Do lipids retard the evaporation of the tear fluid?

PubMed

Rantamäki, Antti H; Javanainen, Matti; Vattulainen, Ilpo; Holopainen, Juha M

2012-09-21

We examined in vitro the potential evaporation-retarding effect of the tear film lipid layer (TFLL). The artificial TFLL compositions used here were based on the present knowledge of TFLL composition. A custom-built system was developed to measure evaporation rates at 35°C. Lipids were applied to an air-water interface, and the evaporation rate through the lipid layer was defined as water loss from the interface. A thick layer of olive oil and a monolayer of long-chain alcohol were used as controls. The artificial TFLLs were composed of 1 to 4 lipid species: polar phosphatidylcholine (PC), nonpolar cholesteryl ester, triglycerides, and wax ester (WE). Brewster angle microscopy (BAM) and interfacial shear rheometry (ISR) were used to assess the lateral structure and shear stress response of the lipid layers, respectively. Olive oil and long-chain alcohol decreased evaporation by 54% and 45%, respectively. The PC monolayer and the four-component mixtures did not retard evaporation. WE was the most important evaporation-retardant TFLL lipid (∼20% decrease). In PC/WE mixtures, an ∼90% proportion of WE was required for evaporation retardation. Based on BAM and ISR, WE resulted in more condensed layers than the non-retardant layers. Highly condensed, solid-like lipid layers, such as those containing high proportions of WEs, are evaporation-retardant. In multi-component lipid layers, the evaporation-retardant interactions between carbon chains decrease and, therefore, these lipid layers do not retard evaporation.

Approach to knowledge of the interaction between the constituents of contact lenses and ocular tears: mixed monolayers of poly(methyl methacrylate) and dipalmitoyl phosphatidyl choline.

PubMed

Miñones Conde, M; Conde, O; Trillo, J M; Miñones, J

2011-04-05

Mixed monolayers of poly(methyl methacrylate) (PMMA), the main component of hard contact lenses, and dipalmitoyl phosphatidyl choline (DPPC), a characteristic phospholipidic constituent of ocular tear films, were selected as an in vitro model in order to observe the behavior of contact lenses on the eye. Using Langmuir monolayer and Brewster angle microscopy (BAM) techniques, the interaction between both components was analyzed from the data of surface pressure-area isotherms, compressional modulus-surface pressure, and relative film thickness versus time elapsed from the beginning of compression, together with BAM images. Regardless of the surface pressure at which the molecular/monomer areas (A(m)) were recorded, the A(m) mole fractions of PMMA (X(PMMA)) plots show that the experimental results match the theoretical values calculated from additivity rule A(m) = X(PMMA)A(PMMA) + X(DPPC)A(DPPC). The application of the Crisp phase rule to the phase diagram of the PMMA-DPPC system can explain the existence of a mixed monolayer made up of miscible components with ideal behavior at surface pressures below 25 mN/m. However, at very high surface pressures, when collapse is reached (at 60 mN/m), the single collapsed components are segregated into two independent phases. These results allows us to argue that PMMA hard contact lenses in the eye do not alter the structural characteristics of the phospholipid (DPPC) in tears.

Nitrobenzoxadiazole-Appended Cell Membrane Modifiers for Efficient Optoporation with Noncoherent Light.

