoring (NP)) to determine recharge rates in micro-irrigated and non-irrigated areas of a semi-arid coastal orchard located in a relatively complex geological environment.Application of the CMB method to estimate recharge rates was difficult owing to the unusually high, variable soil-water chloride concentrations. In addition, contrary to that expected, the chloride concentration distribution at depths below the root zone in the non-irrigated soil profiles was greater than that in the irrigated profiles. The CMB method severely underestimated recharge rates in the non-irrigated areas when compared with the other methods, although the CMB method estimated recharge rates for the irrigated areas, that were similar to those from the other methods, ranging from 42 to 141 mm/year.The SWB method, constructed for a 15-year period, provided insight into the recharge process being driven by winter rains rather than summer irrigation and indicated an average rate of 75 mm/year and 164 mm/year for the 1984 - 98 and 1996 - 98 periods, respectively. Assuming similar soil-water holding capacity, these recharge rates applied to both irrigated and non-irrigated areas. Use of the long period of record was important because it encompassed both drought and heavy rainfall years. Successful application of the SWB method, however, required considerable additional field measurements of orchard ETc, soil-water holding capacity and estimation of rainfall interception - runoff losses.Continuous soil moisture monitoring (NP) was necessary to identify both daily and seasonal seepage processes to corroborate the other recharge estimates. Measured recharge rates during the 1996 - 1998 period in both the orchards and non-irrigated site averaged 180 mm/year. The pattern of soil profile drying during the summer irrigation season, followed by progressive wetting during the winter rainy season was observed in both irrigated and non-irrigated soil profiles, confirming that groundwater recharge was rainfall driven and that micro-irrigation did not predispose the soil profile to excess rainfall recharge. The ability to make this recharge assessment, however, depended on making multiple field measurements associated with all three methods, suggesting that any one should not be used alone.

UOE Pipe Numerical Model: Manufacturing Process And Von Mises Residual Stresses Resulted After Each Technological Step

NASA Astrophysics Data System (ADS)

Delistoian, Dmitri; Chirchor, Mihael

2017-12-01

Fluid transportation from production areas to final customer is effectuated by pipelines. For oil and gas industry, pipeline safety and reliability represents a priority. From this reason, pipe quality guarantee directly influence pipeline designed life, but first of all protects environment. A significant number of longitudinally welded pipes, for onshore/offshore pipelines, are manufactured by UOE method. This method is based on cold forming. In present study, using finite element method is modeled UOE pipe manufacturing process and is obtained von Mises stresses for each step. Numerical simulation is performed for L415 MB (X60) steel plate with 7,9 mm thickness, length 30 mm and width 1250mm, as result it is obtained a DN 400 pipe.

SU-C-207-07: Quantification of Coronary Artery Cross-Sectional Area in CT Angiography Using Integrated Density: A Phantom Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, T; Ding, H; Torabzadeh, M

2015-06-15

Purpose: To investigate the feasibility of quantifying the cross-sectional area (CSA) of coronary arteries using integrated density in a physics-based model with a phantom study. Methods: In this technique the total integrated density of the object as compared with its local background is measured so it is possible to account for the partial volume effect. The proposed method was compared to manual segmentation using CT scans of a 10 cm diameter Lucite cylinder placed inside a chest phantom. Holes with cross-sectional areas from 1.4 to 12.3 mm{sup 2} were drilled into the Lucite and filled with iodine solution, producing amore » contrast-to-noise ratio of approximately 26. Lucite rods 1.6 mm in diameter were used to simulate plaques. The phantom was imaged with and without the Lucite rods placed in the holes to simulate diseased and normal arteries, respectively. Linear regression analysis was used, and the root-mean-square deviations (RMSD) and errors (RMSE) were computed to assess the precision and accuracy of the measurements. In the case of manual segmentation, two readers independently delineated the lumen in order to quantify the inter-reader variability. Results: The precision and accuracy for the normal vessels using the integrated density technique were 0.32 mm{sup 2} and 0.32 mm{sup 2}, respectively. The corresponding results for the manual segmentation were 0.51 mm{sup 2} and 0.56 mm{sup 2}. In the case of diseased vessels, the precision and accuracy of the integrated density technique were 0.46 mm{sup 2} and 0.55 mm{sup 2}, respectively. The corresponding results for the manual segmentation were 0.75 mm{sup 2} and 0.98 mm{sup 2}. The mean percent difference for the two readers was found to be 8.4%. Conclusion: The CSA based on integrated density had improved precision and accuracy as compared with manual segmentation in a Lucite phantom. The results indicate the potential for using integrated density to improve CSA measurements in CT angiography.« less

Assessing the Amount of Interdental Bone in Posterior Areas of the Mandible for Placing Orthodontic Mini-Implants

PubMed Central

Esfahanizadeh, Nasrin; Shahraki, Damoun; Daneshparvar, Hamidreza; Talaei Pour, Ahmad Reza; Saghiri, Mohammad Ali; Sheibaninia, Ahmad; Rashtak, Shadab

2013-01-01

Objective : The aim of this study was to assess the amount of interdental bone in posterior areas of the mandible for placing orthodontic mini-implants to provide and control anchorage in orthodontic treatment. Materials and Methods : The amount of interdental bone in areas between the second premolars and first molars, first and second molars on the right and left sides of the mandible were determined in fifty patients by RVG using periapical radiographs. The images were assessed using Cygnus Media Software to determine the mesio-distal width of the interdental bone, starting at the crest of the alveolar bone (2 mm below the CEJ) every one millimeter up to 12 mm from the CEJ. The actual amount of interdental bone and the effect of related factors were assessed using chi-square test at a 95% confidence interval. Results : The minimum desired interdental bone width for placing mini-implants, 3 mm from the CEJ, between the second premolar and first molar and the first and second molars of the mandible on both sides were significantly different (p<0.01): 1.8 mm (31%) more apical in the area between the second premolar and the first molar. There was also a statistically significant difference between the areas under study on the right side (p<0.002), which was 2.2 mm (44%) more apical in the area of the second premolar and the first molar. Conclusion : The most secure site for placing orthodontic mini-implants in the mandible is between the first and second molars at the height of 5.8 mm from the CEJ. PMID:25512751

Establish susceptibility and risk assessment models for rainfall-induced landslide: A case in Central Taiwan

NASA Astrophysics Data System (ADS)

Wu, Chunhung; Huang, Jyuntai

2017-04-01

Most of the landslide cases in Taiwan were triggered by rainfall or earthquake events. The heavy rainfall in the typhoon seasons, from June to October, causes the landslide hazard more serious. Renai Towhship is of the most large landslide cases after 2009 Typhoon Morakot (from Aug. 5 to Aug. 10, 2009) in Taiwan. Around 2,744 landslides cases with the total landslide area of 21.5 km2 (landslide ratio =1.8%), including 26 large landslide cases, induced after 2009 Typhoon Morakot in Renai Towhship. The area of each large landslides case is more than 0.1 km2, and the area of the largest case is around 0.96 km2. 58% of large landslide cases locate in the area with metamorphosed sandstone. The mean slope of 26 large landslide cases ranges from 15 degree to 56 degree, and the accumulated rainfall during 2009 Typhoon Morakot ranges from 530 mm to 937 mm. Three methods, including frequency ratio method (abbreviated as FR), weights of evidence method (abbreviated as WOE), and logistic regression method (abbreviated as LR), are used in this study to establish the landslides susceptibility in the Renai Township, Nantou County, Taiwan. Eight landslide related-factors, including elevation, slope, aspect, geology, land use, distance to drainage, distance to fault, accumulation rainfall during 2009 Typhoon Morakot, are used to establish the landslide susceptibility models in this study. The landslide inventory after 2009 Typhoon Morakot is also used to test the model performance in this study. The mean accumulated rainfall in Renai Township during 2009 typhoon Morakot was around 735 mm with the maximum 1-hr, 3-hrs, and 6-hrs rainfall intensity of 44 mm/1-hr, 106 mm/3-hrs and 204 mm/6-hrs, respectively. The range of original susceptibility values established by three methods are 4.0 to 20.9 for FR, -33.8 to -16.1 for WOE, and -41.7 to 5.7 for LR, and the mean landslide susceptibility value are 8.0, -24.6 and 0.38, respectively. The AUC values are 0.815 for FR, 0.816 for WOE, and 0.823 for LR. The study normalized the susceptibility value range of three landslide susceptibility models to 0 to 1 to deeply compare the model performance. The normalized landslide susceptibility value > 0.5 and ≦0.5 are regarded as predicted-landslide area and predicted-not-landslide area. The ratio of the area in the predicted-landslide area to the total area is 3.0% for FR, 71.4% for WOE, and 26.5% for LR. And the correct ratio is 65.5% for FR, 61.9% for WOE, 74.5% for LR. The study adopted 14 rainfall stations with more than 20 years daily rainfall data in Renai Township to estimate the 24 hrs accumulated rainfall with different RPYs. Landslide susceptibility map under 24 hrs accumulated rainfall distribution with different RPYs is used to estimate the landslide disaster location and scale. The landslide risk under different RPYs in Renai Township is calculated as 2.62 billion for 5 RPYs, 3.06 billion for 10 RPYs, 4.69 billion for 25 RPYs, 5.97 billion for 50 RPYs, 6.98 billion for 100 RPYs, and 8.23 billion for 200 RPYs, respectively.

Implementations of three OCT angiography (OCTA) methods with 1.7 MHz A-scan rate OCT system on imaging of human retinal and choroidal vasculature

NASA Astrophysics Data System (ADS)

Poddar, Raju; Werner, John S.

2018-06-01

We present noninvasive depth-resolved imaging of human retinal and choroidal microcirculation with an ultrahigh-speed (1.7 MHz A-scans/s), Fourier-domain mode locked (FDML) swept-source optical coherence tomography (SS-OCT) system having a central wavelength of 1065 nm. Three OCT angiography (OCTA) motion based contrast methods, namely phase variance (PV), amplitude decorrelation (AD) and Joint Spectral and Time domain OCT (STdOCT) were implemented. The OCTA imaging was performed with a field of view of 16° (5 mm × 5 mm) and 30° (9 mm × 9 mm), on the retina. A qualitative comparison of images obtained with all three OCTA methods is demonstrated using the same eye of a healthy volunteer. Different parameters, namely acquisition time, scanning area, and scanning density, are discussed. The phase-variance OCTA (PV-OCTA) method produced relatively better results than the other two. Different features regarding the retinal and choroidal vessels are described in different subjects.

Whole-brain high in-plane resolution fMRI using accelerated EPIK for enhanced characterisation of functional areas at 3T

PubMed Central

Yun, Seong Dae

2017-01-01

The relatively high imaging speed of EPI has led to its widespread use in dynamic MRI studies such as functional MRI. An approach to improve the performance of EPI, EPI with Keyhole (EPIK), has been previously presented and its use in fMRI was verified at 1.5T as well as 3T. The method has been proven to achieve a higher temporal resolution and smaller image distortions when compared to single-shot EPI. Furthermore, the performance of EPIK in the detection of functional signals was shown to be comparable to that of EPI. For these reasons, we were motivated to employ EPIK here for high-resolution imaging. The method was optimised to offer the highest possible in-plane resolution and slice coverage under the given imaging constraints: fixed TR/TE, FOV and acceleration factors for parallel imaging and partial Fourier techniques. The performance of EPIK was evaluated in direct comparison to the optimised protocol obtained from EPI. The two imaging methods were applied to visual fMRI experiments involving sixteen subjects. The results showed that enhanced spatial resolution with a whole-brain coverage was achieved by EPIK (1.00 mm × 1.00 mm; 32 slices) when compared to EPI (1.25 mm × 1.25 mm; 28 slices). As a consequence, enhanced characterisation of functional areas has been demonstrated in EPIK particularly for relatively small brain regions such as the lateral geniculate nucleus (LGN) and superior colliculus (SC); overall, a significantly increased t-value and activation area were observed from EPIK data. Lastly, the use of EPIK for fMRI was validated with the simulation of different types of data reconstruction methods. PMID:28945780

Secondary trauma from occlusion: three-dimensional analysis using the finite element method.

PubMed

Geramy, Allahyar; Faghihi, Sharieh

2004-01-01

Clinical effects of forces applied by dental occlusion on the periodontium have been evaluated for decades. Historically, trauma from occlusion has been considered as a major etiologic factor of inflammatory periodontal diseases, while some researchers have interpreted it to be of less importance or without any detectable importance in periodontics. In this study, five three-dimensional models of a maxillary central incisor were created using ANSYS 5.40. The only difference in each model was the height of the alveolar bone that showed from normal height (13 mm of alveolar bone height) to 8 mm of alveolar bone loss (5 mm of alveolar bone height). Five-point forces of 0.3 N summing up to 1.5 N were applied in a parallel line, 1 mm apical to the incisal edge on the palatal side in a palatolabial direction. The maximum (S1) and minimum (S3) principal stresses in the nodes of the labial side of the periodontal ligament (apical to the alveolar crest) were assessed. Analysis was done using the finite element method. An increase of S1 (up to 16 times in the cervical and 11.25 times in the apical area) and S3 (up to 17.13 times in the cervical and 9.9 times in the apical area) in comparison to the normal model was shown. The highest stress levels were traced in the subcervical area, except for the last model (8 mm of the alveolar bone loss). According to the results of this study, 2.5 mm of alveolar bone loss can be considered as a limit beyond which stress alterations were accelerated. Based on the FEM analysis, alveolar bone loss increases stress (S1 and S3) produced in the PDL, in spite of applying the same force vector.

Ex-vivo Assessment of Coronary Artery Atherosclerosis by Magnetic Resonance Imaging: Correlation with Histopathology

PubMed Central

Gomes, Everli P. S. Gonçalves; Rochitte, Carlos Eduardo; Azevedo, Clerio F.; Lemos, Pedro A.; Gutierrez, Paulo Sampaio; César, Luiz Antonio M.

2014-01-01

Introduction: In recent years, high-resolution magnetic resonance imaging (MRI) has emerged as a very promising technique for studying atherosclerotic disease in humans. Aim: In the present study we sought to determine whether MRI allowed for the morphological characterization of the coronary vessel wall and atherosclerotic plaques using histopathological assessment as the reference standard. Methods: The study population consisted of 13 patients who died of acute myocardial infarction and underwent autopsy. The proximal portions of the coronary arteries were excised and were evaluated both by MRI and by histopathology. For each arterial segment, the following parameters were calculated through manual planimetry: 1. total vessel area (TVA); 2. luminal area (LA) and 3. plaque area (PA). Results: A total of 207 coronary artery cross-sections were found to be suitable for analysis by both MRI and histopathology and were included in the final analyses. Both methods demonstrated moderate to good agreement for the quantification of TVA (mean difference = 2.4±2.4 mm2, 95‰ limits of agreement from -2.4 to +7.2 mm2; CCC = 0.69, 95‰ CI from 0.63 to 0.75), LA (mean difference = 0.0±1.7 mm2, 95‰ limits of agreement from -3.3 to + 3.3 mm2; CCC = 0.84, 95‰ CI from 0.80 to 0.88) and PA (mean difference = 2.4±2.4 mm2, 95‰ limits of agreement from -2.3 to + 7.1 mm2; CCC = 0.64, 95‰ CI from 0.58 to 0.71). Conclusion: In this ex vivo experimental model we demonstrated good agreement between coronary artery morphometrical measurements obtained by high-resolution MRI and by histopathology. PMID:24847387

An experimental study of non-destructive testing on glass fibre reinforced polymer composites after high velocity impact event

NASA Astrophysics Data System (ADS)

Razali, N.; Sultan, M. T. H.; Cardona, F.

2016-10-01

A non-destructive testing method on Glass Fibre Reinforced Polymer (GFRP) after high velocity impact event using single stage gas gun (SSGG) is presented. Specimens of C- type and E-type fibreglass reinforcement, which were fabricated with 6mm, 8mm, 10mm and 12mm thicknesses and size 100 mm x 100 mm, were subjected to a high velocity impact with three types of bullets: conical, hemispherical and blunt at various gas gun pressure levels from 6 bar to 60 bar. Visual observation techniques using a lab microscope were used to determine the infringed damage by looking at the crack zone. Dye penetrants were used to inspect the area of damage, and to evaluate internal and external damages on the specimens after impact. The results from visual analysis of the impacted test laminates were discussed and presented. It was found that the impact damage started with induced delamination, fibre cracking and then failure, simultaneously with matrix cracking and breakage, and finally followed by the fibres pulled out. C-type experienced more damaged areas compared to E-type of GFRP.

Robotic hip arthroscopy in human anatomy.

PubMed

Kather, Jens; Hagen, Monika E; Morel, Philippe; Fasel, Jean; Markar, Sheraz; Schueler, Michael

2010-09-01

Robotic technology offers technical advantages that might offer new solutions for hip arthroscopy. Two hip arthroscopies were performed in human cadavers using the da Vinci surgical system. During both surgeries, a robotic camera and 5 or 8 mm da Vinci trocars with instruments were inserted into the hip joint for manipulation. Introduction of cameras and working instruments, docking of the robotic system and instrument manipulation was successful in both cases. The long articulating area of 5 mm instruments limited movements inside the joint; an 8 mm instrument with a shorter area of articulation offered an improved range of motion. Hip arthroscopy using the da Vinci standard system appears a feasible alternative to standard arthroscopy. Instruments and method of application must be modified and improved before routine clinical application but further research in this area seems justified, considering the clinical value of such an approach. Copyright 2010 John Wiley & Sons, Ltd.

Alluvial groundwater recharge estimation in semi-arid environment using remotely sensed data

NASA Astrophysics Data System (ADS)

Coelho, Victor Hugo R.; Montenegro, Suzana; Almeida, Cristiano N.; Silva, Bernardo B.; Oliveira, Leidjane M.; Gusmão, Ana Cláudia V.; Freitas, Emerson S.; Montenegro, Abelardo A. A.

2017-05-01

Data limitations on groundwater (GW) recharge over large areas are still a challenge for efficient water resource management, especially in semi-arid regions. Thus, this study seeks to integrate hydrological cycle variables from satellite imagery to estimate the spatial distribution of GW recharge in the Ipanema river basin (IRB), which is located in the State of Pernambuco in Northeast Brazil. Remote sensing data, including monthly maps (2011-2012) of rainfall, runoff and evapotranspiration, are used as input for the water balance method within Geographic Information Systems (GIS). Rainfall data are derived from the TRMM Multi-satellite Precipitation Analysis (TMPA) Version 7 (3B43V7) product and present the same monthly average temporal distributions from 15 rain gauges that are distributed over the study area (r = 0.93 and MAE = 12.7 mm), with annual average estimates of 894.3 (2011) and 300.7 mm (2012). The runoff from the Natural Resources Conservation Service (NRCS) method, which is based on regional soil information and Thematic Mapper (TM) sensor image, represents 29% of the TMPA rainfall that was observed across two years of study. Actual evapotranspiration data, which were provided by the SEBAL application of MODIS images, present annual averages of 1213 (2011) and 1067 (2012) mm. The water balance results reveal a large inter-annual difference in the IRB GW recharge, which is characterized by different rainfall regimes, with averages of 30.4 (2011) and 4.7 (2012) mm year-1. These recharges were mainly observed between January and July in regions with alluvial sediments and highly permeable soils. The GW recharge approach with remote sensing is compared to the WTF (Water Table Fluctuation) method, which is used in an area of alluvium in the IRB. The estimates from these two methods exhibit reliable annual agreement, with average values of 154.6 (WTF) and 124.6 (water balance) mm in 2011. These values correspond to 14.89 and 13.53% of the rainfall that was recorded at the rain gauges and the TMPA, respectively. Only the WTF method indicates a very low recharge of 15.9 mm for the second year. The values in this paper provide reliable insight regarding the use of remotely sensed data to evaluate the rates of alluvial GW recharge in regions where the potential runoff cannot be disregarded from WB equation and must be calculated spatially.

Sonographic analysis of the intercostal spaces for the application of high-intensity focused ultrasound therapy to the liver.

PubMed

Kim, Young-Sun; Park, Min Jung; Rhim, Hyunchul; Lee, Min Woo; Lim, Hyo Keun

2014-07-01

The purposes of this study were to assess the widths of the intercostal spaces of the right inferior human rib cage through which high-intensity focused ultrasound therapy would be applied for treating liver cancer and to elucidate the demographic factors associated with intercostal space width. From March 2013 to June 2013, the widths of the intercostal spaces and the ribs at six areas of the right inferior rib cage (area 1, lowest intercostal space on anterior axillary line and the adjacent upper rib; area 2, second-lowest intercostal space on anterior axillary line and the adjacent upper rib; areas 3 and 4, lowest and second-lowest spaces on midaxillary line; areas 5 and 6, lowest and second-lowest spaces on posterior axillary line) were sonographically measured in 466 patients (214 men, 252 women; mean age, 53.0 years) after an abdominal sonographic examination. Demographic factors and the presence or absence of chronic liver disease were evaluated by multivariate analysis to investigate which factors influence intercostal width. The width of the intercostal space was 19.7 ± 3.7 mm (range, 9-33 mm) at area 1, 18.3 ± 3.4 mm (range, 9-33 mm) at area 2, 17.4 ± 4.0 mm (range, 7-33 mm) at area 3, 15.4 ± 3.5 mm (range, 5-26 mm) at area 4, 17.2 ± 3.7 mm (range, 7-28 mm) at area 5, and 14.5 ± 3.6 mm (range, 4-26 mm) at area 6. The corresponding widths of the ribs were 15.2 ± 2.3 mm (range, 8-22 mm), 14.5 ± 2.3 mm (range, 9-22 mm), 13.2 ± 2.0 mm (range, 9-20), 14.3 ± 2.2 mm (range, 9-20 mm), 15.0 ± 2.2 mm (range, 10-22 mm), and 15.1 ± 2.3 mm (range, 8-21 mm). Only female sex was significantly associated with the narrower intercostal width at areas 1, 2, 3, and 5 (regression coefficient, 1.124-1.885; p = 0.01-0.04). There was substantial variation in the widths of the intercostal spaces of the right inferior rib cage such that the anterior and inferior aspects of the intercostal space were relatively wider. Women had significantly narrower intercostal spaces than men.

Binding of Single Walled Carbon Nanotube to WT and Mutant HIV-1 Proteases: Analysis of Flap Dynamics and Binding Mechanism

PubMed Central

Meher, Biswa Ranjan; Wang, Yixuan

2012-01-01

Most of the currently treated HIV-1 protease (HIV-PR) inhibitors have been prone to suffer from the mutations associated drug resistance. Therefore, it is necessary to search for potent alternatives against the drug resistance. In the current study we have tested the single-walled carbon nanotube (SWCNT) as an inhibitor in wild type (WT) as well as in three primary mutants (I50VPR, V82APR and I84VPR) of the HIV-1-PR through docking the SWCNT in the active site region, and then performed all-atom MD simulations for the complexes. The conformational dynamics of HIV-PR with a 20 ns trajectory reveals that the SWCNT can effectively bind to the HIV-1-PR active site and regulate the flap dynamics such as maintaining the flap-flap closed. To gain an insight into the binding affinity, we also performed the MM-PBSA based binding free energy calculations for the four HIV-PR/SWCNT complexes. It was observed that, although the binding between the SWCNT and the HIV-PR decreases due to the mutations, the SWCNTs bind to the HIV-PRs 3–5 folds stronger than the most potent HIV-1-PR inhibitor, TMC114. Remarkably, the significant interactions with binding energy higher than 1 kcal/mol focus on the flap and active regions, which favors closing flap-flap and deactivating the active residues of the HIV-PR. The flap dynamics and binding strength information for HIV-PR and SWCNTs can help design SWCNT-based HIV-1-PR inhibitors. PMID:23142620

Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations.

PubMed

Qian, Haiyan; Chen, Jiongjiong; Pan, Youlu; Chen, Jianzhong

2016-09-19

11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

SU-E-I-25: Quantification of Coronary Artery Cross-Sectional Area in CT Angiography Using Integrated Density: A Simulation Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, T; Ding, H; Lipinski, J

2015-06-15

Purpose: To develop a physics-based model for accurate quantification of the cross-sectional area (CSA) of coronary arteries in CT angiography by measuring the integrated density to account for the partial volume effect. Methods: In this technique the integrated density of the object as compared with its local background is measured to account for the partial volume effect. Normal vessels were simulated as circles with diameters in the range of 0.1–3mm. Diseased vessels were simulated as 2, 3, and 4mm diameter vessels with 10–90% area stenosis, created by inserting circular plaques. A simplified two material model was used with the lumenmore » as 8mg/ml Iodine and background as lipid. The contrast-to-noise ratio between lumen and background was approximately 26. Linear fits to the known CSA were calculated. The precision and accuracy of the measurement were quantified using the root-mean-square fit deviations (RMSD) and errors to the known CSA (RMSE). Results compared to manual segmentation of the vessel lumen. To assess the impact of random variations, coefficients of variation (CV) from 10 simulations for each vessel were computed to determine reliability. Measurements with CVs less than 10% were considered reliable. Results: For normal vessels, the precision and accuracy of the integrated density technique were 0.12mm{sup 2} and 0.28mm{sup 2}, respectively. The corresponding results for manual segmentation were 0.27mm{sup 2} and 0.43mm{sup 2}. For diseased vessels, the precision and accuracy of the integrated density technique were 0.14mm{sup 2} and 0.19mm{sup 2}. Corresponding results for manual segmentation were 0.42mm{sup 2} and 0.71mm{sup 2}. Reliable CSAs were obtained for normal vessels with diameters larger than 1 mm and for diseased vessels with area as low as 1.26mm2. Conclusion: The CSA based on integrated density showed improved precision and accuracy as compared with manual segmentation in simulation. These results indicate the potential of using integrated density to quantify CSA of coronary arteries in CT angiography.« less

[Computer aided design and 3-dimensional printing for the production of custom trays of maxillary edentulous jaws based on 3-dimensional scan of primary impression].

PubMed

Chen, H; Zhao, T; Wang, Y; Sun, Y C

2016-10-18

To establish a digital method for production of custom trays for edentulous jaws using fused deposition modeling (FDM) based on three-dimensional (3D) scans of primary jaw impressions, and to quantitatively evaluate the accuracy. A red modeling compound was used to make a primary impression of a standard maxillary edentulous plaster model. The plaster model data and the primary impression tissue surface data were obtained using a 3D scanner. In the Gemomagic 2012 software, several commands were used, such as interactive drawing curves, partial filling holes, local offset, bodily offset, bodily shell, to imitate clinical procedures of drawing tray boundary, filling undercut, buffer, and generating the tray body. A standard shape of tray handle was designed and attached to the tray body and the data saved as stereolithography (STL) format. The data were imported into a computer system connected to a 3D FDM printing device, and the custom tray for the edentulous jaw model was printed layer upon layer at 0.2 mm/layer, using polylactic acid (PLA) filament, the tissue surface of the tray was then scanned with a 3D scanner. The registration functions of Geomagic 2012 was used to register the 3-dimentional surface data, and the point-cloud deviation analysis function of the Imageware 13.0 system was used to analyze the error. The CAD data of the custom tray was registered to the scan data, and the error between them was analyzed. The scanned plaster model surface was registered to the scanned impression surface and the scanned tray data to the CAD data, then the distance between the surface of plaster model and the scanned tissue surface of the custom tray was measured in Imageware 13.0. The deviation between the computer aided design data and the scanned data of the custom tray was (0.17±0.20) mm, with (0.19±0.18) mm in the primary stress-bearing area, (0.17±0.22) mm in the secondary stress-bearing area, (0.30±0.29) mm in the border seal area, (0.08±0.06) mm in the buffer area; the space between the tissue faces of the plaster model and the scanned tissue surface of custom tray was (1.98±0.40) mm, with (1.85±0.24) mm in the primary stress-bearing area, (1.86±0.26) mm in the secondary stress-bearing area, (1.77±0.36) mm in the border seal area, (2.90±0.26) mm in the buffer area. With 3D scanning, computer aided design and FDM technology, an efficient means of custom tray production was established.

Comparative techniques of medial rectus muscle retraction for endoscopic exposure of the medial intraconal space.

PubMed

Lin, Giant C; Freitag, Suzanne K; Kocharyan, Armine; Yoon, Michael K; Lefebvre, Daniel R; Bleier, Benjamin S

2016-05-01

The medial rectus muscle (MRM) is the medial boundary to the intraconal space of the orbit, and retraction of the MRM is oftentimes necessary for endoscopic removal of intraconal tumors, e.g., orbital hemangioma. We evaluated each of the reported methods of MRM retraction for endoscopic orbital surgery and quantified the degree of intraconal exposure conferred by each method. Eight orbits from four cadaver heads were dissected. In each orbit, medial orbital decompression was performed and the MRM was retracted by using four previously described techniques: (1) external MRM retraction at the globe insertion point by using vessel loop (external group), (2) transseptal MRM retraction by using vessel loop (transseptal group), (3) transchoanal retraction of the MRM by using vessel loop (choanal group), and (4) transseptal four-handed technique by using double ball retraction by a second surgeon (transseptal double ball group). The length, height, and area of exposure of the medial intraconal space were quantified and compared. The average ± standard deviation (SD) anterior-posterior exposures for the external group, transseptal group, and transseptal double ball group were 17.51 ± 3.39 mm, 16.59 ± 4.16 mm, and 18.0 ± 15.25 mm, respectively. The choanal group provided significantly less exposure (12.39 ± 3.44 mm, p = 0.049) than the other groups. The average ± SD vertical exposures for the transseptal group, choanal group, and transseptal double ball group were 12.53 ± 4.38 mm, 13.05 ± 5.86 mm, and 13.57 ± 3.74 mm, respectively. The external group provided significantly less exposure (4.51 ± 1.56 mm, p = 0.0072) than the other groups. The transseptal and transseptal double ball groups provided the greatest total access by surface area (58.88 ± 26.96 mm(2) and 62.94 ± 34.74 mm(2), respectively) compared with the external and choanal groups (34.82 ± 23.37 mm(2) and 43.10 ± 23.68 mm(2), respectively). Although the transseptal trajectory of MRM retraction was optimal, the difference in total area of exposure between the static vessel loop retraction and the dynamic, four-handed technique with double ball instrument retraction was not significant. Of note, the exposure provided by the choanal technique required the surgeon to work both above and below the muscle. Retraction of the MRM toward the choanae provided the least length of exposure, and external retraction exposed the least height and total area. Transseptal MRM retraction was most favorable and provided the largest endoscopic corridor to the medial intraconal space. A four-handed approach for endoscopic intraconal surgery of the orbit may offer advantages in dynamic adjustments in retraction.

Clinical evaluation of expanded mesh connective tissue graft in the treatment for multiple adjacent gingival recessions in the esthetic zone

PubMed Central

Shanmugam, M.; Shivakumar, B.; Meenapriya, B.; Anitha, V.; Ashwath, B.

2015-01-01

Background: Multiple approaches have been used to replace lost, damaged or diseased gingival tissues. The connective tissue graft (CTG) procedure is the golden standard method for root coverage. Although multiple sites often need grafting, the palatal mucosa supplies only a limited area of grafting material. To overcome this limitation, expanded mesh graft provides a method whereby a graft can be stretched to cover a large area. The aim of this study was to evaluate the effectiveness and the predictability of expanded mesh CTG (e-MCTG) in the treatment of adjacent multiple gingival recessions. Materials and Methods: Sixteen patients aged 20–50 years contributed to 55 sites, each site falling into at least three adjacent Miller's Class 1 or Class 2 gingival recession. The CTG obtained from the palatal mucosa was expanded to cover the recipient bed, which was 1.5 times larger than the graft. Clinical measurements were recorded at baseline and 3 months, 12 months postoperatively. Results: A mean coverage of 1.96 mm ± 0.66 mm and 2.22 mm ± 0.68 mm was obtained at the end of 3rd and 12th month, respectively. Twelve months after surgery a statistically significant increase in CAL (2.2 mm ± 0.68 mm, P < 0.001) and increasing WKT (1.75 ± 0.78, P < 0.001) were obtained. In 80% of the treated sites, 100% root coverage was achieved (mean 93.5%). Conclusions: The results of this study demonstrated that multiple adjacent recessions were treated by using e-MCTG technique can be applied and highly predictable root coverage can be achieved. PMID:26321829

Friedman tongue position and cone beam computed tomography in patients with obstructive sleep apnea

PubMed Central

O'Brien, Louise; Aronovich, Sharon; Shelgikar, Anita; Hoff, Paul; Palmisano, John; Stanley, Jeffrey

2017-01-01

Objective Evaluate the correlation between Friedman Tongue Position (FTP) and airway cephalometrics in patients with obstructive sleep apnea (OSA). Study Design Retrospective review of adult patients with OSA undergoing Cone Beam Computed Tomography (CBCT). Methods Collected data included age, sex, body mass index, apnea hypopnea index, FTP, and airway cephalometric parameters. Data analyses were performed using ANOVA, dichotomous t‐testing, and linear regression. Results 203 patients were included in the analysis. (M:F 132:71). The mean posterior airway space (PAS) was inversely correlated (p = 0.001, r =.119) with higher FTP grades with means of 12.3 mm, 7.9 mm, 6.6 mm, and 4.3 mm, I‐IV respectively. Minimal cross‐sectional area for patients with FTP I‐IV was 245.7, 179.8, 137.6, and 74.2 mm, 2 respectively (p = 0.002, r = .095). Mean hyoid‐mandibular plane (H‐MP) for FTP I‐IV was 20.6 mm, 20.4 mm, 24.7 mm, and 28.9 mm respectively. No statistically significant difference between H‐MP values when comparing patients with FTP I or II (p = 0.22). There were statistically significant differences when these two groups were individually compared to FTP III and IV (p = 0.002). Linear regression analysis confirmed an independent association between FTP and PAS (β = −2.06, p < 0.001), minimal cross‐sectional area (β = −45.07, p = 0.02), and H‐MP (β = 3.03, p = 0.01) controlling for BMI, age, AHI, and sex. Conclusions Use of FTP is supported by objective CBCT cephalometric results, in particular the PAS, minimal cross‐sectional area, and H‐MP. Understanding the correlation between objective measurements of retroglossal collapse should allow Otolaryngologists to more confidently select patients who may require surgery to address the retroglossal area, particularly when the ability to perform cephalometric analysis is not possible Level of Evidence 4. PMID:29094076

Regression Techniques for Determining the Effective Impervious Area in Southern California Watersheds

NASA Astrophysics Data System (ADS)

Sultana, R.; Mroczek, M.; Dallman, S.; Sengupta, A.; Stein, E. D.

2016-12-01

The portion of the Total Impervious Area (TIA) that is hydraulically connected to the storm drainage network is called the Effective Impervious Area (EIA). The remaining fraction of impervious area, called the non-effective impervious area, drains onto pervious surfaces which do not contribute to runoff for smaller events. Using the TIA instead of EIA in models and calculations can lead to overestimates of runoff volumes peak discharges and oversizing of drainage system since it is assumed all impervious areas produce urban runoff that is directly connected to storm drains. This makes EIA a better predictor of actual runoff from urban catchments for hydraulic design of storm drain systems and modeling non-point source pollution. Compared to TIA, determining the EIA is considerably more difficult to calculate since it cannot be found by using remote sensing techniques, readily available EIA datasets, or aerial imagery interpretation alone. For this study, EIA percentages were calculated by two successive regression methods for five watersheds (with areas of 8.38 - 158mi2) located in Southern California using rainfall-runoff event data for the years 2004 - 2007. Runoff generated from the smaller storm events are considered to be emanating only from the effective impervious areas. Therefore, larger events that were considered to have runoff from both impervious and pervious surfaces were successively removed in the regression methods using a criterion of (1) 1mm and (2) a max (2 , 1mm) above the regression line. MSE is calculated from actual runoff and runoff predicted by the regression. Analysis of standard deviations showed that criterion of max (2 , 1mm) better fit the regression line and is the preferred method in predicting the EIA percentage. The estimated EIAs have shown to be approximately 78% to 43% of the TIA which shows use of EIA instead of TIA can have significant impact on the cost building urban hydraulic systems and stormwater capture devices.

An Evaluation Method for Suppression of Pathogenic Fusarium oxysporum by Soil Microorganisms Using the Dilution Plate Technique.

PubMed

Mitsuboshi, Masahiro; Kioka, Yuuzou; Noguchi, Katsunori; Asakawa, Susumu

2017-01-01

Volume 31, No. 3, Page 307-313, 2016Page 310, Legend for Fig. 4 IncorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm 2 and 36.5 mm, respectively. CorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm 2 and 36.5 mm, respectively. Page 311, Legend for Fig. 5 IncorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm 2 and 40.5 mm, respectively. CorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm 2 and 40.5 mm, respectively. Page 312, Legend for Fig. 7 IncorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha -1 ; MI10, microbial inoculant applied with 10,000 kg ha -1 . Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm 2 and 29.7 mm, respectively. CorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha -1 ; MI10, microbial inoculant applied with 10,000 kg ha -1 . Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm 2 and 29.7 mm, respectively. The authors would like to apologize for these corrections and any inconvenience caused.

Evaluation of Single File Systems Reciproc, Oneshape, and WaveOne using Cone Beam Computed Tomography –An In Vitro Study

PubMed Central

Dhingra, Annil; Miglani, Anjali

2015-01-01

Background Successful endodontic therapy depends on many factor, one of the most important step in any root canal treatment is root canal preparation. In addition, respecting the original shape of the canal is of the same importance; otherwise, canal aberrations such as transportation will be created. Aim The purpose of this study is to compare and evaluate Reciprocating WaveOne ,Reciproc and Rotary Oneshape Single File Instrumentation System On Cervical Dentin Thickness, Cross Sectional Area and Canal Transportation on First Mandibular Molar Using Cone Beam Computed Tomography. Materials and Methods Sixty Mandibular First Molars extracted due to periodontal reason was collected from the Department of Oral and Maxillofacial. Teeth were prepared using one rotary and two reciprocating single file system. Teeth were divided into 3 groups 20 teeth in each group. Pre instrumentation and Post instrumentation scans was done and evaluated for three parameters Canal Transportation, Cervical Dentinal Thickness, Cross-sectional Area. Results were analysed statistically using ANOVA, Post-Hoc Tukey analysis. Results The change in cross-sectional area after filing showed significant difference at 0mm, 1mm, 2mm and 7mm (p<0.001, p =0.006, 0.004 & <0.001 respectively). There was significant difference between wave one and oneshape; oneshape and reciproc at 0mm, 1mm, 2mm & 7mm (p-values for waveone and Oneshape <0.001, 0.022, 0.011 & <0.001 resp. and for oneshape and reciproc < 0.001, p= 0.011, p=0.008 & <0.001). On assessing the transportation of the three file system over a distance of 7 mm (starting from 0mm and then evaluation at 1mm, 2mm, 3mm, 5mm and 7mm), the results showed a significant difference among the file systems at various lengths (p= 0.014, 0.046, 0.004, 0.028, 0.005 & 0.029 respectively). Mean value of cervical dentinal removal is maximum at all the levels for oneshape and minimum for waveone showing the better quality of waveone and reciproc over oneshape file system. Significant difference was found at 9mm, 11mm and 12mm between all the three file systems (p<0.001,< 0.001, <0.001). Conclusion It was concluded that reciprocating motion is better than rotary motion in all the three parameters Canal Transportation, Cross-sectional Area, Cervical Dentinal Thickness. PMID:26023639

Controlled reshaping of the front surface of the cornea through its full-area ablation outside of the optical zone with a Gaussian ArF excimer laser beam

NASA Astrophysics Data System (ADS)

Semchishen, A. V.; Semchishen, V. A.

2014-01-01

We studied in vitro the response of the topography of the cornea to its full-area laser ablation (the laser beam spot diameter is commensurable with the size of the interface) outside of the central zone with an excimer laser having a Gaussian fluence distribution across the beam. Subject to investigation were the topographically controlled surface changes of the anterior cornea in 60 porcine eyes with a 5 ± 1.25-diopter artificially induced astigmatism, the changes being caused by laser ablation of the stromal collagen in two 3.5-mm-dia. circular areas along the weaker astigmatism axis. Experimental relationships are presented between the actual astigmatism correction and the expected correction for the intact optical zones 1, 2, 3, and 4 mm in diameter. The data for each zone were approximated by the least-squares method with the function d = a + bx. The coefficient b is given with the root-mean-square error. The statistical processing of the data yielded the following results: d = (0.14 ± 0.037)x for the 1-mm-dia. optical zone, (1.10 ± 0.036)x for the 2-mm-dia. optical zone, (1.04 ± 0.020)x for the 3-mm-dia. optical zone, and (0.55 ± 0.04)x for the 4-mm-dia. optical zone. Full astigmatism correction was achieved with ablation effected outside of the 3-mm-dia. optical zone. The surface changes of the cornea are shown to be due not only to the removal of the corneal tissue, but also to the biomechanical topographic response of the cornea to its strain caused by the formation of a dense pseudomembrane in the ablation area.

Morphometric analysis of pulp size in maxillary permanent central incisors correlated with age: An indirect digital study.

PubMed

Ravindra, S V; Mamatha, G P; Sunita, J D; Balappanavar, Aswini Y; Sardana, Varun

2015-01-01

Teeth are hardest part of the body and are least affected by the taphonomic process. They are considered as one of the reliable methods of identification of a person in forensic sciences. The aim of the following study is to establish morphometeric measurements by AutoCad 2009 (Autodesk, Inc) of permanent maxillary central incisors in different age groups of Udaipur population. Hospital-based descriptive cross-sectional study carried out in Udaipur. A study was carried out on 308 subjects of both genders with the age range of 9-68 years. Standardized intra-oral radiographs were made by paralleling technique and processed. The radiographs were scanned and the obtained images were standardized to the actual size of radiographic film. This was followed by measuring them using software AutoCad 2009. F-test, post-hoc test, Pearson's correlation test. For left maxillary central incisor, the total pulp area was found to be of 38.41 ± 12.88 mm and 14.32 ± 7.04 mm respectively. For right maxillary central incisor, the total pulp size was 38.39 ± 14.95 mm and 12.35 ± 5 mm respectively. Males (32.50, 32.87 mm(2)) had more pulp area when compared with females (28.82, 30.05 mm(2)). There was a decrease in total pulp area with increasing age which may be attributed to secondary dentin formation.

Three-dimensional quadratic modeling and quantitative evaluation of the diaphragm on a volumetric CT scan in patients with chronic obstructive pulmonary disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Yongjun

Purpose: In patients with chronic obstructive pulmonary disease (COPD), diaphragm function may deteriorate due to reduced muscle fiber length. Quantitative analysis of the morphology of the diaphragm is therefore important. In the authors current study, they propose a diaphragm segmentation method for COPD patients that uses volumetric chest computed tomography (CT) data, and they provide a quantitative analysis of the diaphragmatic dimensions. Methods: Volumetric CT data were obtained from 30 COPD patients and 10 normal control patients using a 16-row multidetector CT scanner (Siemens Sensation 16) with 0.75-mm collimation. Diaphragm segmentation using 3D ray projections on the lower surface ofmore » the lungs was performed to identify the draft diaphragmatic lung surface, which was modeled using quadratic 3D surface fitting and robust regression in order to minimize the effects of segmentation error and parameterize diaphragm morphology. This result was visually evaluated by an expert thoracic radiologist. To take into consideration the shape features of the diaphragm, several quantification parameters—including the shape index on the apex (SIA) (which was computed using gradient set to 0), principal curvatures on the apex on the fitted diaphragm surface (CA), the height between the apex and the base plane (H), the diaphragm lengths along the x-, y-, and z-axes (XL, YL, ZL), quadratic-fitted diaphragm lengths on the z-axis (FZL), average curvature (C), and surface area (SA)—were measured using in-house software and compared with the pulmonary function test (PFT) results. Results: The overall accuracy of the combined segmentation method was 97.22% ± 4.44% while the visual accuracy of the models for the segmented diaphragms was 95.28% ± 2.52% (mean ± SD). The quantitative parameters, including SIA, CA, H, XL, YL, ZL, FZL, C, and SA were 0.85 ± 0.05 (mm{sup −1}), 0.01 ± 0.00 (mm{sup −1}), 17.93 ± 10.78 (mm), 129.80 ± 11.66 (mm), 163.19 ± 13.45 (mm), 71.27 ± 17.52 (mm), 61.59 ± 16.98 (mm), 0.01 ± 0.00 (mm{sup −1}), and 34 380.75 ± 6680.06 (mm{sup 2}), respectively. Several parameters were correlated with the PFT parameters. Conclusions: The authors propose an automatic method for quantitatively evaluating the morphological parameters of the diaphragm on volumetric chest CT in COPD patients. By measuring not only the conventional length and surface area but also the shape features of the diaphragm using quadratic 3D surface modeling, the proposed method is especially useful for quantifying diaphragm characteristics. Their method may be useful for assessing morphological diaphragmatic changes in COPD patients.« less

Poster - 22: Retrospective analysis of portal dosimetry based QA of Prostate VMAT Plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Badu, Shyam; Darko, Johnson; Fleck, Andre

2016-08-15

Purpose: The purpose of this study is to retrospectively analyze the portal dosimetry based quality assurance of prostate VMAT plans. Methods: Our standard quality assurance of VMAT treatment plans are performed using EPID installed on Varian TrueBeam Linac. In our current study we analyzed 84 prostate pretreatment VMAT plans. All plans consisted of two arcs, 7800cGy in 39 fractions with a 6MV beam. For each of these VMAT plans, the measured fluence for each arc is compared with the reference fluence using gamma index analysis. Results: We have compared the gamma passing rates for three criteria; 3%/3mm, 2%/2mm and 1%/1mm.more » Out of 168 arcs measured, the number below the gamma passing rate 95% using the area, Field+1cm, are 0, 2, and 124 for 3%/3mm, 2%/2mm and 1%/1mm criteria respectively. Corresponding numbers for MLC CIAO are 0, 2, and 139 respectively. The average gamma passing rate for all arcs measured using Field+1cm are 99.9±0.4, 99.6±1.2, and 90.9±6.5 for 3%/3mm, 2%/2mm and 1%/1mm respectively. Similarly if the MLC CIAO area is analyzed, a passing rate of 99.9±0.2, 99.2±1.2 and 87.2±8.5 respectively was observed. The average of the maximum gamma was also found to increase with tighter criteria. Conclusion: Analysis of prostate VMAT quality assurance plans indicate that the gamma passing rate is sensitive to the criteria and the area analyzed.« less

Arrhenius parameter determination as a function of heating method and cellular microenvironment based on spatial cell viability analysis.

PubMed

Whitney, Jon; Carswell, William; Rylander, Nichole

2013-06-01

Predictions of injury in response to photothermal therapy in vivo are frequently made using Arrhenius parameters obtained from cell monolayers exposed to laser or water bath heating. However, the impact of different heating methods and cellular microenvironments on Arrhenius predictions has not been thoroughly investigated. This study determined the influence of heating method (water bath and laser irradiation) and cellular microenvironment (cell monolayers and tissue phantoms) on Arrhenius parameters and spatial viability. MDA-MB-231 cells seeded in monolayers and sodium alginate phantoms were heated with a water bath for 3-20 min at 46, 50, and 54 °C or laser irradiated (wavelength of 1064 nm and fluences of 40 W/cm(2) or 3.8 W/cm(2) for 0-4 min) in combination with photoabsorptive carbon nanohorns. Spatial viability was measured using digital image analysis of cells stained with calcein AM and propidium iodide and used to determine Arrhenius parameters. The influence of microenvironment and heating method on Arrhenius parameters and capability of parameters derived from more simplistic experimental conditions (e.g. water bath heating of monolayers) to predict more physiologically relevant systems (e.g. laser heating of phantoms) were assessed. Arrhenius predictions of the treated area (<1% viable) under-predicted the measured areas in photothermally treated phantoms by 23 mm(2) using water bath treated cell monolayer parameters, 26 mm(2) using water bath treated phantom parameters, 27 mm(2) using photothermally treated monolayer parameters, and 0.7 mm(2) using photothermally treated phantom parameters. Heating method and cellular microenvironment influenced Arrhenius parameters, with heating method having the greater impact.

Method for biological tissue temperature measuring in the area of laser radiation exposure with a small size beam profile during laser welding

NASA Astrophysics Data System (ADS)

Ryabkin, Dmitrii I.

2018-04-01

Connection is not strong enough In case of insufficient or excessive temperature of the laser welding. As a result, the temperature measurement in laser welding is an important problem. Measurement area surface is small (3.12 mm2) and measurements shall be carried out by a Non-contact method, which makes them challenging. Method of temperature measurement by an infrared sensor in two positions has been offered. This method allows you to measure the temperature at a distance of up to 5 cm from the measured area with an accuracy of 8%.

Fatigue and In Vivo Validation of a Peritoneum-Lined Self-Expanding Nitinol Stent-Graft

PubMed Central

Bastijanic, Jennifer M.; Etscheidt, Jordan; Sattiraju, Mallika; Bonsignore, Craig; Kopchok, George; White, Rodney; Sarac, Timur P.

2014-01-01

Purpose To assess the fatigue and in vivo performance of a new stent-graft incorporating bovine peritoneum lining that is designed for application in peripheral vascular occlusive disease. Methods Bovine peritoneum-lined stent-grafts were subjected to accelerated in vitro pulsatile fatigue and axial/torsional fatigue testing designed to simulate 10 years of physiological strain on the devices. At specified times the devices were evaluated for stent fracture, suture failure, or tissue tearing. Seven dogs underwent bilateral common iliac artery (CIA) balloon angioplasty injury with unilateral placement of the peritoneum-lined stent-graft. Angiography and intravascular ultrasound were performed prior to treatment, after treatment, and prior to sacrifice at 30 days. Vessels were perfusion fixed and histologically evaluated at 5 regions: above stent, proximal stent, mid stent, distal stent, and below stent. Results No evidence of stent, suture, or tissue failure was present during or after pulsatile and axial/torsional fatigue testing. At 30±0.3 days after implantation, all vessels were patent. The average lumen area at explantation across stented vessels was 25.45 mm2. Lumen areas tended to be reduced above (23.57 mm2) and below (24.17 mm2) the stent. Lumen areas were consistent across stented regions at explantation (proximal stent 27.80 mm2, mid stent 25.88 mm2, and distal stent 25.81 mm2). The mean neointimal area in peritoneum-lined stents was 2.02±1.52 mm2, with a neointima:media ratio of 1.03±0.50. These values were significantly lower in the above and below stent areas than in the stented regions, but there was no difference in either measure within the proximal, mid, or distal stent. Conclusion The custom-designed peritoneum-lined stent-graft is promising for clinical peripheral applications due to its ability to resist relevant long-term physiological stresses and outstanding short-term patency rates in canine implantations. PMID:25290804

Development of 4-Sides Buttable CdTe-ASIC Hybrid Module for X-ray Flat Panel Detector

NASA Astrophysics Data System (ADS)

Tamaki, Mitsuru; Mito, Yoshio; Shuto, Yasuhiro; Kiyuna, Tatsuya; Yamamoto, Masaya; Sagae, Kenichi; Kina, Tooru; Koizumi, Tatsuhiro; Ohno, Ryoichi

2009-08-01

A 4-sides buttable CdTe-ASIC hybrid module suitable for use in an X-ray flat panel detector (FPD) has been developed by applying through silicon via (TSV) technology to the readout ASIC. The ASIC has 128 times 256 channels of charge integration type readout circuitry and an area of 12.9 mm times 25.7 mm. The CdTe sensor of 1 mm thickness, having the same area and pixel of 100 mum pitch, was fabricated from the Cl-doped CdTe single crystal grown by traveling heater method (THM). Then the CdTe pixel sensor was hybridized with the ASIC using the bump-bonding technology. The basic performance of this 4-sides buttable module was evaluated by taking X-ray images, and it was compared with that of a commercially available indirect type CsI(Tl) FPD. A prototype CdTe FPD was made by assembling 9 pieces of the 4-sides buttable modules into 3 times 3 arrays in which the neighboring modules were mounted on the interface board. The FPD covers an active area of 77 mm times 39 mm. The results showed the great potential of this 4-sides buttable module for the new real time X-ray FPD with high spatial resolution.

Regional geoid computation by least squares modified Hotine's formula with additive corrections

NASA Astrophysics Data System (ADS)

Märdla, Silja; Ellmann, Artu; Ågren, Jonas; Sjöberg, Lars E.

2018-03-01

Geoid and quasigeoid modelling from gravity anomalies by the method of least squares modification of Stokes's formula with additive corrections is adapted for the usage with gravity disturbances and Hotine's formula. The biased, unbiased and optimum versions of least squares modification are considered. Equations are presented for the four additive corrections that account for the combined (direct plus indirect) effect of downward continuation (DWC), topographic, atmospheric and ellipsoidal corrections in geoid or quasigeoid modelling. The geoid or quasigeoid modelling scheme by the least squares modified Hotine formula is numerically verified, analysed and compared to the Stokes counterpart in a heterogeneous study area. The resulting geoid models and the additive corrections computed both for use with Stokes's or Hotine's formula differ most in high topography areas. Over the study area (reaching almost 2 km in altitude), the approximate geoid models (before the additive corrections) differ by 7 mm on average with a 3 mm standard deviation (SD) and a maximum of 1.3 cm. The additive corrections, out of which only the DWC correction has a numerically significant difference, improve the agreement between respective geoid or quasigeoid models to an average difference of 5 mm with a 1 mm SD and a maximum of 8 mm.

Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

2018-06-01

Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆G binding  = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation ability, drug release and further development of novel liposome-based pH-responsive nano-drug delivery system with refined structural and chemical features of potential lipid molecule for formulation development.

WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures.

PubMed

Kasam, Vinod; Salzemann, Jean; Botha, Marli; Dacosta, Ana; Degliesposti, Gianluca; Isea, Raul; Kim, Doman; Maass, Astrid; Kenyon, Colin; Rastelli, Giulio; Hofmann-Apitius, Martin; Breton, Vincent

2009-05-01

Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase. In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures. On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed. The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.

Precipitation Modeling over the Greenland and Antarctic Ice Sheets and the Relationship to the Surface Mass Balance and Climate

NASA Technical Reports Server (NTRS)

Bromwich, David H.; Chen, Qui-Shi

2005-01-01

Atmospheric numerical simulation and dynamic retrieval method with atmospheric numerical analyses are used to assess the spatial and temporal variability of Antarctic precipitation for the last two decades. First, the Polar MM5 has been run over Antarctica to study the Antarctic precipitation. With a horizontal resolution of 60km, the Polar MM5 has been run for the period of July 1996 through June 1999 in a series of short-term forecasts from initial and boundary conditions provided by the ECMWF operational analyses. In comparison with climatological maps, the major features of the spatial distribution of Antarctic precipitation are well captured by the Polar MM5. Drift snow effects on redistribution of surface accumulation over Antarctica are also assessed with surface wind fields from Polar MM5 in this study. There are complex divergence and convergence patterns of drift snow transport over Antarctica, especially along the coast. It is found that areas with large drift snow transport convergence and divergence are located around escarpment areas where there is large katabatic wind acceleration. In addition, areas with large snow transport divergence are generally accompanied by areas with large snow transport convergence nearby, indicating that drift snow transport is of local importance for the redistribution of the snowfall

Microscale mass spectrometry systems, devices and related methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramsey, John Michael

Mass spectrometry systems or assemblies therefore include an ionizer that includes at least one planar conductor, a mass analyzer with a planar electrode assembly, and a detector comprising at least one planar conductor. The ionizer, the mass analyzer and the detector are attached together in a compact stack assembly. The stack assembly has a perimeter that bounds an area that is between about 0.01 mm.sup.2 to about 25 cm.sup.2 and the stack assembly has a thickness that is between about 0.1 mm to about 25 mm.

Microscale mass spectrometry systems, devices and related methods

DOEpatents

Ramsey, John Michael

2016-06-21

Mass spectrometry systems or assemblies therefore include an ionizer that includes at least one planar conductor, a mass analyzer with a planar electrode assembly, and a detector comprising at least one planar conductor. The ionizer, the mass analyzer and the detector are attached together in a compact stack assembly. The stack assembly has a perimeter that bounds an area that is between about 0.01 mm.sup.2 to about 25 cm.sup.2 and the stack assembly has a thickness that is between about 0.1 mm to about 25 mm.

Large-Area Fabrication of Droplet Pancake Bouncing Surface and Control of Bouncing State.

PubMed

Song, Jinlong; Gao, Mingqian; Zhao, Changlin; Lu, Yao; Huang, Liu; Liu, Xin; Carmalt, Claire J; Deng, Xu; Parkin, Ivan P

2017-09-26

Superhydrophobic pillar arrays, which can generate the droplet pancake bouncing phenomenon with reduced liquid-solid contact time, have huge application prospects in anti-icing of aircraft wings from freezing rain. However, the previously reported pillar arrays, suitable for obtaining pancake bouncing, have a diameter ≤100 μm and height-diameter ratio >10, which are difficult to fabricate over a large area. Here, we have systematically studied the influence of the dimension of the superhydrophobic pillar arrays on the bouncing dynamics of water droplets. We show that the typical pancake bouncing with 57.8% reduction in contact time with the surface was observed on the superhydrophobic pillar arrays with 1.05 mm diameter, 0.8 mm height, and 0.25 mm space. Such pillar arrays with millimeter diameter and <1 height-diameter ratio can be easily fabricated over large areas. Further, a simple replication-spraying method was developed for the large-area fabrication of the superhydrophobic pillar arrays to induce pancake bouncing. No sacrificial layer was needed to reduce the adhesion in the replication processes. Since the bouncing dynamics were rather sensitive to the space between the pillars, a method to control the contact time, bouncing shape, horizontal bouncing direction, and reversible switch between pancake bouncing and conventional bouncing was realized by adjusting the inclination angle of the shape memory polymer pillars.

Quantifying the Rate of Ellipsoid Zone Loss in Stargardt Disease.

PubMed

Cai, Cindy X; Light, Jacob G; Handa, James T

2018-02-01

To determine a reliable method of using the ellipsoid zone (EZ) on optical coherence tomography (OCT) to track disease progression in Stardgardt disease (STGD). Retrospective reliability study. STGD patients with genetically confirmed ABCA4 gene mutations seen at the Wilmer Eye Institute with follow-up visits separated by at least 12 months were identified. Spectral-domain optical coherence tomography (SD-OCT) macula volume scans centered at the fovea and fundus autofluorescence (FAF) images were obtained. The area of EZ loss was calculated from the SD-OCT and the area of retinal pigment epithelium (RPE) loss from the FAF. Scans were reanalyzed by the primary grader to assess intragrader reliability, and reanalyzed by a second grader to assess intergrader reliability. Sixteen STGD patients (total of 31 eyes) were followed for a mean of 2 years (range 1-4.7 years). The mean rate of EZ loss, 0.31 ± 0.31 mm 2 /year, was similar to the average rate of RPE loss, 0.33 ± 0.38 mm 2 /year. The average area of EZ loss at the initial examination, 4.18 ± 1.91 mm 2 , was larger than the initial area of RPE loss, 2.25 ± 1.66 mm 2 (P < .01). The absolute difference of the area of EZ loss on test-retest for the first grader was 0.12 ± 0.10 mm 2 , and between graders 0.21 ± 0.21 mm 2 . The intraclass correlation (ICC) of both intragrader and intergrader reliability for EZ loss was excellent at 0.99. Tracking the area of EZ loss on SD-OCT macular volume scans longitudinally is a reliable way of monitoring disease progression in STGD. This could be used as a sensitive anatomic outcome measure in clinical trials related to STGD. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

PubMed Central

Ieong, Pek; Amaro, Rommie E.; Li, Wilfred W.

2015-01-01

The antibody immunoglobulin (Ig) 2D1 is effective against the 1918 hemagglutinin (HA) and also known to cross-neutralize the 2009 pandemic H1N1 influenza HA through a similar epitope. However, the detailed mechanism of neutralization remains unclear. We conducted molecular dynamics (MD) simulations to study the interactions between Ig-2D1 and the HAs from the 1918 pandemic flu (A/South Carolina/1/1918, 18HA), the 2009 pandemic flu (A/California/04/2009, 09HA), a 2009 pandemic flu mutant (A/California/04/2009, 09HA_mut), and the 2006 seasonal flu (A/Solomon Islands/3/2006, 06HA). MM-PBSA analyses suggest the approximate free energy of binding (ΔG) between Ig-2D1 and 18HA is −74.4 kcal/mol. In comparison with 18HA, 09HA and 06HA bind Ig-2D1 ∼6 kcal/mol (ΔΔG) weaker, and the 09HA_mut bind Ig-2D1 only half as strong. We also analyzed the contributions of individual epitope residues using the free-energy decomposition method. Two important salt bridges are found between the HAs and Ig-2D1. In 09HA, a serine-to-asparagine mutation coincided with a salt bridge destabilization, hydrogen bond losses, and a water pocket formation between 09HA and Ig-2D1. In 09HA_mut, a lysine-to-glutamic-acid mutation leads to the loss of both salt bridges and destabilizes interactions with Ig-2D1. Even though 06HA has a similar ΔG to 09HA, it is not recognized by Ig-2D1 in vivo. Because 06HA contains two potential glycosylation sites that could mask the epitope, our results suggest that Ig-2D1 may be active against 06HA only in the absence of glycosylation. Overall, our simulation results are in good agreement with observations from biological experiments and offer novel mechanistic insights, to our knowledge, into the immune escape of the influenza virus. PMID:26039171

Estimating nonrigid motion from inconsistent intensity with robust shape features

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Wenyang; Ruan, Dan, E-mail: druan@mednet.ucla.edu; Department of Radiation Oncology, University of California, Los Angeles, California 90095

2013-12-15

Purpose: To develop a nonrigid motion estimation method that is robust to heterogeneous intensity inconsistencies amongst the image pairs or image sequence. Methods: Intensity and contrast variations, as in dynamic contrast enhanced magnetic resonance imaging, present a considerable challenge to registration methods based on general discrepancy metrics. In this study, the authors propose and validate a novel method that is robust to such variations by utilizing shape features. The geometry of interest (GOI) is represented with a flexible zero level set, segmented via well-behaved regularized optimization. The optimization energy drives the zero level set to high image gradient regions, andmore » regularizes it with area and curvature priors. The resulting shape exhibits high consistency even in the presence of intensity or contrast variations. Subsequently, a multiscale nonrigid registration is performed to seek a regular deformation field that minimizes shape discrepancy in the vicinity of GOIs. Results: To establish the working principle, realistic 2D and 3D images were subject to simulated nonrigid motion and synthetic intensity variations, so as to enable quantitative evaluation of registration performance. The proposed method was benchmarked against three alternative registration approaches, specifically, optical flow, B-spline based mutual information, and multimodality demons. When intensity consistency was satisfied, all methods had comparable registration accuracy for the GOIs. When intensities among registration pairs were inconsistent, however, the proposed method yielded pronounced improvement in registration accuracy, with an approximate fivefold reduction in mean absolute error (MAE = 2.25 mm, SD = 0.98 mm), compared to optical flow (MAE = 9.23 mm, SD = 5.36 mm), B-spline based mutual information (MAE = 9.57 mm, SD = 8.74 mm) and mutimodality demons (MAE = 10.07 mm, SD = 4.03 mm). Applying the proposed method on a real MR image sequence also provided qualitatively appealing results, demonstrating good feasibility and applicability of the proposed method. Conclusions: The authors have developed a novel method to estimate the nonrigid motion of GOIs in the presence of spatial intensity and contrast variations, taking advantage of robust shape features. Quantitative analysis and qualitative evaluation demonstrated good promise of the proposed method. Further clinical assessment and validation is being performed.« less

Relationship between Plaque Echo, Thickness and Neovascularization Assessed by Quantitative and Semi-quantitative Contrast-Enhanced Ultrasonography in Different Stenosis Groups.

PubMed

Song, Yan; Feng, Jun; Dang, Ying; Zhao, Chao; Zheng, Jie; Ruan, Litao

2017-12-01

The aim of this study was to determine the relationship between plaque echo, thickness and neovascularization in different stenosis groups using quantitative and semi-quantitative contrast-enhanced ultrasound (CEUS) in patients with carotid atherosclerosis plaque. A total of 224 plaques were divided into mild stenosis (<50%; 135 plaques, 60.27%), moderate stenosis (50%-69%; 39 plaques, 17.41%) and severe stenosis (70%-99%; 50 plaques, 22.32%) groups. Quantitative and semi-quantitative methods were used to assess plaque neovascularization and determine the relationship between plaque echo, thickness and neovascularization. Correlation analysis revealed no relationship of neovascularization with plaque echo in the groups using either quantitative or semi-quantitative methods. Furthermore, there was no correlation of neovascularization with plaque thickness using the semi-quantitative method. The ratio of areas under the curve (RAUC) was negatively correlated with plaque thickness (r = -0.317, p = 0.001) in the mild stenosis group. With the quartile method, plaque thickness of the mild stenosis group was divided into four groups, with significant differences between the 1.5-2.2 mm and ≥3.5 mm groups (p = 0.002), 2.3-2.8 mm and ≥3.5 mm groups (p <0.001) and 2.9-3.4 mm and ≥3.5 mm groups (p <0.001). Both semi-quantitative and quantitative CEUS methods characterizing neovascularization of plaque are equivalent with respect to assessing relationships between neovascularization, echogenicity and thickness. However, the quantitative method could fail for plaque <3.5 mm because of motion artifacts. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Pedicle distraction increases intervertebral and spinal canal area in a cadaver and bone model.