PubMed

Otake, Saya; Okuro, Kou; Bochicchio, Davide; Pavan, Giovanni M; Aida, Takuzo

2018-05-24

FL NBD-BAM PEG2k , bearing a nitrobenzoxadiazole (NBD) unit and an oleyl terminus conjugated via a poly(ethylene glycol) (PEG) spacer ( M n = 2,000), was designed to fluorescently label cell membranes by docking its hydrophobic oleyl terminus. During laser scanning microscopy in a minimal essential medium (MEM), human hepatocellular carcinoma Hep3B cells labeled with FL NBD-BAM PEG2k appeared to undergo optoporation at their plasma membrane. We confirmed this unprecedented possibility by a series of cellular uptake experiments using negatively charged and therefore membrane-impermeable quantum dots (QDs; D h = 4.7 nm). Detailed studies indicated that the photoexcited NBD unit can generate singlet oxygen ( 1 O 2 ), which oxidizes the constituent phospholipids to transiently deteriorate the cell membrane. Reference membrane modifiers FL NBD-Oleyl and FL NBD-BAM PEG8k having shorter or longer hydrophilic spacers between the NBD and oleyl units showed a little or substantially no optoporation. For understanding these results, one must consider the following contradictory factors: (1) The photosensitized 1 O 2 generation efficiently occurs only when the NBD unit is in aqueous media, and (2) the lifetime of 1 O 2 in aqueous media is very short (3.0-3.5 μs). As supported experimentally and computationally, the hydrophilic spacer length of FL NBD-BAM PEG2k is optimal for compromising these factors. Further to note, the optoporation using FL NBD-BAM PEG2k is not accompanied by cytotoxicity.

High dispersibility and enhanced luminescence properties of BaMgAl10O17:Eu2+ phosphors derived from molten salt synthesis

NASA Astrophysics Data System (ADS)

Wang, Xiang; Li, Jin-hong; Shi, Ping-lu; Guan, Wei-min; Zhang, Hong-yao

2015-08-01

BaMgAl10O17:Eu2+ (BAM) phosphors were prepared via the molten salt synthesis (MSS) method. The NaCl-KCl eutectic mixture and LiF were used as the molten salt and flux, respectively. X-ray powder diffraction (XRD) patterns indicate that the BAM phase is formed above 1200 °C and that the addition of LiF leads to an obvious improvement in crystallinity. The emission intensity of the BAM phosphor with 10 wt% LiF is about 85% higher than that of the phosphor without LiF and about 200% higher than that of the phosphor without molten salt and LiF. Scanning electron microscopy (SEM) reveal that the as-prepared phosphors have good crystallinity and regular morphology, and most importantly, they are not aggregated. Li+ doping is benefit for the thermal stability and results in a slightly longer decay times of 1.17 μs.

Perpendicularly oriented barium ferrite thin films with low microwave loss, prepared by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Da-Ming, Chen; Yuan-Xun, Li; Li-Kun, Han; Chao, Long; Huai-Wu, Zhang

2016-06-01

Barium ferrite (BaM) thin films are deposited on platinum coated silicon wafers by pulsed laser deposition (PLD). The effects of deposition substrate temperature on the microstructure, magnetic and microwave properties of BaM thin films are investigated in detail. It is found that microstructure, magnetic and microwave properties of BaM thin film are very sensitive to deposition substrate temperature, and excellent BaM thin film is obtained when deposition temperature is 910 °C and oxygen pressure is 300 mTorr (1 Torr = 1.3332 × 102 Pa). X-ray diffraction patterns and atomic force microscopy images show that the best thin film has perpendicular orientation and hexagonal morphology, and the crystallographic alignment degree can be calculated to be 0.94. Hysteresis loops reveal that the squareness ratio (M r/M s) is as high as 0.93, the saturated magnetization is 4004 Gs (1 Gs = 104 T), and the anisotropy field is 16.5 kOe (1 Oe = 79.5775 A·m-1). Ferromagnetic resonance measurements reveal that the gyromagnetic ratio is 2.8 GHz/kOe, and the ferromagnetic resonance linewith is 108 Oe at 50 GHz, which means that this thin film has low microwave loss. These properties make the BaM thin films have potential applications in microwave devices. Project supported by the Open Foundation of State Key Laboratory of Electronic Thin Films and Integrated Devices (Grant No. KFJJ201506), the Scientific Research Starting Foundation of Hainan University (Grant No. kyqd1539), and the Natural Science Foundation of Hainan Province (Grant No. 20165187).

Sucrose esters as biocompatible surfactants for penetration enhancement: An insight into the mechanism of penetration enhancement studied using stratumcorneum model lipids and Langmuir monolayers.

PubMed

Todosijević, Marija N; Brezesinski, Gerald; Savić, Snežana D; Neubert, Reinhard H H

2017-03-01

Up to now, the molecular mechanism of the penetration enhancing effect of sucrose esters (SEs) on stratumcorneum (SC) has not been explained in details. In this study, variety of surface sensitive techniques, including surface pressure-area (π-A) isotherms, infrared reflection-absorption spectroscopy (IRRAS), and Brewster angle microscopy (BAM), have been used to investigate interactions between SEs and SC intercellular lipids. A monolayer of the mixture of ceramide AS C18:18, stearic acid and cholesterol in the molar ratio of 1:1:0.7 on an aqueous subphase is a good model to mimic a single layer of intercellular SC lipids. The π-A isotherms of mixed monolayers and parameters derived from the curves demonstrated the interaction between nonionic surfactants such as SEs and SC lipids. With increasing SE concentration, the resultant monolayer films became more fluid and better compressible. IRRAS measurements showed that SEs disordered the acyl chains of SC lipids, and the BAM images demonstrated the modification of the domain structures in SC monolayers. Longer chain-SE has a stronger disordering effect and is better miscible with ceramides in comparison to SE with a shorter hydrophobic part. In conclusion, this study demonstrates the disordering effect of SEs on the biomimetic SC model, pointing out that small changes in the structure of surfactant may have a strong influence on a penetration enhancement of lipophilic drugs through intercellular lipids of skin. Copyright © 2016 Elsevier B.V. All rights reserved.

Biophysical characterization of monofilm model systems composed of selected tear film phospholipids.

PubMed

Patterson, Matthew; Vogel, Hans J; Prenner, Elmar J

2016-02-01

The tear film protects the eye from foreign particles and pathogens, prevents excess evaporation, provides lubrication, and maintains a high quality optical surface necessary for vision. The anterior layer of tear film consists of polar and non-polar lipid layers. The polar lipids form a monolayer on the aqueous subphase, acting as surfactants for the non-polar lipid multilayer. A tear film polar lipid biomimetic consisting of dipalmitoyl phosphatidylcholine (DPPC), dipalmitoyl phosphatidylethanolamine (DPPE), palmitoyl glucosylceramide (PGC), and palmitoyl sphingomyelin (PSM) was characterized using Langmuir monolayers and Brewster angle microscopy (BAM). Lipid combinations formed very stable monolayers, especially those containing DPPC or PSM. Surface experiments and elasticity analyses revealed that PGC resulted in more condensed and rigid mixed monolayers. DPPE provided resistance to large changes in lipid ordering over a wide surface pressure range. Ternary mixtures containing DPPE and PGC with either DPPC or PSM experienced the greatest lipid ordering within the natural tear film surface pressure range suggesting that these lipids are important to maintain tear film integrity during the inter-blink period. Finally, BAM images revealed unique structures within monolayers of DPPC, DPPE, and PGC at the natural tear film surface pressure. 3D analysis of these domains suggested either the formation of multilayers or outward protrusions at surface pressures far below the point of irreversible collapse as seen on the isotherm. This entails that the polar lipids of tear film may be capable of multilayer formation or outward folding as a mechanism to prevent rupture of the tear film during a blink. Copyright © 2015 Elsevier B.V. All rights reserved.

Refractive index and thickness determination in Langmuir monolayers of myelin lipids.

PubMed

Pusterla, Julio M; Malfatti-Gasperini, Antonio A; Puentes-Martinez, Ximena E; Cavalcanti, Leide P; Oliveira, Rafael G

2017-05-01

Langmuir monolayers at the air/water interface are widely used as biomembrane models and for amphiphilic molecules studies in general. Under controlled intermolecular organization (lateral molecular area), surface pressure, surface potential, reflectivity (R) and other magnitudes can be precisely determined on these planar monomolecular films. However, some physical parameters such as the refractive index of the monolayer (n) still remain elusive. The refractive index is very relevant because (in combination with R) it allows for the determination of the thickness of the film. The uncertainties of n determine important errors that propagate non-linearly into the calculation of monolayers thickness. Here we present an analytical method for the determination of n in monolayers based on refractive index matching. By using a Brewster angle microscopy (BAM) setup and monolayers spread over subphases with variable refractive index (n 2 ), a minimum in R is search as a function of n 2 . In these conditions, n equals n 2 . The results shown correspond to monolayers of myelin lipids. The n values remain constant at 1.46 upon compression and equals the obtained value for myelin lipid bilayers in suspension. The values for n and R allow for the determination of thickness. We establish comparisons between these thicknesses for the monolayer and those obtained from two X-ray scattering techniques: 1) GIXOS for monolayers at the air/water interface and 2) SAXS for bilayers in bulk suspension. This allows us to conclude that the thickness that we measure by BAM includes the apolar and polar headgroup regions of the monolayer. Copyright © 2017 Elsevier B.V. All rights reserved.