PubMed

Hughes, Matthew; Papadakos, Nikolaos; Bishop, Tim; Bernard, Jason

2018-01-01

Lumbar spinal stenosis is degenerative narrowing of the spinal canal and/or intervertebral foramen causing compression of the spinal cord and nerve roots. Traditional decompression techniques can often cause significant trauma and vertebral instability. This paper evaluates a method of increasing pedicle length to decompress the spinal and intervertebral foramen, which could be done minimally invasive. Three Sawbone (Sawbones Europe, Sweden) and 1 cadaveric lumbar spine underwent bilateral pedicle distraction at L4. A pedicle channel was drilled between the superior articular process and transverse process into the vertebral body. The pedicles underwent osteotomy at the midpoint. Screws were inserted bilaterally and fixated distraction of 0 mm, 2 mm, 4 mm and 6 mm. CT images were taken at each level of distraction. Foramen area was measured in the sagittal plane at L3/4. Spinal canal area was measured at L4 in the axial images. The cadaver was used to evaluate safety of osteotomy and soft tissue interactions preventing distraction. Statistical analysis was by student paired t-test and Pearson rank test. Increasing distraction led to greater Spinal canal area. From 4.27 cm 2 to 5.72 cm 2 (p = 0.002) with 6 mm distraction. A Maximal increase of 34.1%. Vertebral foramen area also increased with increasing pedicle distraction. From 2.43 cm 2 to 3.22 cm 2 (p = 0.022) with 6 mm distraction. A maximal increase of 32.3%. The cadaver spinal canal increased in area by 21.7%. The vertebral foramen increased in area by 36.2% (left) and 22.6% (right). For each increase in pedicle distraction the area of the spinal and vertebral foramen increases. Pedicle distraction could potentially be used to alleviate spinal stenosis and root impingement. A potential osteotomy plane could be at the midpoint of the pedicle with minimal risk to nerve roots and soft tissue restrictions to prevent distraction. © The Authors, published by EDP Sciences, 2018.

Estimating nonrigid motion from inconsistent intensity with robust shape features.

PubMed

Liu, Wenyang; Ruan, Dan

2013-12-01

To develop a nonrigid motion estimation method that is robust to heterogeneous intensity inconsistencies amongst the image pairs or image sequence. Intensity and contrast variations, as in dynamic contrast enhanced magnetic resonance imaging, present a considerable challenge to registration methods based on general discrepancy metrics. In this study, the authors propose and validate a novel method that is robust to such variations by utilizing shape features. The geometry of interest (GOI) is represented with a flexible zero level set, segmented via well-behaved regularized optimization. The optimization energy drives the zero level set to high image gradient regions, and regularizes it with area and curvature priors. The resulting shape exhibits high consistency even in the presence of intensity or contrast variations. Subsequently, a multiscale nonrigid registration is performed to seek a regular deformation field that minimizes shape discrepancy in the vicinity of GOIs. To establish the working principle, realistic 2D and 3D images were subject to simulated nonrigid motion and synthetic intensity variations, so as to enable quantitative evaluation of registration performance. The proposed method was benchmarked against three alternative registration approaches, specifically, optical flow, B-spline based mutual information, and multimodality demons. When intensity consistency was satisfied, all methods had comparable registration accuracy for the GOIs. When intensities among registration pairs were inconsistent, however, the proposed method yielded pronounced improvement in registration accuracy, with an approximate fivefold reduction in mean absolute error (MAE = 2.25 mm, SD = 0.98 mm), compared to optical flow (MAE = 9.23 mm, SD = 5.36 mm), B-spline based mutual information (MAE = 9.57 mm, SD = 8.74 mm) and mutimodality demons (MAE = 10.07 mm, SD = 4.03 mm). Applying the proposed method on a real MR image sequence also provided qualitatively appealing results, demonstrating good feasibility and applicability of the proposed method. The authors have developed a novel method to estimate the nonrigid motion of GOIs in the presence of spatial intensity and contrast variations, taking advantage of robust shape features. Quantitative analysis and qualitative evaluation demonstrated good promise of the proposed method. Further clinical assessment and validation is being performed.

Rapid surface colony counts determination with three new miniaturised techniques.

PubMed

Malik, K A

1977-01-01

Three different miniaturised methods for the rapid surface viable counting are described. The methods were tried in parallel to seven different existing methods (Table 1) for viable counts and were found to be easier, quicker and insome cases more accurate. The techniques require about 10% of the material and time needed for conventional spread-plates method and the results were in no way inferior to that (Table 1 and 2). Mini agar discs were cut aseptically with an especially designed stainless steel agar disc cutter (25 mm internal and 28 mm external diameter, Fig. 1b) or with a test tube of similar diameter. The area of the resulted mini-agar-disc of 25 mm diameter was kept such (about 1/10th of the normal plate) that the ratio of the colony-bearing area to the inoculm remained the same as on big plates in spread-plate-method (Table 2). In normal Petri dishes (about 90 mm diameter) up to seven mini agar discs were possible to cut. Each small agar disc was seperated from the other mini-disc by a distance of at least 6 mm (Fig. 1a). The empty place around the disc was still enlarged during over drying of the plates and during incubation. This created complete isolation from the neighbouring disc. For micro-determination of surface viable counts 10 micronl from each dilution was delivered on a well-dired mini-disc with a piston micropipette. The inoculm was immediately spread on the whole mini-disc with a specially designed flame sterilizable platinum-Mini-spreader (Fig. 2a). No spinning of the plate was needed. Alternatively the dropping pipette and spreader was replaced by a calibrated platinum wire Loop-spreader (Fig. 2b). A loop of 3 mm internal diameter made from a platinum-iridium wire of 0.75 mm thickness proved most useful and carried a drop of 10 micronl. Differences especially in surface tension of various diluting fluids did not influence to drop of this size and no recalibration was needed for water and nutrient broth. The loop was further shaped to Loop-spreader form. From each bacterial suspension 10 micronl were carried and spread on each mini-disc. The method is useful for pathogenic organisms as the loop can readily be flame sterilized. For routine purposes where only approximate numbers of bacteria need to be known a still rapid semiquantitative method was deviced making use of a calibrated stainless steel Stamping-disc (Fig. 2c). A disc of 25mm diameter and 1 mm thickness delivered approximateyl 10 microlitres of supensions and was found to be most useful to stamp seven dilutions on a single plate. In collections and bacteriology laboratories where by conventional methods large number of plates are to be plated and counted the presented techniques could prove most convenient, rapid and economical.

Association of imaging abnormalities of the subcallosal septal area with Alzheimer's disease and mild cognitive impairment.

PubMed

Gan, C L; O'Sullivan, M J; Metzler-Baddeley, C; Halpin, S

2017-11-01

To evaluate the use the distance between the adjacent septal nuclei as a surrogate marker of septal area atrophy seen in Alzheimer's disease (AD). Interseptal distance (ISD) was measured, blind to clinical details, in 250 patients who underwent computed tomography (CT) of the brain at University Hospital of Wales. Clinical details including memory problem history were retrieved. An ISD cut-off value that discriminated those with and without memory symptoms was sought. ISD measurements were also made in 20 AD patients. To test both the method and the defined cut-off, measurements were then made in an independent cohort of 21 mild cognitive impairment (MCI) patients and 45 age-matched healthy controls, in a randomised and blinded fashion. ISD measurement was achieved in all patients. In 28 patients with memory symptoms, the mean ISD was 5.9 mm compared with 2.3 mm in those without overt symptoms (p=0.001). The optimum ISD cut-off value was 4 mm (sensitivity 85.7% and specificity 85.8%). All AD patients had an ISD of >4 mm (mean ISD= 6.1 mm). The mean ISD for MCI patients was 3.84 mm compared with 2.18 mm in age-matched healthy controls (p=0.001). Using a 4 mm cut-off correctly categorised 10 mild cognitive impairment patients (47.6%) and 38 healthy controls (84.4%). ISD is a simple and reliable surrogate measurement for septal area atrophy, applicable to CT and magnetic resonance imaging (MRI). It can be used to help select patients for further investigation. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoupin, Stanislav; Antipov, Sergey; Butler, James E.

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configurationmore » and data analysis using rocking-curve topography. In conclusion, the variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.« less

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics.

PubMed

Stoupin, Stanislav; Antipov, Sergey; Butler, James E; Kolyadin, Alexander V; Katrusha, Andrey

2016-09-01

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking-curve topography. The variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics

DOE PAGES

Stoupin, Stanislav; Antipov, Sergey; Butler, James E.; ...

2016-08-10

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configurationmore » and data analysis using rocking-curve topography. In conclusion, the variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.« less

Efficacy of a sheet combined with fibrin glue in repair of pleural defect at the early phase after lung surgery in a canine model.

PubMed

Sakai, Takashi; Matsutani, Noriyuki; Kanai, Eiichi; Yamauchi, Yoshikane; Uehara, Hirofumi; Iinuma, Hisae; Kawamura, Masafumi

2018-02-01

Polyglycolic acid and oxidized regenerated cellulose have been widely used as a sealant for repairing pulmonary air leakage during respiratory surgery. However, fundamental research of these materials has not been sufficiently conducted. Therefore, we conducted studies to assess the pressure resistance ability of these materials using a canine visceral pleural defect model at the early phase. The 6-mm circular defect and the 12-mm square defect were created on the visceral pleura of anesthetized beagles. These defects were then repaired using one of four methods: method A using polyglycolic acid and fibrin glue; method B using oxidized regenerated cellulose and fibrin glue; method C using oxidized regenerated cellulose; method D using fibrin glue. Airway pressure was measured as bursting pressure when air leakage from the repaired areas occurred at 5 min, 3 h, and 24 h after repair. For the 6-mm circle defect, method A showed higher bursting pressures than the other methods at 5 min and 3 h (p < 0.05); method B showed higher than methods C and D at 5 min and 3 h (p < 0.05). For the 12-mm square defect, method A showed higher bursting pressures than the other methods at all time points (p < 0.05). Moreover, method B showed higher than method C at 24 h (p < 0.05). Visceral pleural repairs using polyglycolic acid combined with fibrin glue showed the highest bursting pressure. Oxidized regenerated cellulose combined with fibrin glue showed sufficiently high bursting pressure in repair of small 6-mm circular defects.

Using remote sensing to characterize and compare evapotranspiration from different irrigation regimes in the Smith River Watershed of central Montana

USGS Publications Warehouse

Sando, Thomas R.; Caldwell, Rodney R.; Blasch, Kyle W.

2017-01-01

According to the 2005 U.S. Geological Survey national water use compilation, irrigation is the second largest use of fresh water in the United States, accounting for 37%, or 484.48 million cubic meters per day, of total freshwater withdrawal. Accurately estimating the amount of water withdrawals and actual consumptive water use (the difference between water withdrawals and return flow) for irrigation at a regional scale is difficult. Remote sensing methods make it possible to compare actual ET (ETa) rates which can serve as a proxy for consumptive water use from different irrigation regimes at a regional scale in a systematic manner. This study investigates crucial components of water use from irrigation such as the difference of ETa rates from flood- and sprinkler-irrigated fields, spatial variability of ETa within a watershed, and the effect of sprinkler irrigation on the water budget of the study area. The mean accumulated ETa depth for the 1,051 square kilometer study area within the upper Smith River watershed was about 467 mm 30-meter per pixel for the 2007 growing season (April through mid-October). The total accumulated volume of ETa for the study area was about 474.705 million cubic meters. The mean accumulated ETa depth from sprinkler-irrigated land was about 687 mm and from flood-irrigated land was about 621 mm from flood-irrigated land. On average, the ETa rate from sprinkler-irrigated fields was 0.25 mm per day higher than flood-irrigated fields over the growing season. Spatial analysis showed that ETa rates within individual fields of a single crop type that are irrigated with a single method (sprinkler or flood) can vary up to about 8 mm per day. It was estimated that the amount of sprinkler irrigation in 2007 accounted for approximately 3% of the total volume of ETa in the study area. When compared to non-irrigated dryland, sprinkler irrigation increases ETa by about 59 to 82% per unit area.

Large area 3-D optical coherence tomography imaging of lumpectomy specimens for radiation treatment planning

NASA Astrophysics Data System (ADS)

Wang, Cuihuan; Kim, Leonard; Barnard, Nicola; Khan, Atif; Pierce, Mark C.

2016-02-01

Our long term goal is to develop a high-resolution imaging method for comprehensive assessment of tissue removed during lumpectomy procedures. By identifying regions of high-grade disease within the excised specimen, we aim to develop patient-specific post-operative radiation treatment regimens. We have assembled a benchtop spectral-domain optical coherence tomography (SD-OCT) system with 1320 nm center wavelength. Automated beam scanning enables "sub-volumes" spanning 5 mm x 5 mm x 2 mm (500 A-lines x 500 B-scans x 2 mm in depth) to be collected in under 15 seconds. A motorized sample positioning stage enables multiple sub-volumes to be acquired across an entire tissue specimen. Sub-volumes are rendered from individual B-scans in 3D Slicer software and en face (XY) images are extracted at specific depths. These images are then tiled together using MosaicJ software to produce a large area en face view (up to 40 mm x 25 mm). After OCT imaging, specimens were sectioned and stained with HE, allowing comparison between OCT image features and disease markers on histopathology. This manuscript describes the technical aspects of image acquisition and reconstruction, and reports initial qualitative comparison between large area en face OCT images and HE stained tissue sections. Future goals include developing image reconstruction algorithms for mapping an entire sample, and registering OCT image volumes with clinical CT and MRI images for post-operative treatment planning.

Methodological comparison of alpine meadow evapotranspiration on the Tibetan Plateau, China.

PubMed

Chang, Yaping; Wang, Jie; Qin, Dahe; Ding, Yongjian; Zhao, Qiudong; Liu, Fengjing; Zhang, Shiqiang

2017-01-01

Estimation of evapotranspiration (ET) for alpine meadow areas in the Tibetan Plateau (TP) is essential for water resource management. However, observation data has been limited due to the extreme climates and complex terrain of this region. To address these issues, four representative methods, Penman-Monteith (PM), Priestley-Taylor (PT), Hargreaves-Samani (HS), and Mahringer (MG) methods, were adopted to estimate ET, which were then compared with ET measured using Eddy Covariance (EC) for five alpine meadow sites during the growing seasons from 2010 to 2014. And each site was measured for one growing season during this period. The results demonstrate that the PT method outperformed at all sites with a coefficient of determination (R2) ranging from 0.76 to 0.94 and root mean square error (RMSE) ranging from 0.41 to 0.62 mm d-1. The PM method showed better performance than HS and MG methods, and the HS method produced relatively acceptable results with higher R2 (0.46) and lower RMSE (0.89 mm d-1) compared to MG method with R2 of 0.16 and RMSE of 1.62 mm d-1, while MG underestimated ET at all alpine meadow sites. Therefore, the PT method, being the simpler approach and less data dependent, is recommended to estimate ET for alpine meadow areas in the Tibetan Plateau. The PM method produced reliable results when available data were sufficient, and the HS method proved to be a complementary method when variables were insufficient. On the contrary, the MG method always underestimated ET and is, thus, not suitable for alpine meadows. These results provide a basis for estimating ET on the Tibetan Plateau for annual data collection, analysis, and future studies.

Methodological comparison of alpine meadow evapotranspiration on the Tibetan Plateau, China

PubMed Central

Chang, Yaping; Wang, Jie; Qin, Dahe; Ding, Yongjian; Zhao, Qiudong; Liu, Fengjing

2017-01-01

Estimation of evapotranspiration (ET) for alpine meadow areas in the Tibetan Plateau (TP) is essential for water resource management. However, observation data has been limited due to the extreme climates and complex terrain of this region. To address these issues, four representative methods, Penman-Monteith (PM), Priestley-Taylor (PT), Hargreaves-Samani (HS), and Mahringer (MG) methods, were adopted to estimate ET, which were then compared with ET measured using Eddy Covariance (EC) for five alpine meadow sites during the growing seasons from 2010 to 2014. And each site was measured for one growing season during this period. The results demonstrate that the PT method outperformed at all sites with a coefficient of determination (R2) ranging from 0.76 to 0.94 and root mean square error (RMSE) ranging from 0.41 to 0.62 mm d-1. The PM method showed better performance than HS and MG methods, and the HS method produced relatively acceptable results with higher R2 (0.46) and lower RMSE (0.89 mm d-1) compared to MG method with R2 of 0.16 and RMSE of 1.62 mm d-1, while MG underestimated ET at all alpine meadow sites. Therefore, the PT method, being the simpler approach and less data dependent, is recommended to estimate ET for alpine meadow areas in the Tibetan Plateau. The PM method produced reliable results when available data were sufficient, and the HS method proved to be a complementary method when variables were insufficient. On the contrary, the MG method always underestimated ET and is, thus, not suitable for alpine meadows. These results provide a basis for estimating ET on the Tibetan Plateau for annual data collection, analysis, and future studies. PMID:29236754

Lumen and calcium characteristics within calcified coronary lesions. Comparison of computed tomography coronary angiography versus intravascular ultrasound.

PubMed

Noll, Dariusz; Kruk, Mariusz; Pręgowski, Jerzy; Kaczmarska, Edyta; Kryczka, Karolina; Pracoń, Radosław; Skwarek, Mirosław; Dzielińska, Zofia; Petryka, Joanna; Spiewak, Mateusz; Lubiszewska, Barbara; Norwa-Otto, Bożena; Opolski, Maksymilian; Witkowski, Adam; Demkow, Marcin; Rużyłło, Witold; Kępka, Cezary

2013-01-01

Computed tomography coronary angiography (CTCA) is a diagnostic method used for exclusion of coronary artery disease. However, lower accuracy of CTCA in assessment of calcified lesions is a significant factor impeding applicability of CTCA for assessment of coronary atherosclerosis. To provide insight into lumen and calcium characteristics assessed with CTCA, we compared these parameters to the reference of intravascular ultrasound (IVUS). Two hundred and fifty-two calcified lesions within 97 arteries of 60 patients (19 women, age 63 ±10 years) underwent assessment with both 2 × 64 slice CT (Somatom Definition, Siemens) and IVUS (s5, Volcano Corp.). Coronary lumen and calcium dimensions within calcified lesions were assessed with CTCA and compared to the reference measurements made with IVUS. On average CTCA underestimated mean lumen diameter (2.8 ±0.7 mm vs. 2.9 ±0.8 mm for IVUS), lumen area (6.4 ±3.4 mm(2) vs. 7.0 ±3.7 mm(2) for IVUS, p < 0.001) and total calcium arc (52 ±35° vs. 83 ±54°). However, analysis of tertiles of the examined parameters revealed that the mean lumen diameter, lumen area and calcium arc did not significantly differ between CTCA and IVUS within the smallest lumens (1(st) tertile of mean lumen diameter at 2.1 mm, and 1(st) tertile of lumen area at 3.7 mm(2)) and lowest calcium arc (mean of 40°). Although, on average, CTCA underestimates lumen diameter and area as well as calcium arc within calcified lesions, the differences are not significant within the smallest vessels and calcium arcs. The low diagnostic accuracy of CTCA within calcified lesions may be attributed to high variance and not to systematic error of measurements.

[Studies on HPLC chromatogram of phenolic constituents of Cortex Magnoliae Officinalis].

PubMed

Huang, Wen-hua; Guo, Bao-lin; Si, Jin-ping

2005-07-01

To study the chemical characteristic, to identify the different forms and to establish the new standard for the quality control of Cortex Magnoliae Officinalis. HPLC method was used with acetonitrile-water (63:37) as the mobile phase at room temperature. The chromatographic column was Lichrospher 100 RP-18e (4.6 mm x 250 mm, 5 microm). The flow rate was 1 mL x min(-1), and the detection wavelength was 294 nm. The chromatograms of 45 individuals from 13 seed resources of Cortex Magnolia Officinalis were recorded. The chemical characteristics analysis and comparability' s calculation of seed resources were made. It was proposed that the area ratio of peak 5 to 6 (characteristic I) and the area ratio of peak 5 and 6 to the total peak areas (characteristic II) are the identification characteristics for different seed resources of Cortex Magnoliae Officinalis. This method can be used effectively to identify the high quality seed resource of Cortex Magnoliae Officinalis.

Ag paste-based nanomesh electrodes for large-area touch screen panels

NASA Astrophysics Data System (ADS)

Chung, Sung-il; Kyeom Kim, Pan; Ha, Tae-gyu

2017-10-01

This study reports a novel method for fabricating a nickel nanomesh mold using phase shift lithography, suitable for use in large-area touch screen panel applications. Generally, the values of light transmittance and sheet resistance of metal mesh transparent conducting electrode (TCE) films are determined by the ratio of the aperture to metal areas. In this study, taking into consideration the optimal light transmittance, sheet resistance, and pattern visibility issues, the line width of the metal mesh pattern was ~1 µm, and the pitch of the pattern was ~100 µm. In addition, a novel method of manufacturing wiring electrodes using a phase shift lithography process was also developed and evaluated. A TCE film with a size of 370 mm  ×  470 mm was prepared and evaluated for its light transmittance and sheet resistance. In addition, wiring electrodes with a length of 70 mm were fabricated and their line resistances evaluated by varying their line width.

Environmental exposure to mineral fibers in New Caledonia: an ecological study

NASA Astrophysics Data System (ADS)

Baumann, F.; Ambrosi, J.

2013-05-01

Inhalation of asbestos and other fibrous minerals causes lung cancer and other malignancies, specifically malignant mesothelioma (MM). MM is an aggressive pleural tumor that presents with a median latency period of 30-40 years from initial fiber exposure. Due to occupational exposure, MM incidence is 4-8 times higher in men as compared to women. In New Caledonia (NC), very high incidences of MM and lung cancer were observed in both men and women, suggesting an environmental origin of exposure. Although nickel mining and the traditional use of tremolite-containing whitewash were suspected causes of MM, numerous MM cases have been observed in areas lacking these risk factors. We carried out an ecological study of MM incidence in NC and identified a study area that included those counties having the highest MM incidences as well as counties lacking MM. We conducted epidemiological and environmental investigations for each of the 100 tribes living within this area. Residential history was assessed for each MM case, and samples of each quarry, road, and whitewash were analyzed to determine the nature of any mineral fibers. We analyzed the environmental determinants of MM, including geology, mineralogy, plant cover, land shape and human activities as well as use of whitewash, by using two univariate and multivariate statistical methods: 1) a logistic regression to compare tribes with and without MM cases and calculate the odds ratios, (OR) 2) the Poisson regression to calculate incidence rate ratios (IRR) for each factor. While most MM cases among Caucasians were observed in men with a mean age of 72, indicating occupational exposure, Melanesians exhibited elevated MM incidence in both men and women at a mean age of 60. A sex ratio close to 1 compounded with the relatively young ages of MM cases confirmed environmental causation within the Melanesian population. We found one significant and two secondary spatial clusters of MM in tribal areas. No temporal cluster was observed. We identified several natural sources of mineral fibers in the study area, including clay-like white soils containing tremolite-actinolite, fibrous antigorite deposits, and veins of chrysotile in peridotite massifs, in addition to multiple serpentinite quarries predominantly containing antigorite. Statistical analyses revealed that the use of serpentinite to pave roads was the greatest risk factor for MM (OR=495.0, 95%CI:46.2-4679.7; multivariate IRR=13.0, 95%CI:10.2-16.6). Other MM risk factors in order of importance were the presence of antigorite, proximity to serpentinite quarries, proximity to peridotite massifs, and presence of chrysotile. Dense vegetation and land slope were protective factors. Whitewash use was not related to MM incidence. Many natural fibrous minerals are not commercially used as asbestos and are therefore not regulated. However, our study demonstrated that non-regulated antigorite fibers are related to cancer, and that soils containing these minerals pose an environmental risk to the population when the fibers are released into the air by weathering or by human activities. Regulation of additional fibrous minerals is therefore suggested.

Reporting numeric values of complete crowns. Part 2: Retention and resistance theories.

PubMed

Tiu, Janine; Al-Amleh, Basil; Waddell, J Neil; Duncan, Warwick J

2015-07-01

Determining the retention and resistance of a tooth preparation for a complete crown has only existed in theory, and these theories have never been measured on tooth preparations performed in vivo. The purpose of this study was to measure the theoretical retention and resistance of clinically produced complete crown preparations by using an objective measuring method. Stone dies from 236 complete crown preparations were collected from dental laboratories. The dies were scanned and analyzed with the coordinate geometry method. Cross-sectional images were captured, and the surface area was measured with a cone frustum and right truncated pyramid formula. Two different theories of resistance form, the "on" or "off" theory (limiting taper) and the linear model (resistance length), were calculated for premolar and molar preparations. The mean surface areas ranged from 33.97 mm(2) to 105.44 mm(2) for the cone frustum formula and 41.75 mm(2) to 117.50 mm(2) for the right truncated pyramid formula. The facial side of maxillary premolars exhibited the highest percentage of resistance form with the limiting taper, at 58%, and the mesial side of the mandibular molars exhibited the lowest percentage of resistance form, at 6%. The objective method used in this study provides a way for retention and resistance theories to be tested and for further clinical implications to be investigated. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Human-motion energy harvester for autonomous body area sensors

NASA Astrophysics Data System (ADS)

Geisler, M.; Boisseau, S.; Perez, M.; Gasnier, P.; Willemin, J.; Ait-Ali, I.; Perraud, S.

2017-03-01

This paper reports on a method to optimize an electromagnetic energy harvester converting the low-frequency body motion and aimed at powering wireless body area sensors. This method is based on recorded accelerations, and mechanical and transduction models that enable an efficient joint optimization of the structural parameters. An optimized prototype of 14.8 mmØ × 52 mm, weighting 20 g, has generated up to 4.95 mW in a resistive load when worn at the arm during a run, and 6.57 mW when hand-shaken. Among the inertial electromagnetic energy harvesters reported so far, this one exhibits one of the highest power densities (up to 730 μW cm-3). The energy harvester was finally used to power a bluetooth low energy wireless sensor node with accelerations measurements at 25 Hz.

Tophaceous gout: quantitative evaluation by direct physical measurement.

PubMed

Schumacher, H Ralph; Becker, Michael A; Palo, William A; Streit, Janet; MacDonald, Patricia A; Joseph-Ridge, Nancy

2005-12-01

The absence of accepted standardized methods for monitoring tophaceous gout limits the ability to track tophus progression or regression. This multicenter study assessed intra- and interrater reproducibility of a simple and direct physical measurement. The quantitative evaluation was the area (mm2) of each measurable tophus and was determined independently by 2 raters on 2 occasions within 10 days. Intra- and interrater reproducibilities were determined by calculating mean differences and average percentage differences (APD) in measurements of areas for the same tophus at each of 2 visits and by each rater, respectively. Fifty-two tophi were measured in 13 subjects: 22 on the hand/wrist, 16 on the elbow, and 14 on the foot/ankle. The mean (+/- SD) difference in tophus areas between visits was -0.2 +/- 835 mm2 (95% CI -162 to 162 mm2) and the mean (+/- SD) APD was 29% +/- 33%. The mean (+/- SD) APD between raters was 32% +/- 27%. The largest variations in measurements were noted for elbow tophi and variations were least for well demarcated tophi on the hands. This simple and reproducible method can be easily utilized in clinical trials and in practice as a measure of efficacy of urate-lowering treatment in tophaceous gout. Among factors contributing to variability in these measurements were the anatomic site of tophi and rater experience with the method. Restriction of measurements to well circumscribed hand or foot tophi could improve reliability, but major changes, as expected with effective therapy, can clearly be documented with this simple technique.

Percutaneous Mitral Valve Dilatation: Single Balloon versus Double Balloon - A Finite Element Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schievano, Silvia; Kunzelman, Karyn; Nicosia, Mark

2009-01-01

Background: Percutaneous mitral valve (MV) dilatation is performed with either a single balloon (SB) or double balloon (DB) technique. The aim of this study was to compare the two balloon system results using the finite element (FE) method. Methods and Results: An established FE model of the MV was modified by fusing the MV leaflet edges at commissure level to simulate a stenotic valve (orifice area=180mm2). A FE model of a 30mm SB (low-pressure, elastomeric balloon) and an 18mm DB system (high-pressure, non-elastic balloon) was created. Both SB and DB simulations resulted in splitting of the commissures and subsequent stenosismore » dilatation (final MV area=610mm2 and 560mm2 respectively). Stresses induced by the two balloon systems varied across the valve. At the end of inflation, SB showed higher stresses in the central part of the leaflets and at the commissures compared to DB simulation, which demonstrated a more uniform stress distribution. The higher stresses in the SB analysis were due to the mismatch of the round balloon shape with the oval mitral orifice. The commissural split was not easily accomplished with the SB due to its high compliance. The high pressure applied to the DB guaranteed the commissural split even when high forces were required to break the commissure welds. Conclusions: The FE model demonstrated that MV dilatation can be accomplished by both SB and DB techniques. However, the DB method resulted in higher probability of splitting of the fused commissures and less damage caused to the MV leaflets by overstretching.« less

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2016-09-01

In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations.

PubMed

Dehury, Budheswar; Behera, Santosh Kumar; Mahapatra, Namita

2017-01-01

The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. Bi-lobed catalytic domain of PfCKI shares a high degree of secondary structure topology with CKI domains of rice, human, and mouse indicating co-evolution of these kinases. Molecular docking study revealed that ATP binds to the active site where the glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with few conserved residues plays a crucial role maintaining stability of the complex. Structural superposition of PfCKI with close structural homologs depicted that the location and length of important loops are different, indicating the dynamic properties of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA displayed that the overall global motion of ATP-bound form is comparatively higher than that of apo form. The present study provides insights into the structural features of PfCKI, which could contribute towards further understanding of related protein structures, dynamics of catalysis and phosphorylation mechanism in these important STKs from malarial parasite in near future. Copyright © 2016 Elsevier Inc. All rights reserved.

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

NASA Astrophysics Data System (ADS)

Cholko, Timothy; Chen, Wei; Tang, Zhiye; Chang, Chia-en A.

2018-05-01

Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.

Molecular insight of isotypes specific β-tubulin interaction of tubulin heterodimer with noscapinoids

NASA Astrophysics Data System (ADS)

Santoshi, Seneha; Naik, Pradeep K.

2014-07-01

Noscapine and its derivatives bind stoichiometrically to tubulin, alter its dynamic instability and thus effectively inhibit the cellular proliferation of a wide variety of cancer cells including many drug-resistant variants. The tubulin molecule is composed of α- and β-tubulin, which exist as various isotypes whose distribution and drug-binding properties are significantly different. Although the noscapinoids bind to a site overlapping with colchicine, their interaction is more biased towards β-tubulin. In fact, their precise interaction and binding affinity with specific isotypes of β-tubulin in the αβ-heterodimer has never been addressed. In this study, the binding affinity of a panel of noscapinoids with each type of tubulin was investigated computationally. We found that the binding score of a specific noscapinoid with each type of tubulin isotype is different. Specifically, amino-noscapine has the highest binding score of -6.4, -7.2, -7.4 and -7.3 kcal/mol with αβI, αβII, αβIII and αβIV isotypes, respectively. Similarly 10 showed higher binding affinity of -6.8 kcal/mol with αβV, whereas 8 had the highest binding affinity of -7.2, -7.1 and -7.2 kcal/mol, respectively with αβVI, αβVII and αβVIII isotypes. More importantly, both amino-noscapine and its clinical derivative, bromo-noscapine have the highest binding affinity of -46.2 and -38.1 kcal/mol against αβIII (overexpression of αβIII has been associated with resistance to a wide range of chemotherapeutic drugs for several human malignancies) as measured using MM-PBSA. Knowledge of the isotype specificity of the noscapinoids may allow for development of novel therapeutic agents based on this class of drugs.

Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor.

PubMed

Ekhteiari Salmas, Ramin; Seeman, Philip; Aksoydan, Busecan; Stein, Matthias; Yurtsever, Mine; Durdagi, Serdar

2017-04-19

The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and it is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homodimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation. The administration of the D2R agonist ligand ACR16 [ 3 H](+)-4-propyl-3,4,4a,5,6,10b-hexahydro-2H-naphtho[1,2-b][1,4]oxazin-9-ol ((+)PHNO) revealed K i values of 32 nM for the D2 high R and 52 μM for the D2 low R. The calculated binding affinities of ACR16 with post processing molecular dynamics (MD) simulations analyses using MM/PBSA for the monomeric and homodimeric forms of the D2 high R were -9.46 and -8.39 kcal/mol, respectively. The data suggests that the dimerization of the D2R leads negative cooperativity for ACR16 binding. The dimerization reaction of the D2 high R is energetically favorable by -22.95 kcal/mol. The dimerization reaction structurally and thermodynamically stabilizes the D2 high R conformation, which may be due to the intermolecular forces formed between the TM4 of each monomer, and the result strongly demonstrates dimerization essential for activation of the D2R.

Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking.

PubMed

Salmas, Ramin Ekhteiari; Seeman, Philip; Aksoydan, Busecan; Erol, Ismail; Kantarcioglu, Isik; Stein, Matthias; Yurtsever, Mine; Durdagi, Serdar

2017-06-21

Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2 High R and D2 Low R dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2 High R and D2 Low R targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2 High R and D2 Low R with binding affinities (K i ) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [ 3 H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2 High R. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2 High R binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2 Low R. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.

Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

NASA Astrophysics Data System (ADS)

Badalkhani-Khamseh, Farideh; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

2017-12-01

Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility improvement and increase in drug loading capacity of PAMAM dendrimers. In this work, fully atomistic MD simulations were employed to study the association of 5-Fluorouracil (5-FU) with amine (NH2)- and hydroxyl (OH)-terminated PAMAM dendrimers of generations 3 and 4 (G3 and G4). MD results show a 1:12, 1:1, 1:27, and 1:4 stoichiometry, respectively, for G3NH2-FU, G3OH-FU, G4NH2-FU, and G4OH-FU complexes, which is in good agreement with the isothermal titration calorimetry results. The results obtained showed that NH2-terminated dendrimers assume segmented open structures with large cavities and more drug molecules can encapsulate inside the dendritic cavities of amine terminated dendrimers. However, OH-terminated have a densely packed structure and therefore, 5-FU drug molecules are more stable to locate close to the surface of the dendrimers. Intermolecular hydrogen bonding analysis showed that 5-FU drug molecules have more tendency to form hydrogen bonds with terminal monomers of OH-terminated dendrimers, while in NH2-terminated these occur both in the inner region and the surface. Furthermore, MM-PBSA analysis revealed that van der Waals and electrostatic energies are both important to stabilize the complexes. We found that drug molecules are distributed uniformly inside the amine and hydroxyl terminated dendrimers and therefore, both dendrimers are promising candidates as drug delivery systems for 5-FU drug molecules.

Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays.

PubMed

Sutthibutpong, Thana; Rattanarojpong, Triwit; Khunrae, Pongsak

2017-12-04

Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three different sites to the thermostability. The first mutation was to replace an unstable negatively charged residue at a surface beta turn near the active site (D32G) by a hydrophobic residue. The second mutation was to create a disulphide bond (S100C/N147C) establishing a strong connection between an alpha helix and a distal beta hairpin associated with the thermally sensitive Thumb loop, and the third mutation add an extra hydrogen bond (A155S) to the same alpha helix. From the MD simulations performed, MM/PBSA energy calculations of the unfolding energy were in a good agreement with the enzyme activities measured from the experiment, as all mutated structures demonstrated the improved thermostability, especially the S100C/N147C proved to be the most stable mutant both by the simulations and the experiment. Local conformational analysis at the catalytic sites and the xylan access region also suggested that mutated xyn11A structures could accommodate xylan binding. However, the analysis of global unfolding pathways showed that structural disruptions at the beta sheet regions near the N-terminal were still imminent. These findings could provide the insight on the molecular mechanisms underlying the enhanced thermostability due to mutagenesis and changes in the protein unfolding pathways for further protein engineering of the GH11 family xylanase enzymes.

Relationship between the Foveal Avascular Zone and Foveal Pit Morphology

PubMed Central

Dubis, Adam M.; Hansen, Benjamin R.; Cooper, Robert F.; Beringer, Joseph; Dubra, Alfredo; Carroll, Joseph

2012-01-01

Purpose. To assess the relationship between foveal pit morphology and size of the foveal avascular zone (FAZ). Methods. Forty-two subjects were recruited. Volumetric images of the macula were obtained using spectral domain optical coherence tomography. Images of the FAZ were obtained using either a modified fundus camera or an adaptive optics scanning light ophthalmoscope. Foveal pit metrics (depth, diameter, slope, volume, and area) were automatically extracted from retinal thickness data, whereas the FAZ was manually segmented by two observers to extract estimates of FAZ diameter and area. Results. Consistent with previous reports, the authors observed significant variation in foveal pit morphology. The average foveal pit volume was 0.081 mm3 (range, 0.022 to 0.190 mm3). The size of the FAZ was also highly variable between persons, with FAZ area ranging from 0.05 to 1.05 mm2 and FAZ diameter ranging from 0.20 to 1.08 mm. FAZ area was significantly correlated with foveal pit area, depth, and volume; deeper and broader foveal pits were associated with larger FAZs. Conclusions. Although these results are consistent with predictions from existing models of foveal development, more work is needed to confirm the developmental link between the size of the FAZ and the degree of foveal pit excavation. In addition, more work is needed to understand the relationship between these and other anatomic features of the human foveal region, including peak cone density, rod-free zone diameter, and Henle fiber layer. PMID:22323466

Design and Development of Card-Sized Virtual Keyboard Using Permanent Magnets and Hall Sensors

NASA Astrophysics Data System (ADS)

Demachi, Kazuyuki; Ohyama, Makoto; Kanemoto, Yoshiki; Masaie, Issei

This paper proposes a method to distinguish the key-type of human fingers attached with the small permanent magnets. The Hall sensors arrayed in the credit card size area feel the distribution of the magnetic field due to the key-typing movement of the human fingers as if the keyboard exists, and the signal is analyzed using the generic algorithm or the neural network algorism to distinguish the typed keys. By this method, the keyboard can be miniaturized to the credit card size (54mm×85mm). We called this system `The virtual keyboard system'.

Use of 35-mm color aerial photography to acquire mallard sex ratio data

USGS Publications Warehouse

Ferguson, Edgar L.; Jorde, Dennis G.; Sease, John L.

1981-01-01

A conventional 35-mm camera equipped with an f2.8 135-mm lens and ASA 64 color film was used to acquire sex ratio data on mallards (Anas platyrhynchos) wintering in the Platte River Valley of south-central Nebraska. Prelight focusing for a distance of 30.5 metres and setting of shutter speed at 1/2000 of a second eliminated focusing and reduced image motion problems and resulted in high-resolution, large-scale aerial photography of small targets. This technique has broad application to the problem of determining sex ratios of various species of waterfowl concentrated on wintering and staging areas. The aerial photographic method was cheaper than the ground ocular method when costs were compared on a per-100 bird basis.

Analysing surface deformation in Surabaya from sentinel-1A data using DInSAR method

NASA Astrophysics Data System (ADS)

Anjasmara, Ira Mutiara; Yusfania, Meiriska; Kurniawan, Akbar; Resmi, Awalina L. C.; Kurniawan, Roni

2017-07-01

The rapid population growth and increasing industrial space in the urban area of Surabaya have caused an excessive ground water use and load of infrastructures. This condition triggers surface deformation, especially the vertical deformation (subsidence or uplift), in Surabaya and its surroundings. The presence of dynamic processes of the Earth and geological form of Surabaya area can also fasten the rate of the surface deformation. In this research, Differential Interferometry Synthetic Aperture Radar (DInSAR) method is chosen to infer the surface deformation over Surabaya area. The DInSAR processing utilized Sentinel 1A satellite images from May 2015 to September 2016 using two-pass interferometric. Two-pass interferometric method is a method that uses two SAR imageries and Digital Elevation Model (DEM). The results from four pairs of DInSAR processing indicate the occurrence of surface deformation in the form of land subsidence and uplift based on the displacement Line of Sight (LOS) in Surabaya. The average rate of surface deformation from May 2015 to September 2016 varies from -3.52 mm/4months to +2.35 mm/4months. The subsidence mostly occurs along the coastal area. However, the result still contains errors from the processing of displacement, due to the value of coherence between the image, noise, geometric distortion of a radar signal and large baseline on image pair.

Quantitative determination and sampling of azathioprine residues for cleaning validation in production area.

PubMed

Fazio, Tatiana Tatit; Singh, Anil Kumar; Kedor-Hackmann, Erika Rosa Maria; Santoro, Maria Inês Rocha Miritello

2007-03-12

Cleaning validation is an integral part of current good manufacturing practices in any pharmaceutical industry. Nowadays, azathioprine and several other pharmacologically potent pharmaceuticals are manufactured in same production area. Carefully designed cleaning validation and its evaluation can ensure that residues of azathioprine will not carry over and cross contaminate the subsequent product. The aim of this study was to validate simple analytical method for verification of residual azathioprine in equipments used in the production area and to confirm efficiency of cleaning procedure. The HPLC method was validated on a LC system using Nova-Pak C18 (3.9 mm x 150 mm, 4 microm) and methanol-water-acetic acid (20:80:1, v/v/v) as mobile phase at a flow rate of 1.0 mL min(-1). UV detection was made at 280 nm. The calibration curve was linear over a concentration range from 2.0 to 22.0 microg mL(-1) with a correlation coefficient of 0.9998. The detection limit (DL) and quantitation limit (QL) were 0.09 and 0.29 microg mL(-1), respectively. The intra-day and inter-day precision expressed as relative standard deviation (R.S.D.) were below 2.0%. The mean recovery of method was 99.19%. The mean extraction-recovery from manufacturing equipments was 83.5%. The developed UV spectrophotometric method could only be used as limit method to qualify or reject cleaning procedure in production area. Nevertheless, the simplicity of spectrophotometric method makes it useful for routine analysis of azathioprine residues on cleaned surface and as an alternative to proposed HPLC method.

Motion Compensation in Extremity Cone-Beam CT Using a Penalized Image Sharpness Criterion

PubMed Central

Sisniega, A.; Stayman, J. W.; Yorkston, J.; Siewerdsen, J. H.; Zbijewski, W.

2017-01-01

Cone-beam CT (CBCT) for musculoskeletal imaging would benefit from a method to reduce the effects of involuntary patient motion. In particular, the continuing improvement in spatial resolution of CBCT may enable tasks such as quantitative assessment of bone microarchitecture (0.1 mm – 0.2 mm detail size), where even subtle, sub-mm motion blur might be detrimental. We propose a purely image based motion compensation method that requires no fiducials, tracking hardware or prior images. A statistical optimization algorithm (CMA-ES) is used to estimate a motion trajectory that optimizes an objective function consisting of an image sharpness criterion augmented by a regularization term that encourages smooth motion trajectories. The objective function is evaluated using a volume of interest (VOI, e.g. a single bone and surrounding area) where the motion can be assumed to be rigid. More complex motions can be addressed by using multiple VOIs. Gradient variance was found to be a suitable sharpness metric for this application. The performance of the compensation algorithm was evaluated in simulated and experimental CBCT data, and in a clinical dataset. Motion-induced artifacts and blurring were significantly reduced across a broad range of motion amplitudes, from 0.5 mm to 10 mm. Structure Similarity Index (SSIM) against a static volume was used in the simulation studies to quantify the performance of the motion compensation. In studies with translational motion, the SSIM improved from 0.86 before compensation to 0.97 after compensation for 0.5 mm motion, from 0.8 to 0.94 for 2 mm motion and from 0.52 to 0.87 for 10 mm motion (~70% increase). Similar reduction of artifacts was observed in a benchtop experiment with controlled translational motion of an anthropomorphic hand phantom, where SSIM (against a reconstruction of a static phantom) improved from 0.3 to 0.8 for 10 mm motion. Application to a clinical dataset of a lower extremity showed dramatic reduction of streaks and improvement in delineation of tissue boundaries and trabecular structures throughout the whole volume. The proposed method will support new applications of extremity CBCT in areas where patient motion may not be sufficiently managed by immobilization, such as imaging under load and quantitative assessment of subchondral bone architecture. PMID:28327471

Design Architecture of field-effect transistor with back gate electrode for biosensor application

NASA Astrophysics Data System (ADS)

Fathil, M. F. M.; Arshad, M. K. Md.; Hashim, U.; Ruslinda, A. R.; Gopinath, Subash C. B.; M. Nuzaihan M., N.; Ayub, R. M.; Adzhri, R.; Zaki, M.; Azman, A. H.

2016-07-01

This paper presents the preparation method of photolithography chrome mask design used in fabrication process of field-effect transistor with back gate biasing based biosensor. Initially, the chrome masks are designed by studying the process flow of the biosensor fabrication, followed by drawing of the actual chrome mask using the AutoCAD software. The overall width and length of the device is optimized at 16 mm and 16 mm, respectively. Fabrication processes of the biosensor required five chrome masks, which included source and drain formation mask, the back gate area formation mask, electrode formation mask, front gate area formation mask, and passivation area formation mask. The complete chrome masks design will be sent for chrome mask fabrication and for future use in biosensor fabrication.

Are catchment-wide erosion rates really "Catchment-Wide"? Effects of grain size on erosion rates determined from 10Be

NASA Astrophysics Data System (ADS)

Reitz, M. A.; Seeber, L.; Schaefer, J. M.; Ferguson, E. K.

2012-12-01

Early studies pioneering the method for catchment wide erosion rates by measuring 10Be in alluvial sediment were taken at river mouths and used the sand size grain fraction from the riverbeds in order to average upstream erosion rates and measure erosion patterns. Finer particles (<0.0625 mm) were excluded to reduce the possibility of a wind-blown component of sediment and coarser particles (>2 mm) were excluded to better approximate erosion from the entire upstream catchment area (coarse grains are generally found near the source). Now that the sensitivity of 10Be measurements is rapidly increasing, we can precisely measure erosion rates from rivers eroding active tectonic regions. These active regions create higher energy drainage systems that erode faster and carry coarser sediment. In these settings, does the sand-sized fraction fully capture the average erosion of the upstream drainage area? Or does a different grain size fraction provide a more accurate measure of upstream erosion? During a study of the Neto River in Calabria, southern Italy, we took 8 samples along the length of the river, focusing on collecting samples just below confluences with major tributaries, in order to use the high-resolution erosion rate data to constrain tectonic motion. The samples we measured were sieved to either a 0.125 mm - 0.710 mm fraction or the 0.125 mm - 4 mm fraction (depending on how much of the former was available). After measuring these 8 samples for 10Be and determining erosion rates, we used the approach by Granger et al. [1996] to calculate the subcatchment erosion rates between each sample point. In the subcatchments of the river where we used grain sizes up to 4 mm, we measured very low 10Be concentrations (corresponding to high erosion rates) and calculated nonsensical subcatchment erosion rates (i.e. negative rates). We, therefore, hypothesize that the coarser grain sizes we included are preferentially sampling a smaller upstream area, and not the entire upstream catchment, which is assumed when measurements are based solely on the sand sized fraction. To test this hypothesis, we used samples with a variety of grain sizes from the Shillong Plateau. We sieved 5 samples into three grain size fractions: 0.125 mm - 710 mm, 710 mm - 4 mm, and >4 mm and measured 10Be concentrations in each fraction. Although there is some variation in the grain size fraction that yields the highest erosion rate, generally, the coarser grain size fractions have higher erosion rates. More significant are the results when calculating the subcatchment erosion rates, which suggest that even medium sized grains (710 mm - 4 mm) are sampling an area smaller than the entire upstream area; this finding is consistent with the nonsensical results from the Neto River study. This result has numerous implications for the interpretations of 10Be erosion rates: most importantly, an alluvial sample may not be averaging the entire upstream area, even when using the sand size fraction - resulting erosion rates more pertinent for that sample point rather than the entire catchment.

Capillary liquid chromatography-mass spectrometry for the rapid identification and quantification of almond flavonoids.

PubMed

Hughey, Christine A; Wilcox, Bruce; Minardi, Carina S; Takehara, Chiyo W; Sundararaman, Meenakshi; Were, Lilian M

2008-05-30

A rapid negative ion ESI high-performance capillary liquid chromatography-mass spectrometry method was developed to identify and quantify flavonoids (e.g., flavanols, flavonols, flavanones and glycosides). Fifteen standards and two varieties of almond skin extract powder (Carmel and Nonpareil) were used to demonstrate the chromatographic separation, reproducibility and accuracy of the method that employed a 150 mm x 0.3 mm ChromXP 3C18-EP-120 column. All standards eluted in less than 10 min, providing a 9-12x reduction in analysis time compared to existing methods (90-120 min). However, isomers (e.g., catechin/epicatechin and galactosides/glucosides) were not resolved and, therefore, identified and quantified collectively. RSDs for retention time and peak area reproducibility (mass spectrometry data) were <0.5% and <5.0%, respectively. Peak area reproducibility was greatly improved (from a RSD>10%) after the implementation of a low-flow metal needle in the ESI source. Quantitation by mass spectrometry also afforded a % error less than 5% for most compounds.

Turkey National Mesothelioma Surveillance and Environmental Asbestos Exposure Control Program

PubMed Central

Metintaş, Selma; Batırel, Hasan Fevzi; Bayram, Hasan; Yılmaz, Ülkü; Karadağ, Mehmet; Ak, Güntülü; Metintaş, Muzaffer

2017-01-01

Malignant mesothelioma (MM) is an important health problem due to ongoing asbestos exposure. Environmental asbestos exposure leads to a high risk of MM in Turkey. The Turkish Mesothelioma Working Group and the Turkish Public Health Institute designed and performed the Turkey National Mesothelioma Surveillance and Environmental Asbestos Exposure Control Program (TUNMES-EAECP). The aim of this study was to analyze the results of the TUNMES-EAECP. Patients diagnosed with MM (code C45.0–C45.9) between 2008 and 2012 were identified. The “from case to the field” method was used to determine the villages with current or previous asbestos exposure. Special public health teams took soil samples from these villages, which were then examined using an X-ray diffractometer. Direct Standardized Average Annual Mesothelioma Incidence Rate (AMIR) and relative risk (RR) of MM were calculated. Finally, a projection on the incidence of MM between 2013 and 2033 was made. The number of confirmed MM cases was 5617 with a male to female ratio of 1.36. Mean age was 61.7 ± 13.4 (20–96) years. The median survival was eight (95% CI 7.6–8.4) months. Asbestos exposure continues in 379 villages, with 158,068 people still living in high risk areas. The standardized AMIR was 2.33/100,000 per year. The risk of MM was higher in males, in both sexes over the age of 40, in asbestos-containing provinces, and in those where the TUNMES was organized. Among the population with continuing asbestos exposure in rural areas, the number of MM cases between 2013 and 2033 was estimated as 2511. As such, the incidence of MM in Turkey is as high as in industrialized countries. Asbestos exposure in rural areas continues to be a serious problem in Turkey, which obviates the necessity for effective preventive measures. PMID:29068368

Turkey National Mesothelioma Surveillance and Environmental Asbestos Exposure Control Program.

PubMed

Metintaş, Selma; Batırel, Hasan Fevzi; Bayram, Hasan; Yılmaz, Ülkü; Karadağ, Mehmet; Ak, Güntülü; Metintaş, Muzaffer

2017-10-25

Malignant mesothelioma (MM) is an important health problem due to ongoing asbestos exposure. Environmental asbestos exposure leads to a high risk of MM in Turkey. The Turkish Mesothelioma Working Group and the Turkish Public Health Institute designed and performed the Turkey National Mesothelioma Surveillance and Environmental Asbestos Exposure Control Program (TUNMES-EAECP). The aim of this study was to analyze the results of the TUNMES-EAECP. Patients diagnosed with MM (code C45.0-C45.9) between 2008 and 2012 were identified. The "from case to the field" method was used to determine the villages with current or previous asbestos exposure. Special public health teams took soil samples from these villages, which were then examined using an X-ray diffractometer. Direct Standardized Average Annual Mesothelioma Incidence Rate (AMIR) and relative risk (RR) of MM were calculated. Finally, a projection on the incidence of MM between 2013 and 2033 was made. The number of confirmed MM cases was 5617 with a male to female ratio of 1.36. Mean age was 61.7 ± 13.4 (20-96) years. The median survival was eight (95% CI 7.6-8.4) months. Asbestos exposure continues in 379 villages, with 158,068 people still living in high risk areas. The standardized AMIR was 2.33/100,000 per year. The risk of MM was higher in males, in both sexes over the age of 40, in asbestos-containing provinces, and in those where the TUNMES was organized. Among the population with continuing asbestos exposure in rural areas, the number of MM cases between 2013 and 2033 was estimated as 2511. As such, the incidence of MM in Turkey is as high as in industrialized countries. Asbestos exposure in rural areas continues to be a serious problem in Turkey, which obviates the necessity for effective preventive measures.

Automated Quantification of Nonperfusion Areas in 3 Vascular Plexuses With Optical Coherence Tomography Angiography in Eyes of Patients With Diabetes.

PubMed

Hwang, Thomas S; Hagag, Ahmed M; Wang, Jie; Zhang, Miao; Smith, Andrew; Wilson, David J; Huang, David; Jia, Yali

2018-06-14

Diabetic retinopathy (DR) is a leading cause of vision loss that is managed primarily through qualitative clinical examination of the retina. Optical coherence tomography angiography (OCTA) may offer an objective and quantitative method of evaluating DR. To quantify capillary nonperfusion in 3 vascular plexuses in the macula of eyes patients with diabetes of various retinopathy severity using projection-resolved OCTA (PR-OCTA). Cross-sectional study at a tertiary academic center comprising 1 eye each from healthy control individuals and patients with diabetes at different severity stages of retinopathy. Data were acquired and analyzed between January 2015 and December 2017. Foveal avascular zone area, extrafoveal avascular area (EAA), and the sensitivity of detecting levels of retinopathy. The study included 39 control individuals (20 women [51%]; mean [SD] age, 43.41 [19.37] years); 16 patients with diabetes without retinopathy (8 women [50%]; mean [SD] age, 56.50 [12.43] years); 23 patients with mild to moderate nonproliferative DR (18 women [78%] ; mean [SD] age, 62.48 [10.55] years); and 32 patients with severe nonproliferative DR or proliferative DR (12 women [38%]; mean age, 53.41 [14.05] years). Mean (SD) foveal avascular zone area was 0.203 (0.103) mm2 for control individuals, 0.192 (0.084) mm2 for patients with diabetes without retinopathy, 0.243 [0.079] mm2 for mild to moderate nonproliferative DR, and 0.359 (0.275) mm2 for severe nonproliferative DR or proliferative DR. Mean (SD) EAA in whole inner retinal slab in these groups, respectively, were 0.020 (0.031) mm2, 0.034 (0.047) mm2, 0.038 (0.040) mm2, and 0.237 (0.235) mm2. The mean (SD) sum of EAA from 3 segmented plexuses in each of the respective groups were 0.103 (0.169) mm2, 0.213 (0.242) mm2, 0.451 (0.243) mm2, and 1.325 (1.140) mm2. With specificity fixed at 95%, using EAA in inner retinal slab, the sensitivity of detecting patients with diabetes from healthy control individuals was 28% (95% CI, 18%-40%), 31% for patients with DR (95% CI, 19%-45%), and 47% for patients with severe DR (95% CI, 29%-65%) from whole inner retinal EAA. With the sum of EAA from 3 individual plexuses, the sensitivities were 69% (95% CI, 57%-80%), 82% (95% CI, 70%-91%), and 97% (95% CI, 85%-100%), respectively. Avascular areas were not associated with signal strength index. The commercial vessel density from the 2-plexus scheme distinguished the groups with lower sensitivity and were dependent on SSI. Automatically quantified avascular areas from a 3-layer segmentation scheme using PR-OCTA distinguished levels of retinopathy with a greater sensitivity than avascular areas from unsegmented inner retinal slab or measurements from a commercially available vessel density in 2-layer scheme. Additional studies are needed to investigate the applicability of nonperfusion parameters in clinical settings.

Accurate electron gun-positioning mechanism for electron beam-mapping of large cross-section magnetic surfaces

NASA Astrophysics Data System (ADS)

Anderson, F. S. B.; Middleton, F.; Colchin, R. J.; Million, D.

1989-04-01

A method of accurately supporting and positioning an electron source inside a large cross-sectional area magnetic field which provides very low electron beam occlusion is reported. The application of electrical discharge machining to the fabrication of a 1-m truss support structure has provided an extremely long, rigid and mechanically strong electron gun support. Reproducible electron gun positioning to within 1 mm has been achieved at any location within a 1×0.6-m2 area. The extremely thin sections of the support truss (≤1.5 mm) have kept the electron beam occlusion to less than 3 mm. The support and drive mechanism have been designed and fabricated at the University of Wisconsin for application to the mapping of the magnetic surface structure of the Advanced Toroidal Facility torsatron1 at the Oak Ridge National Laboratory.

Comparison of 13 equations for determining evapotranspiration from a prairie wetland, Cottonwood Lake Area, North Dakota, USA

USGS Publications Warehouse

Rosenberry, Donald O.; Stannard, David L.; Winter, Thomas C.; Martinez, Margo L.

2004-01-01

Evapotranspiration determined using the energy-budget method at a semi-permanent prairie-pothole wetland in east-central North Dakota, USA was compared with 12 other commonly used methods. The Priestley-Taylor and deBruin-Keijman methods compared best with the energy-budget values; mean differences were less than 0.1 mm d−1, and standard deviations were less than 0.3 mm d−1. Both methods require measurement of air temperature, net radiation, and heat storage in the wetland water. The Penman, Jensen-Haise, and Brutsaert-Stricker methods provided the next-best values for evapotranspiration relative to the energy-budget method. The mass-transfer, deBruin, and Stephens-Stewart methods provided the worst comparisons; the mass-transfer and deBruin comparisons with energy-budget values indicated a large standard deviation, and the deBruin and Stephens-Stewart comparisons indicated a large bias. The Jensen-Haise method proved to be cost effective, providing relatively accurate comparisons with the energy-budget method (mean difference=0.44 mm d−1, standard deviation=0.42 mm d−1) and requiring only measurements of air temperature and solar radiation. The Mather (Thornthwaite) method is the simplest, requiring only measurement of air temperature, and it provided values that compared relatively well with energy-budget values (mean difference=0.47 mm d−1, standard deviation=0.56 mm d−1). Modifications were made to several of the methods to make them more suitable for use in prairie wetlands. The modified Makkink, Jensen-Haise, and Stephens-Stewart methods all provided results that were nearly as close to energy-budget values as were the Priestley-Taylor and deBruin-Keijman methods, and all three of these modified methods only require measurements of air temperature and solar radiation. The modified Hamon method provided values that were within 20 percent of energy-budget values during 95 percent of the comparison periods, and it only requires measurement of air temperature. The mass-transfer coefficient, associated with the commonly used mass-transfer method, varied seasonally, with the largest values occurring during summer.

Trends in evaporation of a large subtropical lake

NASA Astrophysics Data System (ADS)

Hu, Cheng; Wang, Yongwei; Wang, Wei; Liu, Shoudong; Piao, Meihua; Xiao, Wei; Lee, Xuhui

2017-07-01

How rising temperature and changing solar radiation affect evaporation of natural water bodies remains poor understood. In this study, evaporation from Lake Taihu, a large (area 2400 km2) freshwater lake in the Yangtze River Delta, China, was simulated by the CLM4-LISSS offline lake model and estimated with pan evaporation data. Both methods were calibrated against lake evaporation measured directly with eddy covariance in 2012. Results show a significant increasing trend of annual lake evaporation from 1979 to 2013, at a rate of 29.6 mm decade-1 according to the lake model and 25.4 mm decade-1 according to the pan method. The mean annual evaporation during this period shows good agreement between these two methods (977 mm according to the model and 1007 mm according to the pan method). A stepwise linear regression reveals that downward shortwave radiation was the most significant contributor to the modeled evaporation trend, while air temperature was the most significant contributor to the pan evaporation trend. Wind speed had little impact on the modeled lake evaporation but had a negative contribution to the pan evaporation trend offsetting some of the temperature effect. Reference evaporation was not a good proxy for the lake evaporation because it was on average 20.6 % too high and its increasing trend was too large (56.5 mm decade-1).

On the estimation of physical height changes using GRACE satellite mission data - A case study of Central Europe

NASA Astrophysics Data System (ADS)

Godah, Walyeldeen; Szelachowska, Małgorzata; Krynski, Jan

2017-12-01

The dedicated gravity satellite missions, in particular the GRACE (Gravity Recovery and Climate Experiment) mission launched in 2002, provide unique data for studying temporal variations of mass distribution in the Earth's system, and thereby, the geometry and the gravity fi eld changes of the Earth. The main objective of this contribution is to estimate physical height (e.g. the orthometric/normal height) changes over Central Europe using GRACE satellite mission data as well as to analyse them and model over the selected study area. Physical height changes were estimated from temporal variations of height anomalies and vertical displacements of the Earth surface being determined over the investigated area. The release 5 (RL05) GRACE-based global geopotential models as well as load Love numbers from the Preliminary Reference Earth Model (PREM) were used as input data. Analysis of the estimated physical height changes and their modelling were performed using two methods: the seasonal decomposition method and the PCA/ EOF (Principal Component Analysis/Empirical Orthogonal Function) method and the differences obtained were discussed. The main fi ndings reveal that physical height changes over the selected study area reach up to 22.8 mm. The obtained physical height changes can be modelled with an accuracy of 1.4 mm using the seasonal decomposition method.

Diameters of the cavo-sinus-tricuspid area in relation to type I atrial flutter.

PubMed

Kozłowski, Dariusz; Hreczecha, Jolanta; Skwarek, Magdalena; Piwko, Grzegorz; Kosiński, Adam; Gawrysiak, Marcin; Grzybiak, Marek

2003-05-01

Cardiac arrhythmias have troubled patients and fascinated physicians for centuries. The twentieth century was an era of progress, when the mechanism of cardiac disorders became more commonly recognised. Arrhythmias may be due to abnormalities of automaticity, to abnormalities of conduction, or to a combination of both. In order for re-entry to occur, an area of slowing conduction combined with unidirectional block must be present. Much investigation has centred on the underlying re-entry mechanisms of atrial flutter. In the light of these facts, it would seem that a close acquaintance with the detailed topography of the vena cava orifice (cavo), coronary sinus orifice (sinus) and the attachment of the septal leaflet of the tricuspid valve (tricupid) area could be of great interest, especially for invasive cardiologists. The research was conducted carried out on material consisting of 41 hearts of humans of both sexes from the age of 12 to 80 (6 female, 35 male). Classical macroscopic methods of anatomical evaluation were used. The following measurements were made: the shortest distance between the Eustachian valve and the attachment of the tricuspid valve on the left margin of the coronary sinus orifice (diameter 1), the distance between the attachment of the tricuspid valve and the inferior margin of the sinus orifice (diameter 2), the distance between the Eustachian valve and the attachment of the tricuspid valve on the right margin of the coronary sinus orifice (diameter 3), the distance between the inferior margin of the vena cava inferior and the attachment of the tricuspid valve (diameter 4) and, finally, the diameter between the attachment of the septal cusp of the tricuspid valve and the extemal border of the vena cava inferior (diameter 5). No correlation was found between the age and sex of the three groups of the material. The dimensions of the structure examined were similar in the three groups of hearts. In young adult hearts all the diameters measured ranged from 4 to 47 mm. The average diameters were, respectively: 15.02 mm (diameter 1), 8.97 mm (diameter 2), 17.27 mm (diameter 3), 26.87 mm (diameter 4), 36.42 mm (diameter 5). In the mature adult hearts all the diameters measured ranged from 8 to 45 mm; 18.19 mm (diameter 1), 10.54 mm (diameter 2), 19.95 mm (diameter 3), 28.90 mm (diameter 4), 39.63 mm (diameter 5). In the older adults hearts all the diameters measured ranged from 4 to 47 mm. The average diameters were, respectively: 15.65 mm (diameter 1), 8.70 mm (diameter 2), 7.25 mm (diameter 3), 26.80 mm (diameter 4), 35.85 mm (diameter 5). On the basis of our study we were able to conclude that the diameters of the cavo-sinus-tricuspid area were constant and did not differ significantly within the three (young, mature, old) adult groups examined.