Langmuir-Blodgett nanotemplates for protein crystallography.

PubMed

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of sufficient size and quality (order, intensity of diffraction, radiation stability). In this protocol, we provide instructions for performing the Langmuir-Blodgett (LB) nanotemplate method, a crystallization approach that can be used for any protein (including membrane proteins). We describe how to produce highly ordered 2D LB protein monolayers at the air-water interface and deposit them on glass slides. LB-film formation can be observed by surface-pressure measurements and Brewster angle microscopy (BAM), although its quality can be characterized by atomic force microscopy (AFM) and nanogravimetry. Such films are then used as a 2D template for triggering 3D protein crystal formation by hanging-drop vapor diffusion. The procedure for forming the 2D template takes a few minutes. Structural information about the protein reorganization in the LB film during the crystallization process on the nano level can be obtained using an in situ submicron GISAXS (grazing-incidence small-angle X-ray scattering) method. MicroGISAXS spectra, measured directly at the interface of the LB films and protein solution in real time, as described in this protocol, can be interpreted in terms of the buildup of layers, islands, or holes. In our experience, the obtained LB crystals take 1-10 d to prepare and they are more ordered and radiation stable as compared with those produced using other crystallization methods.

Sinusoidal Forcing of Interfacial Films

NASA Astrophysics Data System (ADS)

Rasheed, Fayaz; Raghunandan, Aditya; Hirsa, Amir; Lopez, Juan

2015-11-01

Fluid transport, in vivo, is accomplished via pumping mechanisms of the heart and lungs, which results in biological fluids being subjected to oscillatory shear. Flow is known to influence biological macromolecules, but predicting the effect of shear is incomplete without also accounting for the influence of complex interfaces ubiquitous throughout the body. Here, we investigated the oscillatory response of the structure of aqueous interfacial films using a cylindrical knife edge viscometer. Vitamin K1 was used as a model monolayer because its behaviour has been thoroughly quantified and it doesn't show any measurable hysteresis. The monolayer was subjected to sinusoidal forcing under varied conditions of surface concentrations, periodic frequencies, and knife edge amplitudes. Particle Image Velocimetry(PIV) data was collected using Brewster Angle Microscopy(BAM), revealing the influence of oscillatory interfacial shear stress on the monolayer. Insights were gained as to how the velocity profile dampens at specific distances from the knife edge contact depending on the amplitude, frequency, and concentration of Vitamin K1. Supported by NNX13AQ22G, National Aeronautics and Space Administration.

In vivo roles of BamA, BamB and BamD in the biogenesis of BamA, a core protein of the β-barrel assembly machine of Escherichia coli.

PubMed

Misra, Rajeev; Stikeleather, Ryan; Gabriele, Rebecca

2015-03-13

Assembly of the β-barrel outer membrane proteins (OMPs) is an essential cellular process in Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes--two organelles of bacterial origin. Central to this process is the conserved β-barrel OMP that belongs to the Omp85 superfamily. In Escherichia coli, BamA is the core β-barrel OMP and, together with four outer membrane lipoproteins, BamBCDE, constitutes the β-barrel assembly machine (BAM). In this paper, we investigated the roles of BamD, an essential lipoprotein, and BamB in BamA biogenesis. Depletion of BamD caused impairment in BamA biogenesis and cessation of cell growth. These defects of BamD depletion were partly reversed by single-amino-acid substitutions mapping within the β-barrel domain of BamA. However, in the absence of BamB, the positive effects of the β-barrel substitutions on BamA biogenesis under BamD depletion conditions were nullified. By employing a BamA protein bearing one such substitution, F474L, it was demonstrated that the mutant BamA protein could not only assemble without BamD but also facilitate the assembly of wild-type BamA expressed in trans. Based on these data, we propose a model in which the Bam lipoproteins, which are localized to the outer membrane by the BAM-independent Lol pathway, aid in the creation of new BAM complexes by serving as outer membrane receptors and folding factors for nascent BamA molecules. The newly assembled BAM holocomplex then catalyzes the assembly of substrate OMPs and BamA. These in vivo findings are corroborated by recently published in vitro data. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Essential β-Barrel Assembly Machinery Complex Components BamD and BamA Are Required for Autotransporter Biogenesis▿

PubMed Central

Rossiter, Amanda E.; Leyton, Denisse L.; Tveen-Jensen, Karina; Browning, Douglas F.; Sevastsyanovich, Yanina; Knowles, Timothy J.; Nichols, Katie B.; Cunningham, Adam F.; Overduin, Michael; Schembri, Mark A.; Henderson, Ian R.

2011-01-01

Autotransporter biogenesis is dependent upon BamA, a central component of the β-barrel assembly machinery (BAM) complex. In this report, we detail the role of the other BAM components (BamB-E). We identify the importance of BamD in autotransporter biogenesis and show that BamB, BamC, and BamE are not required. PMID:21665980

β-Amylase1 and β-Amylase3 Are Plastidic Starch Hydrolases in Arabidopsis That Seem to Be Adapted for Different Thermal, pH, and Stress Conditions1[W][OPEN

PubMed Central

Monroe, Jonathan D.; Storm, Amanda R.; Badley, Elizabeth M.; Lehman, Michael D.; Platt, Samantha M.; Saunders, Lauren K.; Schmitz, Jonathan M.; Torres, Catherine E.

2014-01-01

Starch degradation in chloroplasts requires β-amylase (BAM) activity, which is encoded by a multigene family. Of nine Arabidopsis (Arabidopsis thaliana) BAM genes, six encode plastidic enzymes, but only four of these are catalytically active. In vegetative plants, BAM1 acts during the day in guard cells, whereas BAM3 is the dominant activity in mesophyll cells at night. Plastidic BAMs have been difficult to assay in leaf extracts, in part because of a cytosolic activity encoded by BAM5. We generated a series of double mutants lacking BAM5 and each of the active plastidic enzymes (BAM1, BAM2, BAM3, and BAM6) and found that most of the plastidic activity in 5-week-old plants was encoded by BAM1 and BAM3. Both of these activities were relatively constant during the day and the night. Analysis of leaf extracts from double mutants and purified BAM1 and BAM3 proteins revealed that these proteins have distinct properties. Using soluble starch as the substrate, BAM1 and BAM3 had optimum activity at pH 6.0 to 6.5, but at high pH, BAM1 was more active than BAM3, consistent with its known daytime role in the guard cell stroma. The optimum temperature for BAM1, which is transcriptionally induced by heat stress, was about 10°C higher than that of BAM3, which is transcriptionally induced by cold stress. The amino acid composition of BAM1 and BAM3 orthologs reflected differences that are consistent with known adaptations of proteins from heat- and cold-adapted organisms, suggesting that these day- and night-active enzymes have undergone thermal adaptation. PMID:25293962

Surface Colonization and Activity of the 2,6-Dichlorobenzamide (BAM) Degrading Aminobacter sp. Strain MSH1 at Macro- and Micropollutant BAM Concentrations.

PubMed

Sekhar, Aswini; Horemans, Benjamin; Aamand, Jens; Sørensen, Sebastian R; Vanhaecke, Lynn; Bussche, Julie Vanden; Hofkens, Johan; Springael, Dirk

2016-09-20

Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C and N source and is a potential catalyst for biotreatment of BAM-contaminated groundwater in filtration units of drinking water treatment plants (DWTPs). The oligotrophic environment of DWTPs including trace pollutant concentrations, and the high flow rates impose challenges for micropollutant biodegradation in DWTPs. To understand how trace BAM concentrations affect MSH1 surface colonization and BAM degrading activity, MSH1 was cultivated in flow channels fed continuously with BAM macro- and microconcentrations in a N- and C-limiting medium. At all BAM concentrations, MSH1 colonized the flow channel. BAM degradation efficiencies were concentration-dependent, ranging between 70 and 95%. Similarly, BAM concentration affected surface colonization, but at 100 μg/L BAM and lower, colonization was similar to that in systems without BAM, suggesting that assimilable organic carbon and nitrogen other than those supplied by BAM sustained colonization at BAM microconcentrations. Comparison of specific BAM degradation rates in flow channels and in cultures of suspended freshly grown cells indicated that starvation conditions in flow channels receiving BAM microconcentrations resulted into MSH1 biomasses with 10-100-times reduced BAM degrading activity and provided a kinetic model for predicting BAM degradation under continuous C and N starvation.