SU-F-T-383: Robustness for Patient Setup Error in Total Body Irradiation Using Volumetric Modulated Arc Therapy (VMAT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takahashi, Y; National Cancer Center, Kashiwa, Chiba; Tachibana, H

Purpose: Total body irradiation (TBI) and total marrow irradiation (TMI) using Tomotherapy have been reported. A gantry-based linear accelerator uses one isocenter during one rotational irradiation. Thus, 3–5 isocenter points should be used for a whole plan of TBI-VMAT during smoothing out the junctional dose distribution. IGRT provides accurate and precise patient setup for the multiple junctions, however it is evident that some setup errors should occur and affect accuracy of dose distribution in the area. In this study, we evaluated the robustness for patient’s setup error in VMAT-TBI. Methods: VMAT-TBI Planning was performed in an adult whole-body human phantommore » using Eclipse. Eight full arcs with four isocenter points using 6MV-X were used to cover the entire whole body. Dose distribution was optimized using two structures of patient’s body as PTV and lung. The two arcs were shared with one isocenter and the two arcs were 5 cm-overlapped with the other two arcs. Point absolute dose using ionization-chamber and planer relative dose distribution using film in the junctional regions were performed using water-equivalent slab phantom. In the measurements, several setup errors of (+5∼−5mm) were added. Results: The result of the chamber measurement shows the deviations were within ±3% when the setup errors were within ±3 mm. In the planer evaluation, the pass ratio of gamma evaluation (3%/2mm) shows more than 90% if the errors within ±3 mm. However, there were hot/cold areas in the edge of the junction even with acceptable gamma pass ratio. 5 mm setup error caused larger hot and cold areas and the dosimetric acceptable areas were decreased in the overlapped areas. Conclusion: It can be clinically acceptable for VMAT-TBI when patient setup error is within ±3mm. Averaging effects from patient random error would be helpful to blur the hot/cold area in the junction.« less

Novel method of fabricating individual trays for maxillectomy patients by computer-aided design and rapid prototyping.

PubMed

Huang, Zhi; Wang, Xin-zhi; Hou, Yue-Zhong

2015-02-01

Making impressions for maxillectomy patients is an essential but difficult task. This study developed a novel method to fabricate individual trays by computer-aided design (CAD) and rapid prototyping (RP) to simplify the process and enhance patient safety. Five unilateral maxillectomy patients were recruited for this study. For each patient, a computed tomography (CT) scan was taken. Based on the 3D surface reconstruction of the target area, an individual tray was manufactured by CAD/RP. With a conventional custom tray as control, two final impressions were made using the different types of tray for each patient. The trays were sectioned, and in each section the thickness of the material was measured at six evenly distributed points. Descriptive statistics and paired t-test were used to examine the difference of the impression thickness. SAS 9.3 was applied in the statistical analysis. Afterwards, all casts were then optically 3D scanned and compared digitally to evaluate the feasibility of this method. Impressions of all five maxillectomy patients were successfully made with individual trays fabricated by CAD/RP and traditional trays. The descriptive statistics of impression thickness measurement showed slightly more uneven results in the traditional trays, but no statistical significance was shown. A 3D digital comparison showed acceptable discrepancies within 1 mm in the majority of cast areas. The largest difference of 3 mm was observed in the buccal wall of the defective areas. Moderate deviations of 1 to 2 mm were detected in the buccal and labial vestibular groove areas. This study confirmed the feasibility of a novel method of fabricating individual trays by CAD/RP. Impressions made by individual trays manufactured using CAD/RP had a uniform thickness, with an acceptable level of accuracy compared to those made through conventional processes. © 2014 by the American College of Prosthodontists.

Validation of Sampling Protocol and the Promulgation of Method Modifications for the Characterization of Energetic Residues on Military Testing and Training Ranges

DTIC Science & Technology

2009-06-01

Figure 2. Examples of surface vegetation at a firing point (inset) and near the crater of an 81-mm mortar projectile low-order detonation on an artillery... mortar impact range.......................... 7 Figure 3. Fort Richardson and surrounding areas...crater where an 81-mm mortar projectile had low-ordered on an impact range. If vegetation is removed or avoided during sampling, energetic residue

Determination of the Effective Detector Area of an Energy-Dispersive X-Ray Spectrometer at the Scanning Electron Microscope Using Experimental and Theoretical X-Ray Emission Yields.

PubMed

Procop, Mathias; Hodoroaba, Vasile-Dan; Terborg, Ralf; Berger, Dirk

2016-12-01

A method is proposed to determine the effective detector area for energy-dispersive X-ray spectrometers (EDS). Nowadays, detectors are available for a wide range of nominal areas ranging from 10 up to 150 mm2. However, it remains in most cases unknown whether this nominal area coincides with the "net active sensor area" that should be given according to the related standard ISO 15632, or with any other area of the detector device. Moreover, the specific geometry of EDS installation may further reduce a given detector area. The proposed method can be applied to most scanning electron microscope/EDS configurations. The basic idea consists in a comparison of the measured count rate with the count rate resulting from known X-ray yields of copper, titanium, or silicon. The method was successfully tested on three detectors with known effective area and applied further to seven spectrometers from different manufacturers. In most cases the method gave an effective area smaller than the area given in the detector description.

Characterization of highly multiplexed monolithic PET / gamma camera detector modules.

PubMed

Pierce, L A; Pedemonte, S; DeWitt, D; MacDonald, L; Hunter, W C J; Van Leemput, K; Miyaoka, R

2018-03-29

PET detectors use signal multiplexing to reduce the total number of electronics channels needed to cover a given area. Using measured thin-beam calibration data, we tested a principal component based multiplexing scheme for scintillation detectors. The highly-multiplexed detector signal is no longer amenable to standard calibration methodologies. In this study we report results of a prototype multiplexing circuit, and present a new method for calibrating the detector module with multiplexed data. A [Formula: see text] mm 3 LYSO scintillation crystal was affixed to a position-sensitive photomultiplier tube with [Formula: see text] position-outputs and one channel that is the sum of the other 64. The 65-channel signal was multiplexed in a resistive circuit, with 65:5 or 65:7 multiplexing. A 0.9 mm beam of 511 keV photons was scanned across the face of the crystal in a 1.52 mm grid pattern in order to characterize the detector response. New methods are developed to reject scattered events and perform depth-estimation to characterize the detector response of the calibration data. Photon interaction position estimation of the testing data was performed using a Gaussian Maximum Likelihood estimator and the resolution and scatter-rejection capabilities of the detector were analyzed. We found that using a 7-channel multiplexing scheme (65:7 compression ratio) with 1.67 mm depth bins had the best performance with a beam-contour of 1.2 mm FWHM (from the 0.9 mm beam) near the center of the crystal and 1.9 mm FWHM near the edge of the crystal. The positioned events followed the expected Beer-Lambert depth distribution. The proposed calibration and positioning method exhibited a scattered photon rejection rate that was a 55% improvement over the summed signal energy-windowing method.

In silico comparison of the reproducibility of full-arch implant provisional restorations to final restoration between a 3D Scan/CAD/CAM technique and the conventional method.

PubMed

Mino, Takuya; Maekawa, Kenji; Ueda, Akihiro; Higuchi, Shizuo; Sejima, Junichi; Takeuchi, Tetsuo; Hara, Emilio Satoshi; Kimura-Ono, Aya; Sonoyama, Wataru; Kuboki, Takuo

2015-04-01

The aim of this article was to investigate the accuracy in the reproducibility of full-arch implant provisional restorations to final restorations between a 3D Scan/CAD/CAM technique and the conventional method. We fabricated two final restorations for rehabilitation of maxillary and mandibular complete edentulous area and performed a computer-based comparative analysis of the accuracy in the reproducibility of the provisional restoration to final restoration between a 3D scanning and CAD/CAM (Scan/CAD/CAM) technique and the conventional silicone-mold transfer technique. Final restorations fabricated either by the conventional or Scan/CAD/CAM method were successfully installed in the patient. The total concave/convex volume discrepancy observed with the Scan/CAD/CAM technique was 503.50mm(3) and 338.15 mm(3) for maxillary and mandibular implant-supported prostheses (ISPs), respectively. On the other hand, total concave/convex volume discrepancy observed with the conventional method was markedly high (1106.84 mm(3) and 771.23 mm(3) for maxillary and mandibular ISPs, respectively). The results of the present report suggest that Scan/CAD/CAM method enables a more precise and accurate transfer of provisional restorations to final restorations compared to the conventional method. Copyright © 2014 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

Land use policy and agricultural water management of the previous half of century in Africa

NASA Astrophysics Data System (ADS)

Valipour, Mohammad

2015-12-01

This paper examines land use policy and agricultural water management in Africa from 1962 to 2011. For this purpose, data were gathered from Food and Agriculture Organization of the United Nations (FAO) and the World Bank Group. Using the FAO database, ten indices were selected: permanent crops to cultivated area (%), rural population to total population (%), total economically active population in agriculture to total economically active population (%), human development index, national rainfall index (mm/year), value added to gross domestic product by agriculture (%), irrigation water requirement (mm/year), percentage of total cultivated area drained (%), difference between national rainfall index and irrigation water requirement (mm/year), area equipped for irrigation to cultivated area or land use policy index (%). These indices were analyzed for all 53 countries in the study area and the land use policy index was estimated by two different formulas. The results show that value of relative error is <20 %. In addition, an average index was calculated using various methods to assess countries' conditions for agricultural water management. Ability of irrigation and drainage systems was studied using other eight indices with more limited information. These indices are surface irrigation (%), sprinkler irrigation (%), localized irrigation (%), spate irrigation (%), agricultural water withdrawal (10 km3/year), conservation agriculture area as percentage of cultivated area (%), percentage of area equipped for irrigation salinized (%), and area waterlogged by irrigation (%). Finally, tendency of farmers to use irrigation systems for cultivated crops has been presented. The results show that Africa needs governments' policy to encourage farmers to use irrigation systems and raise cropping intensity for irrigated area.

Amalgam Electrode-Based Electrochemical Detector for On-Site Direct Determination of Cadmium(II) and Lead(II) from Soils

PubMed Central

Nejdl, Lukas; Kynicky, Jindrich; Brtnicky, Martin; Vaculovicova, Marketa; Adam, Vojtech

2017-01-01

Toxic metal contamination of the environment is a global issue. In this paper, we present a low-cost and rapid production of amalgam electrodes used for determination of Cd(II) and Pb(II) in environmental samples (soils and wastewaters) by on-site analysis using difference pulse voltammetry. Changes in the electrochemical signals were recorded with a miniaturized potentiostat (width: 80 mm, depth: 54 mm, height: 23 mm) and a portable computer. The limit of detection (LOD) was calculated for the geometric surface of the working electrode 15 mm2 that can be varied as required for analysis. The LODs were 80 ng·mL−1 for Cd(II) and 50 ng·mL−1 for Pb(II), relative standard deviation, RSD ≤ 8% (n = 3). The area of interest (Dolni Rozinka, Czech Republic) was selected because there is a deposit of uranium ore and extreme anthropogenic activity. Environmental samples were taken directly on-site and immediately analysed. Duration of a single analysis was approximately two minutes. The average concentrations of Cd(II) and Pb(II) in this area were below the global average. The obtained values were verified (correlated) by standard electrochemical methods based on hanging drop electrodes and were in good agreement. The advantages of this method are its cost and time effectivity (approximately two minutes per one sample) with direct analysis of turbid samples (soil leach) in a 2 M HNO3 environment. This type of sample cannot be analyzed using the classical analytical methods without pretreatment. PMID:28792458

Streamflow, suspended-sediment, and soil-erosion data from Kaulana and Hakioawa watersheds, Kaho'olawe, Hawai'i,

USGS Publications Warehouse

Izuka, Scot K.; Abbott, Lyman L.

2010-01-01

Various events over the last two centuries have destroyed the vegetation and caused rapid soil erosion on large areas of the small, arid, windy tropical shield-volcano island of Kaho`olawe, Hawai`i. These activities were largely halted in the 1990s, and efforts have been made to restore the island's vegetation in order to stem erosion. In 2003, the Kaho`olawe Island Reserve Commission (KIRC) began restoration efforts using native vegetation. In 2006 to 2010, the U.S. Geological Survey (USGS), in cooperation with the KIRC, monitored streamflow, fluvial suspended-sediment transport, and erosion rates in the Hakioawa and Kaulana watersheds on northeastern Kaho`olawe to provide information needed to assess the effectiveness of restoration efforts. This report presents the results from this monitoring. Results.-Hakioawa and Kaulana gulches were dry about 90 percent of the time during the monitoring period; mean annual flow was 0.06 ft3/s at Hakioawa Gulch gage and 0.01 ft3/s at the Kaulana Gulch gage. For the period when the sediment gages on both gulches were operating concurrently (October 2007 to September 2009), sediment discharge was higher from Hakioawa Gulch than from Kaulana Gulch. The annual suspended-sediment loads for the concurrent period averaged 1,880 tons at the Hakioawa Gulch gage and 276 tons at the Kaulana Gulch gage. Of the 77 erosion-monitoring sites in the Hakioawa and Kaulana watersheds, 50 had overall rates of change indicating erosion for the monitoring period, ranging from -1 to -10 mm/yr and averaging -3 mm/yr. Seven sites had rates of change indicating overall deposition, ranging from 1 to 15 mm/yr and averaging 5 mm/yr. Twenty had rates of change below detection (less than ?1 mm/yr). The average rate of change for the 26 sites in areas that have undergone restoration by the KIRC was below the detection limit of the erosion-monitoring method. In comparison, the 51 sites in nonrestoration areas averaged -2 mm/y. Both of these averages, however, include sites that showed overall erosion as well as sites that showed overall deposition. The average rate of change was -1 mm/yr for both the 32 sites on rills and the 42 sites on interfluves; both categories include sites that showed deposition as well as sites that showed erosion. All three sites on hummocks showed overall erosion, with an average rate of -8 mm/yr. Both the Hakioawa and Kaulana watersheds showed an average rate of change of -1 mm/yr, and both included sites that showed erosion and sites that showed deposition. For sites with negative rates of change indicating erosion, the average rate of change during the monitoring period was -2 mm/yr in restoration areas and -3 mm/yr in nonrestoration areas. For sites with positive rates of change indicating deposition, the average rate of change was 5 mm/yr in restoration areas and 6 mm/yr in nonrestoration sites. The average rate of change for rills was 1 mm/yr in restoration areas and -2 mm/yr in nonrestoration sites. The average rate of change for interfluves was below detection in restoration areas and -1 mm/yr in nonrestoration areas. Potential Use and Limitation of Data.-Additional statistical comparisons of various subsets of erosion data can be used to assess the effectiveness of restoration efforts or how existing landforms, vegetation, climate, and other physical basin characteristics affect erosion and fluvial sediment transport in the watersheds. Further investigation to identify what factors cause the Kaulana watershed to have much lower runoff and sediment loads than the Hakioawa watershed may yield valuable information for developing and modifying restoration strategies. Continued monitoring of streamflow, sediment transport, and erosion is key to assessing the long-term effectiveness of restoration and can provide insight to the island's recovery since the eradication of feral goats and cessation of use as a military bombing range; the results of this study provide the

An ovine model of cerebral catheter venography for implantation of an endovascular neural interface.

PubMed

Oxley, Thomas James; Opie, Nicholas Lachlan; Rind, Gil Simon; Liyanage, Kishan; John, Sam Emmanuel; Ronayne, Stephen; McDonald, Alan James; Dornom, Anthony; Lovell, Timothy John Haynes; Mitchell, Peter John; Bennett, Iwan; Bauquier, Sebastien; Warne, Leon Norris; Steward, Chris; Grayden, David Bruce; Desmond, Patricia; Davis, Stephen M; O'Brien, Terence John; May, Clive N

2018-04-01

OBJECTIVE Neural interface technology may enable the development of novel therapies to treat neurological conditions, including motor prostheses for spinal cord injury. Intracranial neural interfaces currently require a craniotomy to achieve implantation and may result in chronic tissue inflammation. Novel approaches are required that achieve less invasive implantation methods while maintaining high spatial resolution. An endovascular stent electrode array avoids direct brain trauma and is able to record electrocorticography in local cortical tissue from within the venous vasculature. The motor area in sheep runs in a parasagittal plane immediately adjacent to the superior sagittal sinus (SSS). The authors aimed to develop a sheep model of cerebral venography that would enable validation of an endovascular neural interface. METHODS Cerebral catheter venography was performed in 39 consecutive sheep. Contrast-enhanced MRI of the brain was performed on 13 animals. Multiple telescoping coaxial catheter systems were assessed to determine the largest wide-bore delivery catheter that could be delivered into the anterior SSS. Measurements of SSS diameter and distance from the motor area were taken. The location of the motor area was determined in relation to lateral and superior projections of digital subtraction venography images and confirmed on MRI. RESULTS The venous pathway from the common jugular vein (7.4 mm) to the anterior SSS (1.2 mm) was technically challenging to selectively catheterize. The SSS coursed immediately adjacent to the motor cortex (< 1 mm) for a length of 40 mm, or the anterior half of the SSS. Attempted access with 5-Fr and 6-Fr delivery catheters was associated with longer procedure times and higher complication rates. A 4-Fr catheter (internal lumen diameter 1.1 mm) was successful in accessing the SSS in 100% of cases with no associated complications. Complications included procedure-related venous dissection in two major areas: the torcular herophili, and the anterior formation of the SSS. The bifurcation of the cruciate sulcal veins with the SSS was a reliable predictor of the commencement of the motor area. CONCLUSIONS The ovine model for cerebral catheter venography has generalizability to the human cerebral venous system in relation to motor cortex location. This novel model may facilitate the development of the novel field of endovascular neural interfaces that may include preclinical investigations for cortical recording applications such as paralysis and epilepsy, as well as other potential applications in neuromodulation.

The Bare Area of the Proximal Ulna: An Anatomic Study With Relevance to Chevron Osteotomy.

PubMed

Ao, Rongguang; Zhang, Xu; Li, Dejian; Chen, Fancheng; Zhou, Jianhua; Yu, Baoqing

2017-06-01

A chevron osteotomy of the ulna is widely used to obtain intra-articular access to the elbow in the treatment of type C distal humerus fractures. The trochlear notch of the proximal ulna is divided into 2 articular parts by the "bare area." Ideally, the olecranon osteotomy should be centered on the bare area to minimize damage to the joint cartilage. The goals of this study were to describe the anatomy of the bare area and design an ideal chevron-shaped osteotomy. We dissected 38 cadaver elbows and measured the width of the bare area, the distance between the tip of the triceps insertion and the area on the olecranon cortex corresponding to the bare area. We then designed a chevron osteotomy to stay within the bare area and measured the distance from the tip of the triceps insertion to the osteotomy apex as well as the angle of the osteotomy plane and the angle of the chevron cuts. The bare area existed in all 38 cadavers. The mean longitudinal and transverse widths were 4.0 mm (range, 1.0-8.6 mm) and 19.0 mm (range, 16.9-23.8 mm), respectively. The mean distance between the tip of the triceps insertion and the area on the olecranon cortex corresponding to the bare area was 19.0 mm (range, 16.0-23.0 mm). The mean transverse and longitudinal widths of the cortical notch were 3.0 mm (range, 1.6-4.5 mm) and 8.0 mm (range, 6.5-14.8 mm), respectively. The mean distance between the tip of the triceps insertion and the osteotomy apex was 22.0 mm (range, 18.0-24.0 mm) and the mean angle between the osteotomy surface and the vertical plane corresponding to the tangent plane was 20° (range, 10° to 25°). The mean angle of the V shape was 140° (range, 130° to 150°). Using the narrowest edge lacking cartilage (lateral or medial side) as a point of reference to locate the bare area, the designed chevron osteotomy entered the joint in the bare area in most specimens and decreased associated damage to the joint cartilage. This study describes the anatomy of the bare area and the design of the ideal chevron-shaped osteotomy to treat type C distal humerus fractures. Copyright © 2017 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Quantitative analysis of synthetic dyes in lipstick by micellar electrokinetic capillary chromatography.

PubMed

Desiderio, C; Marra, C; Fanali, S

1998-06-01

The separation of synthetic dyes, used as color additives in cosmetics, by micellar electrokinetic capillary chromatography (MEKC) is described in this study. The separation of seven dyes, namely eosine, erythrosine, cyanosine, rhodamine B, orange II, chromotrope FB and tartrazine has been achieved in about 3 min in an untreated fused silica capillary containing as background electrolyte a 25 mM tetraborate/phosphate buffer, pH 8.0, and 30 mM sodium dodecyl sulfate. The electrophoretic method exhibits precision and relatively high sensitivity. A detection limit (LOD, signal/noise = 3) in the range of 5-7.5 X 10(-7) M of standard compounds was recorded. Intra-day repeatability of all the studied dye determinations (8 runs) gave the following results (limit values), % standard deviation: 0.24-1.54% for migration time, 0.99-1.24% for corrected peak areas, 0.99-1.24% for corrected peak area ratio (analyte/internal standard) and 1.56-2.74% for peak areas. The optimized method was successfully applied to the analysis of a lipstick sample where eosine and cyanosine were present.

Evaporation components of a boreal forest: variations during the growing season

NASA Astrophysics Data System (ADS)

Grelle, A.; Lundberg, A.; Lindroth, A.; Morén, A.-S.; Cienciala, E.

1997-10-01

To improve the understanding of interactions between the boreal forest and the climate system as a key issue for global climate change, the water budget of a mixed pine and spruce forest in central Sweden was estimated by measurements of the water flux components and the total evaporation flux during the period 16 May-31 October 1995. Total evaporation was measured using eddy correlation and the components were obtained using measurements of precipitation, throughfall, tree transpiration, and forest floor evaporation. On a daily basis, tree transpiration was the dominant evaporation component during the vegetation period. However, it could be efficiently blocked by a wet canopy associated with large interception evaporation. The accumulated total evaporation was 399 mm, transpiration was 243 mm, forest floor evaporation was 56 mm and interception evaporation was 74 mm. The accumulated sum of interception, transpiration, and floor evaporation was 51 mm larger than the actual measured total evaporation. This difference was mainly attributed to the fact that transpiration was measured in a rather dense 50-year-old stand while total evaporation represented the average conditions of older, roughly 100-year-old stands. To compare eddy-correlation measurements with small-scale measurements of evaporation components, a source area analysis was made to select the flux data that give the best representation of the investigated stand. Especially under stable atmospheric conditions the requirements for surface homogeneity were very high and extreme care had to be taken to be aware of the flux source areas. Canopy water storage was determined by two methods: by the water balance of the canopy, which gave a result of 3.3 mm; and by the so-called minimum method based on plots of throughfall versus precipitation, which gave a much lower value of 1.5 mm. Seasonal interception evaporation constituted 30% of the precipitation.

40 CFR 211.204-2 - Primary label size, print and color.

Code of Federal Regulations, 2011 CFR

2011-07-01

... each area shall be as follows, based upon a scale of 72 points=1 inch: (1) Area A—2.8 millimeters (mm) or 8 point. (2) Area B—7.6 mm or 22 point for the Rating;—1.7 mm or 5 point for -“Decibels”. (3) Area...

Effect of cantilever length and alloy framework on the stress distribution in peri-implant area of cantilevered implant-supported fixed partial dentures

PubMed Central

SUEDAM, Valdey; MORETTI, Rafael Tobias; SOUSA, Edson Antonio Capello; RUBO, José Henrique

2016-01-01

ABSTRACT Because many mechanical variables are present in the oral cavity, the proper load transfer between the prosthesis and the bone is important for treatment planning and for the longevity of the implant-supported fixed partial denture. Objectives To verify the stress generated on the peri-implant area of cantilevered implant-supported fixed partial dentures and the potential effects of such variable. Material and Methods A U-shaped polyurethane model simulating the mandibular bone containing two implants (Ø 3.75 mm) was used. Six groups were formed according to the alloy’s framework (CoCr or PdAg) and the point of load application (5 mm, 10 mm and 15 mm of cantilever arm). A 300 N load was applied in pre-determined reference points. The tension generated on the mesial, lingual, distal and buccal sides of the peri-implant regions was assessed using strain gauges. Results Two-way ANOVA and Tukey statistical tests were applied showing significant differences (p<0.05) between the groups. Pearson correlation test (p<0.05) was applied showing positive correlations between the increase of the cantilever arm and the deformation of the peri-implant area. Conclusions This report demonstrated the CoCr alloy shows larger compression values compared to the PdAg alloy for the same distances of cantilever. The point of load application influences the deformation on the peri-implant area, increasing in accordance with the increase of the lever arm. PMID:27119758

Antibacterial Activity Of ternary semiconductor compounds AgInSe2 Nanoparticles Synthesized by Simple Chemical Method

NASA Astrophysics Data System (ADS)

Shehab, A. A.; Fadaam, S. A.; Abd, A. N.; Mustafa, M. H.

2018-05-01

In this objective AgInSe2Nanoparticles (AgInSe2 NPs) were prepared by a simple chemical method (SCM). The optica structural l and morphological properties of the synthesized AgInSe2 NPs swere investigated by using UVVI absorption atomic force microscopy AFMmf, Fourier Transform Infrared Spectroscopy and x-ray diffraction. The resistance of bacteria represents a trouble and the outlook for the use of antibiotics in the future until now uncertain. Measures must be taken to decrease this problem. Antibacterial activity of the AgInSe2 nanoparticles were exposed against several pathogenic bacteriaa including Klebsiella pneumonia KPa, Staphylococcus aureus, Bacillus subtili, Enterobacter Cloacae and Esherichia Coliby. Using a good spread method the results showed that AgInSe2 NPs had inhibitory effect versus some pathogenic bacteria with suppression area 18, 14 and 17 mm for SAgInSe2 NPs had an inhibitory effect against S Bacillus Subtilis 11 mm K EnterobactercCloacae 12 mm.

Anatomical reconstructions of pediatric airways from endoscopic images: a pilot study of the accuracy of quantitative endoscopy.

PubMed

Meisner, Eric M; Hager, Gregory D; Ishman, Stacey L; Brown, David; Tunkel, David E; Ishii, Masaru

2013-11-01

To evaluate the accuracy of three-dimensional (3D) airway reconstructions obtained using quantitative endoscopy (QE). We developed this novel technique to reconstruct precise 3D representations of airway geometries from endoscopic video streams. This method, based on machine vision methodologies, uses a post-processing step of the standard videos obtained during routine laryngoscopy and bronchoscopy. We hypothesize that this method is precise and will generate assessment of airway size and shape similar to those obtained using computed tomography (CT). This study was approved by the institutional review board (IRB). We analyzed video sequences from pediatric patients receiving rigid bronchoscopy. We generated 3D scaled airway models of the subglottis, trachea, and carina using QE. These models were compared to 3D airway models generated from CT. We used the CT data as the gold standard measure of airway size, and used a mixed linear model to estimate the average error in cross-sectional area and effective diameter for QE. The average error in cross sectional area (area sliced perpendicular to the long axis of the airway) was 7.7 mm(2) (variance 33.447 mm(4)). The average error in effective diameter was 0.38775 mm (variance 2.45 mm(2)), approximately 9% error. Our pilot study suggests that QE can be used to generate precise 3D reconstructions of airways. This technique is atraumatic, does not require ionizing radiation, and integrates easily into standard airway assessment protocols. We conjecture that this technology will be useful for staging airway disease and assessing surgical outcomes. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

On the stability of the relationship between reference evapotranspiration and single tree transpiration: test and validation over several irrigated tree orchards

NASA Astrophysics Data System (ADS)

Ayyoub, Abdellatif; Er-Raki, Salah; Khabba, Saïd; Merlin, Olivier; César Rodriguez, Julio; Ezzahar, Jamal; Bahlaoui, Ahmed; Chehbouni, Abdelghani

2016-04-01

The present work aims to develop a simple approach relating normalized daily sap flow (per unit of leaf area) and daily ET0 (mm/day) calculated by two methods: FAO-Penman-Monteith (FAO-PM) and Hargreaves-Samani (HARG). The data sets used for developing this approach are taken from three experimental sites (olive trees, cv. "Oleaeuropaea L.", olive trees, cv. "Arbequino" and citrus trees cv. "Clementine Afourar") conducted in the Tensift region around Marrakech, Morocco and one experimental site (pecan orchard, cv. "Caryaillinoinensis, Wangenh. K. Koch") conducted in the Yaqui Valley, northwest of Mexico). The results showed that the normalized daily sap flow (volume of transpired water per unit of leaf area) was linearly correlated with ET0 (mm per day) calculated by FAO-PM method. The coefficient of determination (R2) and the slope of this linear regression varied between 0.71 and 0.97 and between 0.30 and 0.35, respectively, depending on the type of orchards. For HARG method, the relationship between both terms is also linear but with less accuracy (R2 =0.7) as expected due to the underestimation of ET0 by this method. Afterward, the validation of the developed linear relationship was performed over an olive orchard ("Oleaeuropaea L.") where the measurements of sap flow were available for another (2004) cropping season. The scatter plot between the normalized measured and estimated sap flow based on FAO-PM method reveals a very good agreement (slope = 1, with R2 = 0.83 and RMSE=0.14 L/m2 leaf area). However, for the estimation of normalized sap flow based on HARG method, the correlation is more scattered with some underestimation (5%). A further validation wasperformed using the measurements of evapotranspiration (ET) by eddy correlation system and the results showed that the correlation between normalized measured ET and estimated normalized sap flow is best when using FAO-PM method (RMSE=0.33 L/m2 leaf area) for estimating ET0 than when using HARG method (RMSE= 0.51 L/m2 leaf area). Finally, the performance of the developed approach was compared to the traditional dual crop coefficient scheme for estimating plant transpiration. Cross-comparison of these two approaches with the measurements data gave satisfactory results with an average value of RMSE equal to about 0.37 mm/day for both approaches.

Determinants and Normal Values of Ascending Aortic Diameter by Age, Gender and Race/Ethnicity in the Multi-Ethnic Study of Atherosclerosis (MESA)

PubMed Central

Turkbey, Evrim B.; Jain, Aditya; Johnson, Craig; Redheuil, Alban; Arai, Andrew E.; Gomes, Antoinette S.; Carr, James; Hundley, W. Gregory; Teixido-Tura, Gisela; Eng, John; Lima, Joao A.C.; Bluemke, David A.

2013-01-01

PURPOSE To determine the normal size and wall thickness of the ascending thoracic aorta (AA) and its relationship with cardiovascular risk factors in a large population-based study. MATERIALS AND METHODS The mean AA luminal diameter was measured in 3573 Multi-Ethnic Study of Atherosclerosis (MESA) participants (age: 45–84 years), using gradient echo phase contrast cine MRI. Multiple linear regression models were used to evaluate the associations between risk factors and AA diameter. The median and upper normal limit (95th percentile) was defined in a “healthy” subgroup as well as AA wall thickness. RESULTS The upper limits of body surface area indexed AA luminal diameter for age categories of 45–54, 55–64, 65–74, and 75–84 years are 21, 22, 22, and 28 mm/m2 in women and 20, 21, 22, 23 mm/m2 in men, respectively. The mean AA wall thickness was 2.8 mm. Age, gender and body surface area were major determinants of AA luminal diameter (~+1 mm/10 years; ~+1.9 mm in men than women; ~+1 mm/ 0.23 m2; p<0.001). The AA diameter in hypertensive subjects was +0.9 mm larger than in normotensives (p<0.001). CONCLUSION AA diameter increases gradually with aging for both genders, among all race/ethnicities. Normal value of AA diameter is provided. PMID:23681649

Effect of Calcifications on Breast Ultrasound Shear Wave Elastography: An Investigational Study

PubMed Central

Gregory, Adriana; Mehrmohammadi, Mohammad; Denis, Max; Bayat, Mahdi; Stan, Daniela L.; Fatemi, Mostafa; Alizad, Azra

2015-01-01

Purpose To investigate the effects of macrocalcifications and clustered microcalcifications associated with benign breast masses on shear wave elastography (SWE). Methods SuperSonic Imagine (SSI) and comb-push ultrasound shear elastography (CUSE) were performed on three sets of phantoms to investigate how calcifications of different sizes and distributions influence measured elasticity. To demonstrate the effect in vivo, three female patients with benign breast masses associated with mammographically-identified calcifications were evaluated by CUSE. Results Apparent maximum elasticity (Emax) estimates resulting from individual macrocalcifications (with diameters of 2mm, 3mm, 5mm, 6mm, 9mm, 11mm, and 15mm) showed values over 50 kPa for all cases, which represents more than 100% increase over background (~21kPa). We considered a 2cm-diameter circular region of interest for all phantom experiments. Mean elasticity (Emean) values varied from 26 kPa to 73 kPa, depending on the macrocalcification size. Highly dense clusters of microcalcifications showed higher Emax values than clusters of microcalcification with low concentrations, but the difference in Emean values was not significant. Conclusions Our results demonstrate that the presence of large isolated macrocalcifications and highly concentrated clusters of microcalcifications can introduce areas with apparent high elasticity in SWE. Considering that benign breast masses normally have significantly lower elasticity values than malignant tumors, such areas with high elasticity appearing due to presence of calcification in benign breast masses may lead to misdiagnosis. PMID:26368939

Anti-Inflammatory Effect of Gallic Acid-Eluting Stent in a Porcine Coronary Restenosis Model

PubMed Central

Seob Lim, Kyung; Park, Jun-Kyu; Ho Jeong, Myung; Ho Bae, In; Sung Park, Dae; Won Shim, Jae; Ha Kim, Jung; Kuk Kim, Hyun; Soo Kim, Sung; Sun Sim, Doo; Joon Hong, Young; Han Kim, Ju; Ahn, Youngkeun

2018-01-01

Background Gallic acid (3,4,5-trihydroxybenzoic acid) is a natural polyphenol and strong natural antioxidant found abundantly in red wine and green tea. The aim of this study was to examine the anti-inflammatory effect of a novel gallic acid-eluting stent in a porcine coronary restenosis model. Methods Fifteen pigs were randomized into three groups; in which a total of 30 coronary arteries (10 in each group) were implanted with gallic acid-eluting stents (GESs, n = 10), gallic acid and sirolimus-eluting stents (GSESs, n = 10), or sirolimus-eluting stents (SESs, n = 10). Histopathologic analysis was performed 28 days after stenting. Results There were no significant differences in injury score and fibrin score among the groups, however there were significant differences in the internal elastic lamina (4.0 ± 0.83 mm2 in GES vs. 3.0 ± 0.53 mm2 in GSES vs. 4.6 ± 1.43 mm2 in SES, p < 0.0001), lumen area (2.3 ± 0.49 mm2 in GES vs. 1.9 ± 0.67 mm2 in GSES vs. 2.9 ± 0.56 mm2 in SES, p < 0.0001), neointimal area (1.7 ± 0.63 mm2 in GES vs. 1.1 ± 0.28 mm2 in GSES vs. 1.7 ± 1.17 mm2 in SES, p < 0.05), and percent area of stenosis (42.4% ± 9.22% in GES vs. 38.2% ± 12.77% in GSES vs. 33.9% ± 15.64% in SES, p < 0.05). The inflammation score was significantly lower in the GES and GSES groups compared to that in the SES group [1.0 (range: 1.0 to 2.0) in GES vs. 1.0 (range: 1.0 to 1.0) in GSES vs. 1.5 (range: 1.0 to 3.0) in SES, p < 0.05]. Conclusions The GES group had a greater percent area of stenosis than the SES group. Although gallic acid in the GES and GSES groups did not show a synergistic effect in suppressing neointimal hyperplasia, it resulted in greater inhibition of the inflammatory reaction in the porcine coronary restenosis model than in the SES group. PMID:29844643

Three-dimensional analysis using finite element method of anterior teeth inclination and center of resistance location.

PubMed

Geramy, Allahyar; Sodagar, Ahmad; Hassanpour, Mehdi

2014-01-01

To locate the centre of resistance of consolidated units of four and six anterior teeth during retraction. Twelve three-dimensional (3D) models were designed in SolidWorks of the anterior segment with four and six teeth and their supporting structure. A proper force system was applied in each model to retract the teeth bodily. The exact location of the centre of resistances (CRes) was determined. It was found that the path of CRes change in four-tooth and six-tooth units according to the anterior teeth torque. A posterior shift of the CRes by increasing the inclination of teeth was shown. However, vertical position has a fluctuant behaviour. First it moves apically, then it moves incisally. Furthermore, results suggest that in en masse retraction, translation can be achieved with a smaller amount of moment-to-force ratio than in four-incisor retraction. In other words, for bodily retraction of anterior incisor segments, we should apply force in a more apical position. Different anterior torques between 7 and 35 degrees, cannot affect the CRes position dramatically. The area of CRes shifting is 0.92 mm (anterioposteriorly) x 0.74 mm (superior-inferiorly) in the six-tooth unit in the teeth model and 0.85 mm (anterioposteriorly) x 0.82 mm (superior-inferiorly) in the teeth and bone model. In the four-tooth model, the area of CRes shifting is 0.97 mm (anterioposteriorly) x 0.93 mm (superior-inferiorly) in tooth model and 0.77 mm (anterioposteriorly) x 0.87 mm (superior-inferiorly) in the teeth and bone model.

Large Area Cd0.9Zn0.1Te Pixelated Detector: Fabrication and Characterization

NASA Astrophysics Data System (ADS)

Chaudhuri, Sandeep K.; Nguyen, Khai; Pak, Rahmi O.; Matei, Liviu; Buliga, Vladimir; Groza, Michael; Burger, Arnold; Mandal, Krishna C.

2014-04-01

Cd0.9Zn0.1Te (CZT) based pixelated radiation detectors have been fabricated and characterized for gamma ray detection. Large area CZT single crystals has been grown using a tellurium solvent method. A 10 ×10 guarded pixelated detector has been fabricated on a 19.5 ×19.5 ×5 mm3 crystal cut out from the grown ingot. The pixel dimensions were 1.3 ×1.3 mm2 and were pitched at 1.8 mm. A guard grid was used to reduce interpixel/inter-electrode leakage. The crystal was characterized in planar configuration using electrical, optical and optoelectronic methods prior to the fabrication of pixelated geometry. Current-voltage (I-V) measurements revealed a leakage current of 27 nA at an operating bias voltage of 1000 V and a resistivity of 3.1 ×1010 Ω-cm. Infrared transmission imaging revealed an average tellurium inclusion/precipitate size less than 8 μm. Pockels measurement has revealed a near-uniform depth-wise distribution of the internal electric field. The mobility-lifetime product in this crystal was calculated to be 6.2 ×10 - 3 cm2/V using alpha ray spectroscopic method. Gamma spectroscopy using a 137Cs source on the pixelated structure showed fully resolved 662 keV gamma peaks for all the pixels, with percentage resolution (FWHM) as high as 1.8%.

A Comprehensive Study of Gridding Methods for GPS Horizontal Velocity Fields

NASA Astrophysics Data System (ADS)

Wu, Yanqiang; Jiang, Zaisen; Liu, Xiaoxia; Wei, Wenxin; Zhu, Shuang; Zhang, Long; Zou, Zhenyu; Xiong, Xiaohui; Wang, Qixin; Du, Jiliang

2017-03-01

Four gridding methods for GPS velocities are compared in terms of their precision, applicability and robustness by analyzing simulated data with uncertainties from 0.0 to ±3.0 mm/a. When the input data are 1° × 1° grid sampled and the uncertainty of the additional error is greater than ±1.0 mm/a, the gridding results show that the least-squares collocation method is highly robust while the robustness of the Kriging method is low. In contrast, the spherical harmonics and the multi-surface function are moderately robust, and the regional singular values for the multi-surface function method and the edge effects for the spherical harmonics method become more significant with increasing uncertainty of the input data. When the input data (with additional errors of ±2.0 mm/a) are decimated by 50% from the 1° × 1° grid data and then erased in three 6° × 12° regions, the gridding results in these three regions indicate that the least-squares collocation and the spherical harmonics methods have good performances, while the multi-surface function and the Kriging methods may lead to singular values. The gridding techniques are also applied to GPS horizontal velocities with an average error of ±0.8 mm/a over the Chinese mainland and the surrounding areas, and the results show that the least-squares collocation method has the best performance, followed by the Kriging and multi-surface function methods. Furthermore, the edge effects of the spherical harmonics method are significantly affected by the sparseness and geometric distribution of the input data. In general, the least-squares collocation method is superior in terms of its robustness, edge effect, error distribution and stability, while the other methods have several positive features.

Sensitivity to detect small coronary artery calcium lesions with varying slice thickness using electron beam tomography.

PubMed

Mao, Songshou; Child, Janis; Carson, Sivi; Liu, Steve C K; Oudiz, Ronald J; Budoff, Matthew J

2003-03-01

To estimate the sensitivity to find small coronary artery calcium lesions with use of different slice widths with electron beam tomography. Two studies were performed. Study 1 utilized double scanning of a stationary cork phantom with three different slice thickness (1.5, 3, and 6 mm). Fifty different calcific lesions (all <20 mm2 in area) fitted in 10 cork coronary arteries were utilized. The calcium foci area, peak value and score were measured and compared. In group 2, 30 patients underwent coronary artery calcium (CAC) screen studies. Each patient was scanned with both 3-mm and 6-mm scan widths in a same study time. Lesions with < 20 mm2 of area of CAC were measured on both 3-mm and 6-mm images. The mean and peak Hounsfield unit measure, and Agatston score were compared between both images. In the cork study, the sensitivity to detect small calcium foci were 96% (48/50), 82% (41/50), and 34% (17/50) in images with 1.5-, 3-, and 6-mm slice thickness, respectively. There is a smaller value in mass, and calcium volume in 6-mm images than 1.5-mm and 3-mm images ( P< 0.001). There was no significant difference between the true value and measured value from 1.5-mm and 3-mm images. In the human study, 18 (30%) of 60 CAC lesions with an area < 20 mm2 defined on 3 mm images were not visible on 6-mm images. Sensitivity of small lesions (P< 5 mm2) was 48% using 6-mm slices. There was a smaller value in CAC area, mean and peak Hounsfield units and score measured from 6-mm images, as compared with 3 mm slices ( P< 0.05). Thinner slice imaging has a higher sensitivity to detect small calcium focus. There was no significant change in score between 3 mm and 1.5 mm on the cork phantom study. However, the use of 6-mm slices should be discouraged, as this protocol both underestimates calcific mass and misses a significant number of calcific lesions in both a phantom and human study.

The contribution of large trees to total transpiration rates in a pre-montane tropical forest and its implications for selective logging practices

NASA Astrophysics Data System (ADS)

Orozco, G.; Moore, G. W.; Miller, G. R.

2012-12-01

In the humid tropics, conservationists generally prefer selective logging practices over clearcutting. Large valuable timber is removed while the remaining forest is left relatively undisturbed. However, little is known about the impact of selective logging on site water balance. Because large trees have very deep sapwood and exposed canopies, they tend to have high transpiration. The first objective was to evaluate the methods used for scaling sap flow measurements to the watershed with particular emphasis on large trees. The second objective of this study was to determine the relative contribution of large trees to site water balance. Our study was conducted in a pre-montane transitional forest at the Texas A&M University Soltis Center in north-central Costa Rica. During the period between January and July 2012, sap flux was monitored in a 30-m diameter plot within a 10-ha watershed. Two pairs of heat dissipation sensors were installed in the outer 0-20 mm of each of 15 trees selected to represent the full range of tree sizes. In six of the largest trees, depth profiles were recorded at 10-mm intervals to a depth of 60 mm using compensation heat pulse sensors. To estimate sapwood basal area of the entire watershed, a stand survey was conducted in three 30-m-diameter plots. In each plot, we measured basal area of all trees and estimated sapwood basal area from sapwood depth measured in nearly half of the trees. An estimated 36.5% of the total sapwood area in this watershed comes from the outer 20 mm of sapwood, with the remaining 63.5% of sapwood from depths deeper than 20 mm. Nearly 13% of sapwood is from depths beyond 60 mm. Sap velocity profiles indicate the highest flow rates occurred in the 0-2 cm depths, with declines of 17% and 25% in the 20-40 mm and 40-60 mm ranges, respectively. Our results demonstrate the need to measure sap velocity profiles in large tropical trees. If total transpiration had been estimated solely from the 0-20 mm heat dissipation probes, it would have been overestimated by at least 15%. Total transpiration averaged 1.49 mm over the 6-month study period. However, the largest 10% of trees contributed disproportionately to this amount. Trees greater than 110 cm in diameter represented over half of the total basal area and 32% of the total sapwood area. These results highlight the importance of large trees in estimating watershed-scale transpiration. From a forest management perspective, selectively logging only the very largest trees, a common practice among these tropical forests of Costa Rica, is likely to disproportionately impact the site water balance unless water use of smaller trees can fully compensate.

Growth of Ca 4YO(BO 3) 3 crystals by vertical Bridgman method

NASA Astrophysics Data System (ADS)

Luo, Jun; Fan, Shiji; Wang, Jinchang; Zhong, Zhenwu; Qian, Guoxing; Sun, Renying

2001-07-01

Growth of single crystals of Ca 4YO(BO 3) 3 (YCOB) by the vertical Bridgman method is reported in this paper. By using near-sealed Pt crucibles to prevent volatilization of B 2O 3, the high-optical-quality YCOB crystals of 25 mm diameter and more than 40 mm in length have been grown at the furnace temperature of 50-80°C above the melting point of YCOB and the crucible lowering rates of 0.2-0.6 mm/h. Owing to the low vertical and radial temperature gradient, crack-free YCOB crystals have been obtained in the <0 1 0> and <0 0 1> directions. At the top of a YCOB boule, the dislocation density was found to decrease from the center to the outer area, and the average dislocation density is about 600/cm 2.

SU-E-T-35: A General Fill Factor Definition Serving to Characterise the MLC Misalignment Detection Capabilities of Two-Dimensional Detector Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stelljes, T.S.; Looe, H.K.; Poppe, B.

Purpose: To present a general definition of the fill factor realistically characterizing the “field coverage”, i.e. the MLC misalignment detection capabilities of a detector array. Methods: According to Gago-Arias et al.{sup 1} the fill factor of a 2D array is defined as the ratio of the area enclosed by the FWHM of the fluence response function KM(x) of a single detector and its cell area defined by the detector spacing. More generally - accounting also for the possible overlap between FWHM’s of neighboured detectors - the fill factor is here defined as that fraction of the sum of the detectormore » cell areas in which a defined MLC misalignment is detectable when the induced percentage signal changes exceed a detection threshold d. Ideally the generalized fill factor may reach 100 %. With user code EGS-chamber and a 2 MeV photon slit beam 0.25 mm wide, both types of the fill factor were calculated for an array with total cell area 100 cm{sup 2} for chamber widths 1–9 mm, using =1mm, d=5%. Results: For single chamber width 5 mm, fill factors were 0.49 (FWHM) and 0.61 (generalized). For chamber width 2 mm the FWHM fill factor was 0.13 whereas the generalized fill factor was 0.32. For chamber widths above 7 mm, the FWHM fill factor exceeds unity, and the general fill factor is exactly 1.00. Conclusions: An updated fill factor definition is introduced which, as a generalization of the FWHM-based definition, more closely estimates the performance of small array chambers and gives a realistic value in the case of overlapping sensitive areas of neighboured chambers. References:{sup 1}A. Gago-Arias, L. Brualla-Gonzalez, D.M. Gonzalez-Castano, F. Gomez, M.S. Garcia, V.L. Vega, J.M. Sueiro, J. Pardo-Montero, “Evaluation of chamber response function influence on IMRT verification using 2D commercial detector arrays,” Phys. Med. Biol. 57, 2005–2020 (2012)« less

Revision 1 Size and position of the healthy meniscus, and its Correlation with sex, height, weight, and bone area- a cross-sectional study

PubMed Central

2011-01-01

Background Meniscus extrusion or hypertrophy may occur in knee osteoarthritis (OA). However, currently no data are available on the position and size of the meniscus in asymptomatic men and women with normal meniscus integrity. Methods Three-dimensional coronal DESSwe MRIs were used to segment and quantitatively measure the size and position of the medial and lateral menisci, and their correlation with sex, height, weight, and tibial plateau area. 102 knees (40 male and 62 female) were drawn from the Osteoarthritis Initiative "non-exposed" reference cohort, including subjects without symptoms, radiographic signs, or risk factors for knee OA. Knees with MRI signs of meniscus lesions were excluded. Results The tibial plateau area was significantly larger (p < 0.001) in male knees than in female ones (+23% medially; +28% laterally), as was total meniscus surface area (p < 0.001, +20% medially; +26% laterally). Ipsi-compartimental tibial plateau area was more strongly correlated with total meniscus surface area in men (r = .72 medially; r = .62 laterally) and women (r = .67; r = .75) than contra-compartimental or total tibial plateau area, body height or weight. The ratio of meniscus versus tibial plateau area was similar between men and women (p = 0.22 medially; p = 0.72 laterally). Tibial coverage by the meniscus was similar between men and women (50% medially; 58% laterally), but "physiological" medial meniscal extrusion was greater in women (1.83 ± 1.06mm) than in men (1.24mm ± 1.18mm; p = 0.011). Conclusions These data suggest that meniscus surface area strongly scales with (ipsilateral) tibial plateau area across both sexes, and that tibial coverage by the meniscus is similar between men and women. PMID:22035074

Large field-of-view tiled grating structures for X-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Schröter, Tobias J.; Koch, Frieder J.; Meyer, Pascal; Kunka, Danays; Meiser, Jan; Willer, Konstantin; Gromann, Lukas; Marco, Fabio D.; Herzen, Julia; Noel, Peter; Yaroshenko, Andre; Hofmann, Andreas; Pfeiffer, Franz; Mohr, Jürgen

2017-01-01

X-ray grating-based interferometry promises unique new diagnostic possibilities in medical imaging and materials analysis. To transfer this method from scientific laboratories or small-animal applications to clinical radiography applications, compact setups with a large field of view (FoV) are required. Currently the FoV is limited by the grating area, which is restricted due to the complex manufacturing process. One possibility to increase the FoV is tiling individual grating tiles to create one large area grating mounted on a carrier substrate. We investigate theoretically the accuracy needed for a tiling process in all degrees of freedom by applying a simulation approach. We show how the resulting precision requirements can be met using a custom-built frame for exact positioning. Precise alignment is achieved by comparing the fringe patterns of two neighboring grating tiles in a grating interferometer. With this method, the FoV can be extended to practically any desired length in one dimension. First results of a phase-contrast scanning setup with a full FoV of 384 mm × 24 mm show the suitability of this method.

Neoplasms treatment by diode laser with and without real time temperature control on operation zone

NASA Astrophysics Data System (ADS)

Belikov, Andrey V.; Gelfond, Mark L.; Shatilova, Ksenia V.; Sosenkova, Svetlana A.; Lazareva, Anastasia A.; Semyashkina, Yulia V.

2016-04-01

Results of nevus, papilloma, dermatofibroma, and basal cell skin cancer in vivo removal by a 980+/-10 nm diode laser with "blackened" tip operating in continuous (CW) mode and automatic power control (APC) mode are presented. The collateral damage width and width of graze wound area around the collateral damage area were demonstrated. The total damage area width was calculated as sum of collateral damage width and graze wound area width. The mean width of total damage area reached 1.538+/-0.254 mm for patient group with nevus removing by 980 nm diode laser operating in CW mode, papilloma - 0.586+/-0.453 mm, dermatofibroma - 1.568+/-0.437 mm, and basal cell skin cancer - 1.603+/-0.613 mm. The mean width of total damage area reached 1.201+/-0.292 mm for patient group with nevus removing by 980 nm diode laser operating in APC mode, papilloma - 0.413+/-0.418 mm, dermatofibroma - 1.240+/-0.546 mm, and basal cell skin cancer - 1.204+/-0.517 mm. It was found that using APC mode decreases the total damage area width at removing of these nosological neoplasms of human skin, and decreases the width of graze wound area at removing of nevus and basal cell skin cancer. At the first time, the dynamic of output laser power and thermal signal during laser removal of nevus in CW and APC mode is presented. It was determined that output laser power during nevus removal for APC mode was 1.6+/-0.05 W and for CW mode - 14.0+/-0.1 W. This difference can explain the decrease of the total damage area width and width of graze wound area for APC mode in comparison with CW mode.

Pencil beam proton radiography using a multilayer ionization chamber

NASA Astrophysics Data System (ADS)

Farace, Paolo; Righetto, Roberto; Meijers, Arturs

2016-06-01

A pencil beam proton radiography (PR) method, using a commercial multilayer ionization chamber (MLIC) integrated with a treatment planning system (TPS) was developed. A Giraffe (IBA Dosimetry) MLIC (±0.5 mm accuracy) was used to obtain pencil beam PR by delivering spots uniformly positioned at a 5.0 mm distance in a 9  ×  9 square of spots. PRs of an electron-density (with tissue-equivalent inserts) phantom and a head phantom were acquired. The integral depth dose (IDD) curves of the delivered spots were computed by the TPS in a volume of water simulating the MLIC, and virtually added to the CT at the exit side of the phantoms. For each spot, measured and calculated IDD were overlapped in order to compute a map of range errors. On the head-phantom, the maximum dose from PR acquisition was estimated. Additionally, on the head phantom the impact on the range errors map was estimated in case of a 1 mm position misalignment. In the electron-density phantom, range errors were within 1 mm in the soft-tissue rods, but greater in the dense-rod. In the head-phantom the range errors were  -0.9  ±  2.7 mm on the whole map and within 1 mm in the brain area. On both phantoms greater errors were observed at inhomogeneity interfaces, due to sensitivity to small misalignment, and inaccurate TPS dose computation. The effect of the 1 mm misalignment was clearly visible on the range error map and produced an increased spread of range errors (-1.0  ±  3.8 mm on the whole map). The dose to the patient for such PR acquisitions would be acceptable as the maximum dose to the head phantom was  <2cGyE. By the described 2D method, allowing to discriminate misalignments, range verification can be performed in selected areas to implement an in vivo quality assurance program.

Pencil beam proton radiography using a multilayer ionization chamber.

PubMed

Farace, Paolo; Righetto, Roberto; Meijers, Arturs

2016-06-07

A pencil beam proton radiography (PR) method, using a commercial multilayer ionization chamber (MLIC) integrated with a treatment planning system (TPS) was developed. A Giraffe (IBA Dosimetry) MLIC (±0.5 mm accuracy) was used to obtain pencil beam PR by delivering spots uniformly positioned at a 5.0 mm distance in a 9  ×  9 square of spots. PRs of an electron-density (with tissue-equivalent inserts) phantom and a head phantom were acquired. The integral depth dose (IDD) curves of the delivered spots were computed by the TPS in a volume of water simulating the MLIC, and virtually added to the CT at the exit side of the phantoms. For each spot, measured and calculated IDD were overlapped in order to compute a map of range errors. On the head-phantom, the maximum dose from PR acquisition was estimated. Additionally, on the head phantom the impact on the range errors map was estimated in case of a 1 mm position misalignment. In the electron-density phantom, range errors were within 1 mm in the soft-tissue rods, but greater in the dense-rod. In the head-phantom the range errors were  -0.9  ±  2.7 mm on the whole map and within 1 mm in the brain area. On both phantoms greater errors were observed at inhomogeneity interfaces, due to sensitivity to small misalignment, and inaccurate TPS dose computation. The effect of the 1 mm misalignment was clearly visible on the range error map and produced an increased spread of range errors (-1.0  ±  3.8 mm on the whole map). The dose to the patient for such PR acquisitions would be acceptable as the maximum dose to the head phantom was  <2cGyE. By the described 2D method, allowing to discriminate misalignments, range verification can be performed in selected areas to implement an in vivo quality assurance program.

Polymeric mercaptosilane-modified platinum electrodes for elimination of interferants in glucose biosensors.

PubMed

Jung, S K; Wilson, G S

1996-02-15

An oxidase-based glucose sensor has been developed that uses a mercaptosilane-modified platinum electrode to achieve selectivity of electrochemical interferants. A platinum-iridium (9:1) wire (0.178 mm o.d., sensing area of 1.12 mm2) is modified with (3-mercaptopropyl)trimethoxysilane. The modified sensors show excellent operational stability for more than 5 days. Glucose oxidase is immobilized on the modified surface (i) by using 3-maleimidopropionic acid as a linker or (ii) by cross-liking with bovine serum albumin using glutaraldehyde. Sensitivities in the range of 9.97 nA/mM glucose are observed when the enzyme is immobilized by method ii. Lower sensitivities (1.13 x 10(-1) nA/mM glucose) are observed when immobilization method i is employed. In terms of linear response range, the sensor enzyme-immobilized by method i is superior to that immobilized by method ii. The linearity is improved upon coating the enzyme layer with polyurethane. The sensor immobilized by method ii and coated with polyurethane exhibits a linear range to 15 mM glucose and excellent selectivity to glucose (0.47 nA/mM) against interferants such as ascorbic acid, uric acid, and acetaminophen.

Estimating spatially and temporally varying recharge and runoff from precipitation and urban irrigation in the Los Angeles Basin, California

USGS Publications Warehouse

Hevesi, Joseph A.; Johnson, Tyler D.

2016-10-17

A daily precipitation-runoff model, referred to as the Los Angeles Basin watershed model (LABWM), was used to estimate recharge and runoff for a 5,047 square kilometer study area that included the greater Los Angeles area and all surface-water drainages potentially contributing recharge to a 1,450 square kilometer groundwater-study area underlying the greater Los Angeles area, referred to as the Los Angeles groundwater-study area. The recharge estimates for the Los Angeles groundwater-study area included spatially distributed recharge in response to the infiltration of precipitation, runoff, and urban irrigation, as well as mountain-front recharge from surface-water drainages bordering the groundwater-study area. The recharge and runoff estimates incorporated a new method for estimating urban irrigation, consisting of residential and commercial landscape watering, based on land use and the percentage of pervious land area.The LABWM used a 201.17-meter gridded discretization of the study area to represent spatially distributed climate and watershed characteristics affecting the surface and shallow sub-surface hydrology for the Los Angeles groundwater study area. Climate data from a local network of 201 monitoring sites and published maps of 30-year-average monthly precipitation and maximum and minimum air temperature were used to develop the climate inputs for the LABWM. Published maps of land use, land cover, soils, vegetation, and surficial geology were used to represent the physical characteristics of the LABWM area. The LABWM was calibrated to available streamflow records at six streamflow-gaging stations.Model results for a 100-year target-simulation period, from water years 1915 through 2014, were used to quantify and evaluate the spatial and temporal variability of water-budget components, including evapotranspiration (ET), recharge, and runoff. The largest outflow of water from the LABWM was ET; the 100-year average ET rate of 362 millimeters per year (mm/yr) accounted for 66 percent of the combined water inflow of 551 mm/yr, including 488 mm/yr from precipitation and 63 mm/yr from urban irrigation. The simulated ET rate varied from a minimum of 0 mm/yr for impervious areas to high values of more than 1,000 mm/yr for many areas, including the south-facing slopes of the San Gabriel Mountains, stream channels underlain by permeable soils and thick root zones, and pervious locations receiving inflows both from urban irrigation and surface water. Runoff was the next largest outflow, averaging 145 mm/yr for the 100-year period, or 26 percent of the combined precipitation and urban-irrigation inflow. Recharge averaged 45 mm/yr, or about 8 percent of the combined inflow from precipitation and urban irrigation.Simulation results indicated that recharge in response to urban irrigation was an important component of spatially distributed recharge, contributing an average of 56 percent of the total recharge to the eight LABWM subdomains containing the Los Angeles groundwater study area. The 100‑year average recharge rate for the eight subdomains was 41 mm/yr, or 8,473 hectare-meters per year (ha-m/yr), with urban irrigation included in the simulation compared to a recharge rate of 18 mm/yr, or 3,741 ha-m/yr, with urban irrigation excluded. In contrast to recharge, the effect of urban irrigation on runoff was slight; runoff was 72,667 ha-m/yr with urban irrigation included compared to 72,618 ha-m/yr with urban irrigation excluded, an increase of only 48 ha-m/yr (about 0.1 percent).Simulation results also indicated that potential recharge from hilly drainages outside of, but bordering and tributary to, the lower-lying area of the Los Angeles groundwater study area, in this study referred to as mountain-front recharge, could provide an important contribution to the total recharge for the groundwater basins. The time-averaged recharge rate was similar to the combined direct and mountain-front recharge components estimated in a previous study and used as input for a calibrated groundwater model. The annual (water year) recharge estimates simulated in this study, however, indicated much greater year-to-year variability, which was dependent on year-to-year variability in the magnitude and distribution of daily precipitation, compared to the previous estimates.

Fully Automatic Software for Retinal Thickness in Eyes With Diabetic Macular Edema From Images Acquired by Cirrus and Spectralis Systems

PubMed Central

Lee, Joo Yong; Chiu, Stephanie J.; Srinivasan, Pratul P.; Izatt, Joseph A.; Toth, Cynthia A.; Farsiu, Sina; Jaffe, Glenn J.

2013-01-01

Purpose. To determine whether a novel automatic segmentation program, the Duke Optical Coherence Tomography Retinal Analysis Program (DOCTRAP), can be applied to spectral-domain optical coherence tomography (SD-OCT) images obtained from different commercially available SD-OCT in eyes with diabetic macular edema (DME). Methods. A novel segmentation framework was used to segment the retina, inner retinal pigment epithelium, and Bruch's membrane on images from eyes with DME acquired by one of two SD-OCT systems, Spectralis or Cirrus high definition (HD)-OCT. Thickness data obtained by the DOCTRAP software were compared with those produced by Spectralis and Cirrus. Measurement agreement and its dependence were assessed using intraclass correlation (ICC). Results. A total of 40 SD-OCT scans from 20 subjects for each machine were included in the analysis. Spectralis: the mean thickness in the 1-mm central area determined by DOCTRAP and Spectralis was 463.8 ± 107.5 μm and 467.0 ± 108.1 μm, respectively (ICC, 0.999). There was also a high level agreement in surrounding areas (out to 3 mm). Cirrus: the mean thickness in the 1-mm central area was 440.8 ± 183.4 μm and 442.7 ± 182.4 μm by DOCTRAP and Cirrus, respectively (ICC, 0.999). The thickness agreement in surrounding areas (out to 3 mm) was more variable due to Cirrus segmentation errors in one subject (ICC, 0.734–0.999). After manual correction of the errors, there was a high level of thickness agreement in surrounding areas (ICC, 0.997–1.000). Conclusions. The DOCTRAP may be useful to compare retinal thicknesses in eyes with DME across OCT platforms. PMID:24084089

Impaired Left Ventricular Filling in COPD and Emphysema: Is It the Heart or the Lungs?

PubMed Central

Smith, Benjamin M.; Prince, Martin R.; Hoffman, Eric A.; Bluemke, David A.; Liu, Chia-Ying; Rabinowitz, Dan; Hueper, Katja; Parikh, Megha A.; Gomes, Antoinette S.; Michos, Erin D.; Lima, João A. C.; Barr, R. Graham

2013-01-01

Background: COPD and heart failure with preserved ejection fraction overlap clinically, and impaired left ventricular (LV) filling is commonly reported in COPD. The mechanism underlying these observations is uncertain, but may include upstream pulmonary dysfunction causing low LV preload or intrinsic LV dysfunction causing high LV preload. The objective of this study is to determine if COPD and emphysema are associated with reduced pulmonary vein dimensions suggestive of low LV preload. Methods: The population-based Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited smokers aged 50 to 79 years who were free of clinical cardiovascular disease. COPD was defined by spirometry. Percent emphysema was defined as regions < −910 Hounsfield units on full-lung CT scan. Ostial pulmonary vein cross-sectional area was measured by contrast-enhanced cardiac magnetic resonance and expressed as the sum of all pulmonary vein areas. Linear regression was used to adjust for age, sex, race/ethnicity, body size, and smoking. Results: Among 165 participants, the mean (± SD) total pulmonary vein area was 558 ± 159 mm2 in patients with COPD and 623 ± 145 mm2 in control subjects. Total pulmonary vein area was smaller in patients with COPD (−57 mm2; 95% CI, −106 to −7 mm2; P = .03) and inversely associated with percent emphysema (P < .001) in fully adjusted models. Significant decrements in total pulmonary vein area were observed among participants with COPD alone, COPD with emphysema on CT scan, and emphysema without spirometrically defined COPD. Conclusions: Pulmonary vein dimensions were reduced in COPD and emphysema. These findings support a mechanism of upstream pulmonary causes of underfilling of the LV in COPD and in patients with emphysema on CT scan. PMID:23764937

Performance optimization of marine propellers

NASA Astrophysics Data System (ADS)

Lee, Chang-Sup; Choi, Young-Dal; Ahn, Byoung-Kwon; Shin, Myoung-Sup; Jang, Hyun-Gil

2010-12-01

Recently a Wide Chord Tip (WCT) propeller has been developed and applied to a commercial ship by STX Offshore & Shipbuilding. It is reported that the WCT propeller significantly reduces pressure fluctuations and also ship's noise and vibration. On the sea trial, vibration magnitude in the accommodations at NCR was measured at 0.9mm/sec which is only 10% of international allowable magnitude of vibration (9mm/sec). In this paper, a design method for increasing performance of the marine propellers including the WCT propeller is suggested. It is described to maximize the performance of the propeller by adjusting expanded areas of the propeller blade. Results show that efficiency can be increased up to over 2% through the suggested design method.