The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation.

PubMed

Soyk, Sebastian; Simková, Klára; Zürcher, Evelyne; Luginbühl, Leonie; Brand, Luise H; Vaughan, Cara K; Wanke, Dierk; Zeeman, Samuel C

2014-04-01

Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be noncatalytic, but they determine the function of the two Arabidopsis thaliana BZR1-BAM isoforms (BAM7 and BAM8) during transcriptional initiation. Removal or swapping of the BAM domains demonstrates that the BAM7 BAM domain restricts DNA binding and transcriptional activation, while the BAM8 BAM domain allows both activities. Furthermore, we demonstrate that BAM7 and BAM8 interact on the protein level and cooperate during transcriptional regulation. Site-directed mutagenesis of residues in the BAM domain of BAM8 shows that its function as a transcriptional activator is independent of catalysis but requires an intact substrate binding site, suggesting it may bind a ligand. Microarray experiments with plants overexpressing truncated versions lacking the BAM domain indicate that the pseudo-enzymatic domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). Side specificity toward the G-box may allow crosstalk to other signaling networks. This work highlights the importance of the enzyme-derived domain of BZR1-BAMs, supporting their potential role as metabolic sensors. © 2014 American Society of Plant Biologists. All rights reserved.

Amylases StAmy23, StBAM1 and StBAM9 regulate cold-induced sweetening of potato tubers in distinct ways

PubMed Central

Hou, Juan; Zhang, Huiling; Liu, Jun; Reid, Stephen; Liu, Tengfei; Xu, Shijing; Tian, Zhendong; Sonnewald, Uwe

2017-01-01

Abstract Cold-induced sweetening (CIS) in potato is detrimental to the quality of processed products. Conversion of starch to reducing sugars (RS) by amylases is considered one of the main pathways in CIS but is not well studied. The amylase genes StAmy23, StBAM1, and StBAM9 were studied for their functions in potato CIS. StAmy23 is localized in the cytoplasm, whereas StBAM1 and StBAM9 are targeted to the plastid stroma and starch granules, respectively. Genetic transformation of these amylases in potatoes by RNA interference showed that β-amylase activity could be decreased in cold-stored tubers by silencing of StBAM1 and collective silencing of StBAM1 and StBAM9. However, StBAM9 silencing did not decrease β-amylase activity. Silencing StBAM1 and StBAM9 caused starch accumulation and lower RS, which was more evident in simultaneously silenced lines, suggesting functional redundancy. Soluble starch content increased in RNAi-StBAM1 lines but decreased in RNAi-StBAM9 lines, suggesting that StBAM1 may regulate CIS by hydrolysing soluble starch and StBAM9 by directly acting on starch granules. Moreover, StBAM9 interacted with StBAM1 on the starch granules. StAmy23 silencing resulted in higher phytoglycogen and lower RS accumulation in cold-stored tubers, implying that StAmy23 regulates CIS by degrading cytosolic phytoglycogen. Our findings suggest that StAmy23, StBAM1, and StBAM9 function in potato CIS with varying levels of impact. PMID:28369567

Structural and magnetic properties of Ni-Zn doped BaM nanocomposite via citrate precursor