Detection of microcalcifications by characteristic magnetic susceptibility effects using MR phase image cross-correlation analysis

PubMed Central

Baheza, Richard A.; Welch, E. Brian; Gochberg, Daniel F.; Sanders, Melinda; Harvey, Sara; Gore, John C.; Yankeelov, Thomas E.

2015-01-01

Purpose: To develop and evaluate a new method for detecting calcium deposits using their characteristic magnetic susceptibility effects on magnetic resonance (MR) images at high fields and demonstrate its potential in practice for detecting breast microcalcifications. Methods: Characteristic dipole signatures of calcium deposits were detected in magnetic resonance phase images by computing the cross-correlation between the acquired data and a library of templates containing simulated phase patterns of spherical deposits. The influence of signal-to-noise ratio and various other MR parameters on the results were assessed using simulations and validated experimentally. The method was tested experimentally for detection of calcium fragments within gel phantoms and calcium-like inhomogeneities within chicken tissue at 7 T with optimized MR acquisition parameters. The method was also evaluated for detection of simulated microcalcifications, modeled from biopsy samples of malignant breast cancer, inserted in silico into breast magnetic resonance imaging (MRIs) of healthy subjects at 7 T. For both assessments of calcium fragments in phantoms and biopsy-based simulated microcalcifications in breast MRIs, receiver operator characteristic curve analyses were performed to determine the cross-correlation index cutoff, for achieving optimal sensitivity and specificity, and the area under the curve (AUC), for measuring the method’s performance. Results: The method detected calcium fragments with sizes of 0.14–0.79 mm, 1 mm calcium-like deposits, and simulated microcalcifications with sizes of 0.4–1.0 mm in images with voxel sizes between (0.2 mm)3 and (0.6 mm)3. In images acquired at 7 T with voxel sizes of (0.2 mm)3–(0.4 mm)3, calcium fragments (size 0.3–0.4 mm) were detected with a sensitivity, specificity, and AUC of 78%–90%, 51%–68%, and 0.77%–0.88%, respectively. In images acquired with a human 7 T scanner, acquisition times below 12 min, and voxel sizes of (0.4 mm)3–(0.6 mm)3, simulated microcalcifications with sizes of 0.6–1.0 mm were detected with a sensitivity, specificity, and AUC of 75%–87%, 54%–87%, and 0.76%–0.90%, respectively. However, different microcalcification shapes were indistinguishable. Conclusions: The new method is promising for detecting relatively large microcalcifications (i.e., 0.6–0.9 mm) within the breast at 7 T in reasonable times. Detection of smaller deposits at high field may be possible with higher spatial resolution, but such images require relatively long scan times. Although mammography can detect and distinguish the shape of smaller microcalcifications with superior sensitivity and specificity, this alternative method does not expose tissue to ionizing radiation, is not affected by breast density, and can be combined with other MRI methods (e.g., dynamic contrast-enhanced MRI and diffusion weighted MRI), to potentially improve diagnostic performance. PMID:25735297

Detection of microcalcifications by characteristic magnetic susceptibility effects using MR phase image cross-correlation analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baheza, Richard A.; Welch, E. Brian; Gochberg, Daniel F.

Purpose: To develop and evaluate a new method for detecting calcium deposits using their characteristic magnetic susceptibility effects on magnetic resonance (MR) images at high fields and demonstrate its potential in practice for detecting breast microcalcifications. Methods: Characteristic dipole signatures of calcium deposits were detected in magnetic resonance phase images by computing the cross-correlation between the acquired data and a library of templates containing simulated phase patterns of spherical deposits. The influence of signal-to-noise ratio and various other MR parameters on the results were assessed using simulations and validated experimentally. The method was tested experimentally for detection of calcium fragmentsmore » within gel phantoms and calcium-like inhomogeneities within chicken tissue at 7 T with optimized MR acquisition parameters. The method was also evaluated for detection of simulated microcalcifications, modeled from biopsy samples of malignant breast cancer, inserted in silico into breast magnetic resonance imaging (MRIs) of healthy subjects at 7 T. For both assessments of calcium fragments in phantoms and biopsy-based simulated microcalcifications in breast MRIs, receiver operator characteristic curve analyses were performed to determine the cross-correlation index cutoff, for achieving optimal sensitivity and specificity, and the area under the curve (AUC), for measuring the method’s performance. Results: The method detected calcium fragments with sizes of 0.14–0.79 mm, 1 mm calcium-like deposits, and simulated microcalcifications with sizes of 0.4–1.0 mm in images with voxel sizes between (0.2 mm){sup 3} and (0.6 mm){sup 3}. In images acquired at 7 T with voxel sizes of (0.2 mm){sup 3}–(0.4 mm){sup 3}, calcium fragments (size 0.3–0.4 mm) were detected with a sensitivity, specificity, and AUC of 78%–90%, 51%–68%, and 0.77%–0.88%, respectively. In images acquired with a human 7 T scanner, acquisition times below 12 min, and voxel sizes of (0.4 mm){sup 3}–(0.6 mm){sup 3}, simulated microcalcifications with sizes of 0.6–1.0 mm were detected with a sensitivity, specificity, and AUC of 75%–87%, 54%–87%, and 0.76%–0.90%, respectively. However, different microcalcification shapes were indistinguishable. Conclusions: The new method is promising for detecting relatively large microcalcifications (i.e., 0.6–0.9 mm) within the breast at 7 T in reasonable times. Detection of smaller deposits at high field may be possible with higher spatial resolution, but such images require relatively long scan times. Although mammography can detect and distinguish the shape of smaller microcalcifications with superior sensitivity and specificity, this alternative method does not expose tissue to ionizing radiation, is not affected by breast density, and can be combined with other MRI methods (e.g., dynamic contrast-enhanced MRI and diffusion weighted MRI), to potentially improve diagnostic performance.« less

Experimental and molecular dynamics studies showed that CBP KIX mutation affects the stability of CBP:c-Myb complex.

PubMed

Odoux, Anne; Jindal, Darren; Tamas, Tamara C; Lim, Benjamin W H; Pollard, Drake; Xu, Wu

2016-06-01

The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright's group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen bonds of the E665:R294 pair exhibited a fast decreasing trend over time during MD simulations. In addition, our data showed that the KIX mutations attenuate CBP's hydrophobic interaction with Leu302 of c-Myb. Furthermore, our 500-ns MD simulations showed that CBP KIX with the mutations has a slightly lower potential energy than wild-type CBP. The CBP KIX structures with or without its interacting protein c-Myb are different for both wild-type and mutant CBP KIX, and this is likewise the case for c-Myb with or without CBP, suggesting that the presence of an interacting protein influences the structure of a protein. Taken together, these analyses will improve our understanding of the exact functions of CBP and its interaction with c-Myb. Published by Elsevier Ltd.

A satellite rainfall retrieval technique over northern Algeria based on the probability of rainfall intensities classification from MSG-SEVIRI

NASA Astrophysics Data System (ADS)

Lazri, Mourad; Ameur, Soltane

2016-09-01

In this paper, an algorithm based on the probability of rainfall intensities classification for rainfall estimation from Meteosat Second Generation/Spinning Enhanced Visible and Infrared Imager (MSG-SEVIRI) has been developed. The classification scheme uses various spectral parameters of SEVIRI that provide information about cloud top temperature and optical and microphysical cloud properties. The presented method is developed and trained for the north of Algeria. The calibration of the method is carried out using as a reference rain classification fields derived from radar for rainy season from November 2006 to March 2007. Rainfall rates are assigned to rain areas previously identified and classified according to the precipitation formation processes. The comparisons between satellite-derived precipitation estimates and validation data show that the developed scheme performs reasonably well. Indeed, the correlation coefficient presents a significant level (r:0.87). The values of POD, POFD and FAR are 80%, 13% and 25%, respectively. Also, for a rainfall estimation of about 614 mm, the RMSD, Bias, MAD and PD indicate 102.06(mm), 2.18(mm), 68.07(mm) and 12.58, respectively.

Performance of 7-cells Dye Sensitized Solar Module in Z-type Series Interconnection

NASA Astrophysics Data System (ADS)

Nur Anggraini, Putri; Muliani, Lia; Maulani Nursam, Natalita; Hidayat, Jojo

2018-01-01

Dye sensitized solar cells (DSSC) is becoming attractive research topic as third generation solar cells technology since it provides clean energy and low cost fabrication. In this study, DSSC was fabricated into module scale, which is important for practical applications. The module was prepared in sandwich structure consisting of TiO2 working electrode and Pt counter electrode on conductive substrate with an area of 100 mm x 100 mm, which was distributed into seven active cells. TiO2 paste was deposited on FTO glass as working electrode with a size of 10 mm x 98 mm per unit cell by screen printing method. Each cell was connected in Z-type series that able to produce high voltage. I - V measurement was applied in two methods consisting of laboratory testing using sun simulator under 500 W/m2 of illumination and outdoor testing using a digital multimeter under direct sunlight. The result shows that DSSC module has photoconversion efficiency of 1.08% and 1.17% for laboratory and outdoor testing, respectively. The module was also tested in three different times to monitor its stability performance.

Top-seeded solution growth and morphology change of RbTiOPO4:Ta single crystal

NASA Astrophysics Data System (ADS)

Li, Ziqing; Chen, Yang; Zhu, Pengfei; Ji, Nianjing; Duan, Xiulan; Jiang, Huaidong

2018-04-01

The RbTiOPO4:Ta single crystal with dimensions of 4 mm × 31 mm × 18 mm was successfully grown by Top Seeded Solution Growth Technique. It is concluded that the doping Ta element can strongly influence the growth and morphology of the RbTiOPO4 crystal. The evident morphology change of RbTiOPO4:Ta crystal with respect to RbTiOPO4 crystal has been observed and the (1 0 0) crystal face was more developed than any other crystal faces. The possible reasons of the morphology change were analyzed through experimental and theoretical methods. Several methods were tried to increase crystallographic a direction dimension of RbTiOPO4:Ta crystals. Finally, the RbTiOPO4:Ta single crystal with crystallographic a direction dimension up to 6 mm was obtained by using thicker seed crystal. This way makes it possible to get isometric RbTiOPO4:Ta crystals, which is beneficial for nonlinear optical applications due to larger area in x-y plane.

Risk factors for worsened muscle strength after the surgical treatment of arteriovenous malformations of the eloquent motor area.

PubMed

Lin, Fuxin; Zhao, Bing; Wu, Jun; Wang, Lijun; Jin, Zhen; Cao, Yong; Wang, Shuo

2016-08-01

OBJECT Case selection for the surgical treatment of arteriovenous malformations (AVMs) of the eloquent motor area remains challenging. The aim of this study was to determine the risk factors for worsened muscle strength after surgery in patients with this disorder. METHODS At their hospital the authors retrospectively studied 48 consecutive patients with AVMs involving motor cortex and/or the descending pathway. All patients had undergone preoperative functional MRI (fMRI) and diffusion tensor imaging (DTI), followed by resection. Both functional and angioarchitectural factors were analyzed with respect to the change in muscle strength. Functional factors included lesion-to-corticospinal tract distance (LCD) on DTI and lesion-to-activation area distance (LAD) and cortical reorganization on fMRI. Based on preoperative muscle strength, the changes in muscle strength at 1 week and 6 months after surgery were defined as short-term and long-term surgical outcomes, respectively. Statistical analysis was performed using the statistical package SPSS (version 20.0.0, IBM Corp.). RESULTS Twenty-one patients (43.8%) had worsened muscle strength 1 week after surgery. However, only 10 patients (20.8%) suffered from muscle strength worsening 6 months after surgery. The LCD was significantly correlated with short-term (p < 0.001) and long-term (p < 0.001) surgical outcomes. For long-term outcomes, patients in the 5 mm ≥ LCD > 0 mm (p = 0.009) and LCD > 5 mm (p < 0.001) categories were significantly associated with a lower risk of permanent motor worsening in comparison with patients in the LCD = 0 mm group. No significant difference was found between patients in the 5 mm ≥ LCD > 0 mm group and LCD > 5 mm group (p = 0.116). Nidus size was the other significant predictor of short-term (p = 0.021) and long-term (p = 0.016) outcomes. For long-term outcomes, the area under the ROC curve (AUC) was 0.728, and the cutoff point was 3.6 cm. Spetzler-Martin grade was not associated with short-term surgical outcomes (0.143), although it was correlated with long-term outcomes (0.038). CONCLUSIONS An AVM with a nidus in contact with tracked eloquent fibers (LCD = 0) and having a large size is more likely to be associated with worsened muscle strength after surgery in patients with eloquent motor area AVMs. Surgical treatment in these patients should be carefully considered. In patients with an LCD > 5 mm, radical resection may be considered to eliminate the risk of hemorrhage.

Trautmann's triangle anatomy with application to posterior transpetrosal and other related skull base procedures.

PubMed

Tubbs, R Shane; Griessenauer, Christoph; Loukas, Marios; Ansari, Shaheryar F; Fritsch, Michael H; Cohen-Gadol, Aaron A

2014-10-01

Trautmann's triangle (TT) faces the cerebellopontine angle and is exposed during posterior transpetrosal approaches. However, reports on the morphometric analysis of this structure are lacking in the literature. The goal was to better understand this important operative corridor. TT was exposed from an external approach (transmastoid) in ten cadavers (20 sides) and from an internal approach on 20 dry adult temporal bones. Measurements included calculation of the area of TT and the distance of the endolymphatic sac from the anterior border of the sigmoid sinus. The area range of TT was 45-210 mm(2) (mean 151 mm(2); SD 37 mm(2)). Three types of triangles were identified based on area. Type I triangles had areas less than 75 mm(2), Type II areas were 75-149 mm(2), and Type III areas were 150 mm(2) and greater. These types were observed in 37.5%, 35%, and 27.5% of sides, respectively. The distance from the jugular bulb's anterior border to the posterior border of the posterior semicircular canal ranged from 6 to 11 mm (mean 8.5 mm). The endolymphatic sac was located in the inferior portion of TT and traveled anterior to the sigmoid sinus. The horizontal distance from the anterior edge of the sigmoid sinus to the posterior edge of the endolymphatic sac ranged from 0 to 13.5 mm (mean 9 mm). Additional anatomic knowledge regarding TT may improve neurosurgical procedures in this region by avoiding intrusion into the endolymphatic sac and sigmoid sinus. © 2014 Wiley Periodicals, Inc.

Potential Bone to Implant Contact Area of Short Versus Standard Implants: An In Vitro Micro-Computed Tomography Analysis.

PubMed

Quaranta, Alessandro; DʼIsidoro, Orlando; Bambini, Fabrizio; Putignano, Angelo

2016-02-01

To compare the available potential bone-implant contact (PBIC) area of standard and short dental implants by micro-computed tomography (μCT) assessment. Three short implants with different diameters (4.5 × 6 mm, 4.1 × 7 mm, and 4.1 × 6 mm) and 2 standard implants (3.5 × 10 mm and 3.3 × 9 mm) with diverse design and surface features were scanned with μCT. Cross-sectional images were obtained. Image data were manually processed to find the plane that corresponds to the most coronal contact point between the crestal bone and implant. The available PBIC was calculated for each sample. Later on, the cross-sectional slices were processed by a 3-dimensional (3D) software, and 3D images of each sample were used for descriptive analysis and display the microtopography and macrotopography. The wide-diameter short implant (4.5 × 6 mm) showed the higher PBIC (210.89 mm) value followed by the standard (178.07 mm and 185.37 mm) and short implants (130.70 mm and 110.70 mm). Wide-diameter short implants show a surface area comparable with standard implants. Micro-CT analysis is a promising technique to evaluate surface area in dental implants with different macrodesign, microdesign, and surface features.

Change in area of geographic atrophy in the Age-Related Eye Disease Study: AREDS report number 26.

PubMed

Lindblad, Anne S; Lloyd, Patricia C; Clemons, Traci E; Gensler, Gary R; Ferris, Frederick L; Klein, Michael L; Armstrong, Jane R

2009-09-01

To characterize progression of geographic atrophy (GA) associated with age-related macular degeneration in AREDS as measured by digitized fundus photographs. Fundus photographs from 181 of 4757 AREDS participants with a GA area of at least 0.5 disc areas at baseline or from participants who developed bilateral GA during follow-up were scanned, digitized, and evaluated longitudinally. Geographic atrophy area was determined using planimetry. Rates of progression from noncentral to central GA and of vision loss following development of central GA included the entire AREDS cohort. Median initial lesion size was 4.3 mm(2). Average change in digital area of GA from baseline was 2.03 mm(2) (standard error of the mean, 0.24 mm(2)) at 1 year, 3.78 mm(2) (0.24 mm(2)) at 2 years, 5.93 mm(2) (0.34 mm(2)) at 3 years, and 1.78 mm(2) (0.086 mm(2)) per year overall. Median time to developing central GA after any GA diagnosis was 2.5 years (95% confidence interval, 2.0-3.0). Average visual acuity decreased by 3.7 letters at first documentation of central GA, and by 22 letters at year 5. Growth of GA area can be reliably measured using standard fundus photographs that are digitized and subsequently graded at a reading center. Development of GA is associated with subsequent further growth of GA, development of central GA, and loss in central vision.

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies.

PubMed

Genheden, Samuel; Ryde, Ulf

2011-11-08

We have evaluated the efficiency of two popular end-point methods to calculate ligand-binding free energies, LIE (linear interaction energy) and MM/GBSA (molecular mechanics with generalized Born surface-area solvation), i.e. the computational effort needed to obtain estimates of a similar precision. As a test case, we use the binding of seven biotin analogues to avidin. The energy terms used by MM/GBSA and LIE exhibit a similar correlation time (∼5 ps), and the equilibration time seems also to be similar, although it varies much between the various ligands. The results show that the LIE method is more effective than MM/GBSA, by a factor of 2-7 for a truncated spherical system with a radius of 26 Å and by a factor of 1.0-2.4 for the full avidin tetramer (radius 47 Å). The reason for this is the cost for the MM/GBSA entropy calculations, which more than compensates for the extra simulation of the free ligand in LIE. On the other hand, LIE requires that the protein is neutralized, whereas MM/GBSA has no such requirements. Our results indicate that both the truncation and neutralization of the proteins may slow the convergence and emphasize small differences in the calculations, e.g., differences between the four subunits in avidin. Moreover, LIE cannot take advantage of the fact that avidin is a tetramer. For this test case, LIE gives poor results with the standard parametrization, but after optimizing the scaling factor of the van der Waals terms, reasonable binding affinities can be obtained, although MM/GBSA still gives a significantly better predictive index and correlation to the experimental affinities.

Effect of soldering techniques and gap distance on tensile strength of soldered Ni-Cr alloy joint

PubMed Central

Lee, Sang-Yeob

2010-01-01

PURPOSE The present study was intended to evaluate the effect of soldering techniques with infrared ray and gas torch under different gap distances (0.3 mm and 0.5 mm) on the tensile strength and surface porosity formation in Ni-Cr base metal alloy. MATERIALS AND METHODS Thirty five dumbbell shaped Ni-Cr alloy specimens were prepared and assigned to 5 groups according to the soldering method and the gap distance. For the soldering methods, gas torch (G group) and infrared ray (IR group) were compared and each group was subdivided by corresponding gap distance (0.3 mm: G3 and IR3, 0.5 mm: G5, IR5). Specimens of the experimental groups were sectioned in the middle with a diamond disk and embedded in solder blocks according to the predetermined distance. As a control group, 7 specimens were prepared without sectioning or soldering. After the soldering procedure, a tensile strength test was performed using universal testing machine at a crosshead speed 1 mm/min. The proportions of porosity on the fractured surface were calculated on the images acquired through the scanning electronic microscope. RESULTS Every specimen of G3, G5, IR3 and IR5 was fractured on the solder joint area. However, there was no significant difference between the test groups (P > .05). There was a negative correlation between porosity formation and tensile strength in all the specimens in the test groups (P < .05). CONCLUSION There was no significant difference in ultimate tensile strength of joints and porosity formations between the gas-oxygen torch soldering and infrared ray soldering technique or between the gap distance of 0.3 mm and 0.5 mm. PMID:21264189

Design and simulation of a novel method for determining depth-of-interaction in a PET scintillation crystal array using a single-ended readout by a multi-anode PMT

NASA Astrophysics Data System (ADS)

Ito, Mikiko; Lee, Jae Sung; Park, Min-Jae; Sim, Kwang-Souk; Jong Hong, Seong

2010-07-01

PET detectors with depth-of-interaction (DOI) encoding capability allow high spatial resolution and high sensitivity to be achieved simultaneously. To obtain DOI information from a mono-layer array of scintillation crystals using a single-ended readout, the authors devised a method based on light spreading within a crystal array and performed Monte Carlo simulations with individual scintillation photon tracking to prove the concept. A scintillation crystal array model was constructed using a grid method. Conventional grids are constructed using comb-shaped reflector strips with rectangular teeth to isolate scintillation crystals optically. However, the authors propose the use of triangularly shaped teeth, such that scintillation photons spread only in the x-direction in the upper halves of crystals and in the y-direction in lower halves. DOI positions can be estimated by considering the extent of two-dimensional light dispersion, which can be determined from the multiple anode outputs of a position-sensitive PMT placed under the crystal array. In the main simulation, a crystal block consisting of a 29 × 29 array of 1.5 mm × 1.5 mm × 20 mm crystals and a multi-anode PMT with 16 × 16 pixels were used. The effects of crystal size and non-uniform PMT output gain were also explored by simulation. The DOI resolution estimated for 1.5 × 1.5 × 20 mm3 crystals was 2.16 mm on average. Although the flood map was depth dependent, each crystal was well identified at all depths when a corner of the crystal array was irradiated with 511 keV gamma rays (peak-to-valley ratio ~9:1). DOI resolution was better than 3 mm up to a crystal length of 28 mm with a 1.5 × 1.5 mm2 or 2.0 × 2.0 mm2 crystal surface area. The devised light-sharing method allowed excellent DOI resolutions to be obtained without the use of dual-ended readout or multiple crystal arrays.

SU-F-T-408: On the Determination of Equivalent Squares for Rectangular Small MV Photon Fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sauer, OA; Wegener, S; Exner, F

Purpose: It is common practice to tabulate dosimetric data like output factors, scatter factors and detector signal correction factors for a set of square fields. In order to get the data for an arbitrary field, it is mapped to an equivalent square, having the same scatter as the field of interest. For rectangular fields both, tabulated data and empiric formula exist. We tested the applicability of such rules for very small fields. Methods: Using the Monte-Carlo method (EGSnrc-doseRZ), the dose to a point in 10cm depth in water was calculated for cylindrical impinging fluence distributions. Radii were from 0.5mm tomore » 11.5mm with 1mm thickness of the rings. Different photon energies were investigated. With these data a matrix was constructed assigning the amount of dose to the field center to each matrix element. By summing up the elements belonging to a certain field, the dose for an arbitrary point in 10cm depth could be determined. This was done for rectangles up to 21mm side length. Comparing the dose to square field results, equivalent squares could be assigned. The results were compared to using the geometrical mean and the 4Xperimeter/area rule. Results: For side length differences less than 2mm, the difference between all methods was in general less than 0.2mm. For more elongated fields, relevant differences of more than 1mm and up to 3mm for the fields investigated occurred. The mean square side length calculated from both empiric formulas fitted much better, deviating hardly more than 1mm and for the very elongated fields only. Conclusion: For small rectangular photon fields, deviating only moderately from square both investigated empiric methods are sufficiently accurate. As the deviations often differ regarding their sign, using the mean improves the accuracy and the useable elongation range. For ratios larger than 2, Monte-Carlo generated data are recommended. SW is funded by Deutsche Forschungsgemeinschaft (SA481/10-1)« less

Full-field ultrasonic inspection for a composite sandwich plate skin-core debonding detection using laser-based ultrasonics

NASA Astrophysics Data System (ADS)

Chong, See Yenn; Victor, Jared J.; Todd, Michael D.

2017-04-01

In this paper, a full-field ultrasonic guided wave method is proposed to inspect a composite sandwich specimen made for an aircraft engine nacelle. The back skin/core interface of the specimen is built with two fabricated disbond defects (diameters of 12.7 mm and 25.4 mm) by removing areas of the adhesive used to bond the back skin to the core. A laser ultrasonic interrogation system (LUIS) incorporated with a disbond detection algorithm is developed. The system consists of a 1-kHz laser ultrasonic scanning system and a single fixed ultrasonic sensor to interrogate ultrasonic guided waves in the sandwich specimen. The interest area of 400 mm × 400 mm is scanned at a 0.5 mm scan interval. The corresponding full-field ultrasonic data is obtained and generated in the three-dimensional (3-D) space-time domain. Then, the 3-D full-field ultrasonic data is Fourier transformed and the ultrasonic frequency spectra are analyzed to determine the dominant frequency that is sensitive to the disbond defects. Continuous wavelet transform (CWT) based on fast Fourier transform (FFT) is implemented as a single-frequency bandpass filter to filter the full-field ultrasonic data in the 3-D space-time domain at the selected dominant frequency. The LUIS has shown the ability to detect the disbond with diameters of 11 mm and 23 mm which match to the pre-determined disbond sizes well. For future research, a robust signal processing algorithm and a model-based matched filter will be investigated to make the detection process autonomous and improve detectability

Groundwater recharge in irrigated semi-arid areas: quantitative hydrological modelling and sensitivity analysis

NASA Astrophysics Data System (ADS)

Jiménez-Martínez, Joaquín; Candela, Lucila; Molinero, Jorge; Tamoh, Karim

2010-12-01

For semi-arid regions, methods of assessing aquifer recharge usually consider the potential evapotranspiration. Actual evapotranspiration rates can be below potential rates for long periods of time, even in irrigated systems. Accurate estimations of aquifer recharge in semi-arid areas under irrigated agriculture are essential for sustainable water-resources management. A method to estimate aquifer recharge from irrigated farmland has been tested. The water-balance-modelling approach was based on VisualBALAN v. 2.0, a computer code that simulates water balance in the soil, vadose zone and aquifer. The study was carried out in the Campo de Cartagena (SE Spain) in the period 1999-2008 for three different groups of crops: annual row crops (lettuce and melon), perennial vegetables (artichoke) and fruit trees (citrus). Computed mean-annual-recharge values (from irrigation+precipitation) during the study period were 397 mm for annual row crops, 201 mm for perennial vegetables and 194 mm for fruit trees: 31.4, 20.7 and 20.5% of the total applied water, respectively. The effects of rainfall events on the final recharge were clearly observed, due to the continuously high water content in soil which facilitated the infiltration process. A sensitivity analysis to assess the reliability and uncertainty of recharge estimations was carried out.

[Evaluation of antihypertensive therapy by ambulatory blood pressure monitoring and establishment of the level of antihypertensive goal on the circadian rhythm of blood pressure].

PubMed

Fujioka, T; Tamaki, S; Fudo, T; Nakae, I; Sugawara, A; Kambara, H

1990-01-01

We have developed a new method for the evaluation of antihypertensive therapy on the circadian rhythm of blood pressure and attempted to determine the indications for antihypertensive therapy and the level of antihypertensive goal. Blood pressures were measured for 24 hours by the use of ambulatory blood pressure monitoring using 630 (ABPM-630) in 50 normotensives, 50 untreated hypertensives and 50 hypertensives undertreatment with various antihypertensive drugs (110 males and 40 females, with a mean age of 53.4 +/- 13.3 yrs). Blood pressure profiles were prepared for determination of the hyperbaric and hypobaric indexes. According to the WHO's definitions for blood pressure, the hyperbaric index was defined as the area above 140 mmHg in systolic blood pressure or 90 mmHg in diastolic blood pressure, and the hypobaric index, as the area below 100 mmHg or 60 mmHg, respectively. The criteria of the hypobaric index was obtained from the mean basal blood pressure (the lowest blood pressure during sleep) of the 50 normotensives. The mean hyperbaric index of the 50 normotensives was 20.4 +/- 40.2/5.5 +/- 15.3 (systole/diastole) mmHg.hour/day and the mean hypobaric index, 12.2 +/- 22.5/9.0 +/- 24.0 mmHg.hour/day. The 50 untreated hypertensives showed a mean hyperbaric index of 281.8 +/- 197.0/156.0 +/- 126.1 mmHg.hour/day and a mean hypobaric index of 0.1 +/- 0.6/0.3 +/- 1.5 mmHg.hour/day. Comparison of the indexes before and after treatment with various antihypertensives showed that a decrease in the hyperbaric index without an increase in the hypobaric index was the most optimal reduction of blood pressure.(ABSTRACT TRUNCATED AT 250 WORDS)

Three-dimensional optimization and sensitivity analysis of dental implant thread parameters using finite element analysis.

PubMed

Geramizadeh, Maryam; Katoozian, Hamidreza; Amid, Reza; Kadkhodazadeh, Mahdi

2018-04-01

This study aimed to optimize the thread depth and pitch of a recently designed dental implant to provide uniform stress distribution by means of a response surface optimization method available in finite element (FE) software. The sensitivity of simulation to different mechanical parameters was also evaluated. A three-dimensional model of a tapered dental implant with micro-threads in the upper area and V-shaped threads in the rest of the body was modeled and analyzed using finite element analysis (FEA). An axial load of 100 N was applied to the top of the implants. The model was optimized for thread depth and pitch to determine the optimal stress distribution. In this analysis, micro-threads had 0.25 to 0.3 mm depth and 0.27 to 0.33 mm pitch, and V-shaped threads had 0.405 to 0.495 mm depth and 0.66 to 0.8 mm pitch. The optimized depth and pitch were 0.307 and 0.286 mm for micro-threads and 0.405 and 0.808 mm for V-shaped threads, respectively. In this design, the most effective parameters on stress distribution were the depth and pitch of the micro-threads based on sensitivity analysis results. Based on the results of this study, the optimal implant design has micro-threads with 0.307 and 0.286 mm depth and pitch, respectively, in the upper area and V-shaped threads with 0.405 and 0.808 mm depth and pitch in the rest of the body. These results indicate that micro-thread parameters have a greater effect on stress and strain values.

The Effect of Annealing on the Elastic Modulus of Orthodontic Wires

NASA Astrophysics Data System (ADS)

Higginbottom, Kyle

Introduction: Nickel Titanium orthodontic wires are currently used in orthodontic treatment due to their heat activated properties and their delivery of constant force. The objective of this study was to determine the effect of annealing on the elastic modulus of Nickel Titanium, Stainless Steel and Beta-titanium (TMA) wires. Different points along the wire were tested in order to determine how far from the annealed ends the elastic modulus of the wires was affected. Methods: Eighty (80) orthodontic wires consisting of 4 equal groups (SS/TMA/Classic NitinolRTM/Super Elastic NitinolRTM) were used as the specimens for this study. All wires were measured and marked at 5mm measurements, and cut into 33.00mm sections. The wires were heated with a butane torch until the first 13.00mm of the wires were red hot. Load deflection tests using an InstronRTM universal testing machine were run at 5mm distances from the end of the wire that had been annealed. The change in elastic modulus was then determined. Results: There was a significant difference (F = 533.001, p = 0.0005) in the change in elastic modulus for the four distances. There was also a significant difference (F = 57.571, p = 0.0005) in the change in elastic modulus for the four wire types. There was a significant interaction (F = 19.601, p = 0.005) between wire type and distance, however this interaction negated the differences between the wires. Conclusion: 1) There are significant differences in the changes in elastic modulus between the areas of the wires within the annealed section and those areas 5mm and 10mm away from the annealed section. The change in elastic modulus within the annealed section was significantly greater at 8 mm than it was at 13mm, and this was significantly greater than 18mm and 23mm (5mm and 10mm beyond the annealed section). However, there was no statistical difference in the change in elastic modulus between 5mm and 10mm away from the annealed section (18mm and 23mm respectively). 2) Regardless of the wire type, no clinically important effects were seen 5mm and 10mm beyond the annealed portion.

Quantification of the internal resistance distribution of microbial fuel cells.

PubMed

Fan, Yanzhen; Sharbrough, Evan; Liu, Hong

2008-11-01

Identifying the limiting factors in a microbial fuel cell (MFC) system requires qualifying the contribution of each component of an MFC to internal resistance. In this study, a new method was developed to calculate the internal resistance distribution of an MFC. Experiments were conducted to identify the limiting factors in single-chamber MFCs by varying the anode surface areas, cathode surface areas, and phosphate buffer concentrations. For the MFCs with equally sized electrodes (7 cm2) and 200 mM phosphate buffer, the anode contributed just 5.4% of the internal resistance, while the cathode and the electrolyte each contributed 47.3%, indicating that the anode was not the limiting factor in power generation. The limitation of the cathode was further revealed by the 780% higher area-specific resistance (284.4 omega cm2) than the 32.3 omega cm2 of the anode. The electrolyte limitation was also evidenced by the greatly increased contribution of electrolyte in internal resistance from 47.3 to 78.2% when the concentration of phosphate buffer was decreased from 200 to 50 mM. An anodic power density of 6860 mW/m2 was achieved at a current density of 2.62 mA/cm2 using the MFCs with an anode/cathode area ratio of 1/14 and 200 mM phosphate buffer. The method was also successfully applied to analyze the internal resistance distribution of the two chamber MFCs from a previously reported study. The comparison of the internal resistances of the two air cathode systems indicates that the much lower resistances, including anode, cathode, and membrane resistances, contributed to the much better performance of the single-chamber MFCs than the two-chamber system.

The water balance components of Mediterranean pine trees on a steep mountain slope during two hydrologically contrasting years

NASA Astrophysics Data System (ADS)

Eliades, Marinos; Bruggeman, Adriana; Lubczynski, Maciek W.; Christou, Andreas; Camera, Corrado; Djuma, Hakan

2018-07-01

Pines in semi-arid mountain environments manage to survive and thrive despite the limited soil water, due to shallow soil depths, and overall water scarcity. This study aims to develop a method for computing soil evaporation, bedrock water uptake and transpiration from a natural, open forest, based on sap flow (Heat Ratio Method), soil moisture and meteorological observations. The water balance of individual trees was conceptualized with a geometric approach, using canopy projected areas and Voronoi (Thiesen) polygons. The canopy approach assumes that the tree's root area extent is equal to its canopy projected area, while the Voronoi approach assumes that the tree roots exploit the open area that is closer to the tree than to any other tree. The methodology was applied in an open Pinus brutia forest (68% canopy cover) in Cyprus, characterized by steep slopes and fractured bedrock, during two hydrologically contrasting years (2015 wet, 2016 dry). Sap flow sensors, soil moisture sensors, throughfall and stemflow gauges were installed on and around eight trees. Rainfall was 507 mm in 2015 and 359 mm in 2016. According to the canopy approach, the sum of tree transpiration and soil evaporation exceeded the throughfall in both years, which implies that the trees' bedrock water uptake exceeds the surface runoff and drainage losses. This indicated that trees extend their roots beyond the canopy-projected areas and the use of the Voronoi polygons captures this effect. According to the stand scale water balance, average throughfall during the two years was 81% of the rainfall. Transpiration was 61% of the rainfall in 2015, but only 32% in 2016. On the contrary, the soil evaporation fraction increased from 26% in 2015 to 35% in the dry year of 2016. The contribution of bedrock water to tree transpiration was 77% of rainfall in 2015 and 66% in 2016. During the summer months, trees relied 100% on the uptake of water from the fractured bedrock to cover their transpiration needs. Average monthly transpiration areas ranged between 0.1 mm d-1 in October 2016 and 1.7 mm d-1 in April 2015. This study shows that bedrock uptake could be an essential water balance component of semi-arid, mountainous pine forests and should be accounted for in hydrologic models.

Esophagogastric junction distensibility assessed using the functional lumen imaging probe

PubMed Central

Chen, Joan W; Rubenstein, Joel H

2017-01-01

AIM To assess reference values in the literature for esophageal distensibility and cross-sectional area in healthy and diseased subjects measured by the functional lumen imaging probe (FLIP). METHODS Systematic search and review of articles in Medline and Embase pertaining to the use of FLIP in the esophagus was conducted in accordance with the PRISMA guidelines. Cross-sectional area and distensibility at the esophagogastric junction (EGJ) were abstracted for normal subjects, achalasia, and gastroesophageal reflux disease (GERD) patients, stratified by balloon length and volume of inflation. RESULTS Six achalasia studies (n = 154), 3 GERD (n = 52), and 5 studies including healthy controls (n = 98) were included in the systematic review. Normative data varied widely amongst studies of healthy volunteers. In contrast, studies in achalasia patients uniformly demonstrated low point estimates in distensibility ≤ 1.6 mm2/mmHg prior to treatment that increased to ≥ 3.4 mm2/mmHg following treatment at 40mL bag volume. In GERD patients, distensibility fell to the range of untreated achalasia (≤ 2.85 mm2/mmHg) following fundoplication. CONCLUSION FLIP may be a useful tool in assessment of treatment efficacy in achalasia. The drastic drop in EGJ distensibility after fundoplication suggests that FLIP measurements need to be interpreted in the context of esophageal body motility and highlights the importance of pre-operative screening for dysmotility. Future studies using standardized FLIP protocol and balloon size are needed. PMID:28275309

Design and verification of the miniature optical system for small object surface profile fast scanning

NASA Astrophysics Data System (ADS)

Chi, Sheng; Lee, Shu-Sheng; Huang, Jen, Jen-Yu; Lai, Ti-Yu; Jan, Chia-Ming; Hu, Po-Chi

2016-04-01

As the progress of optical technologies, different commercial 3D surface contour scanners are on the market nowadays. Most of them are used for reconstructing the surface profile of mold or mechanical objects which are larger than 50 mm×50 mm× 50 mm, and the scanning system size is about 300 mm×300 mm×100 mm. There are seldom optical systems commercialized for surface profile fast scanning for small object size less than 10 mm×10 mm×10 mm. Therefore, a miniature optical system has been designed and developed in this research work for this purpose. Since the most used scanning method of such system is line scan technology, we have developed pseudo-phase shifting digital projection technology by adopting projecting fringes and phase reconstruction method. A projector was used to project a digital fringe patterns on the object, and the fringes intensity images of the reference plane and of the sample object were recorded by a CMOS camera. The phase difference between the plane and object can be calculated from the fringes images, and the surface profile of the object was reconstructed by using the phase differences. The traditional phase shifting method was accomplished by using PZT actuator or precisely controlled motor to adjust the light source or grating and this is one of the limitations for high speed scanning. Compared with the traditional optical setup, we utilized a micro projector to project the digital fringe patterns on the sample. This diminished the phase shifting processing time and the controlled phase differences between the shifted phases become more precise. Besides, the optical path design based on a portable device scanning system was used to minimize the size and reduce the number of the system components. A screwdriver section about 7mm×5mm×5mm has been scanned and its surface profile was successfully restored. The experimental results showed that the measurement area of our system can be smaller than 10mm×10mm, the precision reached to +/-10μm, and the scanning time for each surface of an object was less than 15 seconds. This has proved that our system own the potential to be a fast scanning scanner for small object surface profile scanning.

Characterization of highly multiplexed monolithic PET / gamma camera detector modules

NASA Astrophysics Data System (ADS)

Pierce, L. A.; Pedemonte, S.; DeWitt, D.; MacDonald, L.; Hunter, W. C. J.; Van Leemput, K.; Miyaoka, R.

2018-04-01

PET detectors use signal multiplexing to reduce the total number of electronics channels needed to cover a given area. Using measured thin-beam calibration data, we tested a principal component based multiplexing scheme for scintillation detectors. The highly-multiplexed detector signal is no longer amenable to standard calibration methodologies. In this study we report results of a prototype multiplexing circuit, and present a new method for calibrating the detector module with multiplexed data. A 50 × 50 × 10 mm3 LYSO scintillation crystal was affixed to a position-sensitive photomultiplier tube with 8 × 8 position-outputs and one channel that is the sum of the other 64. The 65-channel signal was multiplexed in a resistive circuit, with 65:5 or 65:7 multiplexing. A 0.9 mm beam of 511 keV photons was scanned across the face of the crystal in a 1.52 mm grid pattern in order to characterize the detector response. New methods are developed to reject scattered events and perform depth-estimation to characterize the detector response of the calibration data. Photon interaction position estimation of the testing data was performed using a Gaussian Maximum Likelihood estimator and the resolution and scatter-rejection capabilities of the detector were analyzed. We found that using a 7-channel multiplexing scheme (65:7 compression ratio) with 1.67 mm depth bins had the best performance with a beam-contour of 1.2 mm FWHM (from the 0.9 mm beam) near the center of the crystal and 1.9 mm FWHM near the edge of the crystal. The positioned events followed the expected Beer–Lambert depth distribution. The proposed calibration and positioning method exhibited a scattered photon rejection rate that was a 55% improvement over the summed signal energy-windowing method.

Maximal Aortic Valve Cusp Separation and Severity of Aortic Stenosis

PubMed Central

Dilu, VP; George, Raju

2017-01-01

Introduction An integrated approach that incorporates two dimensional, M mode and Doppler echocardiographic evaluation has become the standard means for accurate quantification of severity of valvular aortic stenosis. Maximal separation of the aortic valve cusps during systole has been shown to correlate well with the severity of aortic stenosis measured by other echocardiographic parameters. Aim To study the correlation between Maximal Aortic valve Cusp Separation (MACS) and severity of aortic valve stenosis and to find cut-off values of MACS for detecting severe and mild aortic stenosis. Materials and Methods In the present prospective observational study, we have compared the accuracy of MACS distance and the aortic valve area calculated by continuity equation in 59 patients with varying degrees of aortic valve stenosis. Aortic leaflet separation in M mode was identified as the distance between the inner edges of the tips of these structures at mid systole in the parasternal long axis view. Cuspal separation was also measured in 2D echocardiography from the parasternal long axis view and the average of the two values was taken as the MACS. Patients were grouped into mild, moderate and severe aortic stenosis based on the aortic valve area calculated by continuity equation. The resultant data regarding maximal leaflet separation on cross-sectional echocardiogram was then subjected to linear regression analysis in regard to correlation with the peak transvalvular aortic gradient as well as the calculated aortic valve area. A cut-off value for each group was derived using ROC curve. Results There was a strong correlation between MACS and aortic valve area measured by continuity equation and the peak and mean transvalvular aortic gradients. Mean MACS was 6.89 mm in severe aortic stenosis, 9.97 mm in moderate aortic stenosis and 12.36 mm in mild aortic stenosis. MACS below 8.25 mm reliably predicted severe aortic stenosis, with high sensitivity, specificity and positive predictive value. MACS above 11.25 mm practically ruled out significant aortic stenosis. Conclusion Measurement of MACS is a simple echocardio-graphic method to assess the severity of valvular aortic stenosis, with high sensitivity and specificity. MACS can be extremely useful in two clinical situations as a simple screening tool for assessment of stenosis severity and also helps in decision making non invasively when there is discordance between the other echocardiographic parameters of severity of aortic stenosis. PMID:28764221

Fast multigrid-based computation of the induced electric field for transcranial magnetic stimulation

NASA Astrophysics Data System (ADS)

Laakso, Ilkka; Hirata, Akimasa

2012-12-01

In transcranial magnetic stimulation (TMS), the distribution of the induced electric field, and the affected brain areas, depends on the position of the stimulation coil and the individual geometry of the head and brain. The distribution of the induced electric field in realistic anatomies can be modelled using computational methods. However, existing computational methods for accurately determining the induced electric field in realistic anatomical models have suffered from long computation times, typically in the range of tens of minutes or longer. This paper presents a matrix-free implementation of the finite-element method with a geometric multigrid method that can potentially reduce the computation time to several seconds or less even when using an ordinary computer. The performance of the method is studied by computing the induced electric field in two anatomically realistic models. An idealized two-loop coil is used as the stimulating coil. Multiple computational grid resolutions ranging from 2 to 0.25 mm are used. The results show that, for macroscopic modelling of the electric field in an anatomically realistic model, computational grid resolutions of 1 mm or 2 mm appear to provide good numerical accuracy compared to higher resolutions. The multigrid iteration typically converges in less than ten iterations independent of the grid resolution. Even without parallelization, each iteration takes about 1.0 s or 0.1 s for the 1 and 2 mm resolutions, respectively. This suggests that calculating the electric field with sufficient accuracy in real time is feasible.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

Development of time-resolved reflectance diffuse optical tomography for breast cancer monitoring

NASA Astrophysics Data System (ADS)

Yoshimoto, Kenji; Ohmae, Etsuko; Yamashita, Daisuke; Suzuki, Hiroaki; Homma, Shu; Mimura, Tetsuya; Wada, Hiroko; Suzuki, Toshihiko; Yoshizawa, Nobuko; Nasu, Hatsuko; Ogura, Hiroyuki; Sakahara, Harumi; Yamashita, Yutaka; Ueda, Yukio

2017-02-01

We developed a time-resolved reflectance diffuse optical tomography (RDOT) system to measure tumor responses to chemotherapy in breast cancer patients at the bedside. This system irradiates the breast with a three-wavelength pulsed laser (760, 800, and 830 nm) through a source fiber specified by an optical switch. The light collected by detector fibers is guided to a detector unit consisting of variable attenuators and photomultiplier tubes. Thirteen irradiation and 12 detection points were set to a measurement area of 50 × 50 mm for a hand-held probe. The data acquisition time required to obtain the temporal profiles within the measurement area is about 2 minutes. The RDOT system generates topographic and tomographic images of tissue properties such as hemoglobin concentration and tissue oxygen saturation using two imaging methods. Topographic images are obtained from the optical properties determined for each source-detector pair using a curve-fitting method based on the photon diffusion theory, while tomographic images are reconstructed using an iterative image reconstruction method. In an experiment using a tissue-like solid phantom, a tumor-like cylindrical target (15 mm diameter, 15 mm high) embedded in a breast tissue-like background medium was successfully reconstructed. Preliminary clinical measurements indicated that the tumor in a breast cancer patient was detected as a region of high hemoglobin concentration. In addition, the total hemoglobin concentration decreased during chemotherapy. These results demonstrate the potential of RDOT for evaluating the effectiveness of chemotherapy in patients with breast cancer.

Quantification of elemental area densities in multiple metal layers (Au/Ni/Cu) on a Cr-coated quartz glass substrate for certification of NMIJ CRM 5208-a.

PubMed

Ariga, Tomoko; Zhu, Yanbei; Ito, Mika; Takatsuka, Toshiko; Terauchi, Shinya; Kurokawa, Akira; Inagaki, Kazumi

2018-04-01

Area densities of Au/Ni/Cu layers on a Cr-coated quartz substrate were characterized to certify a multiple-metal-layer certified reference material (NMIJ CRM5208-a) that is intended for use in the analysis of the layer area density and the thickness by an X-ray fluorescence spectrometer. The area densities of Au/Ni/Cu layers were calculated from layer mass amounts and area. The layer mass amounts were determined by using wet chemical analyses, namely inductively coupled plasma mass spectrometry (ICP-MS), isotope-dilution (ID-) ICP-MS, and inductively coupled plasma optical emission spectrometry (ICP-OES) after dissolving the layers with diluted mixture of HCl and HNO 3 (1:1, v/v). Analytical results of the layer mass amounts obtained by the methods agreed well with each another within their uncertainty ranges. The area of the layer was determined by using a high-resolution optical scanner calibrated by Japan Calibration Service System (JCSS) standard scales. The property values of area density were 1.84 ± 0.05 μg/mm 2 for Au, 8.69 ± 0.17 μg/mm 2 for Ni, and 8.80 ± 0.14 μg/mm 2 for Cu (mean ± expanded uncertainty, coverage factor k = 2). In order to assess the reliability of these values, the density of each metal layer calculated from the property values of the area density and layer thickness measured by using a scanning electron microscope were compared with available literature values and good agreement between the observed values and values obtained in previous studies.

Relationship between ventral hernia defect area and intra-abdominal pressure: dynamic in vivo measurement.

PubMed

Qandeel, Haitham; O'Dwyer, Patrick J

2016-04-01

It is an acceptable concept that the ventral hernia defect area will increase with a rise in intra-abdominal pressure (IAP). The literature lacks the evidence about how much this increase is in vivo. The aim of this study was to objectively measure the change in the ventral hernia defect area with increasing intra-abdominal pressure. In a prospective study of laparoscopic ventral hernia repair, the area of hernia defect was measured from inside the abdomen using a sterile paper ruler. The horizontal (width) and vertical (length) measurements of the defect were taken at two pressure points: (IAP = 8 mmHg) and (IAP = 15 mmHg). The hernia defect area was calculated as an oval shape using a standard formula. Eighteen consecutive patients with a ventral hernia were included in this study (8 males: 10 females). Median age was 60 years (30-81), body mass index (BMI) was 29.9 (22.6-37.6). Changing the IAP significantly, (P < 0.001) changed the values of horizontal and vertical measurements, and the calculated area of the ventral hernia defect. The median calculated defect area, as an oval shape, was 5.6 cm(2) (Q1-Q3 = 3.5-15.5) and 6.9 cm(2) (Q1-Q3 = 4.5-18.7) at 8 and 15 mmHg IAP, respectively. The calculated area of mesh required to cover the defect with a 5 cm overlap increased by a median of 5% (Q1-Q3 = 3-6%). The change in defect area did not differ significantly between obese and non-obese patients (P = 0.5). Dynamic, rather than static, measurements of ventral hernia area during laparoscopy provide a simple way of in vivo objective measurement that helps the surgeon choose the appropriate area of mesh. When choosing mesh area, we support the trend toward a larger overlap of at least 5 cm if less precise methods of measuring defect area are been used.

Optimal area of lateral mass mini-screws implanted in plated cervical laminoplasty: a radiography anatomy study.

PubMed

Chen, Hua; Li, Huibo; Deng, Yuxiao; Rong, Xin; Gong, Quan; Li, Tao; Song, Yueming; Liu, Hao

2017-04-01

Lateral mass mini-screws used in plated cervical laminoplasty might penetrate into facet joints. The objective is to observe this complication incidence and to identify the optimal areas for 5- and 7-mm-long mini-screws to implant on lateral mass. 47 patients who underwent plated cervical laminoplasty were included. The optimal area for mini-screws implanting was set according to pre-operative 3D CT reconstruction data. Then, each posterior-lateral mass surface was divided into three regions: 7-mm region, 5-mm region, and dangerous area. The mini-screw implanted region was recorded. Post-operative CT images were used to identify whether the mini-screws penetrated into facet joints. 235 mini-plates and 470 lateral mass mini-screws were used in the study. 117 (24.9%) mini-screws penetrated 88 (37.4%) facet joints. The 5-mm-long mini-screw optimal area occupied the upper 72, 65, 65, 64, and 65 % area of the posterior-lateral mass surface for C3-7, while the 7-mm-long mini-screw optimal area encompassed the upper 54, 39, 40, 33, and 32 %. Only 7-mm-long mini-screws were used to fix the plate to the lateral mass. 4 of 240 mini-screws in 7-mm region, 67 of the 179 mini-screws in 5-mm region, and 46 of the 51 mini-screws in dangerous region penetrated into the facet joint. The differences in the rate of facet joint penetration related to region were statistically significant (P < 0.001). The facet joint destruction by mini-screws was not a rare complication in plated cervical laminoplasty. The optimal areas we proposed may help guide the mini-screw implantation positions.

Experimental Evaluation of the Heat Sink Effect in Hepatic Microwave Ablation

PubMed Central

Ringe, Kristina I.; Lutat, Carolin; Rieder, Christian; Schenk, Andrea; Wacker, Frank; Raatschen, Hans-Juergen

2015-01-01

Purpose To demonstrate and quantify the heat sink effect in hepatic microwave ablation (MWA) in a standardized ex vivo model, and to analyze the influence of vessel distance and blood flow on lesion volume and shape. Materials and Methods 108 ex vivo MWA procedures were performed in freshly harvested pig livers. Antennas were inserted parallel to non-perfused and perfused (700,1400 ml/min) glass tubes (diameter 5mm) at different distances (10, 15, 20mm). Ablation zones (radius, area) were analyzed and compared (Kruskal-Wallis Test, Dunn’s multiple comparison Test). Temperature changes adjacent to the tubes were measured throughout the ablation cycle. Results Maximum temperature decreased significantly with increasing flow and distance (p<0.05). Compared to non-perfused tubes, ablation zones were significantly deformed by perfused tubes within 15mm distance to the antenna (p<0.05). At a flow rate of 700ml/min ablation zone radius was reduced to 37.2% and 80.1% at 10 and 15mm tube distance, respectively; ablation zone area was reduced to 50.5% and 89.7%, respectively. Conclusion Significant changes of ablation zones were demonstrated in a pig liver model. Considerable heat sink effect was observed within a diameter of 15mm around simulated vessels, dependent on flow rate. This has to be taken into account when ablating liver lesions close to vessels. PMID:26222431

Comparison of the Tendon Damage Caused by Four Different Anchor Systems Used in Transtendon Rotator Cuff Repair

PubMed Central

Zhang, Qing-Song; Liu, Sen; Zhang, Qiuyang; Xue, Yun; Ge, Dongxia; O'Brien, Michael J.; Savoie, Felix H.; You, Zongbing

2012-01-01

Objectives. The objective of this study was to compare the damage to the rotator cuff tendons caused by four different anchor systems. Methods. 20 cadaveric human shoulder joints were used for transtendon insertion of four anchor systems. The Healix Peek, Fastin RC, Bio-Corkscrew Suture, and Healix Transtend anchors were inserted through the tendons using standard transtendon procedures. The areas of tendon damage were measured. Results. The areas of tendon damage (mean ± standard deviation, n = 7) were 29.1 ± 4.3 mm2 for the Healix Peek anchor, 20.4 ± 2.3 mm2 for the Fastin RC anchor, 23.4 ± 1.2 mm2 for the Bio-Corkscrew Suture anchor, 13.7 ± 3.2 mm2 for the Healix Transtend anchor inserted directly, and 9.1 ± 2.1 mm2 for the Healix Transtend anchor inserted through the Percannula system (P < 0.001 or P < 0.001, compared to other anchors). Conclusions. In a cadaver transtendon rotator cuff repair model, smaller anchors caused less damage to the tendon tissues. The Healix Transtend implant system caused the least damage to the tendon tissues. Our findings suggest that smaller anchors should be considered when performing transtendon procedures to repair partial rotator cuff tears. PMID:22811923

Three-dimensional quantitative analysis of adhesive remnants and enamel loss resulting from debonding orthodontic molar tubes

PubMed Central

2014-01-01

Aims Presenting a new method for direct, quantitative analysis of enamel surface. Measurement of adhesive remnants and enamel loss resulting from debonding molar tubes. Material and methods Buccal surfaces of fifteen extracted human molars were directly scanned with an optic blue-light 3D scanner to the nearest 2 μm. After 20 s etching molar tubes were bonded and after 24 h storing in 0.9% saline - debonded. Then 3D scanning was repeated. Superimposition and comparison were proceeded and shape alterations of the entire objects were analyzed using specialized computer software. Residual adhesive heights as well as enamel loss depths have been obtained for the entire buccal surfaces. Residual adhesive volume and enamel loss volume have been calculated for every tooth. Results The maximum height of adhesive remaining on enamel surface was 0.76 mm and the volume on particular teeth ranged from 0.047 mm3 to 4.16 mm3. The median adhesive remnant volume was 0.988 mm3. Mean depths of enamel loss for particular teeth ranged from 0.0076 mm to 0.0416 mm. Highest maximum depth of enamel loss was 0.207 mm. Median volume of enamel loss was 0.104 mm3 and maximum volume was 1.484 mm3. Conclusions Blue-light 3D scanning is able to provide direct precise scans of the enamel surface, which can be superimposed in order to calculate shape alterations. Debonding molar tubes leaves a certain amount of adhesive remnants on the enamel, however the interface fracture pattern varies for particular teeth and areas of enamel loss are present as well. PMID:25208969

Optical design and evaluation of a 4 mm cost-effective ultra-high-definition arthroscope.

PubMed

Cheng, Dewen; Wang, Yongtian; Yu, Lu; Liu, Xiaohua

2014-08-01

High definition and magnification rigid endoscope plays an important role in modern minimally invasive medical surgery and diagnosis. In this paper, we present the design and evaluation methods of a high definition rigid endoscope, specifically an arthroscope, with a large depth of field (DOF). The incident heights and exit angles of the sampled rays on the relay lens are controlled during the optimization process to ensure an effective field view (70°) and a normal ray path within the limited lens diameter of 2.7 mm. The lens is set up as a multi-configuration system with two extreme and one middle object distances to cover a large DOF. As a result, an entrance pupil of 0.3 mm is achieved for the first time, to bring the theoretical resolution to 23.1 lps/mm in the object space at a working distance of 20 mm, with the wavelength of 0.532 um. The modulation transfer function (MTF) curves approach diffraction limit, and the values are all higher than 0.3 at 160 line pairs/mm (lps/mm) in the image space. Meanwhile, stray light caused by total internal reflection on the inner wall of the rod lenses and the objective lens is eliminated. The measured resolution in the object space at a 20 mm working distance is 22.3 lps/mm, and test results show that other performance characteristics also fulfill design requirements. The relay lenses are designed with only one type of the spacer and two types of lenses to greatly reduce the fabrication and assembly cost. The design method has important research and application values for lens systems used in modern minimally invasive medical surgery and industrial non-destructive testing area.

Development of methods of producing large areas of silicon sheet by the slicing of silicon ingots using Inside Diameter (I.D.) saws

NASA Technical Reports Server (NTRS)

Aharonyan, P.

1980-01-01

Modifications to a 16 inch STC automated saw included: a programmable feed system; a crystal rotating system; and a STC dynatrack blade boring and control system. By controlling the plating operation and by grinding the cutting edge, 16 inch I.D. blades were produced with a cutting edge thickness of .22 mm. Crystal rotation mechanism was used to slice 100 mm diameter crystals with a 16 inch blade down to a thickness of .20 mm. Cutting rates with crystal rotation were generally slower than with standard plunge I.D. slicing techniques. Using programmed feeds and programmed rotation, maximum cutting rates were from 0.3 to 1.0 inches per minute.

Bayesian-based localization of wireless capsule endoscope using received signal strength.

PubMed

Nadimi, Esmaeil S; Blanes-Vidal, Victoria; Tarokh, Vahid; Johansen, Per Michael

2014-01-01

In wireless body area sensor networking (WBASN) applications such as gastrointestinal (GI) tract monitoring using wireless video capsule endoscopy (WCE), the performance of out-of-body wireless link propagating through different body media (i.e. blood, fat, muscle and bone) is still under investigation. Most of the localization algorithms are vulnerable to the variations of path-loss coefficient resulting in unreliable location estimation. In this paper, we propose a novel robust probabilistic Bayesian-based approach using received-signal-strength (RSS) measurements that accounts for Rayleigh fading, variable path-loss exponent and uncertainty in location information received from the neighboring nodes and anchors. The results of this study showed that the localization root mean square error of our Bayesian-based method was 1.6 mm which was very close to the optimum Cramer-Rao lower bound (CRLB) and significantly smaller than that of other existing localization approaches (i.e. classical MDS (64.2mm), dwMDS (32.2mm), MLE (36.3mm) and POCS (2.3mm)).

Crackle template based metallic mesh with highly homogeneous light transmission for high-performance transparent EMI shielding

PubMed Central

Han, Yu; Lin, Jie; Liu, Yuxuan; Fu, Hao; Ma, Yuan; Jin, Peng; Tan, Jiubin

2016-01-01

Our daily electromagnetic environment is becoming increasingly complex with the rapid development of consumer electronics and wireless communication technologies, which in turn necessitates the development of electromagnetic interference (EMI) shielding, especially for transparent components. We engineered a transparent EMI shielding film with crack-template based metallic mesh (CT-MM) that shows highly homogeneous light transmission and strong microwave shielding efficacy. The CT-MM film is fabricated using a cost-effective lift-off method based on a crackle template. It achieves a shielding effectiveness of ~26 dB, optical transmittance of ~91% and negligible impact on optical imaging performance. Moreover, high–quality CT-MM film is demonstrated on a large–calibre spherical surface. These excellent properties of CT-MM film, together with its advantages of facile large-area fabrication and scalability in processing on multi-shaped substrates, make CT-MM a powerful technology for transparent EMI shielding in practical applications. PMID:27151578

[Simultaneous determination of eleven components in Ginkgo biloba leaves by high performance liquid chromatography method].

PubMed

Lv, Jin-Li; Yang, Biao; Li, Meng-Xuan; Meng, Zhao-Qing; Ma, Shi-Ping; Wang, Zhen-Zhong; Ding, Gang; Huang, Wen-Zhe; Xiao, Wei

2017-03-01

To study Ginkgo biloba leaves in different producing area, we establish an HPLC method for the simultaneously determination of seven flavonoids glycosides and four biflavonoids in G. biloba leaves. The analysis was performed on an Agilent ZORBAX SB-C₁₈ column(4.6 mm×250 mm, 5 μm) wich acetonitrile, and 0.4% phosphoric acid as mobile phase at flow rate of 1 mL•min⁻¹ in a gradient edution, and the detection was carried out at 254 nm.The calibration curves of the seven flavonoids glycosides and four biflavonoids had a good linearitiy with good recoveries. The established HPLC method is simple, rapid, accurate, reliable, and sensitive, and can be applied to the identification and quality control of G. biloba leaves. Copyright© by the Chinese Pharmaceutical Association.

Method for producing smooth inner surfaces

DOEpatents

Cooper, Charles A.

2016-05-17

The invention provides a method for preparing superconducting cavities, the method comprising causing polishing media to tumble by centrifugal barrel polishing within the cavities for a time sufficient to attain a surface smoothness of less than 15 nm root mean square roughness over approximately a 1 mm.sup.2 scan area. The method also provides for a method for preparing superconducting cavities, the method comprising causing polishing media bound to a carrier to tumble within the cavities. The method also provides for a method for preparing superconducting cavities, the method comprising causing polishing media in a slurry to tumble within the cavities.

Upper airway expansion after rapid maxillary expansion evaluated with cone beam computed tomography.

PubMed

Ribeiro, Annelise Nazareth Cunha; de Paiva, João Batista; Rino-Neto, José; Illipronti-Filho, Edson; Trivino, Tarcila; Fantini, Solange Mongelli

2012-05-01

Cone-beam computed tomography (CBCT) is a reliable method of assessing the oral cavity and upper airways. We conducted this study to examine the changes introduced by rapid maxillary expansion in the nasal cavity, nasopharynx, and oropharynx as seen with images obtained by CBCT. We evaluated 15 patients with maxillary width deficiency treated with RME. Patients were subjected to CBCT at the beginning of RME and after the retention period of 4 months. The nasal cavity presented a significant transverse increase in the lower third, in the anterior (1.08 mm ± 0.15), medium (1.28 mm ± 0.15), and posterior regions (0.77 mm ± 0.12). No significant change occurred in the nasopharynx in volume (P  =  .11), median sagittal area (P  =  .33), or lower axial area (P  =  .29) resulting from the RME. A significant change was noted in the oropharynx in volume (P  =  .05), median sagittal area (P  =  .01), and lower axial area (P  =  .04) before and immediately after the RME. RME is able to increase the transverse width of the nasal cavity, but it does not have the same effect in the nasopharynx. Changes noted in the oropharynx may be due to the lack of a standardized position of the head and tongue at the time of image acquisition.

Analyzing crack development pattern of masonry structure in seismic oscillation by digital photography

NASA Astrophysics Data System (ADS)

Zhang, Guojian; Yu, Chengxin; Ding, Xinhua

2018-01-01

In this study, digital photography is used to monitor the instantaneous deformation of a masonry wall in seismic oscillation. In order to obtain higher measurement accuracy, the image matching-time baseline parallax method (IM-TBPM) is used to correct errors caused by the change of intrinsic and extrinsic parameters of digital cameras. Results show that the average errors of control point C5 are 0.79mm, 0.44mm and 0.96mm in X, Z and comprehensive direction, respectively. The average errors of control point C6 are 0.49mm, 0.44mm and 0.71mm in X, Z and comprehensive direction, respectively. These suggest that IM-TBPM can meet the accuracy requirements of instantaneous deformation monitoring. In seismic oscillation the middle to lower of the masonry wall develops cracks firstly. Then the shear failure occurs on the middle of masonry wall. This study provides technical basis for analyzing the crack development pattern of masonry structure in seismic oscillation and have significant implications for improved construction of masonry structures in earthquake prone areas.

Factors significantly increasing or inhibiting early stages of malignant melanoma (M.M.) and non-invasive evaluation of new treatment by ingestion and external application of optimal doses of the most effective anti-M.M. substances: haritaki, cilantro, vitamin D3, nori, EPA with DHA, & application of special (+) solar energy stored paper, which reduced the M.M. active area & asbestos rapidly.

PubMed

Omura, Yoshiaki; Jones, Marilyn; Duvvi, Harsha; Paluch, Kamila; Shimotsuura, Yasuhiro; Ohki, Motomu

2013-01-01

Sterilizing the pre-cancer skin of malignant melanoma (M.M.) with 70% Isopropyl alcohol intensified malignancy & the malignant response extended to surrounding normal looking skin, while sterilizing with 80% (vodka) or 12% (plum wine) ethyl alcohol completely inhibited M.M. in the area (both effects lasted for about 90 minutes initially). Burnt food (bread, vegetables, meat, and fish), a variety of smoked & non-smoked fish-skin, many animal's skin, pepper, Vitamin C over 75 mg, mango, pineapple, coconut, almond, sugars, Saccharine & Aspartame, garlic, onion, etc & Electromagnetic field from cellular phones worsened M.M. & induced abnormal M.M. response of surrounding skin. We found the following factors inhibit early stage of M.M. significantly: 1) Increasing normal cell telomere, by taking 500 mg Haritaki, often reached between 400-1150 ng& gradually diminished, but the M.M. response was completely inhibited until normal cell telomeres are reduced to 150 ng, which takes 6-8 hours. More than 70 mg Vitamin C, Orange Juice, & other high Vitamin C containing substances shouldn't be taken because they completely inhibit the effects of Haritaki. 2) We found Chrysotile asbestos & Tremolite asbestos (% of the Chrysotile amount) coexist. A special Cilantro tablet was used to remove asbestos & some toxic metals. 3) Vitamin D3 400 I.U. has a maximum inhibiting effect on M.M. but 800 I.U. or higher promotes malignancy. 4) Noricontaining Iodine, etc., was used. 5) EPA 180 mm with DHA 120 mg was most effectively used after metastasis to the surrounding skin was eliminated. When we combined 1 Cilantro tablet & Vitamin D3 400 I.U. withsmall Nori pieces & EPA with DHA, the effect of complete inhibition of M.M. lasted 9-11 hours. When these anti-M.M.substances (Haritaki, Vitamin D3, Cilantro, Nori, EPA. with DHA) were taken together, the effect lasted 12-14 hoursand M.M. involvement in surrounding normal-looking skin disappeared rapidly & original dark brown or black are as satisfying "ABCD" of M.M. completely fell off. Both oral & frequent external application of mixed solution of plum wine & the same combination of anti-M.M. substances can be used as very effective treatment by taking 2-3 times daily. Additional application of special (+) Solar Energy Stored Paper reduced asbestos & accelerated reduction of M.M. positive area rapidly. This method with individualized optimal doses has also been successfully applied to treat several other types of malignancies.

Gender Differences of Airway Dimensions in Anatomically Matched Sites on CT in Smokers

PubMed Central

Kim, Yu-Il; Schroeder, Joyce; Lynch, David; Newell, John; Make, Barry; Friedlander, Adam; Estépar, Raúl San José; Hanania, Nicola A.; Washko, George; Murphy, James R.; Wilson, Carla; Hokanson, John E.; Zach, Jordan; Butterfield, Kiel; Bowler, Russell P.

2013-01-01

Rationale and Objectives There are limited data on, and controversies regarding gender differences in the airway dimensions of smokers. Multi-detector CT (MDCT) images were analyzed to examine whether gender could explain differences in airway dimensions of anatomically matched airways in smokers. Materials and Methods We used VIDA imaging software to analyze MDCT scans from 2047 smokers (M:F, 1021:1026) from the COPDGene® cohort. The airway dimensions were analyzed from segmental to subsubsegmental bronchi. We compared the differences of luminal area, inner diameter, wall thickness, wall area percentage (WA%) for each airway between men and women, and multiple linear regression including covariates (age, gender, body sizes, and other relevant confounding factors) was used to determine the predictors of each airway dimensions. Results Lumen area, internal diameter and wall thickness were smaller for women than men in all measured airway (18.4 vs 22.5 mm2 for segmental bronchial lumen area, 10.4 vs 12.5 mm2 for subsegmental bronchi, 6.5 vs 7.7 mm2 for subsubsegmental bronchi, respectively p < 0.001). However, women had greater WA% in subsegmental and subsubsegmental bronchi. In multivariate regression, gender remained one of the most significant predictors of WA%, lumen area, inner diameter and wall thickness. Conclusion Women smokers have higher WA%, but lower luminal area, internal diameter and airway thickness in anatomically matched airways as measured by CT scan than do male smokers. This difference may explain, in part, gender differences in the prevalence of COPD and airflow limitation. PMID:21756032

Clinical measurement of the height of the interproximal contact area in maxillary anterior teeth.

PubMed

Sghaireen, Mohd G; Al-Zarea, Bader K; Al-Shorman, Hisham M; Al-Omiri, Mahmoud K

2013-11-01

To clinically quantify the apicoincisal height of interproximal areas directly in patients' mouths. Thirty participants (11 females and 9 males, mean age=26±1.5 years) were recruited into this study. Measurement of interproximal contact areas was carried out directly in patients' mouths using digital caliper (TERENSA, USA) with measuring accuracy of 0.01 mm. The interproximal contact areas that were measured are: central incisor to central incisor, central incisor to lateral incisor, lateral incisor to canine, and canine to first premolar on both sides of the jaw. Statistical significance was based on probability values less than 0.05 (p<0.05). The largest contact point was the one present between central incisors and it ranged from 2.9 to 6.5 mm. On the other hand, the contact point between canine and first premolar was the smallest on both sides of the arch and ranged from 0.6 to 2.5 mm. The dimensions of the contact points declined as we move from anterior area backwards. Statistical analysis using t-test showed that there were significant differences between the measurements of interproximal points of each tooth (P<0.05). the apicogingival dimension of the contact point decreased as we moved from anterior to posterior teeth. The contact area between the central incisors was largest and the one between canine and premolar was the smallest. This study is the first to report direct intra-oral clinical measurement of contact points. Clinical evaluation of contact point dimensions using digital caliber is a viable, quick and accurate method to use.

Optical coherence tomography assessment of efficacy of thrombus aspiration in patients undergoing a primary percutaneous coronary intervention for acute ST-elevation myocardial infarction

PubMed Central

Yamaguchi, Tomoyuki; Ino, Yasushi; Matsuo, Yoshiki; Shiono, Yasutsugu; Yamano, Takashi; Taruya, Akira; Nishiguchi, Tsuyoshi; Shimokado, Aiko; Orii, Makoto; Tanaka, Atsushi; Hozumi, Takeshi; Akasaka, Takashi

2015-01-01

Objective We used optical coherence tomography (OCT) to assess the impact of thrombus aspiration before angioplasty on poststenting tissue protrusions in patients undergoing a primary percutaneous coronary intervention (PCI) for ST-segment elevation myocardial infarction (STEMI). Methods and results A total of 188 patients with STEMI who underwent thrombus-aspiration PCI (n=113) or standard PCI (n=75) were examined in this study. OCT was performed immediately after primary PCI to assess lesion morphology in the stented segment. The minimum stent area was similar between the thrombus-aspiration PCI group and the standard PCI group [7.4 interquartile range (IQR): 5.8–9.4 vs. 7.4 IQR: 5.8–8.9 mm2, P=0.788]. The maximum tissue protrusion area [0.6 (IQR: 0.3–1.1) vs. 1.2 (IQR: 0.8–1.9) mm2, P<0.001], the mean tissue protrusion area [0.1 (IQR: 0.1–0.2) vs. 0.5 (IQR: 0.3–0.8) mm2, P<0.001], and tissue protrusion volume [2.3 (IQR: 1.3–4.3) vs. 8.3 (IQR: 5.4–14.6) mm3, P<0.001] were significantly smaller in the thrombus-aspiration PCI group compared with the standard PCI group. Minimum lumen area was significantly greater in the thrombus-aspiration PCI group compared with the standard PCI group [6.9 (IQR: 5.4–8.8) vs. 6.3 (IQR: 4.6–7.8) mm2, P=0.033]. Conclusion Thrombus aspiration before angioplasty in patients with STEMI was associated with significantly smaller tissue protrusion and larger lumen poststenting compared with standard PCI. Thrombus aspiration in primary PCI favorably influenced lesion morphologies in the stented segment. PMID:26230885

A groundwater recharge perspective on locating tree plantations within low-rainfall catchments to limit water resource losses

NASA Astrophysics Data System (ADS)

Dean, J. F.; Webb, J. A.; Jacobsen, G. E.; Chisari, R.; Dresel, P. E.

2015-02-01

Despite the many studies that consider the impacts of plantation forestry on groundwater recharge, and others that explore the spatial heterogeneity of recharge in low-rainfall regions, there is little marriage of the two subjects in forestry management guidelines and legislation. Here we carry out an in-depth analysis of the impact of reforestation on groundwater recharge in a low-rainfall (< 700 mm annually), high-evapotranspiration paired catchment characterized by ephemeral streams. Water table fluctuation (WTF) estimates of modern recharge indicate that little groundwater recharge occurs along the topographic highs of the catchments (average 18 mm yr-1); instead the steeper slopes in these areas direct runoff downslope to the lowland areas, where most recharge occurs (average 78 mm yr-1). Recharge estimates using the chloride mass balance (CMB) method were corrected by replacing the rainfall input Cl- value with that for streamflow, because most recharge occurs from infiltration of runoff through the streambed and adjacent low gradient slopes. The calculated CMB recharge values (average 10 mm yr-1) are lower than the WTF recharge values (average 47 mm yr-1), because they are representative of groundwater that was mostly recharged prior to European land clearance (> BP 200 years). The tree plantation has caused a progressive drawdown in groundwater levels due to tree water use; the decline is less in the upland areas. The results of this study show that spatial variations in recharge are important considerations for locating tree plantations. To conserve water resources for downstream users in low-rainfall, high-evapotranspiration regions, tree planting should be avoided in the dominant zone of recharge, i.e. the topographically low areas and along the drainage lines, and should be concentrated on the upper slopes, although this may negatively impact the economic viability of the plantation.

Direct Measurements of Water Canopy Storage Capacity of Broadleaf Shrubs under Different Temperature and Wetting Regimes

NASA Astrophysics Data System (ADS)

Yerk, W.

2016-12-01

It is generally agreed that canopy water storage capacity is one of the defining factors of rainfall interception. Multiple studies of storage capacity by shrubs have been published. However, only a fraction of species have been studied. In the presented study the storage capacity of five species (Aronia melanocarpa, Cornus sericea, Hydrangea quercifolia, Itea virginica, and Prunus laurocerasus) was directly measured in an indoor experiment. Effect of the water temperature on the amount of water stored by the canopy was also investigated. Five branches of each species (length 0.25-0.60 m, LAI 1.3-3.6) were selected. Methods of full submergence in water and a simulated rain of intensity of 187.5±9.9 mm/hr were applied. Water of two different temperatures of 30°C and 1.5°C was used for the submergence method. Weight of the branches fixated in a natural position was measured with a digital balance. Storage capacity was expressed as a depth of water retained by the entire branch divided by the one-sided area of all leaves. The storage capacity obtained by submergence was 0.45±0.5 mm for A. melanocarpa, 0.33±0.03 mm for C. sericea, 0.40±0.02 mm for H. quercifolia, 0.48±0.05 mm for I. virginica, and 0.67±0.09 mm for P. laurocerasus. Difference in the storage capacities obtained by both methods was inconsistent. Water temperature exerted a more pronounced effect on the capacity. The canopies stored 0.01 to 0.05 mm more water (p-value < 0.005 for all species except A. melanocarpa). Our findings correspond with the range of storage capacity reported for shrub species. The directly measured storage capacity exceeds the widely used in hydrological modeling value of 0.2 mm. We were able to detect an increase of capacity to store cold water; however, the increase was below the practical level.

Bony contact area and displacement of the temporomandibular joint after high-oblique and bilateral sagittal split osteotomy: a computer-simulated comparison.

PubMed

Möhlhenrich, Stephan Christian; Kamal, Mohammad; Peters, Florian; Fritz, Ulrike; Hölzle, Frank; Modabber, Ali

2016-04-01

The most common way to move the mandible during orthognathic surgery is by bilateral sagittal split osteotomy (BSSO). The high-oblique sagittal split osteotomy (HSSO) is an alternative, although its use is limited by potential complications, mainly to do with the position of the condyle and reduced contact with bone. The aim of this study was to find out the optimal intercondylar distance and area of contact with the surface of the bone for mandibular advancement and setback in BSSO and HSSO. Data from computed tomographic (CT) images from 40 patients were loaded into special planning software, and virtual operations done for mandibular advancement and setback at 3, 5, 8, and 10mm using BSSO and HSSO, which resulted in 640 individual mandibular displacements. The resultant area of bony contact and intercondylar distance were calculated by the software. The mean (SD) areas of contact with the bony surface after 10mm advancement for HSSO and BSSO were 193.94 (63.76) mm(2) and 967.92 (229.21) mm(2), respectively, and after 10mm setback 202.64 (62.30) mm(2) and 1108.86 (247.38) mm(2). The mean corresponding intercondylar distance after maximum advancement were 86.76 (6.40) mm and 86.59 (6.24) mm, and after maximum setback 74.90 (5.73) mm and 73.06 (6.06) mm. There were significant differences between the two for the area of contact with the surface at each displacement distance (p<0.001), but not for intercondylar distance. A larger area of bony contact can be expected at any displacement distance for BSSO, so the changes in intercondylar distance should not be considered when deciding which osteotomy to select. Copyright © 2015 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Design and construction of a guarded hot plate apparatus operating down to liquid nitrogen temperature.

PubMed

Li, Manfeng; Zhang, Hua; Ju, Yonglin

2012-07-01

A double-sided guarded hot plate apparatus (GHP) is specifically designed, fabricated, and constructed for the measurement of thermal conductivities of insulation specimens operated down to liquid nitrogen temperature (-196 °C), at different controlled pressures from 0.005 Pa to 0.105 MPa. The specimens placed in this apparatus are 300 mm in diameter at various thicknesses ranging from 4 mm to 40 mm. The apparatus is different from traditional GHP in terms of structure, supporting and heating method. The details of the design and construction of the hot plate, the cold plates, the suspensions, the clampings, and the vacuum chamber of the system are presented. The measurement methods of the temperatures, the input power, the meter area, and the thickness of the specimens are given. The apparatus is calibrated with teflon plates as sample and the maximum deviation from the published data is about 6% for thermal conductivity. The uncertainties for the measurement are also discussed in this paper.

A cross-sectional analysis of the effects of residential greenness on blood pressure in 10-year old children: results from the GINIplus and LISAplus studies

PubMed Central

2014-01-01

Background According to Ulrich’s psychoevolutionary theory, contact with green environments mitigates stress by activating the parasympathetic system, (specifically, by decreasing blood pressure (BP)). Experimental studies have confirmed this biological effect. However, greenness effects on BP have not yet been explored using an observational study design. We assessed whether surrounding residential greenness is associated with BP in 10 year-old German children. Methods Systolic and diastolic BPs were assessed in 10 year-old children residing in the Munich and Wesel study areas of the German GINIplus and LISAplus birth cohorts. Complete exposure, outcome and covariate data were available for 2,078 children. Residential surrounding greenness was defined as the mean of Normalized Difference Vegetation Index (NDVI) values, derived from Landsat 5 TM satellite images, in circular 500-m buffers around current home addresses of participants. Generalized additive models assessed pooled and area-specific associations between BP and residential greenness categorized into area-specific tertiles. Results In the pooled adjusted model, the systolic BP of children living at residences with low and moderate greenness was 0.90 ± 0.50 mmHg (p-value = 0.073) and 1.23 ± 0.50 mmHg (p-value = 0.014) higher, respectively, than the systolic BP of children living in areas of high greenness. Similarly, the diastolic BP of children living in areas with low and moderate greenness was 0.80 ± 0.38 mmHg (p-value = 0.033) and 0.96 ± 0.38 mmHg (p-value = 0.011) higher, respectively, than children living in areas with high greenness. These associations were not influenced by environmental stressors (temperature, air pollution, noise annoyance, altitude and urbanisation level). When stratified by study area, associations were significant among children residing in the urbanised Munich area but null for those in the rural Wesel area. Conclusions Lower residential greenness was positively associated with higher BP in 10 year-old children living in an urbanised area. Further studies varying in participants’ age, geographical area and urbanisation level are required. PMID:24886243

Ground-water discharge by evapotranspiration in a desert environment of southern Nevada, 1987

USGS Publications Warehouse

Johnson, M.J.

1994-01-01

Evapotranspiration (ET) data were collected at two sites where microclimates are typical of the Mojave Desert in southern Nevada-one site with and one without ground-water contributions to ET--under extremely arid desert conditions. By comparing the rate of evapotranspiration at the two sites, the amount of ground-water ET can be inferred. This method may be useful for quantifying ground-water discharge by ET around basin playas or the summer carbonate-aquifer springs, ET rates are greatest in early spring, but are less than 0.6 millimeter per day (mm/d). As the summer progresses and soil moisture is depleted, ET drops below 0.1 mm/d and vegetation wilts. In areas'with a ground-water contribution, under similar climatic conditions, ET rates increase with increasing solar radiation and plant growth from 1 mm/d in winter to an average of 1.5 to 3.0 mm/d in spring. The highest average is about 5.0 mm/d, in June, July, and August, with fluctuations generally between 3.0 and 7.0 mm/d; the rate then decreases from 3.0 to less than 1.0 mm/d by late autumn. A comparison of monthly ET totals based on average daily rates at the two sites indicates that about 520 millimeters of ground water was lost to ET at Ash Meadows during the 6 months of record, April through September 1987. This is in general agreement with the range of values estimated for areas with native vegetation in the Amargosa Desert where the depth to water was between 0.0 and 1.5 meters. Estimated rates ranged from 320 to 760 millimeters per year.

Vacuum-assisted fluid flow in microchannels to pattern substrates and cells.

PubMed

Shrirao, Anil B; Kung, Frank H; Yip, Derek; Cho, Cheul H; Townes-Anderson, Ellen

2014-09-01

Substrate and cell patterning are widely used techniques in cell biology to study cell-to-cell and cell-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This paper describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. Our method builds upon a previous vacuum-assisted method used for micromolding (Jeon et al 1999 Adv. Mater 11 946) and successfully patterned collagen-I, fibronectin and Sal-1 substrates on glass and polystyrene surfaces, filling microchannels with lengths up to 120 mm and covering areas up to 13 × 10 mm(2). Vacuum-patterned substrates were subsequently used to culture mammalian PC12 and fibroblast cells and amphibian neurons. Cells were also patterned directly by injecting cell suspensions into microchannels using vacuum. Fibroblast and neuronal cells patterned using vacuum showed normal growth and minimal cell death indicating no adverse effects of vacuum on cells. Our method fills reversibly sealed PDMS microchannels. This enables the user to remove the PDMS microchannel cast and access the patterned biomaterial or cells for further experimental purposes. Overall, this is a straightforward technique that has broad applicability for cell biology.

Vacuum-assisted Fluid Flow in Microchannels to Pattern Substrates and Cells

PubMed Central

Shrirao, Anil B.; Kung, Frank H.; Yip, Derek; Cho, Cheul H.; Townes-Anderson, Ellen

2014-01-01

Substrate and cell patterning are widely used techniques in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This paper describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. Our method builds upon a previous vacuum-assisted method used for micromolding (Jeon, Choi et al. 1999) and successfully patterned collagen-I, fibronectin and Sal-1 substrates on glass and polystyrene surfaces, filling microchannels with lengths up to 120 mm and covering areas up to 13 × 10 mm2. Vacuum-patterned substrates were subsequently used to culture mammalian PC12 and fibroblast cells and amphibian neurons. Cells were also patterned directly by injecting cell suspensions into microchannels using vacuum. Fibroblast and neuronal cells patterned using vacuum showed normal growth and minimal cell death indicating no adverse effects of vacuum on cells. Our method fills reversibly sealed PDMS microchannels. This enables the user to remove the PDMS microchannel cast and access the patterned biomaterial or cells for further experimental purposes. Overall, this is a straightforward technique that has broad applicability for cell biology. PMID:24989641

Functional specialization of medial auditory belt cortex in the alert rhesus monkey.

PubMed

Kusmierek, Pawel; Rauschecker, Josef P

2009-09-01

Responses of neural units in two areas of the medial auditory belt (middle medial area [MM] and rostral medial area [RM]) were tested with tones, noise bursts, monkey calls (MC), and environmental sounds (ES) in microelectrode recordings from two alert rhesus monkeys. For comparison, recordings were also performed from two core areas (primary auditory area [A1] and rostral area [R]) of the auditory cortex. All four fields showed cochleotopic organization, with best (center) frequency [BF(c)] gradients running in opposite directions in A1 and MM than in R and RM. The medial belt was characterized by a stronger preference for band-pass noise than for pure tones found medially to the core areas. Response latencies were shorter for the two more posterior (middle) areas MM and A1 than for the two rostral areas R and RM, reaching values as low as 6 ms for high BF(c) in MM and A1, and strongly depended on BF(c). The medial belt areas exhibited a higher selectivity to all stimuli, in particular to noise bursts, than the core areas. An increased selectivity to tones and noise bursts was also found in the anterior fields; the opposite was true for highly temporally modulated ES. Analysis of the structure of neural responses revealed that neurons were driven by low-level acoustic features in all fields. Thus medial belt areas RM and MM have to be considered early stages of auditory cortical processing. The anteroposterior difference in temporal processing indices suggests that R and RM may belong to a different hierarchical level or a different computational network than A1 and MM.

Mediterranean diet and carotid atherosclerosis in the Northern Manhattan Study

PubMed Central

Gardener, Hannah; Wright, Clinton B.; Cabral, Digna; Scarmeas, Nikolaos; Gu, Yian; Cheung, Ken; Elkind, Mitchell S.V.; Sacco, Ralph L.; Rundek, Tatjana

2015-01-01

Objective Adherence to a Mediterranean-style diet (MeDi) may protect against clinical vascular events by reducing atherosclerosis, but data is limited. This is the first observational study of the association between MeDi adherence and carotid plaque thickness and area. Methods The study included 1374 participants of the population-based Northern Manhattan Study with diet assessed and carotid intima-media thickness (cIMT) and plaque measured using B-mode ultrasound (mean age 66 ± 9 years, 60% female, 60% Hispanic, 18% White, 19% Black). A MeDi adherence score (range = 0–9, 9 representing maximal adherence) was examined continuously and in quintiles (3/4/5/6 –9 vs. 0–2). Results Mean cIMT = 0.9 ± 0.1 mm and 57% had plaque (median plaque thickness = 1.5 mm, 75th percentile = 2.2; median plaque area = 4.2 mm2, 75th percentile = 15.8). There was no association between MeDi and cIMT or plaque presence. MeDi adherence was inversely associated with the 75th percentile of plaque thickness and median of plaque area in quantile regression analyses. These associations persisted after controlling for demographics, smoking, physical activity, and total energy consumption (effect of a 1-point increase in MeDi score on the 75th percentile of plaque thickness = −0.049 mm, p = 0.03; median of plaque area = −0.371 mm2, p = 0.03), and when additionally controlling for vascular disease biomarkers, medication use, BMI, and previous cardiac disease. The protective associations appeared strongest for those with a MeDi score of 5 (4th quintile) vs. 0–2 (bottom quintile). Differential effects of a MeDi on plaque thickness and area across race/ethnic groups was suggested. Conclusions Moderate and strict adherence to a MeDi may protect against a higher burden of carotid atherosclerotic plaque, which may mediate the protection against clinical vascular events. Efforts to improve adherence to a MeDi are critical to reducing the burden of atherosclerotic disease. PMID:24721190

Development and validation of an MEKC method for determination of nitrogen-containing drugs in pharmaceutical preparations.

PubMed

Buiarelli, Francesca; Coccioli, Franco; Jasionowska, Renata; Terracciano, Alessandro

2008-09-01

A fast and accurate micellar electrokinetic capillary chromatography method was developed for quality control of pharmaceutical preparations containing cold remedies as acetaminophen, salicylamide, caffeine, phenylephrine, pseudoephedrine, norephedrine and chlorpheniramine. The method optimization was realized on a Beckman P/ACE System MDQ instrument. The baseline separation of seven analytes was performed in an uncoated fused silica capillary internal diameter (ID)=50 microm using tris-borate (20 mM, pH=8.5) containing sodium dodecyl sulphate 30 mM BGE. On line-UV detection at 214 nm was performed and the applied voltage was 10 kV. The operating temperature was 25 degrees C. After experimental conditions optimization, the proposed method was validated. The evaluated parameters were: precision of migration time and of corrected peak area ratio, linearity range, limit of detection, limit of quantification, accuracy (recovery), ruggedness and applicability. The method was then successfully applied for the analysis of three pharmaceutical preparations containing some of the analytes listed before.

Geodetic monitoring of subrosion-induced subsidence processes in urban areas

NASA Astrophysics Data System (ADS)

Kersten, Tobias; Kobe, Martin; Gabriel, Gerald; Timmen, Ludger; Schön, Steffen; Vogel, Detlef

2017-03-01

The research project SIMULTAN applies an advanced combination of geophysical, geodetic, and modelling techniques to gain a better understanding of the evolution and characteristics of sinkholes. Sinkholes are inherently related to surface deformation and, thus, of increasing societal relevance, especially in dense populated urban areas. One work package of SIMULTAN investigates an integrated approach to monitor sinkhole-related mass translations and surface deformations induced by salt dissolution. Datasets from identical and adjacent points are used for a consistent combination of geodetic and geophysical techniques. Monitoring networks are established in Hamburg and Bad Frankenhausen (Thuringia). Levelling surveys indicate subsidence rates of about 4-5 mm per year in the main subsidence areas of Bad Frankenhausen with a local maximum of 10 mm per year around the leaning church tower. Here, the concept of combining geodetic and gravimetric techniques to monitor and characterise geological processes on and below the Earth's surface is exemplary discussed for the focus area Bad Frankenhausen. For the different methods (levelling, GNSS, relative/absolute gravimetry) stable network results at identical points are obtained by the first campaigns, i.e., the results are generally in agreement.

A Method of Accurate Bone Tunnel Placement for Anterior Cruciate Ligament Reconstruction Based on 3-Dimensional Printing Technology: A Cadaveric Study.

PubMed

Ni, Jianlong; Li, Dichen; Mao, Mao; Dang, Xiaoqian; Wang, Kunzheng; He, Jiankang; Shi, Zhibin

2018-02-01

To explore a method of bone tunnel placement for anterior cruciate ligament (ACL) reconstruction based on 3-dimensional (3D) printing technology and to assess its accuracy. Twenty human cadaveric knees were scanned by thin-layer computed tomography (CT). To obtain data on bones used to establish a knee joint model by computer software, customized bone anchors were installed before CT. The reference point was determined at the femoral and tibial footprint areas of the ACL. The site and direction of the bone tunnels of the femur and tibia were designed and calibrated on the knee joint model according to the reference point. The resin template was designed and printed by 3D printing. Placement of the bone tunnels was accomplished by use of templates, and the cadaveric knees were scanned again to compare the concordance of the internal opening of the bone tunnels and reference points. The twenty 3D printing templates were designed and printed successfully. CT data analysis between the planned and actual drilled tunnel positions showed mean deviations of 0.57 mm (range, 0-1.5 mm; standard deviation, 0.42 mm) at the femur and 0.58 mm (range, 0-1.5 mm; standard deviation, 0.47 mm) at the tibia. The accuracy of bone tunnel placement for ACL reconstruction in cadaveric adult knees based on 3D printing technology is high. This method can improve the accuracy of bone tunnel placement for ACL reconstruction in clinical sports medicine. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Comparative evaluation of surface porosities in conventional heat polymerized acrylic resin cured by water bath and microwave energy with microwavable acrylic resin cured by microwave energy

PubMed Central

Singh, Sunint; Palaskar, Jayant N.; Mittal, Sanjeev

2013-01-01

Background: Conventional heat cure poly methyl methacrylate (PMMA) is the most commonly used denture base resin despite having some short comings. Lengthy polymerization time being one of them and in order to overcome this fact microwave curing method was recommended. Unavailability of specially designed microwavable acrylic resin made it unpopular. Therefore, in this study, conventional heat cure PMMA was polymerized by microwave energy. Aim and Objectives: This study was designed to evaluate the surface porosities in PMMA cured by conventional water bath and microwave energy and compare it with microwavable acrylic resin cured by microwave energy. Materials and Methods: Wax samples were obtained by pouring molten wax into a metal mold of 25 mm × 12 mm × 3 mm dimensions. These samples were divided into three groups namely C, CM, and M. Group C denotes conventional heat cure PMMA cured by water bath method, CM denotes conventional heat cure PMMA cured by microwave energy, M denotes specially designed microwavable acrylic denture base resin cured by microwave energy. After polymerization, each sample was scanned in three pre-marked areas for surface porosities using the optical microscope. As per the literature available, this instrument is being used for the first time to measure the porosity in acrylic resin. It is a reliable method of measuring area of surface pores. Portion of the sample being scanned is displayed on the computer and with the help of software area of each pore was measured and data were analyzed. Results: Conventional heat cure PMMA samples cured by microwave energy showed maximum porosities than the samples cured by conventional water bath method and microwavable acrylic resin cured by microwave energy. Higher percentage of porosities was statistically significant, but well within the range to be clinically acceptable. Conclusion: Within the limitations of this in-vitro study, conventional heat cure PMMA can be cured by microwave energy without compromising on its property such as surface porosity. PMID:24015000

Print-to-pattern dry film photoresist lithography

NASA Astrophysics Data System (ADS)

Garland, Shaun P.; Murphy, Terrence M., Jr.; Pan, Tingrui

2014-05-01

Here we present facile microfabrication processes, referred to as print-to-pattern dry film photoresist (DFP) lithography, that utilize the combined advantages of wax printing and DFP to produce micropatterned substrates with high resolution over a large surface area in a non-cleanroom setting. The print-to-pattern methods can be performed in an out-of-cleanroom environment making microfabrication much more accessible to minimally equipped laboratories. Two different approaches employing either wax photomasks or wax etchmasks from a solid ink desktop printer have been demonstrated that allow the DFP to be processed in a negative tone or positive tone fashion, respectively, with resolutions of 100 µm. The effect of wax melting on resolution and as a bonding material was also characterized. In addition, solid ink printers have the capacity to pattern large areas with high resolution, which was demonstrated by stacking DFP layers in a 50 mm × 50 mm woven pattern with 1 mm features. By using an office printer to generate the masking patterns, the mask designs can be easily altered in a graphic user interface to enable rapid prototyping.

a Research on Monitoring Surface Deformation and Relationships with Surface Parameters in Qinghai Tibetan Plateau Permafrost

NASA Astrophysics Data System (ADS)

Mi, S. J.; Li, Y. T.; Wang, F.; Li, L.; Ge, Y.; Luo, L.; Zhang, C. L.; Chen, J. B.

2017-09-01

The Qinghai Tibetan Plateau permafrost has been the largest permafrost region in middle-low latitude in the world for its high altitude. For the large area permafrost, especially surface deformation brought by it, have serious influence on the road engineering, road maintaining and regional economic development. Consequently, it is essential to monitor the surface deformation and study factors that influent it. We monitored an area named Wudaoliang from July 25, 2015 to June 1, 2016 and 15 Sentinel images were obtained during this time. The area we chose is about 35 kilometers long and 2 kilometers wide, and the national road 109 of China passes through the area. The traditional PS-INSAR (Persistent Scatterer Interferometric Synthetic Aperture Radar) method is not suitable because less historical images in the research area and leading to the number of PS (Persistent Scatterer) points is not enough to obtain accurate deformation results. Therefore, in this paper, we used another method which named QUASI-PSInSAR (QUASI Persistent Scatterer Interferometric Synthetic Aperture Radar) to acquire deformation for it has the advantage to weaken or eliminate the effects of spatial and temporal correlation, which has proved by other scholar. After processing 15 images in the SARproz software, we got the conclusions that, 1) the biggest deformation velocity in the whole area was about 127.9mm/year and about 109.3 mm/year in the road; 2) apparent deformation which have surface deformation more than 30mm/year was about 1.7Km in the road. Meanwhile, soil moisture(SM), Land surface temperature (LST) and surface water(SW), which are primary parameters of the land surface over the same time were reversed by using Sentinel data, Landsat data and ZY-3 data, respectively. After analyzing SM, LST , SW and deformation, we obtained that wet areas which had bigger SM, lower LST and more SW, had greater percentage of severe deformation than arid areas; besides, deformation pattern were different in arid areas and wet areas. During the research time, frost heaving firstly accounted for a large proportion both in the arid and wet areas with the decrease of downward radiation from July to December; after December, thaw settlement came into prominence with the increase downward radiation in the arid areas, while in the wet areas, surface put into diverse situations because of water transformation leading to severe deformation. In summary, soil moisture is an important factor that influences the surface deformation. This relationship between deformation process and soil moisture will be researched more in our further work.

Spectral theory of extreme statistics in birth-death systems

NASA Astrophysics Data System (ADS)

Meerson, Baruch

2008-03-01

Statistics of rare events, or large deviations, in chemical reactions and systems of birth-death type have attracted a great deal of interest in many areas of science including cell biochemistry, astrochemistry, epidemiology, population biology, etc. Large deviations become of vital importance when discrete (non-continuum) nature of a population of ``particles'' (molecules, bacteria, cells, animals or even humans) and stochastic character of interactions can drive the population to extinction. I will briefly review the novel spectral method [1-3] for calculating the extreme statistics of a broad class of birth-death processes and reactions involving a single species. The spectral method combines the probability generating function formalism with the Sturm-Liouville theory of linear differential operators. It involves a controlled perturbative treatment based on a natural large parameter of the problem: the average number of particles/individuals in a stationary or metastable state. For extinction (the first passage) problems the method yields accurate results for the extinction statistics and for the quasi-stationary probability distribution, including the tails, of metastable states. I will demonstrate the power of the method on the example of a branching and annihilation reaction, A ->-2.8mm2mm2A,,A ->-2.8mm2mm , representative of a rather general class of processes. *M. Assaf and B. Meerson, Phys. Rev. Lett. 97, 200602 (2006). *M. Assaf and B. Meerson, Phys. Rev. E 74, 041115 (2006). *M. Assaf and B. Meerson, Phys. Rev. E 75, 031122 (2007).

Toward a distributed free-floating wireless implantable neural recording system.

PubMed

Pyungwoo Yeon; Xingyuan Tong; Byunghun Lee; Mirbozorgi, Abdollah; Ash, Bruce; Eckhardt, Helmut; Ghovanloo, Maysam

2016-08-01

To understand the complex correlations between neural networks across different regions in the brain and their functions at high spatiotemporal resolution, a tool is needed for obtaining long-term single unit activity (SUA) across the entire brain area. The concept and preliminary design of a distributed free-floating wireless implantable neural recording (FF-WINeR) system are presented, which can enabling SUA acquisition by dispersedly implanting tens to hundreds of untethered 1 mm3 neural recording probes, floating with the brain and operating wirelessly across the cortical surface. For powering FF-WINeR probes, a 3-coil link with an intermediate high-Q resonator provides a minimum S21 of -22.22 dB (in the body medium) and -21.23 dB (in air) at 2.8 cm coil separation, which translates to 0.76%/759 μW and 0.6%/604 μW of power transfer efficiency (PTE) / power delivered to a 9 kΩ load (PDL), in body and air, respectively. A mock-up FF-WINeR is implemented to explore microassembly method of the 1×1 mm2 micromachined silicon die with a bonding wire-wound coil and a tungsten micro-wire electrode. Circuit design methods to fit the active circuitry in only 0.96 mm2 of die area in a 130 nm standard CMOS process, and satisfy the strict power and performance requirements (in simulations) are discussed.

Morphological Features and Important Parameters of Large Optic Discs for Diagnosing Glaucoma

PubMed Central

Okimoto, Satoshi; Yamashita, Keiko; Shibata, Tetsuo; Kiuchi, Yoshiaki

2015-01-01

Purpose To compare the optic disc parameters of glaucomatous eyes to those of non-glaucomatous eyes with large discs. Methods We studied 225 consecutive eyes with large optic discs (>2.82 mm2): 91 eyes with glaucoma and 134 eyes without glaucoma. An eye was diagnosed with glaucoma when visual field defects were detected by the Humphrey Field Analyzer. All of the Heidelberg Retina Tomograph II (HRT II) parameters were compared between the non-glaucomatous and glaucomatous eyes. A logistic regression analysis of the HRT II parameters was used to establish a new formula for diagnosing glaucoma, and the sensitivity and specificity of the Moorfields Regression Analysis (MRA) was compared to the findings made by our analyses. Results The mean disc area was 3.44±0.50 mm2 in the non-glaucomatous group and 3.40±0.52 mm2 in the glaucoma group. The cup area, cup volume, cup-to-disc area ratio, linear cup/disc ratio, mean cup depth, and the maximum cup depth were significantly larger in glaucomatous eyes than in the non-glaucomatous eyes. The rim area, rim volume, cup shape measurement, mean retinal nerve fiber layer (RNFL) thickness, and RFNL cross-sectional area were significantly smaller in glaucomatous eyes than in non-glaucomatous eyes. The cup-to-disc area ratio, the height variation contour (HVC), and the RNFL cross-sectional area were important parameters for diagnosing the early stage glaucoma, and the cup-to-disc area ratio and cup volume were useful for diagnosing advanced stage glaucoma in eyes with a large optic disc. The new formula had higher sensitivity and specificity for diagnosing glaucoma than MRA. Conclusions The cup-to-disc area ratio, HVC, RNFL cross-sectional area, and cup volume were important parameters for diagnosing glaucoma in eyes with a large optic disc. The important disc parameters to diagnose glaucoma depend on the stage of glaucoma in patients with large discs. PMID:25798580

Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling

NASA Astrophysics Data System (ADS)

Pérez-Castillo, Yunierkis; Froeyen, Matheus; Cabrera-Pérez, Miguel Ángel; Nowé, Ann

2011-04-01

Bacterial β-ketoacyl-acyl carrier protein synthase III (FabH) has become an attractive target for the development of new antibacterial agents which can overcome the increased resistance of these pathogens to antibiotics in clinical use. Despite several efforts have been dedicated to find inhibitors for this enzyme, it is not a straightforward task, mainly due its high flexibility which makes difficult the structure-based design of FabH inhibitors. Here, we present for the first time a Molecular Dynamics (MD) study of the E. colil FabH enzyme to explore its conformational space. We compare the flexibility of this enzyme for the unliganded protein and an enzyme-inhibitor complex and find a correspondence between our modeling results and the experimental evidence previously reported for this enzyme. Furthermore, through a 100 ns MD simulation of the unliganded enzyme we extract useful information related to the concerted motions that take place along the principal components of displacement. We also establish a relation between the presence of water molecules in the oxyanion hole with the conformational stability of structural important loops. Representative conformations of the binding pocket along the whole trajectory of the unliganded protein are selected through cluster analysis and we find that they contain a conformational diversity which is not provided by the X-ray structures of ecFabH. As a proof of this last hypothesis, we use a set of 10 FabH inhibitors and show that they cannot be correctly modeled in any available X-ray structure, while by using our set of conformations extracted from the MD simulations, this task can be accomplish. Finally, we show the ability of short MD simulations for the refinement of the docking binding poses and for MM-PBSA calculations to predict stable protein-inhibitor complexes in this enzyme.

Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations.

PubMed

Parasuraman, Ponnusamy; Murugan, Veeramani; Selvin, Jeyasigamani F A; Gromiha, M Michael; Fukui, Kazuhiko; Veluraja, Kasinadar

2014-08-01

Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics. Copyright © 2014 John Wiley & Sons, Ltd.

Morphometric study of mandibular ramus related to sagittal ramus split osteotomy and osteosynthesis.

PubMed

Vinicius de Oliveira, Marcelo; de Moraes, Paulo Hemerson; Olate, Sergio; Alonso, Maria Beatriz C; Watanabe, Plauto Christopher Aranha; Haiter-Neto, Francisco; de Albergaria-Barbosa, José Ricardo

2012-09-01

The objective of this study was to quantify the cortical bone thickness of the mandibular ramus to determine conditions related to sagittal split ramus osteotomy and placement of screws. The patient sample comprised 44 subjects of ages ranging from 46 to 52 years (mean age, 49 years). The cone-beam computed tomography was performed and realized 3 cuts in the third molar area (section A), 5 mm posterior (section B), and 5 mm posterior to the latter (section C). Measurement in the cortical areas of the superior and inferior levels related to mandibular canal and measurement related to the total width of the mandible was executed. Intraclass correlation coefficient with P < 0.05 was used. The result showed that the buccal and lingual cortical zone did not present statistical differences, and the minor value was 1.5 mm for each one. There were no differences in the superior and inferior cortical bone, and the total width of the mandible was between 15.9 and 8.5 mm in the anterior area, between 17.4 and 12.8 mm in the middle area, and between 18 and 8.8 mm in the posterior area. The distance superiorly to the mandibular canal presented a minimal SD with a mean of 8.5 mm in the anterior region, 10.6 mm for the middle region, and 12.5 mm in the posterior region. In conclusion, the cortical thickness of the mandibular ramus in the adult population is particularly strong and offers a good anchorage for screw insertion in sagittal split ramus osteotomy.

Measurement and properties of the dose-area product ratio in external small-beam radiotherapy.

PubMed

Niemelä, Jarkko; Partanen, Mari; Ojala, Jarkko; Sipilä, Petri; Björkqvist, Mikko; Kapanen, Mika; Keyriläinen, Jani

2017-06-21

In small-beam radiation therapy (RT) the measurement of the beam quality parameter, i.e. the tissue-phantom ratio or TPR 20,10 , using a conventional point detector is a challenge. To obtain reliable results, one has to consider potential sources of error, including volume averaging and adjustment of the point detector into the narrow beam. To overcome these challenges, a different type of beam quality parameter in small beams was studied, namely the dose-area product ratio, or DAPR 20,10 . With this method, the measurement of a dose-area product (DAP) using a large-area plane-parallel chamber (LAC) eliminates the uncertainties in detector positioning and volume averaging that are present when using a point detector. In this study, the properties of the DAPR 20,10 of a cone-collimated 6 MV photon beam were investigated using Monte Carlo (MC) calculations and the obtained values were compared to measurements obtained using two LAC detectors, PTW Type 34073 and PTW Type 34070. In addition, the possibility of determining the DAP using EBT3 film and a Razor diode detector was studied. The determination of the DAPR 20,10 value was found to be feasible in external small-beam radiotherapy using cone-collimated beams with diameters from 4-40 mm, based on the results of the two LACs, the MC calculations and the Razor diode. The measurements indicated a constant DAPR 20,10 value for fields 20-40 mm in diameter, with a maximum relative change of 0.6%, but an increase of 7.0% for fields from 20-4 mm in diameter for the PTW Type 34070 chamber. Simulations and measurements showed an increase of DAPR 20,10 with increasing LAC size or dose integral area for the studied 4-40 mm cone-collimated 6 MV photon beams. This has the consequence that there should be a reference to the size of the used LAC active area or the DAP integration area with the reported DAPR 20,10 value.

Functional optical zone of the cornea.

PubMed

Tabernero, Juan; Klyce, Stephen D; Sarver, Edwin J; Artal, Pablo

2007-03-01

When keratorefractive surgery is used to treat a central corneal diameter smaller than the resting pupil, visual symptoms of polyopia, ghosting, blur, haloes, and glare can be experienced. Progress has been made to enlarge the area of surgical treatment to extend beyond the photopic pupil; however, geometric limitations can pose restrictions to extend the treatment beyond the mesopic pupil diameter and can lead to impediments in night vision. The size of the treated area that has achieved good optical performance has been defined as the functional optical zone (FOZ). In this study the authors developed three objective methods to measure the FOZ. Corneal topography examination results from 1 eye of 34 unoperated normal eyes and 32 myopic eyes corrected by laser in situ keratomileusis (LASIK) were evaluated in three ways. First, a uniform axial power method (FOZ(A)) assessed the area of the postoperative cornea that was within a +/-0.5-D window centered on the mathematical mode. Second, FOZ was determined based on the corneal wavefront true RMS error as a function of the simulated pupil size (FOZ(R)). Third, FOZ was determined from the radial MTF, established at the retinal plane as a function of pupil size (FOZ(M)). Means for each of the FOZ methods (FOZ(A), FOZ(R), and FOZ(M)) were 7.6, 9.1, and 7.7 mm, respectively, for normal eyes. For LASIK-corrected eyes, these means were 6.0, 6.9, and 6.0 mm. Overall, an average decrease of 1.8 mm in the functional optical zone was found after the LASIK procedure. Correlations between the FOZ methods after LASIK showed acceptable and statistically significant values (R = 0.71, 0.70, and 0.61; P < 0.01). These methods will be useful to more fully characterize corneal treatment profiles after keratorefractive surgery. Because of its ease of implementation, direct spatial correspondence to corneal topography, and good correlation to the other more computationally intensive methods, the semiempiric uniform axial power method (FOZ(A)) appears to be most practical in use. The ability to measure the size of the FOZ should permit further evolution of keratorefractive surgical lasers and their algorithms to reduce the night vision impediments that can arise from functional optical zones that do not encompass the entire mesopic pupil.

Utility of Penman-Monteith, Priestley-Taylor, reference evapotranspiration, and pan evaporation methods to estimate pasture evapotranspiration

USGS Publications Warehouse

Sumner, D.M.; Jacobs, J.M.

2005-01-01

Actual evapotranspiration (ETa) was measured at 30-min resolution over a 19-month period (September 28, 2000-April 23, 2002) from a nonirrigated pasture site in Florida, USA, using eddy correlation methods. The relative magnitude of measured ETa (about 66% of long-term annual precipitation at the study site) indicates the importance of accurate ET a estimates for water resources planning. The time and cost associated with direct measurements of ETa and the rarity of historical measurements of ETa make the use of methods relying on more easily obtainable data desirable. Several such methods (Penman-Monteith (PM), modified Priestley-Taylor (PT), reference evapotranspiration (ET 0), and pan evaporation (Ep)) were related to measured ETa using regression methods to estimate PM bulk surface conductance, PT ??, ET0 vegetation coefficient, and Ep pan coefficient. The PT method, where the PT ?? is a function of green-leaf area index (LAI) and solar radiation, provided the best relation with ET a (standard error (SE) for daily ETa of 0.11 mm). The PM method, in which the bulk surface conductance was a function of net radiation and vapor-pressure deficit, was slightly less effective (SE=0.15 mm) than the PT method. Vegetation coefficients for the ET0 method (SE=0.29 mm) were found to be a simple function of LAI. Pan coefficients for the Ep method (SE=0.40 mm) were found to be a function of LAI and Ep. Historical or future meteorological, LAI, and pan evaporation data from the study site could be used, along with the relations developed within this study, to provide estimates of ETa in the absence of direct measurements of ETa. Additionally, relations among PM, PT, and ET0 methods and ETa can provide estimates of ETa in other, environmentally similar, pasture settings for which meteorological and LAI data can be obtained or estimated. ?? 2004 Elsevier B.V. All rights reserved.

Dependence of optic disc parameters on disc area according to Heidelberg Retina Tomograph: Part II.

NASA Astrophysics Data System (ADS)

Machekhin, V.; Manaenkova, G.; Bondarenko, O.

2007-05-01

With the help of Heidelberg Retina Tomograph (HRT-II) optic disc parameters in 211 eyes of 115 healthy patients with refraction Em +/- 3,0 D and 96 eyes of 72 patients with myopia 3,5-14,0 D without any signs of glaucoma were studied. Analysis of optic disc parameters were carried out in 5 groups of patients according to disc area: less than 1,5 mm2, 1,5- 2,5 mm2, 2,5-3,0 mm2, 3,0-3,5 mm2 and more than 3,5 mm2. An accurate depending on disc area was revealed for all optic disc parameters in all sectors, which was manifested by increasing cup disc and rim disc (area and volume) and other parameters. We consider it is necessary to use the proper tables for right interpretation of received data for early diagnosis of glaucoma.

Neuroretinal Rim Area Change in Glaucoma Patients With Visual Field Progression Endpoints and Intraocular Pressure Reduction. The Canadian Glaucoma Study: 4.

PubMed

Malik, Rizwan; O'Leary, Neil; Mikelberg, Frederick S; Balazsi, A Gordon; LeBlanc, Raymond P; Lesk, Mark R; Nicolela, Marcelo T; Trope, Graham E; Chauhan, Balwantray C

2016-03-01

To compare rim area rates in patients with and without the visual field (VF) progression endpoint in the Canadian Glaucoma Study and determine whether intraocular pressure (IOP) reduction following the endpoint altered rim area rate. Prospective multicenter cohort study. setting: University hospitals. Two hundred and six patients with open-angle glaucoma were examined at 4-month intervals with standard automated perimetry and confocal scanning laser tomography. After the endpoint, IOP was reduced by ≥20%. Univariate analysis for change in rim area rate and multivariable analysis to adjust for independent covariates (eg, age, sex, and IOP). Patients with an endpoint (n = 59) had a worse rim area rate prior to the endpoint compared to those without (n = 147; median [interquartile range]: -14 [-32, 11] × 10(-3) mm(2)/y and -5 [-14, 5] × 10(-3) mm(2)/y, respectively, P = .02). In univariate analysis, there was no difference in rim area rate before and after the endpoint (median difference [95% CI], 8 (-10, 24) × 10(-3) mm(2)/y), but the muItivariate analysis showed that IOP reduction >2 mm Hg after the endpoint was strongly linked to a reduction in rim area rate decline (8 × 10(-3) mm(2)/y for each additional 1 mm Hg reduction). Patients with a VF endpoint had a median rim area rate that was nearly 3 times worse than those without an endpoint. Lower mean follow-up IOP was independently associated with a slower decline in rim area. Copyright © 2016 Elsevier Inc. All rights reserved.

An integrated method for atherosclerotic carotid plaque segmentation in ultrasound image.

PubMed

Qian, Chunjun; Yang, Xiaoping

2018-01-01

Carotid artery atherosclerosis is an important cause of stroke. Ultrasound imaging has been widely used in the diagnosis of atherosclerosis. Therefore, segmenting atherosclerotic carotid plaque in ultrasound image is an important task. Accurate plaque segmentation is helpful for the measurement of carotid plaque burden. In this paper, we propose and evaluate a novel learning-based integrated framework for plaque segmentation. In our study, four different classification algorithms, along with the auto-context iterative algorithm, were employed to effectively integrate features from ultrasound images and later also the iteratively estimated and refined probability maps together for pixel-wise classification. The four classification algorithms were support vector machine with linear kernel, support vector machine with radial basis function kernel, AdaBoost and random forest. The plaque segmentation was implemented in the generated probability map. The performance of the four different learning-based plaque segmentation methods was tested on 29 B-mode ultrasound images. The evaluation indices for our proposed methods were consisted of sensitivity, specificity, Dice similarity coefficient, overlap index, error of area, absolute error of area, point-to-point distance, and Hausdorff point-to-point distance, along with the area under the ROC curve. The segmentation method integrated the random forest and an auto-context model obtained the best results (sensitivity 80.4 ± 8.4%, specificity 96.5 ± 2.0%, Dice similarity coefficient 81.0 ± 4.1%, overlap index 68.3 ± 5.8%, error of area -1.02 ± 18.3%, absolute error of area 14.7 ± 10.9%, point-to-point distance 0.34 ± 0.10 mm, Hausdorff point-to-point distance 1.75 ± 1.02 mm, and area under the ROC curve 0.897), which were almost the best, compared with that from the existed methods. Our proposed learning-based integrated framework investigated in this study could be useful for atherosclerotic carotid plaque segmentation, which will be helpful for the measurement of carotid plaque burden. Copyright © 2017 Elsevier B.V. All rights reserved.

Challenges and advantages in wide-field optical coherence tomography angiography imaging of the human retinal and choroidal vasculature at 1.7-MHz A-scan rate

NASA Astrophysics Data System (ADS)

Poddar, Raju; Migacz, Justin V.; Schwartz, Daniel M.; Werner, John S.; Gorczynska, Iwona

2017-10-01

We present noninvasive, three-dimensional, depth-resolved imaging of human retinal and choroidal blood circulation with a swept-source optical coherence tomography (OCT) system at 1065-nm center wavelength. Motion contrast OCT imaging was performed with the phase-variance OCT angiography method. A Fourier-domain mode-locked light source was used to enable an imaging rate of 1.7 MHz. We experimentally demonstrate the challenges and advantages of wide-field OCT angiography (OCTA). In the discussion, we consider acquisition time, scanning area, scanning density, and their influence on visualization of selected features of the retinal and choroidal vascular networks. The OCTA imaging was performed with a field of view of 16 deg (5 mm×5 mm) and 30 deg (9 mm×9 mm). Data were presented in en face projections generated from single volumes and in en face projection mosaics generated from up to 4 datasets. OCTA imaging at 1.7 MHz A-scan rate was compared with results obtained from a commercial OCTA instrument and with conventional ophthalmic diagnostic methods: fundus photography, fluorescein, and indocyanine green angiography. Comparison of images obtained from all methods is demonstrated using the same eye of a healthy volunteer. For example, imaging of retinal pathology is presented in three cases of advanced age-related macular degeneration.

Novel Three-Dimensional Understanding of Maxillary Cleft Distraction.

PubMed

Vaughan, Stephen Michael; Kau, Chung How; Waite, Peter Daniel

2016-09-01

To set forth a universal standard methodology for quantifying volumetric and linear changes in the craniofacial complex, utilizing three-dimensional data captured from a cleft-lip palate patient who underwent rigid external device (RED) distraction. Cone beam computed tomography images of a 14-year-old patient were captured using a Kodak 9500 (Atlanta, GA) Cone Beam system device and a stereophotogrammetric system (3dMDface(TM) Atlanta, GA). The subject was a nonsyndromic unilateral cleft-lip palate patient who received RED distraction as part of maxillary advancement in conjunction with orthodontic treatment. Preop (T1) and postop (T2) images were superimposed using Invivo 5.2.3 (San Jose, CA) software. Volumetric rendering of the airway, bone, and soft tissues, as well as linear measurements were analyzed. Each measurement was captured 10 times to ensure reliability and reproducibility of methodology. Data from T1 to T2 revealed mean differences as follows: airway total volume +5250 mm, minimum cross-sectional area +67.84 mm; bone +1719 mm, soft tissue +44,432 mm. Mean of linear measurements: Pronasale 1.98 mm, Subnasale 3.35 mm, Labial superius 10.79 mm, Labial inferius 4.13 mm, Right alare 5.71 mm, Right cheilion 7.83 mm, Left alare 4.97 mm, Left cheilion 5.50 mm, Pogonion 3.01 mm, B-point 2.49 mm, U1-U1 9.77 mm, and L1-L1 0.00 mm. P values are <0.001 for each analysis. This paper represents a novel and innovative way to look at prepost RED distractions in a three-dimensional format. A universal standard analysis of the craniofacial complex can be implemented using the techniques and method outlined in this study.

Fully automated contour detection of the ascending aorta in cardiac 2D phase-contrast MRI.

PubMed

Codari, Marina; Scarabello, Marco; Secchi, Francesco; Sforza, Chiarella; Baselli, Giuseppe; Sardanelli, Francesco

2018-04-01

In this study we proposed a fully automated method for localizing and segmenting the ascending aortic lumen with phase-contrast magnetic resonance imaging (PC-MRI). Twenty-five phase-contrast series were randomly selected out of a large population dataset of patients whose cardiac MRI examination, performed from September 2008 to October 2013, was unremarkable. The local Ethical Committee approved this retrospective study. The ascending aorta was automatically identified on each phase of the cardiac cycle using a priori knowledge of aortic geometry. The frame that maximized the area, eccentricity, and solidity parameters was chosen for unsupervised initialization. Aortic segmentation was performed on each frame using active contouring without edges techniques. The entire algorithm was developed using Matlab R2016b. To validate the proposed method, the manual segmentation performed by a highly experienced operator was used. Dice similarity coefficient, Bland-Altman analysis, and Pearson's correlation coefficient were used as performance metrics. Comparing automated and manual segmentation of the aortic lumen on 714 images, Bland-Altman analysis showed a bias of -6.68mm 2 , a coefficient of repeatability of 91.22mm 2 , a mean area measurement of 581.40mm 2 , and a reproducibility of 85%. Automated and manual segmentation were highly correlated (R=0.98). The Dice similarity coefficient versus the manual reference standard was 94.6±2.1% (mean±standard deviation). A fully automated and robust method for identification and segmentation of ascending aorta on PC-MRI was developed. Its application on patients with a variety of pathologic conditions is advisable. Copyright © 2017 Elsevier Inc. All rights reserved.

Detecting multiple adulterants in dry milk using Raman chemical imaging

USDA-ARS?s Scientific Manuscript database

A Raman chemical imaging method was developed for detecting the presence of multiple chemical adulterants in dry milk powder. Four chemicals (ammonium sulfate, dicyandiamide, melamine, and urea) were added in equal concentrations, between 0.1% and 5.0%, to nonfat dry milk. An area of 25×25 mm2 for e...

Permanent Scatterer InSAR Analysis and Validation in the Gulf of Corinth.

PubMed

Elias, Panagiotis; Kontoes, Charalabos; Papoutsis, Ioannis; Kotsis, Ioannis; Marinou, Aggeliki; Paradissis, Dimitris; Sakellariou, Dimitris

2009-01-01

The Permanent Scatterers Interferometric SAR technique (PSInSAR) is a method that accurately estimates the near vertical terrain deformation rates, of the order of ∼1 mm year(-1), overcoming the physical and technical restrictions of classic InSAR. In this paper the method is strengthened by creating a robust processing chain, incorporating PSInSAR analysis together with algorithmic adaptations for Permanent Scatterer Candidates (PSCs) and Permanent Scatterers (PSs) selection. The processing chain, called PerSePHONE, was applied and validated in the geophysically active area of the Gulf of Corinth. The analysis indicated a clear subsidence trend in the north-eastern part of the gulf, with the maximum deformation of ∼2.5 mm year(-1) occurring in the region north of the Gulf of Alkyonides. The validity of the results was assessed against geophysical/geological and geodetic studies conducted in the area, which include continuous seismic profiling data and GPS height measurements. All these observations converge to the same deformation pattern as the one derived by the PSInSAR technique.

Permanent Scatterer InSAR Analysis and Validation in the Gulf of Corinth

PubMed Central

Elias, Panagiotis; Kontoes, Charalabos; Papoutsis, Ioannis; Kotsis, Ioannis; Marinou, Aggeliki; Paradissis, Dimitris; Sakellariou, Dimitris

2009-01-01

The Permanent Scatterers Interferometric SAR technique (PSInSAR) is a method that accurately estimates the near vertical terrain deformation rates, of the order of ∼1 mm year-1, overcoming the physical and technical restrictions of classic InSAR. In this paper the method is strengthened by creating a robust processing chain, incorporating PSInSAR analysis together with algorithmic adaptations for Permanent Scatterer Candidates (PSCs) and Permanent Scatterers (PSs) selection. The processing chain, called PerSePHONE, was applied and validated in the geophysically active area of the Gulf of Corinth. The analysis indicated a clear subsidence trend in the north-eastern part of the gulf, with the maximum deformation of ∼2.5 mm year-1 occurring in the region north of the Gulf of Alkyonides. The validity of the results was assessed against geophysical/geological and geodetic studies conducted in the area, which include continuous seismic profiling data and GPS height measurements. All these observations converge to the same deformation pattern as the one derived by the PSInSAR technique. PMID:22389587

Mapping evapotranspiration based on remote sensing: An application to Canada's landmass

NASA Astrophysics Data System (ADS)

Liu, J.; Chen, J. M.; Cihlar, J.

2003-07-01

The evapotranspiration (ET) from all Canadian landmass in 1996 is estimated at daily steps and 1 km resolution using a process model named boreal ecosystem productivity simulator (BEPS). The model is driven by remotely sensed leaf area index and land cover maps as well as soil water holding capacity and daily meteorological data. All the major ET components are considered: transpiration from vegetation, evaporation of canopy-intercepted rainfall, evaporation from soil, sublimation of snow in winter and in permafrost and glacier areas, and sublimation of canopy-intercepted snow. In forested areas the transpiration from both the overstory and understory vegetation is modeled separately. The Penman-Monteith method was applied to sunlit and shaded leaf groups individually in modeling the canopy-level transpiration, a methodological improvement necessary for forest canopies with considerable foliage clumping. The modeled ET map displays pronounced east-west and north-south gradients as well as detailed variations with cover types and vegetation density. It is estimated that for a relative wet year of 1996, the total ET from all Canada's landmass (excluding inland waters) was 2037 km3. If compared with the total precipitation of 5351 km3 based on the data from a medium range meteorological forecast model, the ratio of ET to precipitation was 38%. The ET averaged over Canadian land surface was 228 mm/yr in 1996, partitioned into transpiration of 102 mm yr-1 and evaporation and sublimation of 126 mm yr-1. Forested areas contributed the largest fraction of the total national ET at 59%. Averaged for all cover types, transpiration accounted for 45% of the total ET, while in forested areas, transpiration contributed 51% of ET. Modeled results of daily ET are compared with eddy covariance measurements at three forested sites with a r2 value of 0.61 and a root mean square error of 0.7 mm/day.

Quantifying the Spatial Distribution of Evapotranspiration over Canada With a Process Model Using Remote Sensing, Meteorological, and Soil Data

NASA Astrophysics Data System (ADS)

Liu, J.; Chen, J.; Cihlar, J.

2004-12-01

The evapotranspiration (ET) from all Canadian landmass is estimated at daily steps and 1 km resolution using a process model named Boreal Ecosystem Productivity Simulator (BEPS). The model is driven by remotely sensed leaf area index and land cover maps, as well as soil water holding capacity and daily meteorological data. All the major ET components are considered: transpiration from vegetation, evaporation of canopy-intercepted rainfall, evaporation from soil, sublimation of snow in winter and in permafrost and glacier areas, and sublimation of canopy-intercepted snow. In forested areas, the transpiration from both the overstory and understory vegetation is modelled separately. The Penman-Monteith method was applied to sunlit and shaded leaf groups individually in modelling the canopy-level transpiration, a methodological improvement necessary for forest canopies with considerable foliage clumping. The modelled ET map displays pronounced east-west and north-south gradients as well as detailed variations with cover types and vegetation density. It is estimated that, for a relative wet year of 1996, the total ET from all Canada's landmass (excluding inland waters) was 2037 km3. If compared with the total precipitation of 5351 km3 based on the data from a medium range meteorological forecast model, the ratio of ET to precipitation was 38 %. The ET averaged over Canadian land surface was 228 mm/yr in 1996, partitioned into transpiration of 102 mm/yr and evaporation and sublimation of 126 mm/yr. Forested areas contributed the largest fraction of the total national ET at 59 %. Averaged for all cover types, transpiration accounted for 45 % of the total ET, while in forested areas, transpiration was contributed 51 % of ET. Modelled results of daily ET are compared with eddy covariance measurements at three forested sites with a r2 value of 0.61 and a root mean square error of 0.7 mm/day.

Large area x-ray detectors for cargo radiography

NASA Astrophysics Data System (ADS)

Bueno, C.; Albagli, D.; Bendahan, J.; Castleberry, D.; Gordon, C.; Hopkins, F.; Ross, W.

2007-04-01

Large area x-ray detectors based on phosphors coupled to flat panel amorphous silicon diode technology offer significant advances for cargo radiologic imaging. Flat panel area detectors provide large object coverage offering high throughput inspections to meet the high flow rate of container commerce. These detectors provide excellent spatial resolution when needed, and enhanced SNR through low noise electronics. If the resolution is reduced through pixel binning, further advances in SNR are achievable. Extended exposure imaging and frame averaging enables improved x-ray penetration of ultra-thick objects, or "select-your-own" contrast sensitivity at a rate many times faster than LDAs. The areal coverage of flat panel technology provides inherent volumetric imaging with the appropriate scanning methods. Flat panel area detectors have flexible designs in terms of electronic control, scintillator selection, pixel pitch, and frame rates. Their cost is becoming more competitive as production ramps up for the healthcare, nondestructive testing (NDT), and homeland protection industries. Typically used medical and industrial polycrystalline phosphor materials such as Gd2O2S:Tb (GOS) can be applied to megavolt applications if the phosphor layer is sufficiently thick to enhance x-ray absorption, and if a metal radiator is used to augment the quantum detection efficiency and reduce x-ray scatter. Phosphor layers ranging from 0.2-mm to 1-mm can be "sandwiched" between amorphous silicon flat panel diode arrays and metal radiators. Metal plates consisting of W, Pb or Cu, with thicknesses ranging from 0.25-mm to well over 1-mm can be used by covering the entire area of the phosphor plate. In some combinations of high density metal and phosphor layers, the metal plate provides an intensification of 25% in signal due to electron emission from the plate and subsequent excitation within the phosphor material. This further improves the SNR of the system.

3D and 2D marginal fit of pressed and CAD/CAM lithium disilicate crowns made from digital and conventional impressions.

PubMed

Anadioti, Evanthia; Aquilino, Steven A; Gratton, David G; Holloway, Julie A; Denry, Isabelle; Thomas, Geb W; Qian, Fang

2014-12-01

This in vitro study evaluated the 3D and 2D marginal fit of pressed and computer-aided-designed/computer-aided-manufactured (CAD/CAM) all-ceramic crowns made from digital and conventional impressions. A dentoform tooth (#30) was prepared for an all-ceramic crown (master die). Thirty type IV definitive casts were made from 30 polyvinyl siloxane (PVS) impressions. Thirty resin models were produced from thirty Lava Chairside Oral Scanner impressions. Thirty crowns were pressed in lithium disilicate (IPS e.max Press; 15/impression technique). Thirty crowns were milled from lithium disilicate blocks (IPS e.max CAD; 15/impression technique) using the E4D scanner and milling engine. The master die and the intaglio of the crowns were digitized using a 3D laser coordinate measurement machine with accuracy of ±0.00898 mm. For each specimen a separate data set was created for the Qualify 2012 software. The digital master die and the digital intaglio of each crown were merged using best-fitting alignment. An area above the margin with 0.75 mm occlusal-gingival width circumferentially was defined. The 3D marginal fit of each specimen was an average of all 3D gap values on that area. For the 2D measurements, the marginal gap was measured at two standardized points (on the margin and at 0.75 mm above the margin), from standardized facial-lingual and mesial-distal digitized sections. One-way ANOVA with post hoc Tukey's honestly significant difference and two-way ANOVA tests were used, separately, for statistical analysis of the 3D and 2D marginal data (alpha = 0.05). One-way ANOVA revealed that both 3D and 2D mean marginal gap for group A: PVS impression/IPS e.max Press (0.048 mm ± 0.009 and 0.040 mm ± 0.009) were significantly smaller than those obtained from the other three groups (p < 0.0001), while no significant differences were found among groups B: PVS impression/IPS e.max CAD (0.088 mm ± 0.024 and 0.076 mm ± 0.023), C: digital impression/IPS e.max Press (0.089 mm ± 0.020 and 0.075 mm ± 0.015) and D: digital impression/IPS e.max CAD (0.084 mm ± 0.021 and 0.074 mm ± 0.026). The results of two-way ANOVA revealed a significant interaction between impression techniques and crown fabrication methods for both 3D and 2D measurements. The combination of PVS impression method and press fabrication technique produced the most accurate 3D and 2D marginal fits. © 2014 by the American College of Prosthodontists.

Land subsidence in the San Joaquin Valley, California, USA, 2007-2014

NASA Astrophysics Data System (ADS)

Sneed, M.; Brandt, J. T.

2015-11-01

Rapid land subsidence was recently measured using multiple methods in two areas of the San Joaquin Valley (SJV): between Merced and Fresno (El Nido), and between Fresno and Bakersfield (Pixley). Recent land-use changes and diminished surface-water availability have led to increased groundwater pumping, groundwater-level declines, and land subsidence. Differential land subsidence has reduced the flow capacity of water-conveyance systems in these areas, exacerbating flood hazards and affecting the delivery of irrigation water. Vertical land-surface changes during 2007-2014 were determined by using Interferometric Synthetic Aperture Radar (InSAR), Continuous Global Positioning System (CGPS), and extensometer data. Results of the InSAR analysis indicate that about 7600 km2 subsided 50-540 mm during 2008-2010; CGPS and extensometer data indicate that these rates continued or accelerated through December 2014. The maximum InSAR-measured rate of 270 mm yr-1 occurred in the El Nido area, and is among the largest rates ever measured in the SJV. In the Pixley area, the maximum InSAR-measured rate during 2008-2010 was 90 mm yr-1. Groundwater was an important part of the water supply in both areas, and pumping increased when land use changed or when surface water was less available. This increased pumping caused groundwater-level declines to near or below historical lows during the drought periods 2007-2009 and 2012-present. Long-term groundwater-level and land-subsidence monitoring in the SJV is critical for understanding the interconnection of land use, groundwater levels, and subsidence, and evaluating management strategies that help mitigate subsidence hazards to infrastructure while optimizing water supplies.

Nanoarmoring of Enzymes by Interlocking in Cellulose Fibers With Poly(Acrylic Acid).

PubMed

Riccardi, Caterina M; Kasi, Rajeswari M; Kumar, Challa V

2017-01-01

A simple method for interlocking glucose oxidase (GOx) and horseradish peroxidase (HRP) in cellulose fibers using poly(acrylic acid) (PAA) as an armor around the enzyme, without any need for activation of the cellulose support, is reported here. The resulting enzyme paper is an inexpensive, stable, simple, wearable, and washable biosensor. PAA functions as a multifunctional tether to interlock the enzyme molecules around the paper fibers so that the enzymes are protected against thermal/chemical denaturation and not released from the paper when washed with a detergent. The decreased conformational entropy of the interlocked enzyme protected by the nanoarmor is likely responsible for increased enzyme stability to heat and chemical denaturants (retained ≥70 percent enzyme activity after washing with urea or SDS for 30min), and the polymer protects the enzyme against inactivation by proteases, bacteria, inhibitors, etc. The kinetics of the interlocked enzyme were similar to that of the enzyme in solution. The V max was 6(±0.5)mM per minute before washing, then increased slightly to 9(±1.4)mM per minute after washing with water. The K m was 22(±6.4mM), which was slightly higher compared to GOx in solution (25-27mM). Because the surface area of the paper does not limit the enzyme loading, about 20% of enzyme was successfully loaded onto the paper (0.2g enzyme per gram of paper), and ≥95% of the enzyme was retained after washing. Interlocking works with other enzymes such as laccase, where ≥60% of the enzyme activity is retained. This novel methodology provides a low cost, simple, modular approach of achieving high enzyme loadings in ordinary filter paper, not limited by cellulose surface area, and there has been no need for complex methods of enzyme engineering or toxic methods of activation of the solid support to prepare highly active biocatalysts. © 2017 Elsevier Inc. All rights reserved.

A new Doppler-echo method to quantify regurgitant volume.

PubMed

Wang, S S; Rubenstein, J J; Goldman, M; Sidd, J J

1992-01-01

An in vitro technique using color flow imaging and continuous wave Doppler was developed to measure the initial regurgitant flow jet diameter and velocity integral to yield the parameters for a volume calculation. Jets were produced by volume-controlled injection through tubes of various diameters (1.3, 1.9, 2.8, and 3.5 mm) to deliver volumes from 1 to 7 ml over 100 to 300 msec at pressures from 40 to 200 mm Hg. One hundred forty-five samples were obtained. Flow jet diameter consistently overestimated tube diameter by 2 mm when injected volume was 1.5 to 7 ml and by 1.5 mm when injected volume was less than 1.5 ml. This offset was stable with various transducers (2.5, 3.5, 5.0 MHz) at normal gain setting (just under noise). Therefore, corrected flow jet diameter (FJD) = FJD - 2 mm, and Doppler volume = corrected flow jet area x velocity integral. A range of injectates from 1.1 to 7 ml generated Doppler volume of 1.0 to 8.2 ml. The relation between Doppler volume (DV) and injected volume (IV) was DV = 1.079 IV - 0.22, r2 = 0.945, p less than 0.01. This relation was not altered by tube diameter. Thus a method combining color flow imaging and continuous wave Doppler provides a reliable and accurate measure of in vitro flow volume.

Permeability enhancement by shock cooling

NASA Astrophysics Data System (ADS)

Griffiths, Luke; Heap, Michael; Reuschlé, Thierry; Baud, Patrick; Schmittbuhl, Jean

2015-04-01

The permeability of an efficient reservoir, e.g. a geothermal reservoir, should be sufficient to permit the circulation of fluids. Generally speaking, permeability decreases over the life cycle of the geothermal system. As a result, is usually necessary to artificially maintain and enhance the natural permeability of these systems. One of the methods of enhancement -- studied here -- is thermal stimulation (injecting cold water at low pressure). This goal of this method is to encourage new thermal cracks within the reservoir host rocks, thereby increasing reservoir permeability. To investigate the development of thermal microcracking in the laboratory we selected two granites: a fine-grained (Garibaldi Grey granite, grain size = 0.5 mm) and a course-grained granite (Lanhelin granite, grain size = 2 mm). Both granites have an initial porosity of about 1%. Our samples were heated to a range of temperatures (100-1000 °C) and were either cooled slowly (1 °C/min) or shock cooled (100 °C/s). A systematic microstructural (2D crack area density, using standard stereological techniques, and 3D BET specific surface area measurements) and rock physical property (porosity, P-wave velocity, uniaxial compressive strength, and permeability) analysis was undertaken to understand the influence of slow and shock cooling on our reservoir granites. Microstructurally, we observe that the 2D crack surface area per unit volume and the specific surface area increase as a result of thermal stressing, and, for the same maximum temperature, crack surface area is higher in the shock cooled samples. This observation is echoed by our rock physical property measurements: we see greater changes for the shock cooled samples. We can conclude that shock cooling is an extremely efficient method of generating thermal microcracks and modifying rock physical properties. Our study highlights that thermal treatments are likely to be an efficient method for the "matrix" permeability enhancement of granitic geothermal reservoirs.

Standardized quantitative measurements of wrist cartilage in healthy humans using 3T magnetic resonance imaging

PubMed Central

Zink, Jean-Vincent; Souteyrand, Philippe; Guis, Sandrine; Chagnaud, Christophe; Fur, Yann Le; Militianu, Daniela; Mattei, Jean-Pierre; Rozenbaum, Michael; Rosner, Itzhak; Guye, Maxime; Bernard, Monique; Bendahan, David

2015-01-01

AIM: To quantify the wrist cartilage cross-sectional area in humans from a 3D magnetic resonance imaging (MRI) dataset and to assess the corresponding reproducibility. METHODS: The study was conducted in 14 healthy volunteers (6 females and 8 males) between 30 and 58 years old and devoid of articular pain. Subjects were asked to lie down in the supine position with the right hand positioned above the pelvic region on top of a home-built rigid platform attached to the scanner bed. The wrist was wrapped with a flexible surface coil. MRI investigations were performed at 3T (Verio-Siemens) using volume interpolated breath hold examination (VIBE) and dual echo steady state (DESS) MRI sequences. Cartilage cross sectional area (CSA) was measured on a slice of interest selected from a 3D dataset of the entire carpus and metacarpal-phalangeal areas on the basis of anatomical criteria using conventional image processing radiology software. Cartilage cross-sectional areas between opposite bones in the carpal region were manually selected and quantified using a thresholding method. RESULTS: Cartilage CSA measurements performed on a selected predefined slice were 292.4 ± 39 mm2 using the VIBE sequence and slightly lower, 270.4 ± 50.6 mm2, with the DESS sequence. The inter (14.1%) and intra (2.4%) subject variability was similar for both MRI methods. The coefficients of variation computed for the repeated measurements were also comparable for the VIBE (2.4%) and the DESS (4.8%) sequences. The carpus length averaged over the group was 37.5 ± 2.8 mm with a 7.45% between-subjects coefficient of variation. Of note, wrist cartilage CSA measured with either the VIBE or the DESS sequences was linearly related to the carpal bone length. The variability between subjects was significantly reduced to 8.4% when the CSA was normalized with respect to the carpal bone length. CONCLUSION: The ratio between wrist cartilage CSA and carpal bone length is a highly reproducible standardized measurement which normalizes the natural diversity between individuals. PMID:26396941

Analysis of spiramycin by capillary electrophoresis.

PubMed

González-Hernández, R; Li, Y M; Van Schepdael, A; Roets, E; Hoogmartens, J

1999-09-01

The development and validation of an analytical method for the determination of spiramycin I in the presence of its related substances by capillary electrophoresis is shown. The separation, performed in a phosphate buffer (80 mM, pH 7.5) containing 12 mM cetyltrimethylammonium bromide (CTAB) and 20 mM sodium cholate, with a 50 microm ID and 44 cm long fused-silica capillary (36 cm effective length), applying a voltage of 12 kV (l approximately 80 microA), at 25 degrees C, is achieved in 15 min. Good selectivity among spiramycin I and its related substances was obtained. The influence of the buffer pH, and of the CTAB and sodium cholate concentrations was investigated. The method robustness, examined by means of a full-fraction factorial design, shows that it can be used within the limits set for the three parameters that were investigated. The method is linear (r = 0.9992) and precise (day-to-day corrected peak area repeatability, n = 18, relative standard deviation = 1.3%). The limits of detection and quantitation are 7 pg (0.025%) and 22 pg (0.08%), respectively, relative to a 2 mg/mL solution.

A method of LED free-form tilted lens rapid modeling based on scheme language

NASA Astrophysics Data System (ADS)

Dai, Yidan

2017-10-01

According to nonimaging optical principle and traditional LED free-form surface lens, a new kind of LED free-form tilted lens was designed. And a method of rapid modeling based on Scheme language was proposed. The mesh division method was applied to obtain the corresponding surface configuration according to the character of the light source and the desired energy distribution on the illumination plane. Then 3D modeling software and the Scheme language programming are used to generate lens model respectively. With the help of optical simulation software, a light source with the size of 1mm*1mm*1mm in volume is used in experiment, and the lateral migration distance of illumination area is 0.5m, in which total one million rays are computed. We could acquire the simulated results of both models. The simulated output result shows that the Scheme language can prevent the model deformation problems caused by the process of the model transfer, and the degree of illumination uniformity is reached to 82%, and the offset angle is 26°. Also, the efficiency of modeling process is greatly increased by using Scheme language.

LOGISMOS-B for primates: primate cortical surface reconstruction and thickness measurement

NASA Astrophysics Data System (ADS)

Oguz, Ipek; Styner, Martin; Sanchez, Mar; Shi, Yundi; Sonka, Milan

2015-03-01

Cortical thickness and surface area are important morphological measures with implications for many psychiatric and neurological conditions. Automated segmentation and reconstruction of the cortical surface from 3D MRI scans is challenging due to the variable anatomy of the cortex and its highly complex geometry. While many methods exist for this task in the context of the human brain, these methods are typically not readily applicable to the primate brain. We propose an innovative approach based on our recently proposed human cortical reconstruction algorithm, LOGISMOS-B, and the Laplace-based thickness measurement method. Quantitative evaluation of our approach was performed based on a dataset of T1- and T2-weighted MRI scans from 12-month-old macaques where labeling by our anatomical experts was used as independent standard. In this dataset, LOGISMOS-B has an average signed surface error of 0.01 +/- 0.03mm and an unsigned surface error of 0.42 +/- 0.03mm over the whole brain. Excluding the rather problematic temporal pole region further improves unsigned surface distance to 0.34 +/- 0.03mm. This high level of accuracy reached by our algorithm even in this challenging developmental dataset illustrates its robustness and its potential for primate brain studies.

Analysis of the Factors Affecting Surgical Success of Implants Placed in Iranian Warfare Victims

PubMed Central

Jafarian, Mohammad; Bayat, Mohammad; Pakravan, Amir-Hossein; Emadi, Naghmeh

2016-01-01

Objective The aim was to evaluate the survival time and success rates of dental implants in warfare victims and factors that affect implant success. Subjects and Methods This retrospective study involved 250 Iranian warfare victims who received dental implants from 2003 to 2013. Patients' demographic characteristics, as well as the brand, diameter, length, location and failure rate of the implants were retrieved from patients' dental records and radiographs. The associations between these data and the survival rate were analyzed. Statistical analysis was carried out with χ2 and log-rank tests. Results Overall, out of the 1,533 dental implants, 61 (4s%) failed. The maxillary canine area had the highest failure rate [9 of 132 implants (6.8s%)], while the mandibular incisor region had the least number of failures [3 of 147 implants (2.0s%)] and the longest survival time (approximately 3,182 days). Maxillary canine areas had the shortest survival (about 2,996 days). The longest survival time was observed in implants with 11 mm length (3,179.72 ± 30.139 days) and 3.75-4 mm diameter (3,131.161 ± 35.96 days), and the shortest survival was found in implants with 11.5 mm length (2,317.79 ± 18.71 days) and 6.5 mm diameter (2,241.45 ± 182.21 days). Moreover, implants with 10 mm length (10.7s%) and 5.5-6 mm diameter (22.2s%) had the highest failure rate; however, the least failure rate occurred when the implants were 11.5 mm in length (1.9s%) and 3-3.5 mm in diameter (3.1s%). Conclusions The brand, length and diameter of implants affected the survival time, failure rate and time to failure. The location of the implant was not statistically significant regarding the mentioned factors, although it has clinical significance. PMID:27322534

New type of multijunction thermopile IR detector

NASA Astrophysics Data System (ADS)

Sun, Tietun; Guo, Lihui

1996-09-01

A newly designed thin-film thermopile infrared detector, which as an absorption layer and a sensitive area on two sides are fabricated using integrated-circuit technology. The device uses a series-connected thermocouples array whose `hot' junction are supported on a thin Myler film of 1 - 3 micrometers thickness. By a special method of fasting the shadow mask, the thermopile with 48 Bi-Sb couples for 2 X 2 mm(superscript 2) area produces a responsivity of 50 - 70 V/W and relaxation time of about 70 ms.

Light-controlled biphasic current stimulator IC using CMOS image sensors for high-resolution retinal prosthesis and in vitro experimental results with rd1 mouse.

PubMed

Oh, Sungjin; Ahn, Jae-Hyun; Lee, Sangmin; Ko, Hyoungho; Seo, Jong Mo; Goo, Yong-Sook; Cho, Dong-il Dan

2015-01-01

Retinal prosthetic devices stimulate retinal nerve cells with electrical signals proportional to the incident light intensities. For a high-resolution retinal prosthesis, it is necessary to reduce the size of the stimulator pixels as much as possible, because the retinal nerve cells are concentrated in a small area of approximately 5 mm × 5 mm. In this paper, a miniaturized biphasic current stimulator integrated circuit is developed for subretinal stimulation and tested in vitro. The stimulator pixel is miniaturized by using a complementary metal-oxide-semiconductor (CMOS) image sensor composed of three transistors. Compared to a pixel that uses a four-transistor CMOS image sensor, this new design reduces the pixel size by 8.3%. The pixel size is further reduced by simplifying the stimulation-current generating circuit, which provides a 43.9% size reduction when compared to the design reported to be the most advanced version to date for subretinal stimulation. The proposed design is fabricated using a 0.35 μm bipolar-CMOS-DMOS process. Each pixel is designed to fit in a 50 μ m × 55 μm area, which theoretically allows implementing more than 5000 pixels in the 5 mm × 5 mm area. Experimental results show that a biphasic current in the range of 0 to 300 μA at 12 V can be generated as a function of incident light intensities. Results from in vitro experiments with rd1 mice indicate that the proposed method can be effectively used for retinal prosthesis with a high resolution.

Modeling evapotranspiration over China's landmass from 1979-2012 using three surface models

NASA Astrophysics Data System (ADS)

Sun, Shaobo; Chen, Baozhang; Zhang, Huifang; Lin, Xiaofeng

2017-04-01

Land surface models (LSMs) are useful tools to estimate land evapotranspiration at a grid scale and for a long-term applications. Here, the Community Land Model 4.0 (CLM4.0), Dynamic Land Model (DLM) and Variable Infiltration Capacity (VIC) model were driven with observation-based forcing data sets, and a multiple LSM ensemble-averaged evapotranspiration (ET) product (LSMs-ET) was developed and its spatial-temporal variations were analyzed for the China landmass over the period 1979-2012. Evaluations against measurements from nine flux towers at site scale and surface water budget based ET at regional scale showed that the LSMs-ET had good performance in most areas of China's landmass. The inter-comparisons between the ET estimates and the independent ET products from remote sensing and upscaling methods suggested that there were a fairly consistent patterns between each data sets. The LSMs-ET produced a mean annual ET of 351.24±10.7 mm yr-1 over 1979-2012, and its spatial-temporal variation analyses showed that (i) there was an overall significant ET increasing trend, with a value of 0.72 mm yr-1 (p < 0.01); (ii) 36.01% of Chinese land had significant increasing trends, ranging from 1 to 9 mm yr-1, while only 6.41% of the area showed significant decreasing trends, ranging from -6.28 to -0.08 mm yr-1. Analyses of ET variations in each climate region clearly showed that the Tibetan Plateau areas were the main contributors to the overall increasing ET trends of China.

Delamination failure of multilaminated adhesively bonded joints at low temperatures

NASA Astrophysics Data System (ADS)

Lee, Chi-Seung; Chun, Min-Sung; Kim, Myung-Hyun; Lee, Jae-Myung

2011-08-01

A series of experimental investigations of multilaminated joints adhesively bonded by epoxy/polyurethane (PU) glue were conducted in order to examine the delamination failure characteristics under in-plane shear loading at low temperatures. In order to observe these phenomena, a series of lap-shear tests were carried out at various low temperatures (20 °C, -110 °C and -163 °C) and various adhesion areas (15 mm × 50 mm, 30 mm × 50 mm, 50 mm × 50 mm, 75 mm × 50 mm and 100 mm × 50 mm). The test results were used to investigate the delamination and material characteristics, as well as the material properties, e.g., ultimate shear stress and shear elongation. Furthermore, the dependencies of the characteristics of multilaminated adhesively bonded joints (MABJs) on temperature and adhesion area was analyzed using the stress-strain relationship, and closed form formulas that are functions of the dependent parameters are proposed.

Variation of Vegetation Ecological Water Consumption and Its Response to Vegetation Coverage Changes in the Rocky Desertification Areas in South China

PubMed Central

Zhou, Jinxing; Guo, Hongyan; Cui, Ming; Liu, Yuguo; Ning, Like; Tang, Fukai

2016-01-01

Over the past several decades, rocky desertification has led to severe ecological problems in karst areas in South China. After a rocky desertification treatment project was completed, the vegetation coverage changed greatly and, consequently, increased the ecology water consumption (approximately equal to the actual evapotranspiration) of the regional vegetation. Thus, it intensified the regional water stresses. This study explored the changes in the actual evapotranspiration (ETa) response to the vegetation coverage changes in the rocky desertification areas in South China based on the precipitation (P), potential evapotranspiration (ETp) and NDVI (the normalized difference vegetation index) datasets. The revised Bagrov model was used to simulate the actual evapotranspiration changes with the supposed increasing NDVI. The results indicated that the average NDVI value was lower when the rocky desertification was more severe. The ETa, evapotranspiration efficiency (ETa/ETp) and potential humidity (P/ETp) generally increased with the increasing NDVI. The sensitivity of the ETa response to vegetation coverage changes varied due to different precipitation conditions and different rocky desertification severities. The ETa was more sensitive under drought conditions. When a drought occurred, the ETa exhibited an average increase of 40~60 mm with the NDVI increasing of 0.1 in the rocky desertification areas. Among the 5 different severity categories of rocky desertification, the ETa values’ responses to NDVI changes were less sensitive in the severe rocky desertification areas but more sensitive in the extremely and potential rocky desertification areas. For example, with the NDVI increasing of 0.025, 0.05, 0.075, and 0.1, the corresponding ETa changes increased by an average of 2.64 mm, 10.62 mm, 19.19 mm, and 27.58 mm, respectively, in severe rocky desertification areas but by 4.94 mm, 14.99 mm, 26.80, and 37.13 mm, respectively, in extremely severe rocky desertification areas. Understanding the vegetation ecological water consumption response to the vegetation coverage changes is essential for the vegetation restoration and water stresses mitigation in rocky desertification areas. PMID:27798642

Variation of Vegetation Ecological Water Consumption and Its Response to Vegetation Coverage Changes in the Rocky Desertification Areas in South China.

PubMed

Wan, Long; Tong, Jing; Zhou, Jinxing; Guo, Hongyan; Cui, Ming; Liu, Yuguo; Ning, Like; Tang, Fukai

2016-01-01

Over the past several decades, rocky desertification has led to severe ecological problems in karst areas in South China. After a rocky desertification treatment project was completed, the vegetation coverage changed greatly and, consequently, increased the ecology water consumption (approximately equal to the actual evapotranspiration) of the regional vegetation. Thus, it intensified the regional water stresses. This study explored the changes in the actual evapotranspiration (ETa) response to the vegetation coverage changes in the rocky desertification areas in South China based on the precipitation (P), potential evapotranspiration (ETp) and NDVI (the normalized difference vegetation index) datasets. The revised Bagrov model was used to simulate the actual evapotranspiration changes with the supposed increasing NDVI. The results indicated that the average NDVI value was lower when the rocky desertification was more severe. The ETa, evapotranspiration efficiency (ETa/ETp) and potential humidity (P/ETp) generally increased with the increasing NDVI. The sensitivity of the ETa response to vegetation coverage changes varied due to different precipitation conditions and different rocky desertification severities. The ETa was more sensitive under drought conditions. When a drought occurred, the ETa exhibited an average increase of 40~60 mm with the NDVI increasing of 0.1 in the rocky desertification areas. Among the 5 different severity categories of rocky desertification, the ETa values' responses to NDVI changes were less sensitive in the severe rocky desertification areas but more sensitive in the extremely and potential rocky desertification areas. For example, with the NDVI increasing of 0.025, 0.05, 0.075, and 0.1, the corresponding ETa changes increased by an average of 2.64 mm, 10.62 mm, 19.19 mm, and 27.58 mm, respectively, in severe rocky desertification areas but by 4.94 mm, 14.99 mm, 26.80, and 37.13 mm, respectively, in extremely severe rocky desertification areas. Understanding the vegetation ecological water consumption response to the vegetation coverage changes is essential for the vegetation restoration and water stresses mitigation in rocky desertification areas.

Women Build Long Bones With Less Cortical Mass Relative to Body Size and Bone Size Compared With Men.

PubMed

Jepsen, Karl J; Bigelow, Erin M R; Schlecht, Stephen H

2015-08-01

The twofold greater lifetime risk of fracturing a bone for white women compared with white men and black women has been attributed in part to differences in how the skeletal system accumulates bone mass during growth. On average, women build more slender long bones with less cortical area compared with men. Although slender bones are known to have a naturally lower cortical area compared with wider bones, it remains unclear whether the relatively lower cortical area of women is consistent with their increased slenderness or is reduced beyond that expected for the sex-specific differences in bone size and body size. Whether this sexual dimorphism is consistent with ethnic background and is recapitulated in the widely used mouse model also remains unclear. We asked (1) do black women build bones with reduced cortical area compared with black men; (2) do white women build bones with reduced cortical area compared with white men; and (3) do female mice build bones with reduced cortical area compared with male mice? Bone strength and cross-sectional morphology of adult human and mouse bone were calculated from quantitative CT images of the femoral midshaft. The data were tested for normality and regression analyses were used to test for differences in cortical area between men and women after adjusting for body size and bone size by general linear model (GLM). Linear regression analysis showed that the femurs of black women had 11% lower cortical area compared with those of black men after adjusting for body size and bone size (women: mean=357.7 mm2; 95% confidence interval [CI], 347.9-367.5 mm2; men: mean=400.1 mm2; 95% CI, 391.5-408.7 mm2; effect size=1.2; p<0.001, GLM). Likewise, the femurs of white women had 12% less cortical area compared with those of white men after adjusting for body size and bone size (women: mean=350.1 mm2; 95% CI, 340.4-359.8 mm2; men: mean=394.3 mm2; 95% CI, 386.5-402.1 mm2; effect size=1.3; p<0.001, GLM). In contrast, female and male femora from recombinant inbred mouse strains showed the opposite trend; femurs from female mice had a 4% larger cortical area compared with those of male mice after adjusting for body size and bone size (female: mean=0.73 mm2; 95% CI, 0.71-0.74 mm2; male: mean=0.70 mm2; 95% CI, 0.68-0.71 mm2; effect size=0.74; p=0.04, GLM). Female femurs are not simply a more slender version of male femurs. Women acquire substantially less mass (cortical area) for their body size and bone size compared with men. Our analysis questions whether mouse long bone is a suitable model to study human sexual dimorphism. Identifying differences in the way bones are constructed may be clinically important for developing sex-specific diagnostics and treatment strategies to reduce fragility fractures.

Morphological changes in the cervical intervertebral foramen dimensions with unilateral facet joint dislocation.

PubMed

Ebraheim, Nabil A; Liu, Jiayong; Ramineni, Satheesh K; Liu, Xiaochen; Xie, Joe; Hartman, Ryan G; Goel, Vijay K

2009-11-01

Many investigators have conducted studies to determine the biomechanics, causes, complications and treatment of unilateral facet joint dislocation in the cervical spine. However, there is no quantitative data available on morphological changes in the intervertebral foramen of the cervical spine following unilateral facet joint dislocation. These data are important to understand the cause of neurological compromise following unilateral facet joint dislocation. Eight embalmed human cadaver cervical spine specimens ranging from level C1-T1 were used. The nerve roots of these specimens at C5-C6 level were marked by wrapping a 0.12mm diameter wire around them. Unilateral facet dislocation at C5-C6 level was simulated by serially sectioning the corresponding ligamentous structures. A CT scan of the specimens was obtained before and after the dislocation was simulated. A sagittal plane through the centre of the pedicle and facet joint was constructed and used for measurement. The height and area of the intervertebral foramen, the facet joint space, nerve root diameter and area, and vertebral alignment both before and after dislocation were evaluated. The intervertebral foramen area changed from 50.72+/-0.88mm(2) to 67.82+/-4.77mm(2) on the non-dislocated side and from 41.39+/-1.11mm(2) to 113.77+/-5.65mm(2) on the dislocated side. The foraminal heights changed from 9.02+/-0.30mm to 10.52+/-0.50mm on the non-dislocated side and 10.43+/-0.50mm to 17.04+/-0.96mm on the dislocated side. The facet space area in the sagittal plane changed from 6.80+/-0.80mm(2) to 40.02+/-1.40mm(2) on the non-dislocated side. The C-5 anterior displacement showed a great change from 0mm to 5.40+/-0.24mm on the non-dislocated side and from 0mm to 3.42+/-0.20mm on the dislocated side. Neither of the nerve roots on either side showed a significant change in size. The lack of change in nerve root area indicates that the associated nerve injury with unilateral facet joint dislocation is probably due to distraction rather than due to direct nerve root compression.

Phase Composition Maps integrate mineral compositions with rock textures from the micro-meter to the thin section scale

NASA Astrophysics Data System (ADS)

Willis, Kyle V.; Srogi, LeeAnn; Lutz, Tim; Monson, Frederick C.; Pollock, Meagen

2017-12-01

Textures and compositions are critical information for interpreting rock formation. Existing methods to integrate both types of information favor high-resolution images of mineral compositions over small areas or low-resolution images of larger areas for phase identification. The method in this paper produces images of individual phases in which textural and compositional details are resolved over three orders of magnitude, from tens of micrometers to tens of millimeters. To construct these images, called Phase Composition Maps (PCMs), we make use of the resolution in backscattered electron (BSE) images and calibrate the gray scale values with mineral analyses by energy-dispersive X-ray spectrometry (EDS). The resulting images show the area of a standard thin section (roughly 40 mm × 20 mm) with spatial resolution as good as 3.5 μm/pixel, or more than 81 000 pixels/mm2, comparable to the resolution of X-ray element maps produced by wavelength-dispersive spectrometry (WDS). Procedures to create PCMs for mafic igneous rocks with multivariate linear regression models for minerals with solid solution (olivine, plagioclase feldspar, and pyroxenes) are presented and are applicable to other rock types. PCMs are processed using threshold functions based on the regression models to image specific composition ranges of minerals. PCMs are constructed using widely-available instrumentation: a scanning-electron microscope (SEM) with BSE and EDS X-ray detectors and standard image processing software such as ImageJ and Adobe Photoshop. Three brief applications illustrate the use of PCMs as petrologic tools: to reveal mineral composition patterns at multiple scales; to generate crystal size distributions for intracrystalline compositional zones and compare growth over time; and to image spatial distributions of minerals at different stages of magma crystallization by integrating textures and compositions with thermodynamic modeling.

Quantifying Digital Ulcers in Systemic Sclerosis: Reliability of Computer-Assisted Planimetry in Measuring Lesion Size.

PubMed

Simpson, V; Hughes, M; Wilkinson, J; Herrick, A L; Dinsdale, G

2018-03-01

Digital ulcers are a major problem in patients with systemic sclerosis (SSc), causing severe pain and impairment of hand function. In addition, digital ulcers heal slowly and sometimes become infected, which can lead to gangrene and necessitate amputation if appropriate intervention is not taken. A reliable, objective method for assessing digital ulcer healing or progression is needed in both the clinical and research arenas. This study was undertaken to compare 2 computer-assisted planimetry methods of measurement of digital ulcer area on photographs (ellipse and freehand regions of interest [ROIs]), and to assess the reliability of photographic calibration and the 2 methods of area measurement. Photographs were taken of 107 digital ulcers in 36 patients with SSc spectrum disease. Three raters assessed the photographs. Custom software allowed raters to calibrate photograph dimensions and draw ellipse or freehand ROIs. The shapes and dimensions of the ROIs were saved for further analysis. Calibration (by a single rater performing 5 repeats per image) produced an intraclass correlation coefficient (intrarater reliability) of 0.99. The mean ± SD areas of digital ulcers assessed using ellipse and freehand ROIs were 18.7 ± 20.2 mm 2 and 17.6 ± 19.3 mm 2 , respectively. Intrarater and interrater reliability of the ellipse ROI were 0.97 and 0.77, respectively. For the freehand ROI, the intrarater and interrater reliability were 0.98 and 0.76, respectively. Our findings indicate that computer-assisted planimetry methods applied to SSc-related digital ulcers can be extremely reliable. Further work is needed to move toward applying these methods as outcome measures for clinical trials and in clinical settings. © 2017, American College of Rheumatology.

Novel CO2 laser robotic controller outperforms experienced laser operators in tasks of accuracy and performance repeatability.

PubMed

Wong, Yu-Tung; Finley, Charles C; Giallo, Joseph F; Buckmire, Robert A

2011-08-01

To introduce a novel method of combining robotics and the CO(2) laser micromanipulator to provide excellent precision and performance repeatability designed for surgical applications. Pilot feasibility study. We developed a portable robotic controller that appends to a standard CO(2) laser micromanipulator. The robotic accuracy and laser beam path repeatability were compared to six experienced users of the industry standard micromanipulator performing the same simulated surgical tasks. Helium-neon laser beam video tracking techniques were employed. The robotic controller demonstrated superiority over experienced human manual micromanipulator control in accuracy (laser path within 1 mm of idealized centerline), 97.42% (standard deviation [SD] 2.65%), versus 85.11% (SD 14.51%), P = .018; and laser beam path repeatability (area of laser path divergence on successive trials), 21.42 mm(2) (SD 4.35 mm(2) ) versus 65.84 mm(2) (SD 11.93 mm(2) ), P = .006. Robotic micromanipulator control enhances accuracy and repeatability for specific laser tasks. Computerized control opens opportunity for alternative user interfaces and additional safety features. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

Ground measured evapotranspiration scaled to stand level using MODIS and Landsat sensors to study Tamarix spp.response to repeated defoliation by the Tamarix leaf beetle at two sites

NASA Astrophysics Data System (ADS)

Pearlstein, S.; Nagler, P. L.; Glenn, E. P.; Hultine, K. R.

2012-12-01

The Dolores River in Southern Utah and the Virgin River in Southern Nevada are ecosystems under pressure from increased groundwater withdrawal due to growing populations and introduced riparian species. We studied the impact of the biocontrol Tamarix leaf beetles (Dirohabda carinulata and D. elongata) on the introduced riparian species, Tamarix spp., phenology and water use over multiple cycles of annual defoliation. Heat balance sap flow measurements, leaf area index (LAI), well data, allometry and satellite imagery from Landsat Thematic Mapper 5 and EOS-1 Moderate Resolution Imaging Spectrometer (MODIS) sensors were used to assess the distribution of beetle defoliation and its effect on evapotranspiration (ET). Study objectives for the Virgin River were to measure pre-beetle arrival ET, while the Dolores River site has had defoliation since 2004 and is a site of long-term beetle effect monitoring. This study focuses on measurements conducted over two seasons, 2010 and 2011. At the Dolores River site, results from 2010 were inconclusive due to sensor malfunctions but plant ET by sap flow in 2011 averaged 1.02 mm/m^2 leaf area/day before beetle arrival, dropping to an average of 0.75 mm/m^2 leaf area/day after beetle arrival. Stand level estimations from May - December, 2010 by MODIS were about 0.63 mm/ day, results from Landsat were 0.51 mm/day in June and 0.78 in August. For January -September, 2011, MODIS values were about 0.6 mm/day, and Landsat was 0.57 mm/day in June and 0.62 mm/day in August. These values are lower than previously reported ET values for this site meaning that repeated defoliation does diminish stand level water use. The Virgin River site showed plant ET from sap flow averaged about 3.9-4 mm/m^2 leaf area/day from mid-May - September, 2010. In 2011, ET from sap flow averaged 3.83 mm/m^2 leaf area/day during June - July, but dropped to 3.73 mm/ m^2 leaf area/day after beetle arrival in August. The slight drop in plant ET is not significant, meaning that the first year of beetle arrival at this site did not result in significant water savings. Stand level ET by MODIS was about 2.2 mm/day in 2010, beetle arrival was captured in 2011 and about 1.5 mm/day in 2011. Landsat results in 2010 were 1.9 mm/day in June and 2.2 mm/day in August, in 2011 ET was 1.4 mm/day in June and 0.9 mm/day in August.

Tibial tunnel defect size as a risk factor in growth arrest following paediatric transphyseal anterior cruciate ligament reconstruction: an anatomical study.

PubMed

Pananwala, Hasitha; Jabbar, Yaser; Mills, Leonora; Symes, Michael; Nandapalan, Haren; Sefton, Andrew; Delungahawatte, Lasitha; Dao, Quang

2016-09-01

There is ongoing controversy regarding growth disturbances in younger patients undergoing anterior cruciate ligament reconstructions. Animal models have shown that an injury of 7-9% of the physeal area is a risk factor for growth disturbances. A total of 39 magnetic resonance imaging studies of the knee were examined. The proximal tibial physeal area was determined using a calibrated 'region of interest' ligature encompassing the tibial physis in the axial plane. The potential defect left by commonly used drill sizes was calculated as a percentage of the physeal area. A 7-mm drill leaves a mean defect of 1.45% physeal area (range: 1.11-1.89%, SD: 0.28, 95% CI: ±0.09), 8-mm drill leaves a 1.84% mean defect (range: 1.43-2.49%, SD: 0.38, 95% CI: ±0.12) and a 9-mm drill leaves a 2.30% mean defect (range: 1.83-3.19%, SD: 0.58, 95% CI: ±0.17). At 55°, 7-mm drill leaves a mean defect of 1.96% (range: 1.32-2.28%, SD: 0.37, 95% CI: ±0.12), 8-mm drill leaves a mean defect of 2.19% (range: 1.71-2.95%, SD: 0.46, 95% CI: ±0.14) and a 9-mm drill leaves a mean defect of 2.76% (range: 2.16-3.73%, SD: 0.58, 95% CI: ±0.18). There was a statistically significant difference in the tunnel area with a change of drill angle (7-mm drill P = 0.005, 8-mm drill P = 0.001, 9-mm drill P = 0.001). On the basis of this study in the context of animal model and observational evidence, the area of physeal injury using drill tunnels for anterior cruciate ligament reconstruction would not appear to contribute to potential growth disturbances. © 2016 Royal Australasian College of Surgeons.

[Relationship between image quality and cross-sectional area of phantom in three-dimensional positron emission tomography scan].

PubMed

Osawa, Atsushi; Miwa, Kenta; Wagatsuma, Kei; Takiguchi, Tomohiro; Tamura, Shintaro; Akimoto, Kenta

2012-01-01

The image quality in (18)FDG PET/CT often degrades as the body size increases. The purpose of this study was to evaluate the relationship between image quality and the body size using original phantoms of variable cross-sectional areas in PET/CT. We produced five water phantoms with different cross-sectional areas. The long axis of phantom was 925 mm, and the cross-sectional area was from 324 to 1189 cm(2). These phantoms with the sphere (diameter 10 mm) were filled with (18)F-FDG solution. The radioactivity concentration of background in the phantom was 1.37, 2.73, 4.09 and 5.46 kBq/mL. The scanning duration was 30 min in list mode acquisition for each measurement. Background variability (N(10 mm)), noise equivalent count rates (NECR(phantom)), hot sphere contrast (Q(H,10 mm)) as physical evaluation and visual score of sphere detection were measured, respectively. The relationship between image quality and the various cross-sectional areas was also analyzed under the above-mentioned conditions. As cross-sectional area increased, NECR(phantom) progressively decreased. Furthermore, as cross-sectional area increased, N(10 mm) increased and Q(H,10 mm) decreased. Image quality became degraded as body weight increased because noise and contrast contributed to image quality. The visual score of sphere detection deteriorated in high background radioactivity concentration because a false positive detection in cross-sectional area of the phantom increased. However, additional increases in scanning periods could improve the visual score. We assessed tendencies in the relationship between image quality and body size in PET/CT. Our results showed that time adjustment was more effective than dose adjustment for stable image quality of heavier patients in terms of the large cross-sectional area.

Validation of a Method To Screen for Pulmonary Hypertension in Advanced Idiopathic Pulmonary Fibrosis*

PubMed Central

Zisman, David A.; Karlamangla, Arun S.; Kawut, Steven M.; Shlobin, Oksana A.; Saggar, Rajeev; Ross, David J.; Schwarz, Marvin I.; Belperio, John A.; Ardehali, Abbas; Lynch, Joseph P.; Nathan, Steven D.

2008-01-01

Background We have developed a method to screen for pulmonary hypertension (PH) in idiopathic pulmonary fibrosis (IPF) patients, based on a formula to predict mean pulmonary artery pressure (MPAP) from standard lung function measurements. The objective of this study was to validate this method in a separate group of IPF patients. Methods Cross-sectional study of 60 IPF patients from two institutions. The accuracy of the MPAP estimation was assessed by examining the correlation between the predicted and measured MPAPs and the magnitude of the estimation error. The discriminatory ability of the method for PH was assessed using the area under the receiver operating characteristic curve (AUC). Results There was strong correlation in the expected direction between the predicted and measured MPAPs (r = 0.72; p < 0.0001). The estimated MPAP was within 5 mm Hg of the measured MPAP 72% of the time. The AUC for predicting PH was 0.85, and did not differ by institution. A formula-predicted MPAP > 21 mm Hg was associated with a sensitivity, specificity, positive predictive value, and negative predictive value of 95%, 58%, 51%, and 96%, respectively, for PH defined as MPAP from right-heart catheterization > 25 mm Hg. Conclusions A prediction formula for MPAP using standard lung function measurements can be used to screen for PH in IPF patients. PMID:18198245

Three-dimensional tomographic mapping related to primary stability and structural miniscrew characteristics.

PubMed

Silvestrini Biavati, A; Tecco, S; Migliorati, M; Festa, F; Panza, G; Marzo, G; Gherlone, E; Tetè, S

2011-05-01

To evaluate the maxilla, mandible, and cortical plates on computerized tomographic (CT) scans to achieve accurate three-dimensional bone thickness measurements. We selected the CT scans of 25 subjects (among 102), aged 18-58 years (10 men, 15 women), with nearly complete dentition. We performed interradicular and bucco-lingual (including cortical plate thickness) measurements in dental areas distal to the canines in both alveolar arches, at three levels (5, 8, and 11 mm) from the alveolar ridge. The mean thicknesses of the cortical plates in the maxilla were 1.10 mm buccally and 1.27 mm on the palatal side (p < 0.05). In the mandible, cortical plates were 2.23 mm buccally and 2.02 mm lingually. Mandibular buccal and lingual cortical plates became thicker distally in the second and third molar areas. There was considerable variation in cortical thickness (from 0.25 to 5.50 mm). Based on interradicular distances, only 13% of measured sites in the maxilla were suitable for miniscrew insertion (≥3.3 mm), but 63% of sites were suitable in the mandible. This study showed considerable individual variation in bone thickness. Our data suggested that the palatal/lingual side may provide greater primary stability for miniscrews. The palatal area, between the second upper bicuspid and the first molar, appeared to be the most suitable area for tapered 7- to 9-mm miniscrews, starting at 1.5-2 mm from the alveolar crest. © 2011 John Wiley & Sons A/S.

Three-dimensional analysis of elbow soft tissue footprints and anatomy.

PubMed

Capo, John T; Collins, Christopher; Beutel, Bryan G; Danna, Natalie R; Manigrasso, Michaele; Uko, Linda A; Chen, Linda Y

2014-11-01

Tendinous and ligamentous injuries commonly occur in the elbow. This study characterized the location, surface areas, and origin and insertional footprints of major elbow capsuloligamentous and tendinous structures in relation to bony landmarks with the use of a precision 3-dimensional modeling system. Nine unpaired cadaveric elbow specimens were dissected and mounted on a custom jig. Mapping of the medial collateral ligament (MCL), lateral ulnar collateral ligament (LUCL), triceps, biceps, brachialis, and capsular reflections was then performed with 3-dimensional digitizing technology. The location, surface areas, and footprints of the soft tissues were calculated. The MCL had a mean origin (humeral) footprint of 216 mm(2), insertional footprint of 154 mm(2), and surface area of 421 mm(2). The LUCL had a mean origin footprint of 136 mm(2), an insertional footprint of 142 mm(2), and a surface area of 532 mm(2). Of the tendons, the triceps maintained the largest insertional footprint, followed by the brachialis and the biceps (P < .001-.03). The MCL, LUCL, and biceps footprint locations were consistent, with little variability. The surface areas of the anterior (1251 mm(2)) and posterior (1147 mm(2)) capsular reflections were similar (P = .82), and the anterior capsule extended farther proximally. Restoring the normal anatomy of key elbow capsuloligamentous and tendinous structures is crucial for effective reconstruction after bony or soft tissue trauma. This study provides the upper extremity surgeon with information that may aid in restoring elbow biomechanics and preserving range of motion in these patients. Copyright © 2014 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Attenuated total reflection-Fourier transform infrared imaging of large areas using inverted prism crystals and combining imaging and mapping.

PubMed

Chan, K L Andrew; Kazarian, Sergei G

2008-10-01

Attenuated total reflection-Fourier transform infrared (ATR-FT-IR) imaging is a very useful tool for capturing chemical images of various materials due to the simple sample preparation and the ability to measure wet samples or samples in an aqueous environment. However, the size of the array detector used for image acquisition is often limited and there is usually a trade off between spatial resolution and the field of view (FOV). The combination of mapping and imaging can be used to acquire images with a larger FOV without sacrificing spatial resolution. Previous attempts have demonstrated this using an infrared microscope and a Germanium hemispherical ATR crystal to achieve images of up to 2.5 mm x 2.5 mm but with varying spatial resolution and depth of penetration across the imaged area. In this paper, we demonstrate a combination of mapping and imaging with a different approach using an external optics housing for large ATR accessories and inverted ATR prisms to achieve ATR-FT-IR images with a large FOV and reasonable spatial resolution. The results have shown that a FOV of 10 mm x 14 mm can be obtained with a spatial resolution of approximately 40-60 microm when using an accessory that gives no magnification. A FOV of 1.3 mm x 1.3 mm can be obtained with spatial resolution of approximately 15-20 microm when using a diamond ATR imaging accessory with 4x magnification. No significant change in image quality such as spatial resolution or depth of penetration has been observed across the whole FOV with this method and the measurement time was approximately 15 minutes for an image consisting of 16 image tiles.

The effect of the X-Stop implantation on intervertebral foramen, segmental spinal canal length and disc space in elderly patients with lumbar spinal stenosis.

PubMed

Wan, Zongmiao; Wang, Shaobai; Kozanek, Michal; Xia, Qun; Mansfield, Frederick L; Lü, Guohua; Wood, Kirkham B; Li, Guoan

2012-03-01

To evaluate the biomechanical effect of the X-Stop device on the intervertebral foramen (IVF) and segmental spinal canal length (SSCL), as well as the intervertebral disc space at the implanted and the adjacent segments in patients with lumbar spinal stenosis (LSS). Eight elderly patients with LSS, scheduled for X-stop implantation, were CT or MRI scanned to construct 3D vertebral models (L2-S1). Before and after the surgery, each patient was also imaged using a dual-fluoroscopic image system during weight-bearing standing and maximum extension-flexion. The positions of the vertebrae were then determined using an established 2D-3D model matching method. The data revealed that the postoperative IVF area was significantly increased by 32.9% (or 32 mm2) (p<0.05) and the IVF width was increased by 24.4% (or 1.1 mm, p=0.06) during extension, but with minimal change in standing and flexion. The IVF heights were significantly (p<0.05) increased at standing by 1.2 mm and extension by 1.8 mm, but not at flexion. The SSCL were significantly (p<0.05) increased at extension by 1.2 mm, but not at standing and flexion. Anterior disc space of the implanted level was significantly decreased from 8.0 to 6.6 mm during standing. The X-Stop implantation efficiently enlarged the IVF area in the elderly patients with LSS at the operated level with little biomechanical effect immediately on the superior and inferior adjacent levels. However, it reduced the anterior disc space at the implanted level.

Effect of soldering techniques and gap distance on tensile strength of soldered Ni-Cr alloy joint.

PubMed

Lee, Sang-Yeob; Lee, Jong-Hyuk

2010-12-01

The present study was intended to evaluate the effect of soldering techniques with infrared ray and gas torch under different gap distances (0.3 mm and 0.5 mm) on the tensile strength and surface porosity formation in Ni-Cr base metal alloy. Thirty five dumbbell shaped Ni-Cr alloy specimens were prepared and assigned to 5 groups according to the soldering method and the gap distance. For the soldering methods, gas torch (G group) and infrared ray (IR group) were compared and each group was subdivided by corresponding gap distance (0.3 mm: G3 and IR3, 0.5 mm: G5, IR5). Specimens of the experimental groups were sectioned in the middle with a diamond disk and embedded in solder blocks according to the predetermined distance. As a control group, 7 specimens were prepared without sectioning or soldering. After the soldering procedure, a tensile strength test was performed using universal testing machine at a crosshead speed 1 mm/min. The proportions of porosity on the fractured surface were calculated on the images acquired through the scanning electronic microscope. Every specimen of G3, G5, IR3 and IR5 was fractured on the solder joint area. However, there was no significant difference between the test groups (P > .05). There was a negative correlation between porosity formation and tensile strength in all the specimens in the test groups (P < .05). There was no significant difference in ultimate tensile strength of joints and porosity formations between the gas-oxygen torch soldering and infrared ray soldering technique or between the gap distance of 0.3 mm and 0.5 mm.

Tidal Volume Single Breath Washout of Two Tracer Gases - A Practical and Promising Lung Function Test

PubMed Central

Singer, Florian; Stern, Georgette; Thamrin, Cindy; Fuchs, Oliver; Riedel, Thomas; Gustafsson, Per; Frey, Urs; Latzin, Philipp

2011-01-01

Background Small airway disease frequently occurs in chronic lung diseases and may cause ventilation inhomogeneity (VI), which can be assessed by washout tests of inert tracer gas. Using two tracer gases with unequal molar mass (MM) and diffusivity increases specificity for VI in different lung zones. Currently washout tests are underutilised due to the time and effort required for measurements. The aim of this study was to develop and validate a simple technique for a new tidal single breath washout test (SBW) of sulfur hexafluoride (SF6) and helium (He) using an ultrasonic flowmeter (USFM). Methods The tracer gas mixture contained 5% SF6 and 26.3% He, had similar total MM as air, and was applied for a single tidal breath in 13 healthy adults. The USFM measured MM, which was then plotted against expired volume. USFM and mass spectrometer signals were compared in six subjects performing three SBW. Repeatability and reproducibility of SBW, i.e., area under the MM curve (AUC), were determined in seven subjects performing three SBW 24 hours apart. Results USFM reliably measured MM during all SBW tests (n = 60). MM from USFM reflected SF6 and He washout patterns measured by mass spectrometer. USFM signals were highly associated with mass spectrometer signals, e.g., for MM, linear regression r-squared was 0.98. Intra-subject coefficient of variation of AUC was 6.8%, and coefficient of repeatability was 11.8%. Conclusion The USFM accurately measured relative changes in SF6 and He washout. SBW tests were repeatable and reproducible in healthy adults. We have developed a fast, reliable, and straightforward USFM based SBW method, which provides valid information on SF6 and He washout patterns during tidal breathing. PMID:21423739

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

PubMed

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

Fabrication of double-sided thallium bromide strip detectors

NASA Astrophysics Data System (ADS)

Hitomi, Keitaro; Nagano, Nobumichi; Onodera, Toshiyuki; Kim, Seong-Yun; Ito, Tatsuya; Ishii, Keizo

2016-07-01

Double-sided strip detectors were fabricated from thallium bromide (TlBr) crystals grown by the traveling-molten zone method using zone-purified materials. The detectors had three 3.4-mm-long strips with 1-mm widths and a surrounding electrode placed orthogonally on opposite surfaces of the crystals at approximately 6.5×6.5 mm2 in area and 5 mm in thickness. Excellent charge transport properties for both electrons and holes were observed from the TlBr crystals. The mobility-lifetime products for electrons and holes in the detector were measured to be ~3×10-3 cm2/V and ~1×10-3 cm2/V, respectively. The 137Cs spectra corresponding to the gamma-ray interaction position were obtained from the detector. An energy resolution of 3.4% of full width at half maximum for 662-keV gamma rays was obtained from one "pixel" (an intersection of the strips) of the detector at room temperature.

Investigation of radiant millimeter wave/terahertz radiation from low-infrared signature targets

NASA Astrophysics Data System (ADS)

Aytaç, B.; Alkuş, Ü.; Sivaslıgil, M.; Şahin, A. B.; Altan, H.

2017-10-01

Millimeter (mm) and sub-mm wave radiation is increasingly becoming a region of interest as better methods are developed to detect in this wavelength range. The development of sensitive focal plane array (FPA) architectures as well as single pixel scanners has opened up a new field of passive detection and imaging. Spectral signatures of objects, a long standing area of interest in the Short Wave Infrared (SWIR), Mid-Wave (MWIR) and Long Wave-IR (LWIR) bands can now be assessed in the mm-wave/terahertz (THz) region. The advantage is that this form of radiation is not as adversely affected by poor atmospheric conditions compared to other bands. In this study, a preliminary experiment in a laboratory environment is performed to assess the radiance from targets with low infrared signatures in the millimeter wave/terahertz (THz) band (<1 THz). The goal of this approach is to be able to model the experimental results to better understand the mm-wave/THz signature of targets with low observability in the IR bands.

Comparison of drusen area detected by spectral domain optical coherence tomography and color fundus imaging.

PubMed

Yehoshua, Zohar; Gregori, Giovanni; Sadda, SriniVas R; Penha, Fernando M; Goldhardt, Raquel; Nittala, Muneeswar G; Konduru, Ranjith K; Feuer, William J; Gupta, Pooja; Li, Ying; Rosenfeld, Philip J

2013-04-03

To compare the measurements of drusen area from manual segmentation of color fundus photographs with those generated by an automated algorithm designed to detect elevations of the retinal pigment epithelium (RPE) on spectral domain optical coherence tomography (SD-OCT) images. Fifty eyes with drusen secondary to nonexudative age-related macular degeneration were enrolled. All eyes were imaged with a high-definition OCT instrument using a 200 × 200 A-scan raster pattern covering a 6 mm × 6 mm area centered on the fovea. Digital color fundus images were taken on the same day. Drusen were traced manually on the fundus photos by graders at the Doheny Image Reading Center, whereas quantitative OCT measurements of drusen were obtained by using a fully automated algorithm. The color fundus images were registered to the OCT data set and measurements within corresponding 3- and 5-mm circles centered at the fovea were compared. The mean areas (± SD [range]) for the 3-mm circles were SD-OCT = 1.57 (± 1.08 [0.03-4.44]); 3-mm color fundus = 1.92 (± 1.08 [0.20-3.95]); 5-mm SD-OCT = 2.12 (± 1.55 [0.03-5.40]); and 5-mm color fundus = 3.38 (± 1.90 [0.39-7.49]). The mean differences between color images and the SD-OCT (color - SD-OCT) were 0.36 (± 0.93) (P = 0.008) for the 3-mm circle and 1.26 (± 1.38) (P < 0.001) for the 5-mm circle measurements. Intraclass correlation coefficients of agreements for 3- and 5-mm measurements were 0.599 and 0.540, respectively. There was only fair agreement between drusen area measurements obtained from SD-OCT images and color fundus photos. Drusen area measurements on color fundus images were larger than those with SD-OCT scans. This difference can be attributed to the fact that the OCT algorithm defines drusen in terms of RPE deformations above a certain threshold, and will not include small, flat drusen and subretinal drusenoid deposits. The two approaches provide complementary information about drusen.

Omnidirectional angle constraint based dynamic six-degree-of-freedom measurement for spacecraft rendezvous and docking simulation

NASA Astrophysics Data System (ADS)

Shi, Shendong; Yang, Linghui; Lin, Jiarui; Ren, Yongjie; Guo, Siyang; Zhu, Jigui

2018-04-01

In this paper we present a novel omnidirectional angle constraint based method for dynamic 6-DOF (six-degree-of-freedom) measurement. A photoelectric scanning measurement network is employed whose photoelectric receivers are fixed on the measured target. They are in a loop distribution and receive signals from rotating transmitters. Each receiver indicates an angle constraint direction. Therefore, omnidirectional angle constraints can be constructed in each rotation cycle. By solving the constrained optimization problem, 6-DOF information can be obtained, which is independent of traditional rigid coordinate system transformation. For the dynamic error caused by the measurement principle, we present an interpolation method for error reduction. Accuracy testing is performed in an 8  ×  8 m measurement area with four transmitters. The experimental results show that the dynamic orientation RMSEs (root-mean-square errors) are reduced from 0.077° to 0.044°, 0.040° to 0.030° and 0.032° to 0.015° in the X, Y, and Z axes, respectively. The dynamic position RMSE is reduced from 0.65 mm to 0.24 mm. This method is applied during the final approach phase in the rendezvous and docking simulation. Experiments under different conditions are performed in a 40  ×  30 m area, and the method is verified to be effective.

Development of an Omnidirectional-Capable Electromagnetic Shock Wave Generator for Lipolysis

PubMed Central

Lin, San Yih

2017-01-01

Traditional methods for adipose tissue removal have progressed from invasive methods such as liposuction to more modern methods of noninvasive lipolysis. This research entails the development and evaluation of an omnidirectional-capable flat-coil electromagnetic shock wave generator (EMSWG) for lipolysis. The developed EMSWG has the advantage of omnidirectional-capable operation. This capability increases the eventual clinical usability by adding three designed supports to the aluminum disk of the EMSWG to allow omnidirectional operation. The focal pressures of the developed EMSWG for different operating voltages were measured, and its corresponding energy intensities were calculated. The developed EMSWG was mounted in a downward orientation for lipolysis and evaluated as proof of concept. In vitro tests on porcine fatty tissues have been carried out. It is found that at a 6 kV operating voltage with 1500 shock wave exposures, a 2 cm thick subcutaneous hypodermis of porcine fatty tissue can be ruptured, resulting in a damaged area of 1.39 mm2. At a 6.5 kV operating voltage with 2000 shock wave exposures, the damaged area is increased to about 5.20 mm2, which can be enlarged by changing the focal point location, resulting in significant lipolysis for use in clinical applications. PMID:29065664

[Influence of combination on the specific chromatogram of Glycyrrhiza in sini decoctions by HPLC].

PubMed

Zhao, Huai-Bin; Hong, Yan-Long; Wang, You-Jie; Shen, Lan; Wu, Fei; Feng, Yi; Ruan, Ke-Feng

2012-04-01

The paper is to report the establishment of an HPLC specific chromatogram of Glycyrrhiza in Sini decoctions and the influence of combination on the specific chromatogram. The RP-HPLC method was used with a Phenomenex Gemini C18 column (250 mm x 4.6 mm ID, 5 microm), and acetonitrile-0.05% trifluoroacetic acid (gradient elution) as mobile phase. Flow rate was 0.8 mL x min(-1) and the detection wavelength was set at 232 nm. The temperature of column was 30 degrees C. The method is stable and reliable with a good reproducibility, it can be used to determine the specific chromatogram of Glycyrrhiza in Sini Decoctions. Twenty peaks were selected as specific peaks in Sini Decoction with liquiritin peak as the reference peak. Six of them were from Glycyrrhiza and the other 6 peaks were from both Glycyrrhiza and Ganjiangfuzi Decoction. The areas of specific peaks of Sini Decoctions were smaller than those in the chromatogram of Glycyrrhiza. The specific chromatogram of Glycyrrhiza in Sini Decoctions is markedly influenced by Radix Aconiti Carmichaeli and Rhizoma Zingiberis. The areas of the specific peaks in Sini Decoctions were reduced obviously. The method is stable and reliable with a good reproducibility, it can be used to determine the specific chromatogram of Glycyrrhiza in Sini Decoctions.

Development of an Omnidirectional-Capable Electromagnetic Shock Wave Generator for Lipolysis.

PubMed

Chang, Ming Hau; Lin, San Yih

2017-01-01

Traditional methods for adipose tissue removal have progressed from invasive methods such as liposuction to more modern methods of noninvasive lipolysis. This research entails the development and evaluation of an omnidirectional-capable flat-coil electromagnetic shock wave generator (EMSWG) for lipolysis. The developed EMSWG has the advantage of omnidirectional-capable operation. This capability increases the eventual clinical usability by adding three designed supports to the aluminum disk of the EMSWG to allow omnidirectional operation. The focal pressures of the developed EMSWG for different operating voltages were measured, and its corresponding energy intensities were calculated. The developed EMSWG was mounted in a downward orientation for lipolysis and evaluated as proof of concept. In vitro tests on porcine fatty tissues have been carried out. It is found that at a 6 kV operating voltage with 1500 shock wave exposures, a 2 cm thick subcutaneous hypodermis of porcine fatty tissue can be ruptured, resulting in a damaged area of 1.39 mm 2 . At a 6.5 kV operating voltage with 2000 shock wave exposures, the damaged area is increased to about 5.20 mm 2 , which can be enlarged by changing the focal point location, resulting in significant lipolysis for use in clinical applications.

An application of second-order UV-derivative spectrophotometry for study of solvolysis of a novel fluocinolone acetonide ester

NASA Astrophysics Data System (ADS)

Markovic, Bojan; Vladimirov, Sote; Cudina, Olivera; Savic, Vladimir; Karljikovic-Rajic, Katarina

2010-02-01

A novel topical corticosteroid FA-21-PhP, 2-phenoxypropionate ester of fluocinolone acetonide, has been synthesized in order to investigate the possibility of decreasing systemic side effects. In this study model system for in vitro solvolytic reaction of FA-21-PhP has been analyzed in ethanol/water (90:10, v/v) with excess of sodium hydrogen carbonate. The selected conditions have been used as in vitro model for activation of corticosteroid C-21 ester prodrug. The second-order derivative spectrophotometric method (DS) using zero-crossing technique was developed for monitoring ternary mixture of solvolysis. Fluocinolone acetonide (FA) as a solvolyte was determined in the mixture in the concentration range 0.062-0.312 mM using amplitude 2D 274.96. Experimentally determined LOD value was 0.0295 mM. The accuracy of proposed DS method was confirmed with HPLC referent method. Peak area of parent ester FA-21-PhP was used for solvolysis monitoring to ensure the initial stage of changes. Linear relationship in HPLC assay for parent ester was obtained in the concentration range 0.054-0.54 mM, with experimentally determined LOD value of 0.0041 mM. Investigated solvolytic reaction in the presence of excess of NaHCO 3 proceeded via a pseudo-first-order kinetic with significant correlation coefficients 0.9891 and 0.9997 for DS and HPLC, respectively. The values of solvolysis rate constant calculated according to DS and HPLC methods are in good accordance 0.038 and 0.043 h -1, respectively.

Poor symptom control is associated with reduced CT scan segmental airway lumen area in smokers with asthma.

PubMed

Thomson, Neil C; Chaudhuri, Rekha; Spears, Mark; Messow, Claudia-Martina; MacNee, William; Connell, Martin; Murchison, John T; Sproule, Michael; McSharry, Charles

2015-03-01

Cigarette smoking is associated with worse symptoms in asthma and abnormal segmental airways in healthy subjects. We tested the hypothesis that current symptom control in smokers with asthma is associated with altered segmental airway dimensions measured by CT scan. In 93 subjects with mild, moderate, and severe asthma (smokers and never smokers), we recorded Asthma Control Questionnaire-6 (ACQ-6) score, spirometry (FEV1; forced expiratory flow rate, midexpiratory phase [FEF(25%-75%)]), residual volume (RV), total lung capacity (TLC), and CT scan measures of the right bronchial (RB) and left bronchial (LB) segmental airway dimensions (wall thickness, mm; lumen area, mm²) in the RB3/LB3, RB6/LB6, and RB10/LB10 (smaller) airways. The CT scan segmental airway (RB10 and LB10) lumen area was reduced in smokers with asthma compared with never smokers with asthma; RB10, 16.6 mm² (interquartile range, 12.4-19.2 mm²) vs 19.6 mm² (14.7-24.2 mm²) (P = .01); LB10, 14.8 mm² (12.1-19.0 mm²) vs 19.9 mm² (14.5-25.0 mm²) (P = .003), particularly in severe disease, with no differences in wall thickness or in larger airway (RB3 and LB3) dimensions. In smokers with asthma, a reduced lumen area in fifth-generation airways (RB10 or LB10) was associated with poor symptom control (higher ACQ-6 score) (-0.463 [-0.666 to -0.196], P = .001, and -0.401 [-0.619 to -0.126], P = .007, respectively) and reduced postbronchodilator FEF(25%-75%) (0.521 [0.292-0.694], P < .001, and [0.471 [0.236-0.654], P = .001, respectively) and higher RV/TLC %. The CT scan segmental airway lumen area is reduced in smokers with asthma compared with never smokers with asthma, particularly in severe disease, and is associated with worse current symptom control and small airway dysfunction.

Torque test measurement in segmental bone defects using porous calcium phosphate cement implants.

PubMed

Kroese-Deutman, Henriette C; Wolke, Joop G C; Spauwen, Paul H M; Jansen, John A

2010-10-01

This study was performed to assess the bone healing supporting characteristics of porous calcium phosphate (Ca-P) cement when implanted in a rabbit segmental defect model as well as to determine the reliability of torque testing as a method to verify bone healing. The middiaphyseal radius was chosen as the area to create bilaterally increasing defect sizes (5, 10, and 15 mm), which were either filled with porous Ca-P cement or left open as a control. After 12 weeks of implantation, torque test measurements as well as histological and radiographic evaluation were performed. In two of the open 15 mm control defects, bone bridging was visible at the radiographic and histological evaluation. Bone was observed to be present in all porous Ca-P cement implants (5, 10, and 15 mm defects) after 12 weeks. No significant differences in torque measurements were observed between the 5 and 10 mm filled and open control defects using a t-test. In addition, the mechanical strength of all operated specimens was similar compared with nonoperated bone samples. The torsion data for the 15 mm open defect appeared to be lower compared with the filled 15 mm defect, but no significant difference could be proven. Within the limitation of the study design, porous Ca-P cement implants demonstrated osteoconductive properties and confirmed to be a suitable scaffold material in a weight-bearing situation. Further, the used torque testing method was found to be unreliable for testing the mechanical properties of the healed bone defect.

Interpretation Criteria for Comparative Intradermal Tuberculin Test for Diagnosis of Bovine Tuberculosis in Cattle in Maroua Area of Cameroon

PubMed Central

Temwa, J.; Mouiche, M. M.; Iyawa, D.; Zoli, P. A.

2016-01-01

Intradermal tuberculin test (TST) is the choice method for diagnosis of bovine tuberculosis (Tb) in live animals. This work was done to assess the performance of single intradermal comparative cervical tuberculin (SICCT) test in randomly selected cattle in Maroua, Cameroon, against detection of Tb lesions and detection of Tb lesions plus acid fast bacilli in lesions. While 22.28% of slaughtered cattle presented Tb lesions at meat inspection, detection rates of anti-bovine-Tb antibody, Tb lesions, and Tb lesions plus acid fast bacilli were 68.57%, 32.95%, and 22.35%, respectively. SICCT-bovine-Tb positive cattle were 35.29%, 29.41%, 25.88%, 24.7%, and 21.18% at ≥2 mm, ≥2.5 mm, ≥3 mm, ≥3.5 mm, and ≥4 mm cut-offs, respectively. Higher sensitivity and predictive values were obtained at severe interpretations. The best performance was at ≥3 mm and ≥3.5 mm cut-offs. Against detection of Tb lesions, ≥3 mm and ≥3.5 mm showed sensitivity of 67.8% and specificity of 94.7% and 96.5%, respectively. For detection of Tb lesions accompanied with acid fast bacilli in lesions, ≥3 mm and ≥3.5 mm showed sensitivity of 89.4% and specificity of 92.4% and 93.9%, respectively. These findings revealed that interpretations of SICCT-bovine-Tb should be at ≥3 mm and/or ≥3.5 mm cut-offs. Severe interpretation of TST is essential for optimal diagnosis of bovine Tb in cattle in Maroua, Cameroon. PMID:27563481

[Localization of perforators in the lower leg by digital antomy imaging methods].

PubMed

Wei, Peng; Ma, Liang-Liang; Fang, Ye-Dong; Xia, Wei-Zhi; Ding, Mao-Chao; Mei, Jin

2012-03-01

To offer both the accurate three-dimensional anatomical information and algorithmic morphology of perforators in the lower leg for perforator flaps design. The cadaver was injected with a modified lead oxide-gelatin mixture. Radiography was first performed and the images were analyzed using the software Photoshop and Scion Image. Then spiral CT scan was also performed and 3-dimensional images were reconstructed with MIMICS 10.01 software. There are (27 +/- 4) perforators whose outer diameter > or = 0.5 mm ( average, 0.8 +/- 0.2 mm). The average pedicle length within the superficial fascia is (37.3 +/- 18.6) mm. The average supplied area of each perforator is (49.5 +/- 25.5) cm2. The three-dimensional model displayed accurate morphology structure and three-dimensional distribution of the perforator-to- perforator and perforator-to-source artery. The 3D reconstruction model can clearly show the geometric, local details and three-dimensional distribution. It is a considerable method for the study of morphological characteristics of the individual perforators in human calf and preoperative planning of the perforator flap.

Electronic desalting for controlling the ionic environment in droplet-based biosensing platforms

NASA Astrophysics Data System (ADS)

Swaminathan, Vikhram Vilasur; Dak, Piyush; Reddy, Bobby; Salm, Eric; Duarte-Guevara, Carlos; Zhong, Yu; Fischer, Andrew; Liu, Yi-Shao; Alam, Muhammad A.; Bashir, Rashid

2015-02-01

The ability to control the ionic environment in saline waters and aqueous electrolytes is useful for desalination as well as electronic biosensing. We demonstrate a method of electronic desalting at micro-scale through on-chip micro electrodes. We show that, while desalting is limited in bulk solutions with unlimited availability of salts, significant desalting of ≥1 mM solutions can be achieved in sub-nanoliter volume droplets with diameters of ˜250 μm. Within these droplets, by using platinum-black microelectrodes and electrochemical surface treatments, we can enhance the electrode surface area to achieve >99% and 41% salt removal in 1 mM and 10 mM salt concentrations, respectively. Through self-consistent simulations and experimental measurements, we demonstrate that conventional double-layer theory over-predicts the desalting capacity and, hence, cannot be used to model systems that are mass limited or undergoing significant salt removal from the bulk. Our results will provide a better understanding of capacitive desalination, as well as a method for salt manipulation in high-throughput droplet-based microfluidic sensing platforms.

RELATIONSHIP BETWEEN RIGIDITY OF EXTERNAL FIXATOR AND NUMBER OF PINS: COMPUTER ANALYSIS USING FINITE ELEMENTS

PubMed Central

Sternick, Marcelo Back; Dallacosta, Darlan; Bento, Daniela Águida; do Reis, Marcelo Lemos

2015-01-01

Objective: To analyze the rigidity of a platform-type external fixator assembly, according to different numbers of pins on each clamp. Methods: Computer simulation on a large-sized Cromus dynamic external fixator (Baumer SA) was performed using a finite element method, in accordance with the standard ASTM F1541. The models were generated with approximately 450,000 quadratic tetrahedral elements. Assemblies with two, three and four Schanz pins of 5.5 mm in diameter in each clamp were compared. Every model was subjected to a maximum force of 200 N, divided into 10 sub-steps. For the components, the behavior of the material was assumed to be linear, elastic, isotropic and homogeneous. For each model, the rigidity of the assembly and the Von Mises stress distribution were evaluated. Results: The rigidity of the system was 307.6 N/mm for two pins, 369.0 N/mm for three and 437.9 N/mm for four. Conclusion: The results showed that four Schanz pins in each clamp promoted rigidity that was 19% greater than in the configuration with three pins and 42% greater than with two pins. Higher tension occurred in configurations with fewer pins. In the models analyzed, the maximum tension occurred on the surface of the pin, close to the fixation area. PMID:27047879

Evapotranspiration and water balance in a hot pepper (Capsicum frutescens L.) field during a dry season in the tropics

NASA Astrophysics Data System (ADS)

Laban, S.; Oue, H.; Rampisela, D. A.

2018-05-01

Evapotranspiration and water balance in a hot pepper (Capsicum frutescens L.) field during the 2nd dry season were analyzed in this study. Actual evapotranspiration (ET) was estimated by Bowen Ratio Energy Budget (BREB) method, potential evaporation (EP) was calculated by Penman method, and irrigation volume of water was measured manually. Meteorological instruments were installed in the experimental field during hot pepper cultivation. Leaf area index increased during the growing stages where the highest LAI of 1.65 in the generative stage. The daily average of ET was 1.94 and EP was 6.71 mm resulting in low Kc. The Kc values were significantly different between stage to stage under T-test analysis (α = 0.05). Moreover, Kc in every stage could be related to soil water content (SWC) in logarithmic function. Totally, ET during hot pepper cultivation was 179.19 mm, while rainfall was 180.0 mm and irrigation water was 27.42 mm. However, there was a water shortages during vegetative and generative stages. This study suggested that consumptive water of hot pepper was complimented by soil and groundwater under the condition of water shortages in the vegetative and generative stages during the 2nd dry season.

Monitoring Ground Deformation of Subway Area during the Construction Based on the Method of Multi-Temporal Coherent Targets Analysis

NASA Astrophysics Data System (ADS)

Zhang, L.; Wu, J.; Zhao, J.; Yuan, M.

2018-04-01

Multi-temporal coherent targets analysis is a high-precision and high-spatial-resolution monitoring method for urban surface deformation based on Differential Synthetic Aperture Radar (DInSAR), and has been successfully applied to measure land subsidence, landslide and strain accumulation caused by fault movement and so on. In this paper, the multi-temporal coherent targets analysis is used to study the settlement of subway area during the period of subway construction. The eastern extension of Shanghai Metro Line. 2 is taking as an example to study the subway settlement during the construction period. The eastern extension of Shanghai Metro Line. 2 starts from Longyang Road and ends at Pudong airport. Its length is 29.9 kilometers from east to west and it is a key transportation line to the Pudong Airport. 17 PalSAR images during 2007 and 2010 are applied to analyze and invert the settlement of the buildings nearby the subway based on the multi-temporal coherent targets analysis. But there are three significant deformation areas nearby the Line 2 between 2007 and 2010, with maximum subsidence rate up to 30 mm/y in LOS. The settlement near the Longyang Road station and Chuansha Town are both caused by newly construction and city expansion. The deformation of the coastal dikes suffer from heavy settlement and the rate is up to -30 mm/y. In general, the area close to the subway line is relatively stable during the construction period.

Fetal sigmoid colon mesentery - In relevance in fetal ultrasound application. A pilot study.

PubMed

Wozniak, Slawomir; Florjanski, Jerzy; Kordecki, Henryk; Podhorska-Okolow, Marzena; Domagala, Zygmunt

2018-03-01

Ultrasound examinations during pregnancy are routine procedures used to detect fetal congenital malformations. Ultrasound monitoring of sigmoid colon mesenterial development could be useful for early detection of subjects at risk of sigmoid colon volvulus. The aim of our paper was to assess the sigmoid colon length, and sigmoid colon mesentery width and height in the late fetal period, and, using the results, to estimate the surface area of the mesocolon (in mm 2 ) in living fetuses. Moreover, we attempted to repeat some of these measurements in living fetuses using ultrasound imaging. The study was carried out on 209 formalin fixed human fetuses (100 female and 109 male) aged from 4th to 7th gestational months (102-203 days), with a crown-rump length of 132-342mm. The length of the sigmoid colon, as well as the height and width of its mesentery were measured. The surface area of the mesocolon was estimated. Correction for formalin induced shrinkage was applied. Pilot ultrasound examinations of live fetuses were performed. Mean values of sigmoid colon length, mesenteric width and height (formalin fixed fetuses) for respective gestational ages were: month 4: 21.46±6.7mm, 6.80±2.1mm, 5.5±1.49mm; month 5: 27.32±1.2mm, 7.62±2.01mm, 7.33±2.17mm; month 6: 47.56±9.57mm, 11.68±3.8mm, 10.3±3.05mm; month 7: 56.92±17.48mm. 15.32±8 mm, 12.81±3.16mm. The surface area ranges of the sigmoid colon mesentery found for respective gestational months (intrauterine fetuses) were as follows: month 4: 33.24-51.95mm 2 ; month 5: 49.63-77.6mm 2 ; month 6: 106.89-167.15mm 2 and month 7: 145.69-272.53mm 2 . The surface area of the sigmoid colon mesentery can be used as a simple parameter applied in fetal ultrasonographic evaluation. The development of the sigmoid colon accelerates in the 6th gestational month, and decelerates in the 7th gestational month. The sigmoid colon mesentery width was larger than its height between the 4th and 7th gestational months. Copyright © 2017 Elsevier GmbH. All rights reserved.

Evaluation of Single File Systems Reciproc, Oneshape, and WaveOne using Cone Beam Computed Tomography -An In Vitro Study.

PubMed

Dhingra, Annil; Ruhal, Nidhi; Miglani, Anjali

2015-04-01

Successful endodontic therapy depends on many factor, one of the most important step in any root canal treatment is root canal preparation. In addition, respecting the original shape of the canal is of the same importance; otherwise, canal aberrations such as transportation will be created. The purpose of this study is to compare and evaluate Reciprocating WaveOne ,Reciproc and Rotary Oneshape Single File Instrumentation System On Cervical Dentin Thickness, Cross Sectional Area and Canal Transportation on First Mandibular Molar Using Cone Beam Computed Tomography. Sixty Mandibular First Molars extracted due to periodontal reason was collected from the Department of Oral and Maxillofacial. Teeth were prepared using one rotary and two reciprocating single file system. Teeth were divided into 3 groups 20 teeth in each group. Pre instrumentation and Post instrumentation scans was done and evaluated for three parameters Canal Transportation, Cervical Dentinal Thickness, Cross-sectional Area. Results were analysed statistically using ANOVA, Post-Hoc Tukey analysis. The change in cross-sectional area after filing showed significant difference at 0mm, 1mm, 2mm and 7mm (p<0.001, p =0.006, 0.004 & <0.001 respectively). There was significant difference between wave one and oneshape; oneshape and reciproc at 0mm, 1mm, 2mm & 7mm (p-values for waveone and Oneshape <0.001, 0.022, 0.011 & <0.001 resp. and for oneshape and reciproc < 0.001, p= 0.011, p=0.008 & <0.001). On assessing the transportation of the three file system over a distance of 7 mm (starting from 0mm and then evaluation at 1mm, 2mm, 3mm, 5mm and 7mm), the results showed a significant difference among the file systems at various lengths (p= 0.014, 0.046, 0.004, 0.028, 0.005 & 0.029 respectively). Mean value of cervical dentinal removal is maximum at all the levels for oneshape and minimum for waveone showing the better quality of waveone and reciproc over oneshape file system. Significant difference was found at 9mm, 11mm and 12mm between all the three file systems (p<0.001,< 0.001, <0.001). It was concluded that reciprocating motion is better than rotary motion in all the three parameters Canal Transportation, Cross-sectional Area, Cervical Dentinal Thickness.

Content determination of aniracetam in aniracetam inclusion complex by HPLC.

PubMed

Li, Yongjian; Hu, Dejian; Sun, Yong

2009-01-01

We established a HPLC method for content determination of aniracetam in aniracetam inclusion complex. The chromato column was Agilent ODS (4.6mm x 150mm, 5 microm), the mobile phase was methanol-0.01 mol/L Potassium dihydrogen phosphate buffer solution (25:75, pH 3.0), with the flow rate of 1.0 ml/min, column temperature of 30 degrees and the detection wave at 280 nm, the sample size was 20microL. A good linear relationship was obtained between the peak areas and the concentrations of aniracetam in the range from 5- 80microg/ml (r=0.9998), the mean recovery was 100.1% (n=15), RSD=0.19%. This method is convenient, rapid, accurate, and brings about good recovery; it can be used for content determination of aniracetam in aniracetam inclusion complex.

Pattern of maxillary and mandibular proximal enamel thickness at the contact area of the permanent dentition from first molar to first molar.

PubMed

Sarig, Rachel; Vardimon, Alexander D; Sussan, Celine; Benny, Lea; Sarne, Ofer; Hershkovitz, Israel; Shpack, Nir

2015-04-01

Proximal enamel thickness (PET) at the mesial and distal contact areas of the complete permanent dentition has not been previously reported. Anatomic investigation of PET is essential for interproximal reduction treatment. Our objectives were to measure the PETs of the complete maxillary and mandibular dentitions at the contact areas, to compare the PETs of adjacent teeth, and to evaluate the vertical position of each contact area. We evaluated 720 extracted teeth; of these, 109 intact teeth were selected. The mesial and distal contact areas were demarcated, and each tooth was embedded in transparent epoxy resin. Blocks were prepared so that the 2 demarcated contact areas were exposed, and 6 measurements were taken and statistically analyzed. Both jaws showed the same PET pattern characterized by 5 features: PET increased progressively from incisor (0.63 mm) to first molar (1.48 mm). Per tooth, mesial and distal PET did not differ. Total maxillary (26.86 mm) and mandibular (24.52 mm) PETs were similar. Paired PETs at the interproximal interface were similar, with the exception of the lateral incisor-canine interfaces. From incisor to first molar, the contact area becomes located farther gingivally. The existing guideline of maximal 0.5-mm interproximal reduction per 2 adjacent teeth should be kept in the anterior region and could be increased to 1 mm in the posterior region, when an equal amount is removed. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

A randomised controlled comparison of injection, thermal, and mechanical endoscopic methods of haemostasis on mesenteric vessels.

PubMed

Hepworth, C C; Kadirkamanathan, S S; Gong, F; Swain, C P

1998-04-01

A randomised controlled comparison of haemostatic efficacy of mechanical, injection, and thermal methods of haemostasis was undertaken using canine mesenteric vessels to test the hypothesis that mechanical methods of haemostasis are more effective in controlling haemorrhage than injection or thermal methods. The diameter of arteries in human bleeding ulcers measures up to 3.45 mm; mesenteric vessels up to 5 mm were therefore studied. Mesenteric vessels were randomised to treatment with injection sclerotherapy (adrenaline and ethanolamine), bipolar diathermy, or mechanical methods (band, clips, sewing machine, endoloops). The vessels were severed and haemostasis recorded. Injection sclerotherapy and clips failed to stop bleeding from vessels of 1 mm (n = 20) and 2 mm (n = 20). Bipolar diathermy was effective on 8/10 vessels of 2 mm but failed on 3 mm vessels (n = 5). Unstretched elastic bands succeeded on 13/15 vessels of 2 mm but on only 3/10 vessels of 3 mm. The sewing machine achieved haemostasis on 8/10 vessels of 4 mm but failed on 5 mm vessels (n = 5); endoloops were effective on all 5 mm vessels (n = 5). Only mechanical methods were effective on vessels greater than 2 mm in diameter. Some mechanical methods (banding and clips) were less effective than expected and need modification. Thermal and (effective) mechanical methods were significantly (p < 0.01) more effective than injection sclerotherapy. The most effective mechanical methods were significantly more effective (p < 0.01) than thermal or injection on vessels greater than 2 mm.

Estimating groundwater evapotranspiration by a subtropical pine plantation using diurnal water table fluctuations: Implications from night-time water use

NASA Astrophysics Data System (ADS)

Fan, Junliang; Ostergaard, Kasper T.; Guyot, Adrien; Fujiwara, Stephen; Lockington, David A.

2016-11-01

Exotic pine plantations have replaced large areas of the native forests for timber production in the subtropical coastal Australia. To evaluate potential impacts of changes in vegetation on local groundwater discharge, we estimated groundwater evapotranspiration (ETg) by the pine plantation using diurnal water table fluctuations for the dry season of 2012 from August 1st to December 31st. The modified White method was used to estimate the ETg, considering the night-time water use by pine trees (Tn). Depth-dependent specific yields were also determined both experimentally and numerically for estimation of ETg. Night-time water use by pine trees was comprehensively investigated using a combination of groundwater level, sap flow, tree growth, specific yield, soil matric potential and climatic variables measurements. Results reveal a constant average transpiration flux of 0.02 mm h-1 at the plot scale from 23:00 to 05:00 during the study period, which verified the presence of night-time water use. The total ETg for the period investigated was 259.0 mm with an accumulated Tn of 64.5 mm, resulting in an error of 25% on accumulated evapotranspiration from the groundwater if night-time water use was neglected. The results indicate that the development of commercial pine plantations may result in groundwater losses in these areas. It is also recommended that any future application of diurnal water table fluctuation based methods investigate the validity of the zero night-time water use assumption prior to use.

Screening of extraction methods for glycoproteins from jellyfish ( Rhopilema esculentum) oral-arms by high performance liquid chromatography

NASA Astrophysics Data System (ADS)

Ren, Guoyan; Li, Bafang; Zhao, Xue; Zhuang, Yongliang; Yan, Mingyan; Hou, Hu; Zhang, Xiukun; Chen, Li

2009-03-01

In order to select an optimum extraction method for the target glycoprotein (TGP) from jellyfish ( Rhopilema esculentum) oral-arms, a high performance liquid chromatography (HPLC)-assay for the determination of the TGP was developed. Purified target glycoprotein was taken as a standard glycoprotein. The results showed that the calibration curves for peak area plotted against concentration for TGP were linear ( r = 0.9984, y = 4.5895 x+47.601) over concentrations ranging from 50 to 400 mgL-1. The mean extraction recovery was 97.84% (CV2.60%). The fractions containing TGP were isolated from jellyfish ( R. esculentum) oral-arms by four extraction methods: 1) water extraction (WE), 2) phosphate buffer solution (PBS) extraction (PE), 3) ultrasound-assisted water extraction (UA-WE), 4) ultrasound-assisted PBS extraction (UA-PE). The lyophilized extract was dissolved in Milli-Q water and analyzed directly on a short TSK-GEL G4000PWXL (7.8 mm×300 mm) column. Our results indicated that the UA-PE method was the optimum extraction method selected by HPLC.

Preclinical evaluation of a novel abluminal surface coated sirolimus eluting stent with biodegradable polymer matrix

PubMed Central

Doshi, Manish; Galloni, Marco; Vignolini, Christina; Vyas, Ashwin; Chevli, Bhavesh; Sheiban, Imad

2015-01-01

Background Second generation of drug eluting stents (DES) has attempted to improve safety using abluminal sirolimus drug delivery with biodegradable polymers matrix. The present preclinical study was designed to investigate the safety and efficacy profile of Abluminus™ stents (SES). This is a new coronary stent with sirolimus and biodegradable polymer matrix coated on abluminal stent and balloon surface. Methods SES were compared with two controls: bare metal stent (BMS) and BMS + polymer coated stents (PC). All devices (40 stents) were implanted in porcine coronary arteries with primary endpoint of endothelialization at 7 days and subsequent histological and morphometric evaluations at 7, 30 and 90 days. Results Early endothelialization at seven days was complete in all stents. Histology at 30 days revealed minimum inflammation in all groups and increased at 90 days in PC group while it was absent at 180 days. Thirty day morphometry showed significantly reduction of neointimal area in Abluminus™ (SES 0.96±0.48 mm2; BMS 1.83±0.34 mm2; PC 1.76±0.55 mm2; P<0.05); after 90 days neointimal area was 1.10±0.54 mm2 for SES; 1.92±0.36 mm2 for BMS; and 1.94±0.48 mm2 for PC; P<0.05). Neointimal thickness at 30 and 90 days respectively was 0.15±0.07 and 0.18±0.10 mm for SES, 0.57±0.08 and 0.61±0.09 mm for BMS and 0.52±0.09 and 0.59±0.08 mm, P<0.001 for PC group. Conclusions The most significant experimental evidence appears to be earlier endothelialization at 7 days for SES which led to safety of the device. Efficacy of the device was also observed by a reduced neointimal thickness and minimized inflammatory score at all follow-ups. Termination of antiplatelet at 30 days has not shown any further complications. Polymer thickness was almost in negligible amount at 180 days with no inflammation. PMID:26331109

A Comparison between the Kawase and Extended Retrosigmoid Approaches (Retrosigmoid Transtentorial and Retrosigmoid Intradural Suprameatal Approaches) for Accessing the Petroclival Tumors. A Cadaveric Study

PubMed Central

Sharma, Mayur; Ambekar, Sudheer; Guthikonda, Bharat; Nanda, Anil

2014-01-01

Background The aim of our study was to compare the area of exposure at the ventral brainstem and petroclival region offered by the Kawase, retrosigmoid transtentorial (RTT), and the retrosigmoid intradural suprameatal (RISA) approaches in cadaveric models. Methods We performed 15 approaches (five each of the Kawase, RISA, and RTT approaches) on silicone-injected adult cadaver heads. Ventral brainstem and petroclival areas of exposure were measured and compared. Results The mean ventral brainstem area exposed by the Kawase approach was 55.00 ± 24.1 mm2, significantly less than that exposed by RTT (441 ± 63.3 mm2) and RISA (311 ± 61 mm2) (p < 0.05). The area of ventral brainstem exposure was significantly more via RTT than through RISA (p = 0.01). The mean petroclival area of exposure through the Kawase approach was significantly smaller than that obtained through the RTT and RISA approaches (101.7 ± 545.01 mm2, 696 ± 57.7 mm2, and 716.7 ± 51.4 mm2, respectively). Conclusion Retrosigmoid approaches provide a greater exposure of the brainstem and petroclival areas. The Kawase approach is ideally suited for lesions around the Meckel cave with an extension into the middle fossa. These approaches can be used in conjunction with one another to access petroclival tumors. PMID:24967151

7 CFR 51.2340 - Classification of defects.

Code of Federal Regulations, 2012 CFR

2012-01-01

... flesh extends more than 1/16 inch (1.6 mm) in depth When surface of fruit is indented and discoloration of the flesh extends deeper than 1/8 inch (3.2 mm), or causing slight discoloration exceeding the area of a circle 3/8 inch (9.5 mm) in diameter, or lesser bruises aggregating an area of a circle 3/8...

7 CFR 51.2340 - Classification of defects.

Code of Federal Regulations, 2010 CFR

2010-01-01

... flesh extends more than 1/16 inch (1.6 mm) in depth When surface of fruit is indented and discoloration of the flesh extends deeper than 1/8 inch (3.2 mm), or causing slight discoloration exceeding the area of a circle 3/8 inch (9.5 mm) in diameter, or lesser bruises aggregating an area of a circle 3/8...

7 CFR 51.2340 - Classification of defects.

Code of Federal Regulations, 2011 CFR

2011-01-01

... flesh extends more than 1/16 inch (1.6 mm) in depth When surface of fruit is indented and discoloration of the flesh extends deeper than 1/8 inch (3.2 mm), or causing slight discoloration exceeding the area of a circle 3/8 inch (9.5 mm) in diameter, or lesser bruises aggregating an area of a circle 3/8...

Wafer-scale fabrication of polymer-based microdevices via injection molding and photolithographic micropatterning protocols.

PubMed

Lee, Dae-Sik; Yang, Haesik; Chung, Kwang-Hyo; Pyo, Hyeon-Bong

2005-08-15

Because of their broad applications in biomedical analysis, integrated, polymer-based microdevices incorporating micropatterned metallic and insulating layers are significant in contemporary research. In this study, micropatterns for temperature sensing and microelectrode sets for electroanalysis have been implemented on an injection-molded thin polymer membrane by employing conventional semiconductor processing techniques (i.e., standard photolithographic methods). Cyclic olefin copolymer (COC) is chosen as the polymer substrate because of its high chemical and thermal stability. A COC 5-in. wafer (1-mm thickness) is manufactured using an injection molding method, in which polymer membranes (approximately 130 microm thick and 3 mm x 6 mm in area) are implemented simultaneously in order to reduce local thermal mass around micropatterned heaters and temperature sensors. The highly polished surface (approximately 4 nm within 40 microm x 40 microm area) of the fabricated COC wafer as well as its good resistance to typical process chemicals makes it possible to use the standard photolithographic and etching protocols on the COC wafer. Gold micropatterns with a minimum 5-microm line width are fabricated for making microheaters, temperature sensors, and microelectrodes. An insulating layer of aluminum oxide (Al2O3) is prepared at a COC-endurable low temperature (approximately 120 degrees C) by using atomic layer deposition and micropatterning for the electrode contacts. The fabricated microdevice for heating and temperature sensing shows improved performance of thermal isolation, and microelectrodes display good electrochemical performances for electrochemical sensors. Thus, this novel 5-in. wafer-level microfabrication method is a simple and cost-effective protocol to prepare polymer substrate and demonstrates good potential for application to highly integrated and miniaturized biomedical devices.

qFibrosis: A fully-quantitative innovative method incorporating histological features to facilitate accurate fibrosis scoring in animal model and chronic hepatitis B patients

PubMed Central

Tai, Dean C.S.; Wang, Shi; Cheng, Chee Leong; Peng, Qiwen; Yan, Jie; Chen, Yongpeng; Sun, Jian; Liang, Xieer; Zhu, Youfu; Rajapakse, Jagath C.; Welsch, Roy E.; So, Peter T.C.; Wee, Aileen; Hou, Jinlin; Yu, Hanry

2014-01-01

Background & Aims There is increasing need for accurate assessment of liver fibrosis/cirrhosis. We aimed to develop qFibrosis, a fully-automated assessment method combining quantification of histopathological architectural features, to address unmet needs in core biopsy evaluation of fibrosis in chronic hepatitis B (CHB) patients. Methods qFibrosis was established as a combined index based on 87 parameters of architectural features. Images acquired from 25 Thioacetamide-treated rat samples and 162 CHB core biopsies were used to train and test qFibrosis and to demonstrate its reproducibility. qFibrosis scoring was analyzed employing Metavir and Ishak fibrosis staging as standard references, and collagen proportionate area (CPA) measurement for comparison. Results qFibrosis faithfully and reliably recapitulates Metavir fibrosis scores, as it can identify differences between all stages in both animal samples (p <0.001) and human biopsies (p <0.05). It is robust to sampling size, allowing for discrimination of different stages in samples of different sizes (area under the curve (AUC): 0.93–0.99 for animal samples: 1–16 mm2; AUC: 0.84–0.97 for biopsies: 10–44 mm in length). qFibrosis can significantly predict staging underestimation in suboptimal biopsies (<15 mm) and under- and over-scoring by different pathologists (p <0.001). qFibrosis can also differentiate between Ishak stages 5 and 6 (AUC: 0.73, p = 0.008), suggesting the possibility of monitoring intra-stage cirrhosis changes. Best of all, qFibrosis demonstrates superior performance to CPA on all counts. Conclusions qFibrosis can improve fibrosis scoring accuracy and throughput, thus allowing for reproducible and reliable analysis of efficacies of anti-fibrotic therapies in clinical research and practice. PMID:24583249

Tensile properties of the transverse carpal ligament and carpal tunnel complex.

PubMed

Ugbolue, Ukadike C; Gislason, Magnus K; Carter, Mark; Fogg, Quentin A; Riches, Philip E; Rowe, Philip J

2015-08-01

A new sophisticated method that uses video analysis techniques together with a Maillon Rapide Delta to determine the tensile properties of the transverse carpal ligament-carpal tunnel complex has been developed. Six embalmed cadaveric specimens amputated at the mid-forearm and aged (mean (SD)): 82 (6.29) years were tested. The six hands were from three males (four hands) and one female (two hands). Using trigonometry and geometry the elongation and strain of the transverse carpal ligament and carpal arch were calculated. The cross-sectional area of the transverse carpal ligament was determined. Tensile properties of the transverse carpal ligament-carpal tunnel complex and Load-Displacement data were also obtained. Descriptive statistics, one-way ANOVA together with a post-hoc analysis (Tukey) and t-tests were incorporated. A transverse carpal ligament-carpal tunnel complex novel testing method has been developed. The results suggest that there were no significant differences between the original transverse carpal ligament width and transverse carpal ligament at peak elongation (P=0.108). There were significant differences between the original carpal arch width and carpal arch width at peak elongation (P=0.002). The transverse carpal ligament failed either at the mid-substance or at their bony attachments. At maximum deformation the peak load and maximum transverse carpal ligament displacements ranged from 285.74N to 1369.66N and 7.09mm to 18.55mm respectively. The transverse carpal ligament cross-sectional area mean (SD) was 27.21 (3.41)mm(2). Using this method the results provide useful biomechanical information and data about the tensile properties of the transverse carpal ligament-carpal tunnel complex. Copyright © 2015 Elsevier Ltd. All rights reserved.

Micro-finite element analysis applied to high-resolution MRI reveals improved bone mechanical competence in the distal femur of female pre-professional dancers

PubMed Central

Rajapakse, C. S.; Diamond, M.; Honig, S.; Recht, M. P.; Weiss, D. S.; Regatte, R. R.

2013-01-01

Summary Micro-finite element analysis applied to high-resolution (0.234-mm length scale) MRI reveals greater whole and cancellous bone stiffness, but not greater cortical bone stiffness, in the distal femur of female dancers compared to controls. Greater whole bone stiffness appears to be mediated by cancellous, rather than cortical bone adaptation. Introduction The purpose of this study was to compare bone mechanical competence (stiffness) in the distal femur of female dancers compared to healthy, relatively inactive female controls. Methods This study had institutional review board approval. We recruited nine female modern dancers (25.7± 5.8 years, 1.63±0.06 m, 57.1±4.6 kg) and ten relatively inactive, healthy female controls matched for age, height, and weight (32.1±4.8 years, 1.6±0.04 m, 55.8±5.9 kg). We scanned the distal femur using a 7-T MRI scanner and a three-dimensional fast low-angle shot sequence (TR/TE= 31 ms/5.1 ms, 0.234 mm×0.234 mm×1 mm, 80 slices). We applied micro-finite element analysis to 10-mm-thick volumes of interest at the distal femoral diaphysis, metaphysis, and epiphysis to compute stiffness and cross-sectional area of whole, cortical, and cancellous bone, as well as cortical thickness. We applied two-tailed t-tests and ANCOVA to compare groups. Results Dancers demonstrated greater whole and cancellous bone stiffness and cross-sectional area at all locations (p< 0.05). Cortical bone stiffness, cross-sectional area, and thickness did not differ between groups (>0.08). At all locations, the percent of intact whole bone stiffness for cortical bone alone was lower in dancers (p<0.05). Adjustment for cancellous bone cross-sectional area eliminated significant differences in whole bone stiffness between groups (p>0.07), but adjustment for cortical bone cross-sectional area did not (p<0.03). Conclusions Modern dancers have greater whole and cancellous bone stiffness in the distal femur compared to controls. Elevated whole bone stiffness in dancers may be mediated via cancellous, rather than cortical bone adaptation. PMID:22893356

Thermal distribution of microwave antenna for atrial fibrillation catheter ablation.

PubMed

Zhang, Huijuan; Nan, Qun; Liu, Youjun

2013-09-01

The aim of this study is to investigate the effects of ablation parameters on thermal distribution during microwave atrial fibrillation catheter ablation, such as ablation time, ablation power, blood condition and antenna placement, and give proper ablative parameters to realise transmural ablation. In this paper, simplified 3D antenna-myocardium-blood finite element method models were built to simulate the endocardial ablation operation. Thermal distribution was obtained based on the coupled electromagnetic-thermal analysis. Under different antenna placement conditions and different microwave power inputs within 60 s, the lesion dimensions (maximum depth, maximum width) of the ablation zones were analysed. The ablation width and depth increased with the ablation time. The increase rate significantly slowed down after 10 s. The maximum temperature was located in 1 mm under the antenna tip when perpendicular to the endocardium, while 1.5 mm away from the antenna axis and 26 mm along the antenna (with antenna length about 30 mm) in the myocardium when parallel to the endocardium. The maximum temperature in the ablated area decreased and the effective ablation area (with the temperature raised to 50°C) shifted deeper into the myocardium due to the blood cooling. The research validated that the microwave antenna can provide continuous long and linear lesions for the treatment of atrial fibrillation. The dimensions of the created lesion widths were all larger than those of the depths. It is easy for the microwave antenna to produce transmural lesions for an atrial wall thickness of 2-6 mm by adjusting the applied power and ablation time.

Computational fluid dynamics in the assessment of patients' postoperative status after glottis-widening surgery.

PubMed

Marków, Magdalena; Janecki, Daniel; Orecka, Bogusława; Misiołek, Maciej; Warmuziński, Krzysztof

2017-09-01

Computational fluid dynamics (CFD), a rapidly developing instrument with a number of practical applications, allows calculation and visualization of the changing parameters of airflow in the upper respiratory tract. The aim of this study was to demonstrate the advantages of CFD as an instrument for noninvasive tests of the larynx in patients who had undergone surgical treatment due to bilateral vocal fold paralysis. Surface measurements of the glottic space were made during maximum adduction of the vocal folds. Additionally, the following spirometric parameters were determined: forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), and peak expiratory flow (PEF) rate. Based on the measurements, commercial mesh generation software was used to develop a geometrical model of the glottic space. The computations were carried out using a general purpose CFD code. The analysis included patients who were surgically treated for BVFP in the authors' department between 1999 and 2012. The study group consisted of 22 women (91.67%) and 2 men (8.33%). It was observed that the pressure drop calculated for free breathing depends on the area of the glottis and is independent of its shape. Importantly, for areas below approx. 40 mm2, a sudden rise occurred in the resistance to flow; for the smallest glottic areas studied, the pressure drop was almost 6 times higher than for an area of 40 mm2. Consequently, in cases of areas below 40 mm2 even minor enlargement of the glottic opening can lead to a marked improvement in breathing comfort. Computational fluid dynamics is a useful method for calculating and visualizing the changing parameters of airflow in the upper respiratory tract.

Local Variability of Parameters for Characterization of the Corneal Subbasal Nerve Plexus.

PubMed

Winter, Karsten; Scheibe, Patrick; Köhler, Bernd; Allgeier, Stephan; Guthoff, Rudolf F; Stachs, Oliver

2016-01-01

The corneal subbasal nerve plexus (SNP) offers high potential for early diagnosis of diabetic peripheral neuropathy. Changes in subbasal nerve fibers can be assessed in vivo by confocal laser scanning microscopy (CLSM) and quantified using specific parameters. While current study results agree regarding parameter tendency, there are considerable differences in terms of absolute values. The present study set out to identify factors that might account for this high parameter variability. In three healthy subjects, we used a novel method of software-based large-scale reconstruction that provided SNP images of the central cornea, decomposed the image areas into all possible image sections corresponding to the size of a single conventional CLSM image (0.16 mm2), and calculated a set of parameters for each image section. In order to carry out a large number of virtual examinations within the reconstructed image areas, an extensive simulation procedure (10,000 runs per image) was implemented. The three analyzed images ranged in size from 3.75 mm2 to 4.27 mm2. The spatial configuration of the subbasal nerve fiber networks varied greatly across the cornea and thus caused heavily location-dependent results as well as wide value ranges for the parameters assessed. Distributions of SNP parameter values varied greatly between the three images and showed significant differences between all images for every parameter calculated (p < 0.001 in each case). The relatively small size of the conventionally evaluated SNP area is a contributory factor in high SNP parameter variability. Averaging of parameter values based on multiple CLSM frames does not necessarily result in good approximations of the respective reference values of the whole image area. This illustrates the potential for examiner bias when selecting SNP images in the central corneal area.

Land subsidence in the San Joaquin Valley, California, USA, 2007-14

USGS Publications Warehouse

Sneed, Michelle; Brandt, Justin

2015-01-01

Rapid land subsidence was recently measured using multiple methods in two areas of the San Joaquin Valley (SJV): between Merced and Fresno (El Nido), and between Fresno and Bakersfield (Pixley). Recent land-use changes and diminished surface-water availability have led to increased groundwater pumping, groundwater-level declines, and land subsidence. Differential land subsidence has reduced the flow capacity of water-conveyance systems in these areas, exacerbating flood hazards and affecting the delivery of irrigation water. Vertical land-surface changes during 2007–2014 were determined by using Interferometric Synthetic Aperture Radar (InSAR), Continuous Global Positioning System (CGPS), and extensometer data. Results of the InSAR analysis indicate that about 7600 km2 subsided 50–540 mm during 2008–2010; CGPS and extensometer data indicate that these rates continued or accelerated through December 2014. The maximum InSAR-measured rate of 270 mm yr−1 occurred in the El Nido area, and is among the largest rates ever measured in the SJV. In the Pixley area, the maximum InSAR-measured rate during 2008–2010 was 90 mm yr−1. Groundwater was an important part of the water supply in both areas, and pumping increased when land use changed or when surface water was less available. This increased pumping caused groundwater-level declines to near or below historical lows during the drought periods 2007–2009 and 2012–present. Long-term groundwater-level and land-subsidence monitoring in the SJV is critical for understanding the interconnection of land use, groundwater levels, and subsidence, and evaluating management strategies that help mitigate subsidence hazards to infrastructure while optimizing water supplies.

Normal Cerebellar Growth by Using Three-dimensional US in the Preterm Infant from Birth to Term-corrected Age.

PubMed

Benavente-Fernández, Isabel; Rodríguez-Zafra, Enrique; León-Martínez, Jesús; Jiménez-Gómez, Gema; Ruiz-González, Estefanía; Fernández-Colina, Rosalía Campuzano; Lechuga-Sancho, Alfonso M; Lubián-López, Simón P

2018-04-03

Purpose To establish cross-sectional and longitudinal reference values for cerebellar size in preterm infants with normal neuroimaging findings and normal 2-year neurodevelopmental outcome by using cranial ultrasonography (US). Materials and Methods This prospective study consecutively enrolled preterm infants admitted to a neonatal intensive care unit from June 2011 to June 2014 with a birth weight of less than or equal to 1500 g and/or gestational age (GA) of less than or equal to 32 weeks. They underwent weekly cranial US from birth to term-equivalent age and magnetic resonance (MR) imaging at term-equivalent age. The infants underwent neurodevelopmental assessments at age 2 years with Bayley Scales of Infant and Toddler Development, 3rd edition (BSID-III). Patients with adverse outcomes (death or abnormal neuroimaging findings and/or BSID-III score of <85) were excluded. The following measurements were performed: vermis height, craniocaudal diameter, superior width, inferior width, vermis area, and transcerebellar diameter. Statistical analyses were conducted by using multilevel analyses. Results A total of 137 infants with a mean GA at birth of 29.4 weeks (range, 25-32 weeks) were included. Transcerebellar diameter increased by 1.04 mm per week on average; vermis height and craniocaudal diameter increased by 0.55 mm and 0.59 mm, respectively. Superior vermian width increased by an average of 0.45 mm, whereas inferior vermian width increased by an average of 0.51 mm per week. Vermis area was found to increase by 0.22 cm 2 per week on average. The sex effect was significant (female lower than male) for vermis height (P < .05), craniocaudal diameter (P < .05), inferior vermian width (P <. 05), and vermis area (P <. 05). Conclusion Cross-sectional and longitudinal reference values were established for cerebellar growth in preterm infants, which may be included in routine cranial US. © RSNA, 2018 Online supplemental material is available for this article.

Validation of High Resolution Orbital Precipitation Over Upper Mahanadi River Basin, India

NASA Astrophysics Data System (ADS)

Gautam, A. K.; Pandey, A.

2016-12-01

Precipitation is one of the most important component of hydrologic cycle and used for various applications i.e. hydrological modeling, structure design to water management policy. Satellite based precipitation, radar rainfall and rain-gauge networks are supporting to each other, in relation to their spatial coverage and ability of observing precipitation. In the absence of rainfall data, satellite precipitation products can be used in the developing countries and over complex terrain where precipitation observations are either sparse or not available. However, satellite precipitation estimates are affected by different errors (AghaKouchak, et al., 2012.). Therefore, ground validation of satellite precipitation estimates is essential. In this study, the upper Mahanadi River Basin (A Part of Central India), has been selected for evaluation of the TRMM multi-satellite precipitation analysis (TMPA) and IMERG (Integrated Multi-satellite Retrievals for GPM) satellite Based Precipitation Products for the period of April 2014 - December 2015. The TMPA (3B42V7) and IMERG (late run) precipitation estimates were evaluated using statistical, contingency table and volumetric method for available 112 rain gauge stations in the study area. Results indicated that, both IMERG and TMPA precipitation overestimated the daily precipitation. The results also revealed that IMERG precipitation estimates provide better accuracy than TMPA precipitation estimates for very light rain (0.1-2.5 mm day-1), light rain (2.5-7.5 mm day-1), moderate rain (7.5-35.5 mm day-1), heavy rain (35.5-64.5 mm day-1) and very heavy rain (>64.5 mm day-1). Although, the detection capability of daily TMPA precipitation performed better in heavy rain. The results showed a good correlation (as high as 0.84) and poor correlation (as low as 0.012) with GPM satellite data over the most parts of the study area. The analyses suggest that, there is a need for improvement in precipitation estimation algorithm and accuracy verification against raingauge precipitation measurement to capture the rain events reliably in the study area.

Improved estimation of ligand macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods

NASA Astrophysics Data System (ADS)

Khandelwal, Akash; Balaz, Stefan

2007-01-01

Structure-based predictions of binding affinities of ligands binding to proteins by coordination bonds with transition metals, covalent bonds, and bonds involving charge re-distributions are hindered by the absence of proper force fields. This shortcoming affects all methods which use force-field-based molecular simulation data on complex formation for affinity predictions. One of the most frequently used methods in this category is the Linear Response (LR) approach of Åquist, correlating binding affinities with van der Waals and electrostatic energies, as extended by Jorgensen's inclusion of solvent-accessible surface areas. All these terms represent the differences, upon binding, in the ensemble averages of pertinent quantities, obtained from molecular dynamics (MD) or Monte Carlo simulations of the complex and of single components. Here we report a modification of the LR approach by: (1) the replacement of the two energy terms through the single-point QM/MM energy of the time-averaged complex structure from an MD simulation; and (2) a rigorous consideration of multiple modes (mm) of binding. The first extension alleviates the force-field related problems, while the second extension deals with the ligands exhibiting large-scale motions in the course of an MD simulation. The second modification results in the correlation equation that is nonlinear in optimized coefficients, but does not lead to an increase in the number of optimized coefficients. The application of the resulting mm QM/MM LR approach to the inhibition of zinc-dependent gelatinase B (matrix metalloproteinase 9) by 28 hydroxamate ligands indicates a significant improvement of descriptive and predictive abilities.

Emerging pollutants in sewage, surface and drinking water in Galicia (NW Spain).

PubMed

Rodil, Rosario; Quintana, José Benito; Concha-Graña, Estefanía; López-Mahía, Purificación; Muniategui-Lorenzo, Soledad; Prada-Rodríguez, Darío

2012-03-01

A monitoring programme was carried out on wastewater, surface and drinking water on the NW area of Spain during the four seasons of a year period (November 2007-September 2008). This study covered a series of emerging pollutants of different classes, including pharmaceuticals, neutral and acidic organophosphorus flame retardant/plasticizers (OPs), triclosan, phenoxy-herbicides, insect repellents and UV filters. From the total set of 53 compounds, 19 were found in raw wastewater with median concentrations higher than 0.1 μg L(-1). Among them, salicylic acid, ibuprofen and the UV filter benzophenone-4 (BP-4) were the most concentrated, exceeding the 1 μg L(-1) median value. Subsequently, 11 of these contaminants are not efficiently enough removed in the small WWTPs tested and their median concentrations in effluents still surpassed the 0.1 μg L(-1), so that they can spread through surface water. These chemicals are the pharmaceuticals naproxen, diclofenac and atenolol; the OPs tri(2-chloroethyl) phosphate (TCEP), tri(chloropropyl) phosphate (TCPP), tri-n-butyl phosphate (TnBP), diphenyl phosphate (DPhP) and diethylhexyl phosphate (DEHP); and the sulphonate UV filters BP-4 and 2-phenylbenzimidazole-5-sulphonic acid (PBSA). These OPs were then the dominant emerging pollutants occurring in surface and drinking water, where they are detected in the 20-200 ng L(-1) range. Pharmaceuticals and UV filters are typically below the 10 ng L(-1) level. Finally, herbicides were only detected in the last sampling campaign under the 100 ng L(-1) drinking water European Union limit. Copyright © 2011 Elsevier Ltd. All rights reserved.

Influence of meniscus on cartilage and subchondral bone features of knees from older individuals: A cadaver study

PubMed Central

Touraine, Sébastien; Bouhadoun, Hamid; Engelke, Klaus; Laredo, Jean Denis; Chappard, Christine

2017-01-01

Objective Cartilage and subchondral bone form a functional unit. Here, we aimed to examine the effect of meniscus coverage on the characteristics of this unit in knees of older individuals. Methods We assessed the hyaline cartilage, subchondral cortical plate (SCP), and subchondral trabecular bone in areas covered or uncovered by the meniscus from normal cadaver knees (without degeneration). Bone cores harvested from the medial tibial plateau at locations uncovered (central), partially covered (posterior), and completely covered (peripheral) by the meniscus were imaged by micro-CT. The following were measured on images: cartilage volume (Cart.Vol, mm3) and thickness (Cart.Th, mm); SCP thickness (SCP.Th, μm) and porosity (SCP.Por, %); bone volume to total volume fraction (BV/TV, %); trabecular thickness (Tb.Th, μm), spacing (Tb.Sp, μm), and number (Tb.N, 1/mm); structure model index (SMI); trabecular pattern factor (Tb.Pf); and degree of anisotropy (DA). Results Among the 28 specimens studied (18 females) from individuals with mean age 82.8±10.2 years, cartilage and SCP were thicker at the central site uncovered by the meniscus than the posterior and peripheral sites, and Cart.Vol was greater. SCP.Por was highest in posterior samples. In the upper 1–5 mm of subchondral bone, central samples were characterized by higher values for BV/TV, Tb.N, Tb.Th, and connectivity (Tb.Pf), a more plate-like trabecular structure and lower anisotropy than with other samples. Deeper down, at 6–10 mm, the differences were slightly higher for Tb.Th centrally, DA peripherally and SMI posteriorly. Conclusions The coverage or not by meniscus in the knee of older individuals is significantly associated with Cart.Th, SCP.Th, SCP.Por and trabecular microarchitectural parameters in the most superficial 5 mm and to a lesser extent the deepest area of subchondral trabecular bone. These results suggest an effect of differences in local loading conditions. In subchondral bone uncovered by the meniscus, the trabecular architecture resembles that of highly loaded areas. PMID:28797093

SU-F-J-206: Systematic Evaluation of the Minimum Detectable Shift Using a Range- Finding Camera

DOE Office of Scientific and Technical Information (OSTI.GOV)

Platt, M; Platt, M; Lamba, M

2016-06-15

Purpose: The robotic table used for patient alignment in proton therapy is calibrated only at commissioning under well-defined conditions and table shifts may vary over time and with differing conditions. The purpose of this study is to systematically investigate minimum detectable shifts using a time-of-flight (TOF) range-finding camera for table position feedback. Methods: A TOF camera was used to acquire one hundred 424 × 512 range images from a flat surface before and after known shifts. Range was assigned by averaging central regions of the image across multiple images. Depth resolution was determined by evaluating the difference between the actualmore » shift of the surface and the measured shift. Depth resolution was evaluated for number of images averaged, area of sensor over which depth was averaged, distance from camera to surface, central versus peripheral image regions, and angle of surface relative to camera. Results: For one to one thousand images with a shift of one millimeter the range in error was 0.852 ± 0.27 mm to 0.004 ± 0.01 mm (95% C.I.). For varying regions of the camera sensor the range in error was 0.02 ± 0.05 mm to 0.47 ± 0.04 mm. The following results are for 10 image averages. For areas ranging from one pixel to 9 × 9 pixels the range in error was 0.15 ± 0.09 to 0.29 ± 0.15 mm (1σ). For distances ranging from two to four meters the range in error was 0.15 ± 0.09 to 0.28 ± 0.15 mm. For an angle of incidence between thirty degrees and ninety degrees the average range in error was 0.11 ± 0.08 to 0.17 ± 0.09 mm. Conclusion: It is feasible to use a TOF camera for measuring shifts in flat surfaces under clinically relevant conditions with submillimeter precision.« less

A Study on the Development of a Robot-Assisted Automatic Laser Hair Removal System

PubMed Central

Lim, Hyoung-woo; Park, Sungwoo; Noh, Seungwoo; Lee, Dong-Hun; Yoon, Chiyul; Koh, Wooseok; Kim, Youdan; Chung, Jin Ho; Kim, Hee Chan

2014-01-01

Abstract Background and Objective: The robot-assisted automatic laser hair removal (LHR) system is developed to automatically detect any arbitrary shape of the desired LHR treatment area and to provide uniform laser irradiation to the designated skin area. Methods: For uniform delivery of laser energy, a unit of a commercial LHR device, a laser distance sensor, and a high-resolution webcam are attached at the six axis industrial robot's end-effector, which can be easily controlled using a graphical user interface (GUI). During the treatment, the system provides real-time treatment progress as well as the total number of “pick and place” automatically. Results: During the test, it was demonstrated that the arbitrary shapes were detected, and that the laser was delivered uniformly. The localization error test and the area-per-spot test produced satisfactory outcome averages of 1.04 mm error and 38.22 mm2/spot, respectively. Conclusions: Results showed that the system successfully demonstrated accuracy and effectiveness. The proposed system is expected to become a promising device in LHR treatment. PMID:25343281

Characterization of macromolecular baseline of human brain using metabolite cycled semi-LASER at 9.4T.

PubMed

Giapitzakis, Ioannis-Angelos; Avdievich, Nikolai; Henning, Anke

2018-08-01

Macromolecular resonances (MM) arise mainly from cytosolic proteins and overlap with metabolites, influencing metabolite quantification. Macromolecules can serve as valuable biomarkers for diseases and pathologies. The objectives of this study were to characterize MM at 9.4T in the human brain (occipital and left parietal lobe) and to describe the RF coil setup used for MM acquisition in the two regions. An adiabatic inversion pulse was optimised for metabolite nulling at 9.4T using double inversion recovery and was combined for the first time with metabolite cycled (MC) semi-LASER and appropriate coil configuration. MM spectra (seven volunteers) from two brain locations were averaged and smoothed creating MM templates, which were then parametrized using simulated Voigt-shaped lines within LCModel. Quantification was performed on individual data sets, including corrections for different tissue composition and the T 1 and T 2 relaxation of water. Our coil configuration method resulted in efficient B1+ (>30 T/√kW) for both brain regions. The 15 MM components were detected and quantified in MM baselines of the two brain areas. No significant differences in concentration levels of MM between different regions were found. Two new MM peaks were reported (M7 & M8). Double inversion, which was combined with MC semi-LASER, enabled the acquisition of high spectral resolution MM spectra for both brain regions at 9.4T. The 15 MM components were detected and quantified. Two new MM peaks were reported for the first time (M7 & M8) and preliminarily assigned to β-methylene protons of aspartyl-groups. Magn Reson Med 80:462-473, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

The efficacy of two electrodes radiofrequency technique: comparison study using a cadaveric interspinous ligament and temperature measurement using egg white.

PubMed

Lee, Chang-Hyung; Derby, Richard; Choi, Hyun-Seok; Lee, Sang-Heon; Kim, Se Hoon; Kang, Yoon Kyu

2010-01-01

One technique in radiofrequency neurotomies uses 2 electrodes that are simultaneously placed to lie parallel to one another. Comparing lesions on cadaveric interspinous ligament tissue and measuring the temperature change in egg white allows us to accurately measure quantitatively the area of the lesion. Fresh cadaver spinal tissue and egg white tissue were used. A series of samples were prepared with the electrodes placed 1 to 7 mm apart. Using radiofrequency, the needle electrodes were heated in sequential or simultaneous order and the distance of the escaped lesion area and temperature were measured. Samples of cadaver interspinous ligament showed sequential heating of the needles limits the placement of the needle electrodes up to 2 mm apart from each other and up to 4 mm apart when heated simultaneously. The temperature at the escaped lesion area decreased according to the distance for egg white. There was a significant difference in temperature at the escaped lesion area up to 6 mm apart and the temperature was above 50 degrees celsius up to 5 mm in simultaneous lesion and 3 mm in the sequential lesion. The limitations of this study include cadaveric experimentation and use of intraspinous ligament rather than medial branch of the dorsal ramus which is difficult to identify. Heating the 2 electrodes simultaneously appears to coagulate a wider area and potentially produce better results in less time.

Dynamic cycling in atrial size and flow during obstructive apnoea

PubMed Central

Pressman, Gregg S; Cepeda-Valery, Beatriz; Codolosa, Nicolas; Orban, Marek; Samuel, Solomon P; Somers, Virend K

2016-01-01

Objective Obstructive sleep apnoea (OSA) is strongly associated with cardiovascular disease. However, acute cardiovascular effects of repetitive airway obstruction are poorly understood. While past research used a sustained Mueller manoeuver to simulate OSA we employed a series of gasping efforts to better simulate true obstructive apnoeas. This report describes acute changes in cardiac anatomy and flow related to sudden changes in intrathoracic pressure. Methods and results 26 healthy, normal weight participants performed 5–6 gasping efforts (target intrathoracic pressure −40 mm Hg) while undergoing Doppler echocardiography. 14 participants had sufficient echocardiographic images to allow comparison of atrial areas during the manoeuver with baseline measurements. Mitral and tricuspid E-wave and A-wave velocities postmanoeuver were compared with baseline in all participants. Average atrial areas changed little during the manoeuver, but variance in both atrial areas was significantly greater than baseline. Further, an inverse relationship was noted with left atrial collapse and right atrial enlargement at onset of inspiratory effort. Significant inverse changes were noted in Doppler flow when comparing the first beat postmanoeuver (pMM1) with baseline. Mitral E-wave velocity increased 9.1 cm/s while tricuspid E-wave velocity decreased 7.0 cm/s; by the eighth beat postmanoeuver (pMM8) values were not different from baseline. Mitral and tricuspid A-wave velocities were not different from baseline at pMM1, but both were significantly higher by pMM8. Conclusions Repetitive obstructive apnoeas produce dynamic, inverse changes in atrial size and Doppler flow across the atrioventricular valves. These observations have important implications for understanding the pathophysiology of OSA. PMID:27127636

Intraoral versus extraoral measurement of the height of the interproximal contact area in maxillary anterior teeth.

PubMed

Sghaireen, Mohd G; Albhiran, Heyam Mobark; Alzoubi, Ibrahim A; Lynch, Edward; Al-Omiri, Mahmoud K

2015-01-01

This study aimed to clinically quantify the apicoincisal height of the upper interproximal areas directly in patients' mouths compared to measurements on stone models. One hundred and fifty participants (75 females and 75 males, age range 20-45 years) were recruited for this study. A digital caliper was used to measure the anterior maxillary interproximal contact areas directly in patients' mouths and on stone models. The digital caliper accuracy was up to 0.01. The Statistical Package for Social Sciences software (SPSS, version 19.0, Chicago, Ill., USA) was used for statistical analysis. Statistical significance was based on probability values <0.05. The intraoral measurement of proximal contacts as well as the measurement on stone models showed that the dimensions of interproximal contacts on both sides of each tooth were significantly different (p < 0.001) and that the dimension of the mesial contact point was larger than that of the distal contact point of each tooth. The largest contact point was the one between the central incisors (direct intraoral measurement = 2.9-6.49 mm; model measurement = 3.31-6.91 mm). On the other hand, the contact point between the canine and first premolar was the smallest on both sides of the arch (0.63-2.52 mm intraorally, 0.98-2.88 mm on models). The intraoral measurement of contact points was more accurate than model measurements, and the differences were statistically significant (p < 0.001). The clinical evaluation of contact point dimensions using a digital caliper was more precise than measuring contact points on stone models; hence, it is a viable, quick and adequate method to be used routinely. © 2015 S. Karger AG, Basel.

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ojeda-May, Pedro; Pu, Jingzhi, E-mail: jpu@iupui.edu

The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r{sup −1} term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as amore » Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN{sub 2} reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN{sub 2} reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.« less

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

PubMed

Ojeda-May, Pedro; Pu, Jingzhi

2015-11-07

The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

NASA Astrophysics Data System (ADS)

Ojeda-May, Pedro; Pu, Jingzhi

2015-11-01

The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r-1 term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.

Intralaryngeal thyroarytaenoid lateralisation using the Fast-Fix 360 system: a canine cadaveric study

PubMed Central

Stegen, Ludo; Kitshoff, Adriaan M.; Van Goethem, Bart; Vandekerckhove, Peter; de Rooster, Hilde

2015-01-01

Introduction Laryngeal paralysis is a condition in which failure of arytaenoid abduction results in a reduced rima glottidis cross-sectional area. The most commonly performed surgical techniques rely on unilateral abduction of the arytaenoid, requiring a lateral or ventral surgical approach to the larynx. Aims and objectives The aim of the study was to investigate a novel minimally invasive intralaryngeal thyroarytaenoid lateralisation technique, using the Fast-Fix 360 meniscal repair system. Materials and methods Larynges were harvested from large breed canine cadavers. With the aid of Kirschner wires placed between the centre of the vocal process and the centre of an imaginary line between the cranial thyroid fissure and the cricothyroid articulation, the mean insertion angle was calculated. Results The Fast-Fix 360 delivery needle inserted intralaryngeally (n=10), according to a simplified insertion angle (70°), resulted in thyroid penetration (>2.5 mm from margin) in all patients. The Fast-Fix was applied unilaterally at 70° with the first toggle fired on the lateral aspect of the thyroid cartilage and inside the laryngeal cavity on retraction. The suture was tightened. Preprocedural (61.06±9.21 mm2) and postprocedural (138.37±26.12 mm2) rima glottidis cross-sectional area was significantly different (P<0.0001). The mean percentage increase in rima glottidis cross-sectional area was 125.96 per cent (±16.54 per cent). Conclusion Intralaryngeal thyroarytaenoid laterlisation using the Fast-Fix 360 meniscal repair system ex vivo increased the rima glottidis cross-sectional area significantly. PMID:26392907

A simple method for estimating basin-scale groundwater discharge by vegetation in the basin and range province of Arizona using remote sensing information and geographic information systems

USGS Publications Warehouse

Tillman, F.D.; Callegary, J.B.; Nagler, P.L.; Glenn, E.P.

2012-01-01

Groundwater is a vital water resource in the arid to semi-arid southwestern United States. Accurate accounting of inflows to and outflows from the groundwater system is necessary to effectively manage this shared resource, including the important outflow component of groundwater discharge by vegetation. A simple method for estimating basin-scale groundwater discharge by vegetation is presented that uses remote sensing data from satellites, geographic information systems (GIS) land cover and stream location information, and a regression equation developed within the Southern Arizona study area relating the Enhanced Vegetation Index from the MODIS sensors on the Terra satellite to measured evapotranspiration. Results computed for 16-day composited satellite passes over the study area during the 2000 through 2007 time period demonstrate a sinusoidal pattern of annual groundwater discharge by vegetation with median values ranging from around 0.3 mm per day in the cooler winter months to around 1.5 mm per day during summer. Maximum estimated annual volume of groundwater discharge by vegetation was between 1.4 and 1.9 billion m3 per year with an annual average of 1.6 billion m3. A simplified accounting of the contribution of precipitation to vegetation greenness was developed whereby monthly precipitation data were subtracted from computed vegetation discharge values, resulting in estimates of minimum groundwater discharge by vegetation. Basin-scale estimates of minimum and maximum groundwater discharge by vegetation produced by this simple method are useful bounding values for groundwater budgets and groundwater flow models, and the method may be applicable to other areas with similar vegetation types.

Quality evaluation of Semen Cassiae (Cassia obtusifolia L.) by using ultra-high performance liquid chromatography coupled with mass spectrometry.

PubMed

Zhang, Wei-Dong; Wang, Ying; Wang, Qing; Yang, Wan-Jun; Gu, Yi; Wang, Rong; Song, Xiao-Mei; Wang, Xiao-Juan

2012-08-01

A sensitive and reliable ultra-high performance liquid chromatography-electrospray ionization-tandem mass spectrometry has been developed and partially validated to evaluate the quality of Semen Cassiae (Cassia obtusifolia L.) through simultaneous determination of 11 anthraquinones and two naphtha-γ-pyrone compounds. The analysis was achieved on a Poroshell 120 EC-C(18) column (100 mm × 2.1 mm, 2.7 μm; Agilent, Palo Alto, CA, USA) with gradient elution using a mobile phase that consisted of acetonitrile-water (30 mM ammonium acetate) at a flow rate of 0.4 mL/min. For quantitative analysis, all calibration curves showed perfect linear regression (r(2) > 0.99) within the testing range. This method was also validated with respect to precision and accuracy, and was successfully applied to quantify the 13 components in nine batches of Semen Cassiae samples from different areas. The performance of developed method was compared with that of conventional high-performance liquid chromatography method. The significant advantages of the former include high-speed chromatographic separation, four times faster than high-performance liquid chromatography with conventional columns, and great enhancement in sensitivity. This developed method provided a new basis for overall assessment on quality of Semen Cassiae. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantifying shape changes of silicone breast implants in a murine model using in vivo micro-CT.

PubMed

Anderson, Emily E; Perilli, Egon; Carati, Colin J; Reynolds, Karen J

2017-08-01

A major complication of silicone breast implants is the formation of a capsule around the implant known as capsular contracture which results in the distortion of the implant. Recently, a mouse model for studying capsular contracture was examined using micro-computed tomography (micro-CT), however, only qualitative changes were reported. The aim of this study was to develop a quantitative method for comparing the shape changes of silicone implants using in vivo micro-CT. Mice were bilaterally implanted with silicone implants and underwent ionizing radiation to induce capsular contracture. On day 28 post-surgery mice were examined in vivo using micro-CT. The reconstructed cross-section images were visually inspected to identify distortion. Measurements were taken in 2D and 3D to quantify the shape of the implants in the normal (n = 11) and distorted (n = 5) groups. The degree of anisotropy was significantly higher in the distorted implants in the transaxial view (0.99 vs. 1.19, p = 0.002) and the y-axis lengths were significantly shorter in the sagittal (9.27 mm vs. 8.55 mm, p = 0.015) and coronal (9.24 mm vs. 8.76 mm, p = 0.031) views, indicating a deviation from the circular cross-section and shortening of the long axis. The 3D analysis revealed a significantly lower average thickness (sphere-fitting method) in distorted implants (6.86 mm vs. 5.49 mm, p = 0.002), whereas the volume and surface area did not show significant changes. Statistically significant differences between normal and distorted implants were found in 2D and 3D using distance measurements performed via micro-CT. This objective analysis method can be useful for a range of studies involving deformable implants using in vivo micro-CT. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1447-1452, 2017. © 2016 Wiley Periodicals, Inc.

Development and calibration of a new gamma camera detector using large square Photomultiplier Tubes

NASA Astrophysics Data System (ADS)

Zeraatkar, N.; Sajedi, S.; Teimourian Fard, B.; Kaviani, S.; Akbarzadeh, A.; Farahani, M. H.; Sarkar, S.; Ay, M. R.

2017-09-01

Large area scintillation detectors applied in gamma cameras as well as Single Photon Computed Tomography (SPECT) systems, have a major role in in-vivo functional imaging. Most of the gamma detectors utilize hexagonal arrangement of Photomultiplier Tubes (PMTs). In this work we applied large square-shaped PMTs with row/column arrangement and positioning. The Use of large square PMTs reduces dead zones in the detector surface. However, the conventional center of gravity method for positioning may not introduce an acceptable result. Hence, the digital correlated signal enhancement (CSE) algorithm was optimized to obtain better linearity and spatial resolution in the developed detector. The performance of the developed detector was evaluated based on NEMA-NU1-2007 standard. The acquired images using this method showed acceptable uniformity and linearity comparing to three commercial gamma cameras. Also the intrinsic and extrinsic spatial resolutions with low-energy high-resolution (LEHR) collimator at 10 cm from surface of the detector were 3.7 mm and 7.5 mm, respectively. The energy resolution of the camera was measured 9.5%. The performance evaluation demonstrated that the developed detector maintains image quality with a reduced number of used PMTs relative to the detection area.

AlGaN/GaN high electron mobility transistors with selective area grown p-GaN gates

NASA Astrophysics Data System (ADS)

Yuliang, Huang; Lian, Zhang; Zhe, Cheng; Yun, Zhang; Yujie, Ai; Yongbing, Zhao; Hongxi, Lu; Junxi, Wang; Jinmin, Li

2016-11-01

We report a selective area growth (SAG) method to define the p-GaN gate of AlGaN/GaN high electron mobility transistors (HEMTs) by metal-organic chemical vapor deposition. Compared with Schottky gate HEMTs, the SAG p-GaN gate HEMTs show more positive threshold voltage (V th) and better gate control ability. The influence of Cp2Mg flux of SAG p-GaN gate on the AlGaN/GaN HEMTs has also been studied. With the increasing Cp2Mg from 0.16 μmol/min to 0.20 μmol/min, the V th raises from -0.67 V to -0.37 V. The maximum transconductance of the SAG HEMT at a drain voltage of 10 V is 113.9 mS/mm while that value of the Schottky HEMT is 51.6 mS/mm. The SAG method paves a promising way for achieving p-GaN gate normally-off AlGaN/GaN HEMTs without dry etching damage. Project supported by the National Natural Sciences Foundation of China (Nos. 61376090, 61306008) and the National High Technology Program of China (No. 2014AA032606).

Influence of the weighing bar size to determine optimal time of biodiesel-glycerol separation by using the buoyancy weighing-bar method

NASA Astrophysics Data System (ADS)

Tambun, R.; Sibagariang, Y.; Manurung, J.

2018-02-01

The buoyancy weighing-bar method is a novel method in the particle size distribution measurement. This method can measure particle size distributions of the settling particles and floating particles. In this study, the buoyancy weighing-bar method is applied to determine optimal time of biodiesel-glycerol separation. The buoyancy weighing-bar method can be applied to determine the separation time because biodiesel and glycerol have the different densities. The influences of diameter of weighing-bar by using the buoyancy weighing-bar method would be experimentally investigated. The diameters of weighing-bar in this experiment are 8 mm, 10 mm, 15 mm and 20 mm, while the graduated cylinder (diameter : 65 mm) is used as vessel. The samples used in this experiment are the mixture of 95 % of biodiesel and 5 % of glycerol. The data obtained by the buoyancy weighing-bar method are analized by using the gas chromatography to determine the purity of biodiesel. Based on the data obtained, the buoyancy weighing-bar method can be used to detect the separation time of biodiesel-glycerol by using the weighing-bar diameter of 8 mm, 10 mm, 15 mm and 20 mm, but the most accuracy in determination the biodiesel-glycerol separation time is obtained by using the weighing-bar diameter of 20 mm. The biodiesel purity of 97.97 % could be detected at 64 minutes by using the buoyancy weighing-bar method when the weighing-bar diameter of 20 mm is used.

A new markerless patient-to-image registration method using a portable 3D scanner.

PubMed

Fan, Yifeng; Jiang, Dongsheng; Wang, Manning; Song, Zhijian

2014-10-01

Patient-to-image registration is critical to providing surgeons with reliable guidance information in the application of image-guided neurosurgery systems. The conventional point-matching registration method, which is based on skin markers, requires expensive and time-consuming logistic support. Surface-matching registration with facial surface scans is an alternative method, but the registration accuracy is unstable and the error in the more posterior parts of the head is usually large because the scan range is limited. This study proposes a new surface-matching method using a portable 3D scanner to acquire a point cloud of the entire head to perform the patient-to-image registration. A new method for transforming the scan points from the device space into the patient space without calibration and tracking was developed. Five positioning targets were attached on a reference star, and their coordinates in the patient space were measured prior. During registration, the authors moved the scanner around the head to scan its entire surface as well as the positioning targets, and the scanner generated a unique point cloud in the device space. The coordinates of the positioning targets in the device space were automatically detected by the scanner, and a spatial transformation from the device space to the patient space could be calculated by registering them to their coordinates in the patient space that had been measured prior. A three-step registration algorithm was then used to register the patient space to the image space. The authors evaluated their method on a rigid head phantom and an elastic head phantom to verify its practicality and to calculate the target registration error (TRE) in different regions of the head phantoms. The authors also conducted an experiment with a real patient's data to test the feasibility of their method in the clinical environment. In the phantom experiments, the mean fiducial registration error between the device space and the patient space, the mean surface registration error, and the mean TRE of 15 targets on the surface of each phantom were 0.34 ± 0.01 mm and 0.33 ± 0.02 mm, 1.17 ± 0.02 mm and 1.34 ± 0.10 mm, and 1.06 ± 0.11 mm and 1.48 ± 0.21 mm, respectively. When grouping the targets according to their positions on the head, high accuracy was achieved in all parts of the head, and the TREs were similar across different regions. The authors compared their method with the current surface registration methods that use only a part of the facial surface on the elastic phantom, and the mean TRE of 15 targets was 1.48 ± 0.21 mm and 1.98 ± 0.53 mm, respectively. In a clinical experiment, the mean TRE of seven targets on the patient's head surface was 1.92 ± 0.18 mm, which was sufficient to meet clinical requirements. The proposed surface-matching registration method provides sufficient registration accuracy even in the posterior area of the head. The 3D point cloud of the entire head, including the facial surface and the back of the head, can be easily acquired using a portable 3D scanner. The scanner does not need to be calibrated prior or tracked by the optical tracking system during scanning.

Quantitative evaluation of deep and shallow tissue layers' contribution to fNIRS signal using multi-distance optodes and independent component analysis.

PubMed

Funane, Tsukasa; Atsumori, Hirokazu; Katura, Takusige; Obata, Akiko N; Sato, Hiroki; Tanikawa, Yukari; Okada, Eiji; Kiguchi, Masashi

2014-01-15

To quantify the effect of absorption changes in the deep tissue (cerebral) and shallow tissue (scalp, skin) layers on functional near-infrared spectroscopy (fNIRS) signals, a method using multi-distance (MD) optodes and independent component analysis (ICA), referred to as the MD-ICA method, is proposed. In previous studies, when the signal from the shallow tissue layer (shallow signal) needs to be eliminated, it was often assumed that the shallow signal had no correlation with the signal from the deep tissue layer (deep signal). In this study, no relationship between the waveforms of deep and shallow signals is assumed, and instead, it is assumed that both signals are linear combinations of multiple signal sources, which allows the inclusion of a "shared component" (such as systemic signals) that is contained in both layers. The method also assumes that the partial optical path length of the shallow layer does not change, whereas that of the deep layer linearly increases along with the increase of the source-detector (S-D) distance. Deep- and shallow-layer contribution ratios of each independent component (IC) are calculated using the dependence of the weight of each IC on the S-D distance. Reconstruction of deep- and shallow-layer signals are performed by the sum of ICs weighted by the deep and shallow contribution ratio. Experimental validation of the principle of this technique was conducted using a dynamic phantom with two absorbing layers. Results showed that our method is effective for evaluating deep-layer contributions even if there are high correlations between deep and shallow signals. Next, we applied the method to fNIRS signals obtained on a human head with 5-, 15-, and 30-mm S-D distances during a verbal fluency task, a verbal working memory task (prefrontal area), a finger tapping task (motor area), and a tetrametric visual checker-board task (occipital area) and then estimated the deep-layer contribution ratio. To evaluate the signal separation performance of our method, we used the correlation coefficients of a laser-Doppler flowmetry (LDF) signal and a nearest 5-mm S-D distance channel signal with the shallow signal. We demonstrated that the shallow signals have a higher temporal correlation with the LDF signals and with the 5-mm S-D distance channel than the deep signals. These results show the MD-ICA method can discriminate between deep and shallow signals. Copyright © 2013 Elsevier Inc. All rights reserved.

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement.

PubMed

Cao, Lili; Caldararu, Octav; Ryde, Ulf

2017-09-07

Nitrogenase is the only enzyme that can break the triple bond in N 2 to form two molecules of ammonia. The enzyme has been thoroughly studied with both experimental and computational methods, but there is still no consensus regarding the atomic details of the reaction mechanism. In the most common form, the active site is a MoFe 7 S 9 C(homocitrate) cluster. The homocitrate ligand contains one alcohol and three carboxylate groups. In water solution, the triply deprotonated form dominates, but because the alcohol (and one of the carboxylate groups) coordinate to the Mo ion, this may change in the enzyme. We have performed a series of computational calculations with molecular dynamics (MD), quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), QM/MM with Poisson-Boltzmann and surface area solvation, QM/MM thermodynamic cycle perturbations, and quantum refinement methods to settle the most probable protonation state of the homocitrate ligand in nitrogenase. The results quite conclusively point out a triply deprotonated form (net charge -3) with a proton shared between the alcohol and one of the carboxylate groups as the most stable at pH 7. Moreover, we have studied eight ionizable protein residues close to the active site with MD simulations and determined the most likely protonation states.

Validation of a HPLC method for determination of hydroxymethylfurfural in crude palm oil.

PubMed

Ariffin, Abdul Azis; Ghazali, H M; Kavousi, Parviz

2014-07-01

For the first time 5-hydroxymethyl-2-furaldehyde (HMF) was separated from crude palm oil (CPO), and its authenticity was determined using an RP-HPLC method. Separation was accomplished with isocratic elution of a mobile phase comprising water and methanol (92:8 v/v) on a Purospher Star RP-18e column (250mm×4.6mm, 5.0μm). The flow rate was adjusted to 1ml/min and detection was performed at 284nm. The method was validated, and results obtained exhibit a good recovery (95.58% to 98.39%). Assessment of precision showed that the relative standard deviations (RSD%) of retention times and peak areas of spiked samples were less than 0.59% and 2.66%, respectively. Further, the limit of detection (LOD) and LOQ were 0.02, 0.05mg/kg, respectively, and the response was linear across the applied ranges. The crude palm oil samples analysed exhibited HMF content less than 2.27mg/kg. Copyright © 2014 Elsevier Ltd. All rights reserved.

Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography.

PubMed

Croft, Daniel E; van Hemert, Jano; Wykoff, Charles C; Clifton, David; Verhoek, Michael; Fleming, Alan; Brown, David M

2014-01-01

Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. Copyright 2014, SLACK Incorporated.

Templated synthesis of highly ordered mesoporous cobalt ferrite and its microwave absorption properties

NASA Astrophysics Data System (ADS)

Li, Guo-Min; Wang, Lian-Cheng; Xu, Yao

2014-08-01

Based on the nanocasting strategy, highly ordered mesoporous CoFe2O4 is synthesized via the ‘two-solvent’ impregnation method using a mesoporous SBA-15 template. An ordered two-dimensional (P6mm) structure is preserved for the CoFe2O4/SBA-15 composite after the nanocasting. After the SBA-15 template is dissolved by NaOH solution, a mesoporous structure composed of aligned nanoparticles can be obtained, and the P6mm structure of the parent SBA-15 is preserved. With a high specific surface area (above 90 m2/g) and ferromagnetic behavior, the obtained material shows potential in light weight microwave absorption application. The minimum reflection loss (RL) can reach -18 dB at about 16 GHz with a thickness of 2 mm and the corresponding absorption bandwidth is 4.5 GHz.

Methods for quantitative measurement of tooth wear using the area and volume of virtual model cusps

PubMed Central

2018-01-01

Purpose Clinicians must examine tooth wear to make a proper diagnosis. However, qualitative methods of measuring tooth wear have many disadvantages. Therefore, this study aimed to develop and evaluate quantitative parameters using the cusp area and volume of virtual dental models. Methods The subjects of this study were the same virtual models that were used in our former study. The same age group classification and new tooth wear index (NTWI) scoring system were also reused. A virtual occlusal plane was generated with the highest cusp points and lowered vertically from 0.2 to 0.8 mm to create offset planes. The area and volume of each cusp was then measured and added together. In addition to the former analysis, the differential features of each cusp were analyzed. Results The scores of the new parameters differentiated the age and NTWI groups better than those analyzed in the former study. The Spearman ρ coefficients between the total area and the area of each cusp also showed higher scores at the levels of 0.6 mm (0.6A) and 0.8A. The mesiolingual cusp (MLC) showed a statistically significant difference (P<0.01) from the other cusps in the paired t-test. Additionally, the MLC exhibited the highest percentage of change at 0.6A in some age and NTWI groups. Regarding the age groups, the MLC showed the highest score in groups 1 and 2. For the NTWI groups, the MLC was not significantly different in groups 3 and 4. These results support the proposal that the lingual cusp exhibits rapid wear because it serves as a functional cusp. Conclusions Although this study has limitations due to its cross-sectional nature, it suggests better quantitative parameters and analytical tools for the characteristics of cusp wear. PMID:29770241

Bi-Directional Theta Modulation between the Septo-Hippocampal System and the Mammillary Area in Free-Moving Rats

PubMed Central

Ruan, Ming; Young, Calvin K.; McNaughton, Neil

2017-01-01

Hippocampal (HPC) theta oscillations have long been linked to various functions of the brain. Many cortical and subcortical areas that also exhibit theta oscillations have been linked to functional circuits with the hippocampus on the basis of coupled activities at theta frequencies. We examine, in freely moving rats, the characteristics of diencephalic theta local field potentials (LFPs) recorded in the supramammillary/mammillary (SuM/MM) areas that are bi-directionally connected to the HPC through the septal complex. Using partial directed coherence (PDC), we find support for previous suggestions that SuM modulates HPC theta at higher frequencies. We find weak separation of SuM and MM by dominant theta frequency recorded locally. Contrary to oscillatory cell activities under anesthesia where SuM is insensitive, but MM is sensitive to medial septal (MS) inactivation, theta LFPs persisted and became indistinguishable after MS-inactivation. However, MS-inactivation attenuated SuM/MM theta power, while increasing the frequency of SuM/MM theta. MS-inactivation also reduced root mean squared power in both HPC and SuM/MM equally, but reduced theta power differentially in the time domain. We provide converging evidence that SuM is preferentially involved in coding HPC theta at higher frequencies, and that the MS-HPC circuit normally imposes a frequency-limiting modulation over the SuM/MM area as suggested by cell-based recordings in anesthetized animals. In addition, we provide evidence that the postulated SuM-MS-HPC-MM circuit is under complex bi-directional control, rather than SuM and MM having roles as unidirectional relays in the network. PMID:28955209

A randomised controlled comparison of injection, thermal, and mechanical endoscopic methods of haemostasis on mesenteric vessels

PubMed Central

Hepworth, C; Kadirkamanathan, S; Gong, F; Swain, C

1998-01-01

Background and aims—A randomised controlled comparison of haemostatic efficacy of mechanical, injection, and thermal methods of haemostasis was undertaken using canine mesenteric vessels to test the hypothesis that mechanical methods of haemostasis are more effective in controlling haemorrhage than injection or thermal methods. The diameter of arteries in human bleeding ulcers measures up to 3.45 mm; mesenteric vessels up to 5 mm were therefore studied. 
Methods—Mesenteric vessels were randomised to treatment with injection sclerotherapy (adrenaline and ethanolamine), bipolar diathermy, or mechanical methods (band, clips, sewing machine, endoloops). The vessels were severed and haemostasis recorded. 
Results—Injection sclerotherapy and clips failed to stop bleeding from vessels of 1 mm (n=20) and 2 mm (n=20). Bipolar diathermy was effective on 8/10 vessels of 2 mm but failed on 3 mm vessels (n=5). Unstretched elastic bands succeeded on 13/15 vessels of 2 mm but on only 3/10 vessels of 3 mm. The sewing machine achieved haemostasis on 8/10 vessels of 4 mm but failed on 5 mm vessels (n=5); endoloops were effective on all 5 mm vessels (n=5). 
Conclusions—Only mechanical methods were effective on vessels greater than 2 mm in diameter. Some mechanical methods (banding and clips) were less effective than expected and need modification. Thermal and (effective) mechanical methods were significantly (p<0.01) more effective than injection sclerotherapy. The most effective mechanical methods were significantly more effective (p<0.01) than thermal or injection on vessels greater than 2mm. 

 Keywords: endoscopic haemostasis; mesenteric vessels PMID:9616305

Determining Subsidence Rates with a Combination of RTK GNSS Data and National Geodetic Survey Data Sheets: A Case Study from SE Texas

NASA Astrophysics Data System (ADS)

Kruger, J. M.

2016-12-01

This study determines the rates of subsidence or uplift in coastal areas of SE Texas by comparing recent GNSS measurements to the original orthometric heights of previously installed National Geodetic Survey (NGS) benchmarks. Understanding subsidence rates in coastal areas of SE Texas is critical when determining its vulnerability to local sea level rise and flooding, as well as for accurate survey control. The study area includes major metropolitan and industrial areas as well as more rural areas at risk for flooding and hurricane surge. The resurveying methods used in this RTK GNSS study allow a large area to be covered relatively quickly with enough detail to determine subsidence rates that are averaged over several decades, and identify at-risk regions that can be monitored more closely with permanent or campaign-style measurements. The most recent measurements were acquired using a Trimble R8 GNSS system on all NGS benchmarks found in the study area. Differential corrections were applied in real time using a VRS network of base stations. Nominal vertical accuracies were 1.5 to 3.0 cm for a 2 to 5 minute reading. Usually three readings were measured and averaged for the final result. A total of 340 benchmarks were used for vertical rate calculations. Original NGS elevations were subtracted from the new elevations and divided by the number of years between the two elevation measurements to determine the average subsidence or uplift rate of the benchmark. Besides inaccuracies in the NGS datasheet and re-measured elevations, another source of error includes uncertainties in the year the NGS datasheet elevations were measured. Overall, vertical rates of change vary from -6 to -15 mm/yr subsidence in Port Arthur, Nederland, and other areas of Jefferson County, as well as in areas northwest of Beaumont, Texas. Other areas with subsidence rates between -10 and -4 mm/yr include parts of the Bolivar Peninsula in Galveston County, northeastern Chambers County, and the Mont Belvieu area. Surprisingly, areas of uplift, with rates as great as +5 mm/yr, were found in some parts of the study area, mostly around Liberty, Texas, western Chambers County, east-central Beaumont, and in the northern part of the study area near Jasper, Texas.

A new method for temperature-field reconstruction during ultrasound-monitored cryosurgery using potential-field analogy.

PubMed

Thaokar, Chandrajit; Rossi, Michael R; Rabin, Yoed

2016-02-01

The current study aims at developing computational tools in order to gain information about the thermal history in areas invisible to ultrasound imaging during cryosurgery. This invisibility results from the high absorption rate of the ultrasound energy by the frozen region, which leads to an apparent opacity in the cryotreated area and a shadow behind it. A proof-of-concept for freezing-front estimation is demonstrated in the current study, using the new potential-field analogy method (PFAM). This method is further integrated with a recently developed temperature-field reconstruction method (TFRM) to estimate the temperature distribution within the frozen region. This study uses prostate cryosurgery as a developmental model and trans-rectal ultrasound imaging as a choice of practice. Results of this study indicate that the proposed PFAM is a viable and computationally inexpensive solution to estimate the extent of freezing in the acoustic shadow region. Comparison of PFAM estimations and experimental data shows an average mismatch of less than 2 mm in freezing-front location, which is comparable to the uncertainty in ultrasound imaging. Comparison of the integrated PFAM + TFRM scheme with a full-scale finite-elements analysis (FEA) indicates an average mismatch of 0.9 mm for the freezing front location and 0.1 mm for the lethal temperature isotherm of -45 °C. Comparison of the integrated PFAM + TFRM scheme with experimental temperature measurements show a difference in the range of 2 °C and 6 °C for selected points of measurement. Results of this study demonstrate the integrated PFAM + TFRM scheme as a viable and computationally inexpensive means to gain information about the thermal history in the frozen region during ultrasound-monitored cryosurgery. Copyright © 2015 Elsevier Inc. All rights reserved.

Influence of critical closing pressure on systemic vascular resistance and total arterial compliance: A clinical invasive study.

PubMed

Chemla, Denis; Lau, Edmund M T; Hervé, Philippe; Millasseau, Sandrine; Brahimi, Mabrouk; Zhu, Kaixian; Sattler, Caroline; Garcia, Gilles; Attal, Pierre; Nitenberg, Alain

2017-12-01

Systemic vascular resistance (SVR) and total arterial compliance (TAC) modulate systemic arterial load, and their product is the time constant (Tau) of the Windkessel. Previous studies have assumed that aortic pressure decays towards a pressure asymptote (P∞) close to 0mmHg, as right atrial pressure is considered the outflow pressure. Using these assumptions, aortic Tau values of ∼1.5seconds have been documented. However, a zero P∞ may not be physiological because of the high critical closing pressure previously documented in vivo. To calculate precisely the Tau and P∞ of the Windkessel, and to determine the implications for the indices of systemic arterial load. Aortic pressure decay was analysed using high-fidelity recordings in 16 subjects. Tau was calculated assuming P∞=0mmHg, and by two methods that make no assumptions regarding P∞ (the derivative and best-fit methods). Assuming P∞=0mmHg, we documented a Tau value of 1372±308ms, with only 29% of Windkessel function manifested by end-diastole. In contrast, Tau values of 306±109 and 353±106ms were found from the derivative and best-fit methods, with P∞ values of 75±12 and 71±12mmHg, and with ∼80% completion of Windkessel function. The "effective" resistance and compliance were ∼70% and ∼40% less than SVR and TAC (area method), respectively. We did not challenge the Windkessel model, but rather the estimation technique of model variables (Tau, SVR, TAC) that assumes P∞=0. The study favoured a shorter Tau of the Windkessel and a higher P∞ compared with previous studies. This calls for a reappraisal of the quantification of systemic arterial load. Crown Copyright © 2017. Published by Elsevier Masson SAS. All rights reserved.

Rapid Method of Determining Factors Limiting Bacterial Growth in Soil

PubMed Central

Aldén, L.; Demoling, F.; Bååth, E.

2001-01-01

A technique to determine which nutrients limit bacterial growth in soil was developed. The method was based on measuring the thymidine incorporation rate of bacteria after the addition of C, N, and P in different combinations to soil samples. First, the thymidine incorporation method was tested in two different soils: an agricultural soil and a forest humus soil. Carbon (as glucose) was found to be the limiting substance for bacterial growth in both of these soils. The effect of adding different amounts of nutrients was studied, and tests were performed to determine whether the additions affected the soil pH and subsequent bacterial activity. The incubation time required to detect bacterial growth after adding substrate to the soil was also evaluated. Second, the method was used in experiments in which three different size fractions of straw (1 to 2, 0.25 to 1, and <0.25 mm) were mixed into the agricultural soil in order to induce N limitation for bacterial growth. When the straw fraction was small enough (<0.25 mm), N became the limiting nutrient for bacterial growth after about 3 weeks. After the addition of the larger straw fractions (1 to 2 and 0.25 to 1 mm), the soil bacteria were C limited throughout the incubation period (10 weeks), although an increase in the thymidine incorporation rate after the addition of C and N together compared with adding them separately was seen in the sample containing the size fraction from 0.25 to 1 mm. Third, soils from high-pH, limestone-rich areas were examined. P limitation was observed in one of these soils, while tendencies toward P limitation were seen in some of the other soils. PMID:11282640

Comparison of corneal endothelial image analysis by Konan SP8000 noncontact and Bio-Optics Bambi systems.

PubMed

Benetz, B A; Diaconu, E; Bowlin, S J; Oak, S S; Laing, R A; Lass, J H

1999-01-01

Compare corneal endothelial image analysis by Konan SP8000 and Bio-Optics Bambi image-analysis systems. Corneal endothelial images from 98 individuals (191 eyes), ranging in age from 4 to 87 years, with a normal slit-lamp examination and no history of ocular trauma, intraocular surgery, or intraocular inflammation were obtained by the Konan SP8000 noncontact specular microscope. One observer analyzed these images by using the Konan system and a second observer by using the Bio-Optics Bambi system. Three methods of analyses were used: a fixed-frame method to obtain cell density (for both Konan and Bio-Optics Bambi) and a "dot" (Konan) or "corners" (Bio-Optics Bambi) method to determine morphometric parameters. The cell density determined by the Konan fixed-frame method was significantly higher (157 cells/mm2) than the Bio-Optics Bambi fixed-frame method determination (p<0.0001). However, the difference in cell density, although still statistically significant, was smaller and reversed comparing the Konan fixed-frame method with both Konan dot and Bio-Optics Bambi comers method (-74 cells/mm2, p<0.0001; -55 cells/mm2, p<0.0001, respectively). Small but statistically significant morphometric analyses differences between Konan and Bio-Optics Bambi were seen: cell density, +19 cells/mm2 (p = 0.03); cell area, -3.0 microm2 (p = 0.008); and coefficient of variation, +1.0 (p = 0.003). There was no statistically significant difference between these two methods in the percentage of six-sided cells detected (p = 0.55). Cell densities measured by the Konan fixed-frame method were comparable with Konan and Bio-Optics Bambi's morphometric analysis, but not with the Bio-Optics Bambi fixed-frame method. The two morphometric analyses were comparable with minimal or no differences for the parameters that were studied. The Konan SP8000 endothelial image-analysis system may be useful for large-scale clinical trials determining cell loss; its noncontact system has many clinical benefits (including patient comfort, safety, ease of use, and short procedure time) and provides reliable cell-density calculations.

Comparative Evaluation of Cone-beam Computed Tomography versus Direct Surgical Measurements in the Diagnosis of Mandibular Molar Furcation Involvement

PubMed Central

Padmanabhan, Shyam; Dommy, Ahila; Guru, Sanjeela R.; Joseph, Ajesh

2017-01-01

Aim: Periodontists frequently experience inconvenience in accurate assessment and treatment of furcation areas affected by periodontal disease. Furcation involvement (FI) most commonly affects the mandibular molars. Diagnosis of furcation-involved teeth is mainly by the assessment of probing pocket depth, clinical attachment level, furcation entrance probing, and intraoral periapical radiographs. Three-dimensional imaging has provided advantage to the clinician in assessment of bone morphology. Thus, the present study aimed to compare the diagnostic efficacy of cone-beam computed tomography (CBCT) as against direct intrasurgical measurements of furcation defects in mandibular molars. Subjects and Methods: Study population included 14 patients with 25 mandibular molar furcation sites. CBCT was performed to measure height, width, and depth of furcation defects of mandibular molars with Grade II and Grade III FI. Intrasurgical measurements of the FI were assessed during periodontal flap surgery in indicated teeth which were compared with CBCT measurements. Statistical analysis was done using paired t-test and Bland–Altman plot. Results: The CBCT versus intrasurgical furcation measurements were 2.18 ± 0.86 mm and 2.30 ± 0.89 mm for furcation height, 1.87 ± 0.52 mm and 1.84 ± 0.49 mm for furcation width, and 3.81 ± 1.37 mm and 4.05 ± 1.49 mm for furcation depth, respectively. Results showed that there was no statistical significance between the measured parameters, indicating that the two methods were statistically similar. Conclusion: Accuracy of assessment of mandibular molar FI by CBCT was comparable to that of direct surgical measurements. These findings indicate that CBCT is an excellent adjunctive diagnostic tool in periodontal treatment planning. PMID:29042732

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

PubMed

Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

2015-12-03

Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

Facile and Scalable Fabrication of Highly Efficient Lead Iodide Perovskite Thin-Film Solar Cells in Air Using Gas Pump Method.

PubMed

Ding, Bin; Gao, Lili; Liang, Lusheng; Chu, Qianqian; Song, Xiaoxuan; Li, Yan; Yang, Guanjun; Fan, Bin; Wang, Mingkui; Li, Chengxin; Li, Changjiu

2016-08-10

Control of the perovskite film formation process to produce high-quality organic-inorganic metal halide perovskite thin films with uniform morphology, high surface coverage, and minimum pinholes is of great importance to highly efficient solar cells. Herein, we report on large-area light-absorbing perovskite films fabrication with a new facile and scalable gas pump method. By decreasing the total pressure in the evaporation environment, the gas pump method can significantly enhance the solvent evaporation rate by 8 times faster and thereby produce an extremely dense, uniform, and full-coverage perovskite thin film. The resulting planar perovskite solar cells can achieve an impressive power conversion efficiency up to 19.00% with an average efficiency of 17.38 ± 0.70% for 32 devices with an area of 5 × 2 mm, 13.91% for devices with a large area up to 1.13 cm(2). The perovskite films can be easily fabricated in air conditions with a relative humidity of 45-55%, which definitely has a promising prospect in industrial application of large-area perovskite solar panels.

Methods for quantitative measurement of tooth wear using the area and volume of virtual model cusps.

PubMed

Kim, Soo-Hyun; Park, Young-Seok; Kim, Min-Kyoung; Kim, Sulhee; Lee, Seung-Pyo

2018-04-01

Clinicians must examine tooth wear to make a proper diagnosis. However, qualitative methods of measuring tooth wear have many disadvantages. Therefore, this study aimed to develop and evaluate quantitative parameters using the cusp area and volume of virtual dental models. The subjects of this study were the same virtual models that were used in our former study. The same age group classification and new tooth wear index (NTWI) scoring system were also reused. A virtual occlusal plane was generated with the highest cusp points and lowered vertically from 0.2 to 0.8 mm to create offset planes. The area and volume of each cusp was then measured and added together. In addition to the former analysis, the differential features of each cusp were analyzed. The scores of the new parameters differentiated the age and NTWI groups better than those analyzed in the former study. The Spearman ρ coefficients between the total area and the area of each cusp also showed higher scores at the levels of 0.6 mm (0.6A) and 0.8A. The mesiolingual cusp (MLC) showed a statistically significant difference ( P <0.01) from the other cusps in the paired t -test. Additionally, the MLC exhibited the highest percentage of change at 0.6A in some age and NTWI groups. Regarding the age groups, the MLC showed the highest score in groups 1 and 2. For the NTWI groups, the MLC was not significantly different in groups 3 and 4. These results support the proposal that the lingual cusp exhibits rapid wear because it serves as a functional cusp. Although this study has limitations due to its cross-sectional nature, it suggests better quantitative parameters and analytical tools for the characteristics of cusp wear.

Sex differences in fingerprint ridge density in a Turkish young adult population: a sample of Baskent University.

PubMed

Oktem, Hale; Kurkcuoglu, Ayla; Pelin, Ismail Can; Yazici, Ayse Canan; Aktaş, Gulnihal; Altunay, Fikret

2015-05-01

Fingerprints are considered to be one of the most reliable methods of identification. Identification of an individual plays a vital part of any medico-legal investigations. Dermatoglyphics is a branch of science that studies epidermal ridges and ridge patterns. Epidermal ridges are polygenic characteristics that form intrauterine 10-18 weeks and considered fully developed by the sixth month of fetal growth. Fingerprints are permanent morphological characteristics and criminal detection based on fingerprints is based on the principle that no two people can have identical fingerprints. Sex determination from fingerprints has been examined in different population. In this study we aimed to study fingerprint ridge density in Turkish population sample of Baskent University students. Fingerprints were obtained from 118 women, 88 men a total of 206 students aged between 17 and 28 years old by means of simple inking method. Fingerprints from all right and left hands fingers were collected in three different area of each. The ridges on fingerprints were counted diagonally on squares measuring 5 mm × 5 mm on radial, ulnar and inferior areas. The fingerprint ridge density in radial, ulnar and inferior areas and between sexes was compared statistically Mann Whitney U test and Friedman test. The ridge density was significantly greater in women in every region studied and in all fingers when compared to men. The fingerprint ridge density in the ulnar and radial areas of the fingerprints was significantly greater than the lower area. Fingerprint ridge density can be used by medico-legal examination for sex identification. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Design architecture of double spiral interdigitated electrode with back gate electrode for biosensor application

NASA Astrophysics Data System (ADS)

Fathil, M. F. M.; Arshad, M. K. Md.; Hashim, U.; Ruslinda, A. R.; Gopinath, Subash C. B.; M. Nuzaihan M., N.; Ayub, R. M.; Adzhri, R.; Zaki, M.; Azman, A. H.

2016-07-01

This paper presents the preparation method of photolithography chrome mask design used in fabrication process of double spiral interdigitated electrode with back gate biasing based biosensor. By learning the fabrication process flow of the biosensor, the chrome masks are designed through drawing using the AutoCAD software. The overall width and length of the device is optimized at 7.0 mm and 10.0 mm, respectively. Fabrication processes of the biosensor required three chrome masks, which included back gate opening, spiral IDE formation, and passivation area formation. The complete chrome masks design will be sent for chrome mask fabrication and for future use in biosensor fabrication.

A millimeter-wave reflectometer for whole-body hydration sensing

NASA Astrophysics Data System (ADS)

Zhang, W.-D.; Brown, E. R.

2016-05-01

This paper demonstrates a non-invasive method to determine the hydration level of human skin by measuring the reflectance of W-band (75-110 GHz) and Ka-band (26-40 GHz) radiation. Ka-band provides higher hydration accuracy (<1%) and greater depth of penetration (> 1 mm), thereby allowing access to the important dermis layer of skin. W-band provides less depth of penetration but finer spatial resolution (~2 mm). Both the hydration sensing concept and experimental results are presented here. The goal is to make a human hydration sensor that is 1% accurate or better, operable by mechanically scanning, and fast enough to measure large areas of the human body in seconds.

[HPLC fingerprint of the antiarrhythmic fraction of Valeriana officinalis].

PubMed

Duan, Xue-Yun; Gong, Zhan-Feng; Chen, Shu-He; Fang, Ying; Liu, Yan-Wen

2009-06-01

To establish HPLC fingerprints of the Antiarrhythmic fraction of Valeriana officinalis. Agilent C18 (250 mm x 4.6 mm, 5 microm) column was used and the acetonitrile-water was chosen as the mobile phase in a gradient mode. The column temperature was 380 degrees C and the detection wavelength was 218 nm. The detection time was 70 min, and the flow rate was 1.0 mL/ min. Fifteen characteristic peaks were indicated in HPLC fingerprints. The relative retention time and the ranges of relative areas of the common peaks were also determined. This method is simple and accurate with a good reproducibility and provides a reference standard for the quality control of Valeriana officinalis.

TH-C-12A-03: Development of Expanded Field Irradiation Technique with Gimbaled X-Ray Head

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, T; Miyabe, Y; Yamada, M

2014-06-15

Purpose: The Vero4DRT has a maximum field size of 150×150 mm{sup 2}. The purposes of this study were to develop an expanded field irradiation technique using a unique gimbaled x-ray head of Vero4DRT and to evaluate its dosimetric characteristic. Methods: The expanded field irradiation consisted of four separate fields with 2.39 degree gimbal rotation around orthogonal two axes. The central beam axis for each field shifted 40 mm from the isocenter for longitudinal and lateral directions, and thus, the field size was expanded up to 230×230 mm{sup 2}. Adjacent region were created at the isocenter (center-adjacent expanded-field) and 20 mmmore » from isocenter (offadjacent expanded-field). To create flat dose distribution in the combined piecewise-fields, the overlapping and gaps regions on the isocenter plane were adjusted with the gimbal rotating and the MLC. To evaluate dosimetric characteristic of the expanded-field, films inserted in water-equivalent phantoms at 50, 100 and 150 mm depth were irradiated and the field size, penumbra, flatness and symmetry were analyzed.In addition, the expandedfield irradiation technique was applied to IMRT. A head and neck IMRT field, which was planned for the conventional linac (Varian Clinac iX), was reproduced with the expanded-field of the Vero4DRT. The simulated dose distribution for the expanded IMRT field was compared to the measured dose distribution. Results: The field size, penumbra, flatness and symmetry of center- and off- adjacent expanded-fields were 230.2–232.1 mm, 7.8–10.7 mm, 2.3–6.5% and –0.5–0.4% at 100 mm depth. The 82.1% area of the expanded IMRT dose distribution was within 5% difference between measurement and simulation, which was analyzed upper 50% dose area, and the 3%/3 mm gamma pass rate was 98.4%. Conclusions: The expandedfield technique was developed using the gimbaled x-ray head. To extend applied targets, such as whole breast irradiations or head and neck IMRT, the expanded-field technique would be effective.« less

Displacement prediction of Baijiabao landslide based on empirical mode decomposition and long short-term memory neural network in Three Gorges area, China

NASA Astrophysics Data System (ADS)

Xu, Shiluo; Niu, Ruiqing

2018-02-01

Every year, landslides pose huge threats to thousands of people in China, especially those in the Three Gorges area. It is thus necessary to establish an early warning system to help prevent property damage and save peoples' lives. Most of the landslide displacement prediction models that have been proposed are static models. However, landslides are dynamic systems. In this paper, the total accumulative displacement of the Baijiabao landslide is divided into trend and periodic components using empirical mode decomposition. The trend component is predicted using an S-curve estimation, and the total periodic component is predicted using a long short-term memory neural network (LSTM). LSTM is a dynamic model that can remember historical information and apply it to the current output. Six triggering factors are chosen to predict the periodic term using the Pearson cross-correlation coefficient and mutual information. These factors include the cumulative precipitation during the previous month, the cumulative precipitation during a two-month period, the reservoir level during the current month, the change in the reservoir level during the previous month, the cumulative increment of the reservoir level during the current month, and the cumulative displacement during the previous month. When using one-step-ahead prediction, LSTM yields a root mean squared error (RMSE) value of 6.112 mm, while the support vector machine for regression (SVR) and the back-propagation neural network (BP) yield values of 10.686 mm and 8.237 mm, respectively. Meanwhile, the Elman network (Elman) yields an RMSE value of 6.579 mm. In addition, when using multi-step-ahead prediction, LSTM obtains an RMSE value of 8.648 mm, while SVR, BP and the Elman network obtains RSME values of 13.418 mm, 13.014 mm, and 13.370 mm. The predicted results indicate that, to some extent, the dynamic model (LSTM) achieves results that are more accurate than those of the static models (i.e., SVR and BP). LSTM even displays better performance than the Elman network, which is also a dynamic method.

Correction of differential renal function for asymmetric renal area ratio in unilateral hydronephrosis.

PubMed

Aktaş, Gul Ege; Sarıkaya, Ali

2015-11-01

Children with unilateral hydronephrosis are followed up with anteroposterior pelvic diameter (APD), hydronephrosis grade, mercaptoacetyltriglycine (MAG-3) drainage pattern and differential renal function (DRF). Indeterminate drainage preserved DRF in higher grades of hydronephrosis, in some situations, complicating the decision-making process. Due to an asymmetric renal area ratio, falsely negative DRF estimations can result in missed optimal surgery times. This study was designed to assess whether correcting the DRF estimation according to kidney area could reflect the clinical situation of a hydronephrotic kidney better than a classical DRF calculation, concurrently with the hydronephrosis grade, APD and MAG-3 drainage pattern. We reviewed the MAG-3, dimercaptosuccinic acid (DMSA) scans and ultrasonography (US) of 23 children (6 girls, 17 boys, mean age: 29 ± 50 months) with unilateral hydronephrosis. MAG-3 and DMSA scans were performed within 3 months (mean 25.4 ± 30.7 days). The closest US findings (mean 41.5 ± 28.2 days) were used. DMSA DRF estimations were obtained using the geometric mean method. Secondary calculations were performed to correct the counts (the total counts divided by the number of pixels in ROI) according to kidney area. The renogram patterns of patients were evaluated and separated into subgroups. The visual assessment of DMSA scans was noted and the hydronephrotic kidney was classified in comparison to the normal contralateral kidney's uptake. The correlations of the DRF values of classical and area-corrected methods with MAG-3 renogram patterns, the visual classification of DMSA scan, the hydronephrosis grade and the APD were assessed. DRF estimations of two methods were statistically different (p: 0.001). The categories of 12 hydronephrotic kidneys were changed. There were no correlations between classical DRF estimations and the hydronephrosis grade, APD, visual classification of the DMSA scan and uptake evaluation. The DRF distributions according to MAG-3 drainage patterns were not different. Area-corrected DRF estimations correlated with all: with an increasing hydronephrosis grade and APD, DRF estimations decreased and MAG-3 drainage patterns worsened. A decrease in DRF (< 45 %) was determined when APD was ≥ 10 mm. When APD was ≥ 26 mm, a reduction of DRF below 40 % was determined. Our results suggest that correcting DRF estimation for asymmetric renal area ratio in unilateral hydronephrosis can be more robust than the classical method, especially for higher grades of hydronephrotic kidneys, under equivocal circumstances.

Metal artifact reduction by filter-based dual-energy cone-beam computed tomography on a bench-top micro-CBCT system: concept and demonstration.

PubMed

Iramina, Hiraku; Hamaguchi, Takumi; Nakamura, Mitsuhiro; Mizowaki, Takashi; Kanno, Ikuo

2018-04-30

We evaluated two dual-energy cone-beam computed tomography (DE-CBCT) methodologies for a bench-top micro-CBCT system to reduce metal artifacts on reconstructed images. Two filter-based DE-CBCT methodologies were tested: (i) alternative spectral switching and (ii) simultaneous beam splitting. We employed filters of 0.6-mm-thick tin and 0.1-mm-thick tungsten to generate high- and low-energy spectra from 120 kVp X-rays, respectively. The spectral switching method was imitated by two half scans with different filters (pseudo-switching). Filters were placed and between the X-ray tube and a phantom ('1-u,' '2-u'), a phantom and a flat panel detector ('1-d,' '2-d'), and compared with (iii) two half scans at 80 and 140 kVp [pseudo-(80,140)]. For the splitting method, two half-width filters were aligned along a rotating axis. Projections were separated into halves and merged with corresponding areas of opposed projections after one full rotation. A solid 30-mm-diameter acrylic phantom and an acrylic phantom with four 5-mm-diameter titanium rods were used. DE images were generated by weighted summation of the high- and low-energy images. The blending factor was changed from 0 to +5 in increments of 0.01. Relative errors (REs) of the linear attenuation coefficients of the two phantoms and the contrast-to-noise ratios (CNRs) between the titanium and acrylic regions were compared. All methods showed zero REs except for the method (2-d). CNRs for pseudo-switching with upstream placement were 1.4-fold larger than CNRs for the pseudo-(80,140) method. CNRs for the downstream placements were small. It was concluded that the pseudo-switching method with upstream placement is appropriate for reducing metal artifacts.

Factors predicting language lateralization in patients with perisylvian vascular malformations

PubMed Central

Lee, Darrin J.; Pouratian, Nader; Bookheimer, Susan Y.; Martin, Neil A.

2017-01-01

Object The authors conducted a study to determine the factors associated with right-sided language dominance in patients with cerebrovascular malformations. Methods Twenty-two patients with either arteriovenous malformations (AVMs [15 cases]) or cavernous malformations (7 cases) underwent functional MR (fMR) imaging studies of language function; a 3.0-T head-only unit was used. Lateralization indices were calculated separately for Broca and Wernicke areas. Lesion size, Spetzler-Martin grade, and the distance between the lesion and anatomically defined language cortex were calculated for each patient. Results Right-sided language dominance occurred in 5 patients, all of whom had AVMs within 10 mm of canonical language areas. Three patients had right-sided language dominance in the Wernicke area alone whereas 2 had right-sided language dominance in both Broca and Wernicke areas. Wada testing and intraoperative electrocortical stimulation were performed as clinically indicated to corroborate fMR imaging findings. Conclusions The primary factor associated with right-sided language dominance was the AVM being within 10 mm of anatomically defined language areas. The lesion size and the Spetzler-Martin grade were not significant factors. Anomalous fMR imaging laterality was typically confined to the language area proximate to the lesion, with the distal language area remaining in the left hemisphere dominant. This study emphasizes the need to map each case individually in patients with left perisylvian AVMs. Assumptions about eloquent cortex based on anatomical landmarks (a key component of Spetzler-Martin grading) may have to be reconsidered. PMID:20302390

Design and fabrication of a large area freestanding compressive stress SiO2 optical window

NASA Astrophysics Data System (ADS)

Van Toan, Nguyen; Sangu, Suguru; Ono, Takahito

2016-07-01

This paper reports the design and fabrication of a 7.2 mm  ×  9.6 mm freestanding compressive stress SiO2 optical window without buckling. An application of the SiO2 optical window with and without liquid penetration has been demonstrated for an optical modulator and its optical characteristic is evaluated by using an image sensor. Two methods for SiO2 optical window fabrication have been presented. The first method is a combination of silicon etching and a thermal oxidation process. Silicon capillaries fabricated by deep reactive ion etching (deep RIE) are completely oxidized to form the SiO2 capillaries. The large compressive stress of the oxide causes buckling of the optical window, which is reduced by optimizing the design of the device structure. A magnetron-type RIE, which is investigated for deep SiO2 etching, is the second method. This method achieves deep SiO2 etching together with smooth surfaces, vertical shapes and a high aspect ratio. Additionally, in order to avoid a wrinkling optical window, the idea of a Peano curve structure has been proposed to achieve a freestanding compressive stress SiO2 optical window. A 7.2 mm  ×  9.6 mm optical window area without buckling integrated with an image sensor for an optical modulator has been successfully fabricated. The qualitative and quantitative evaluations have been performed in cases with and without liquid penetration.

Applications of Hybrid Algorithm (Successive Over Relaxation and Inverse Distance Weighting) for Interpolating Rainfall Data Obtained from a Dense Network of Meteorological Stations in Metro Manila, Philippines

NASA Astrophysics Data System (ADS)

Yao, J. G.; Lagrosas, N.; Ampil, L. J. Y.; Lorenzo, G. R. H.; Simpas, J.

2016-12-01

A hybrid piecewise rainfall value interpolation algorithm was formulated using the commonly known Inverse Distance Weighting (IDW) and Gauss-Seidel variant Successive Over Relaxation (SOR) to interpolate rainfall values over Metro Manila, Philippines. Due to the fact that the SOR requires boundary values for its algorithm to work, the IDW method has been used to estimate rainfall values at the boundary. Iterations using SOR were then done on the defined boundaries to obtain the desired results corresponding to the lowest RMSE value. The hybrid method was applied to rainfall datasets obtained from a dense network of 30 stations in Metro Manila which has been collecting meteorological data every 5 minutes since 2012. Implementing the Davis Vantage Pro 2 Plus weather monitoring system, each station sends data to a central server which could be accessed through the website metroweather.com.ph. The stations are spread over approximately 625 sq km of area such that each station is approximately within 25 sq km from each other. The locations of the stations determined by the Metro Manila Development Authority (MMDA) are in critical sections of Metro Manila such as watersheds and flood-prone areas. Three cases have been investigated in this study, one for each type of rainfall present in Metro Manila: monsoon-induced (8/20/13), typhoon (6/29/13), and thunderstorm (7/3/15 & 7/4/15). The area where the rainfall stations are located is divided such that large measured rainfall values are used as part of the boundaries for the SOR. Measured station values found inside the area where SOR is implemented are compared with results from interpolated values. Root mean square error (RMSE) and correlation trends between measured and interpolated results are quantified. Results from typhoon, thunderstorm and monsoon cases show RMSE values ranged from 0.25 to 2.46 mm for typhoons, 1.55 to 10.69 mm for monsoon-induced rain and 0.01 to 6.27 mm for thunderstorms. R2 values, on the other hand, are 0.91, 0.89 and 0.76 for typhoons, monsoon-induced rain and thunderstorms, respectively. This study has shown that the method of approximating rainfall works and can be used in improved prediction, analysis and real time flood map generation.

Geohazards Monitoring in Roma from InSAR and In Situ Data: Outcomes of the PanGeo Project

NASA Astrophysics Data System (ADS)

Comerci, Valerio; Vittori, Eutizio; Cipolloni, Carlo; Di Manna, Pio; Guerrieri, Luca; Nisio, Stefania; Succhiarelli, Claudio; Ciuffreda, Maria; Bertoletti, Erika

2015-11-01

Within the PanGeo project (financed by the European Commission under the 7th Framework Program), the Geological Survey of Italy ( ISPRA) and the Urban Planning Department of the City of Roma developed a geodatabase and map of the geological hazards for the territory of Roma, integrating remotely sensed data (PSInSAR—Permanent Scatterer Interferometry Synthetic Aperture Radar) and in situ geological information. Numerous thematic layers, maps and inventories of hazards (e.g., landslides, sinkholes, cavities), geological and hydrogeological data added to historical and recent urbanization information were compared to the permanent scatterer (PS) data from the European Remote Sensing satellites (ERS-1/2, 1992-2000) and ENVISAT (2002-2005) descending scenes, in order to produce a ground stability layer (GSL). Based on the PS data, most of the territory appears stable (almost 70 % of PS velocities are within ±1 mm/year). About 14 % of the PSs show positive line-of-sight (LOS) velocities (measured along the LOS of the satellite) between 1 and 3 mm/year and more than 2 % exceed 3 mm/year; more than 11 % of PSs show negative LOS velocities between -1 and -3 mm/year, while about 3 % exceed -3 mm/year (with tens of the PSs showing velocities over -20 mm/year). The GSL is comprised of polygons or multi-polygons (multipart polygons grouping individual polygons under a single identifier geohazard) enclosing areas where geohazards have been pointed out by PS data and/or in situ surveys (observed instabilities), and by polygons enclosing areas potentially affected by geohazards, based on the available knowledge of the territory (potential instabilities). In Roma's GSL, 18 multi-polygons (covering ca. 600 km2) related to observed instabilities have been outlined, where ground movements could be detected through InSAR data or where landslides and sinkholes are known to have occurred. Other 13 multi-polygons (covering nearly 900 km2) concern areas where the potential occurrence of geohazards was inferred by combining geological and/or geothematic data (potential instabilities). The geohazards mapped in Roma have been: landslides, collapsible grounds, compressible grounds, groundwater abstraction, mining, man-made ground, tectonic movements, and volcanic inflation/deflation. The lattermost is the likely cause of the significant uplift observed in the Alban Hills area. However, this paper focuses on two more currently impending hazards: subsidence and sinkholes. In general, sinkhole-prone areas (areas of dense underground cavities) are hard to discern from satellite data, but can be revealed by ruling out other potential causes of observed ground movement based on in situ data. Subsiding zones are effectively detected by the available PSInSAR dataset over a total extent of about 60 km2, mostly overlapping the recent alluvial areas of the Tiber and its tributaries. PSs show a very different behaviour inside and outside the historical centre. Inside, loading by anthropogenic construction and man-made ground since ancient times has led to an almost complete consolidation of the recent river deposits, marked by modest to absent subsidence. In contrast, outside, subsidence clearly stands out, with negative LOS velocities that, although generally within several mm/year, can locally exceed -25 mm/year. PS data have provided motion information at both a regional and local scale (up to the scale of a single building). Closer to the sea, in the Tiber delta area, velocities increase, especially above recently reclaimed marsh areas, rich in peat and organic clays. Velocities can change significantly over short distances, as in the international airport area, reflecting the local stratigraphic setting. The same occurs in the two subsiding areas located within the Alban Hills volcanic complex, which is generally affected by ground uplift. As a whole, PSInSAR ground motion velocities offer a significant contribution to susceptibility and hazard recognition studies. In particular, such a method provides a fast and effective tool available to local authorities to monitor ground and building behaviour, possibly allowing for timely prevention activities, especially when coupled with appropriate in situ knowledge.

Diffuse reflectance spectroscopy from 400-1600 nm to evaluate tumor resection margins during head and neck surgery (Conference Presentation)

NASA Astrophysics Data System (ADS)

Brouwer de Koning, Susan G.; Baltussen, E. J. M.; Karakullukcu, M. Baris; Smit, L.; van Veen, R. L. P.; Hendriks, Benno H. W.; Sterenborg, H. J. C. M.; Ruers, Theo J. M.

2017-02-01

This ex vivo study evaluates the feasibility of diffuse reflectance spectroscopy (DRS) for discriminating tumor from healthy oral tissue, with the aim to develop a technique that can be used to determine a complete excision of tumor through intraoperative margin assessment. DRS spectra were acquired on fresh surgical specimens from patients with an oral squamous cell carcinoma. The spectra represent a measure of diffuse light reflectance (wavelength range of 400-1600 nm), detected after illuminating tissue with a source fiber at 1.0 and 2.0 mm distances from a detection fiber. Spectra were obtained from 23 locations of tumor tissue and 16 locations of healthy muscle tissue. Biopsies were taken from all measured locations to facilitate an optimal correlation between spectra and pathological information. The area under the spectrum was used as a parameter to classify spectra of tumor and healthy tissue. Next, a receiver operating characteristics (ROC) analysis was performed to provide the area under the receiver operating curve (AUROC) as a measure for discriminative power. The area under the spectrum between 650 and 750 nm was used in the ROC analysis and provided AUROC values of 0.99 and 0.97, for distances of 1 mm and 2 mm between source and detector fiber, respectively. DRS can discriminate tumor from healthy oral tissue in an ex vivo setting. More specimens are needed to further evaluate this technique with component analyses and classification methods, prior to in vivo patient measurements.

Comparative fixation methods of cervical disc arthroplasty versus conventional methods of anterior cervical arthrodesis: serration, teeth, keels, or screws?

PubMed

Cunningham, Bryan W; Hu, Nianbin; Zorn, Candace M; McAfee, Paul C

2010-02-01

Using a synthetic vertebral model, the authors quantified the comparative fixation strengths and failure mechanisms of 6 cervical disc arthroplasty devices versus 2 conventional methods of cervical arthrodesis, highlighting biomechanical advantages of prosthetic endplate fixation properties. Eight cervical implant configurations were evaluated in the current investigation: 1) PCM Low Profile; 2) PCM V-Teeth; 3) PCM Modular Flange; 4) PCM Fixed Flange; 5) Prestige LP; 6) Kineflex/C disc; 7) anterior cervical plate + interbody cage; and 8) tricortical iliac crest. All PCM treatments contained a serrated implant surface (0.4 mm). The PCM V-Teeth and Prestige contained 2 additional rows of teeth, which were 1 mm and 2 mm high, respectively. The PCM Modular and Fixed Flanged devices and anterior cervical plate were augmented with 4 vertebral screws. Eight pullout tests were performed for each of the 8 conditions by using a synthetic fixation model consisting of solid rigid polyurethane foam blocks. Biomechanical testing was conducted using an 858 Bionix test system configured with an unconstrained testing platform. Implants were positioned between testing blocks, using a compressive preload of -267 N. Tensile load-to-failure testing was performed at 2.5 mm/second, with quantification of peak load at failure (in Newtons), implant surface area (in square millimeters), and failure mechanisms. The mean loads at failure for the 8 implants were as follows: 257.4 +/- 28.54 for the PCM Low Profile; 308.8 +/- 15.31 for PCM V-Teeth; 496.36 +/- 40.01 for PCM Modular Flange; 528.03+/- 127.8 for PCM Fixed Flange; 306.4 +/- 31.3 for Prestige LP; 286.9 +/- 18.4 for Kineflex/C disc; 635.53 +/- 112.62 for anterior cervical plate + interbody cage; and 161.61 +/- 16.58 for tricortical iliac crest. The anterior plate exhibited the highest load at failure compared with all other treatments (p < 0.05). The PCM Modular and Fixed Flange PCM constructs in which screw fixation was used exhibited higher pullout loads than all other treatments except the anterior plate (p < 0.05). The PCM VTeeth and Prestige and Kineflex/C implants exhibited higher pullout loads than the PCM Low Profile and tricortical iliac crest (p < 0.05). Tricortical iliac crest exhibited the lowest pullout strength, which was different from all other treatments (p < 0.05). The surface area of endplate contact, measuring 300 mm(2) (PCM treatments), 275 mm(2) (Prestige LP), 250 mm(2) (Kineflex/C disc), 180 mm(2) (plate + cage), and 235 mm(2) (tricortical iliac crest), did not correlate with pullout strength (p > 0.05). The PCM, Prestige, and Kineflex constructs, which did not use screw fixation, all failed by direct pullout. Screw fixation devices, including anterior plates, led to test block fracture, and tricortical iliac crest failed by direct pullout. These results demonstrate a continuum of fixation strength based on prosthetic endplate design. Disc arthroplasty constructs implanted using vertebral body screw fixation exhibited the highest pullout strength. Prosthetic endplates containing toothed ridges (>or= 1 mm) or keels placed second in fixation strength, whereas endplates containing serrated edges exhibited the lowest fixation strength. All treatments exhibited greater fixation strength than conventional tricortical iliac crest. The current study offers insights into the benefits of various prosthetic endplate designs, which may potentially improve acute fixation following cervical disc arthroplasty.

Quantitation of tacrolimus in whole blood using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS).

PubMed

Donaldson, Keri J; Shaw, Leslie M

2010-01-01

We describe a multiple reaction monitoring positive ion HPLC/tandem mass spectrometric method for quantification of tacrolimus in human whole blood with online extraction and cleanup. Included in this procedure: API 2000 triple quadrupole mass spectrometer with turbo-ion spray source (Applied Biosystems, Foster City, CA); 10-port diverter/switching valve (Valco, Houston, TX); HPLC system (Agilent Technologies series 1100, Wilmington, DE); 10 mm (C(18)) guard cartridge (Perkin Elmer, Norwalk, CT) used as an extraction column; a Nova-Pak C18 analytical column (2.1 x 150 mm I.D., 4 microm, Waters Corp, Milford, MA); washing solution, methanol: 30 mM ammonium acetate pH 5.1 (80:20); eluting solution, methanol:30 mM ammonium acetate pH 5.1 (97:3); flow rate 0.8 mL/min; and a run-time of 2.8 min. The first and third quadrupoles were set to detect the ammonium adduct ion and a high mass fragment of tacrolimus (m/z 821.5-->768.3), and of an internal standard (ascomycin) (m/z 901.8-->834.4). The lower limit of quantification of this method is 3.75 mg/L. The concentration of drug is determined by comparing peak-area ratios for tacrolimus and internal standard to a standard curve constructed using non-weighted linear through zero regression.

Phyllanthus wightianus Müll. Arg.: A Potential Source for Natural Antimicrobial Agents

PubMed Central

Natarajan, D.; Srinivasan, R.; Shivakumar, M. S.

2014-01-01

Phyllanthus wightianus belongs to Euphorbiaceae family having ethnobotanical importance. The present study deals with validating the antimicrobial potential of solvent leaf extracts of P. wightianus. 11 human bacterial pathogens (Bacillus subtilis, Streptococcus pneumoniae, Staphylococcus epidermidis, Proteus vulgaris, Pseudomonas aeruginosa, Klebsiella pneumoniae, Salmonella typhimurium, Escherichia coli, Shigella flexneri, Proteus vulgaris, and Serratia marcescens) and 4 fungal pathogens (Candida albicans, Cryptococcus neoformans, Mucor racemosus, and Aspergillus niger) were also challenged with solvent leaf extracts usingagar well and disc diffusion methods. Further, identification of the active component present in the bioactive extract was done using GC-MS analysis. Results show that all extracts exhibited broad spectrum (6–29 mm) of antibacterial activity on most of the tested organisms. The results highlight the fact that the well in agar method was more effective than disc diffusion method. Significant antimicrobial activity was detected in methanol extract against S. pneumoniae (29 mm) with MIC and MBC values of 15.62 μg/mL. GC-MS analysis revealed that 29 bioactive constituents were present in methanolic extract of P. wightianus, of which 9,12-octadecaenioic acid (peak area 22.82%; RT-23.97) and N-hexadecanoic acid (peak area 21.55% RT-21.796) are the major compounds. The findings of this study show that P. wightianus extracts may be used as an anti-infective agent in folklore medicine. PMID:24883301

Comparison of the Outcome of Silicone Ahmed Glaucoma Valve Implantation with a Surface Area between 96 and 184 mm2 in Adult Eyes

PubMed Central

Koh, Kyung Min; Hwang, Young Hoon; Jung, Jong Jin; Sohn, Yong Ho

2013-01-01

Purpose To compare the success rates, complications, and visual outcomes between silicone Ahmed glaucoma valve (AGV) implantation with 96 mm2 (FP8) or 184 mm2 (FP7) surface areas. Methods This study is a retrospective review of the records from 132 adult patients (134 eyes) that underwent silicone AGV implant surgery. Among them, the outcomes of 24 eyes from 24 patients with refractory glaucoma who underwent FP8 AGV implantation were compared with 76 eyes from 76 patients who underwent FP7 AGV implantation. Preoperative and postoperative data, including intraocular pressure (IOP), visual acuity, number of medications, and complications were compared between the 2 groups. Results There were no significant differences in baseline characteristics between the 2 groups (p > 0.05). The postoperative visual acuity of the patients in the FP8 group was better than that of the patients in the FP7 group in some early postoperative periods (p < 0.05); however, after 10 postoperative months, visual acuity was not significantly different through the 3-year follow-up period (p > 0.05). Postoperative IOP was not significantly different between the 2 groups (p > 0.05) except for IOP on postoperative day 1 (11.42 mmHg for the FP7 group and 7.42 mmHg for the FP8 group; p = 0.031). There was no statistical difference in success rates, final IOP, number of medications, or complication rates between the 2 groups (p > 0.05). Conclusions The FP7 and FP8 AGV implants showed no difference in terms of vision preservation, IOP reduction, and number of glaucoma medications required. PMID:24082774