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

Rana, Kush; Thakur, Preeti; Thakur, Atul, E-mail: atulphysics@gmail.com

2016-05-23

Ni-Zn substituted M-type barium ferrite nanocomposite has been prepared via citrate precursor method. Nanocomposite having composition BaNi{sub 0.5}Zn{sub 0.5}Fe{sub 11}O{sub 19} was sintered at 900°C for 3hrs and characterized by using different characterization techniques. X-ray diffraction (XRD) confirmed the formation of double phase with most prominent peak at (114). Average crystallite size for pure BaM and BNZFO were found to be 36 nm & 45 nm. Field emission scanning electron microscopy (FESEM) confirmed the formation of hexagonal platelets with a layered structure. Magnetic properties of these samples were investigated by using vibrating sample magnetometer (VSM). Magnetic parameters like saturation magnetization (M{sub s}),more » coericivity (H{sub c}) and squareness ratio (SQR) of nanocomposite were found to be 60 emu/g, 3663 Oe and 0.6163 respectively. These values were noticed to be higher as compared to pure BaM. Enhanced magnetic properties of nanocomposite were strongly dependent on exchange coupling. Therefore these properties make this nanocomposite a suitable candidate for magnetic recording and high frequency applications.« less

Preparation of Scandium-Doped, Textured, M-Type Barium Ferrite via a Wet Magnetizing Orientation Process

NASA Astrophysics Data System (ADS)

Wang, Yu; Liu, Yingli; Zhang, Huaiwu; Li, Jie; Gao, Liwen; Chen, Daming; Chen, Yong

2018-02-01

In this paper, a wet magnetizing orientation process was applied to synthesize c-axis-textured, M-type barium ferrite (BaFe12O19 or BaM), which is widely used to produce hard magnetic materials. To modify the magnetic properties of the BaM ferrite and make it suitable for certain operating frequencies, Sc3+ was substituted into Fe3+ sites of the BaM crystal structure. A BaSc x Fe12- x O19 ferrite with a typical relative density of ˜ 75% was successfully obtained. We used x-ray diffraction, scanning electronic microscopy, and a vibrating sample magnetometer to obtain phase information, detail of the microstructure, and magnetic properties of the BaSc x Fe12- x O19, respectively. The composition BaSc x Fe12- x O19 ( x = 0.1) featured a superior squareness ratio of ˜ 67% and a saturation magnetization ( M S) of ˜ 5300 Gauss in magnetic hysteresis loop measurements. These features match well with requirements for self-biased passive devices. Moreover, the site preference of Sc3+ in the hexagonal crystal structure was investigated.

Augmenting β-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins.

PubMed

Heuck, Alexander; Schleiffer, Alexander; Clausen, Tim

2011-03-11

β-Barrel proteins are frequently found in the outer membrane of mitochondria, chloroplasts and Gram-negative bacteria. In Escherichia coli, these proteins are inserted in the outer membrane by the Bam (β-barrel assembly machinery) complex, a multiprotein machinery formed by the β-barrel protein BamA and the four peripheral membrane proteins BamB, BamC, BamD and BamE. The periplasmic part of BamA binds prefolded β-barrel proteins by a β-augmentation mechanism, thereby stabilizing the precursors prior to their membrane insertion. However, the role of the associated proteins within the Bam complex remains unknown. Here, we describe the crystal structure of BamB, a nonessential component of the Bam complex. The structure shows a typical eight-bladed β-propeller fold. Two sequence stretches of BamB were previously identified to be important for interaction with BamA. In our structure, both motifs are located in close proximity to each other and contribute to a conserved region forming a narrow groove on the top of the propeller. Moreover, crystal contacts reveal two interaction modes of how BamB might bind unfolded β-barrel proteins. In the crystal lattice, BamB binds to exposed β-strands by β-augmentation, whereas peptide stretches rich in aromatic residues can be accommodated in hydrophobic pockets located at the bottom of the propeller. Thus, BamB could simultaneously bind to BamA and prefolded β-barrel proteins, thereby enhancing the folding and membrane insertion capability of the Bam complex. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core.

PubMed

Bergal, Hans Thor; Hopkins, Alex Hunt; Metzner, Sandra Ines; Sousa, Marcelo Carlos

2016-02-02

The β-barrel assembly machine (BAM) mediates folding and insertion of integral β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Of the five BAM subunits, only BamA and BamD are essential for cell viability. Here we present the crystal structure of a fusion between BamA POTRA4-5 and BamD from Rhodothermus marinus. The POTRA5 domain binds BamD between its tetratricopeptide repeats 3 and 4. The interface structural elements are conserved in the Escherichia coli proteins, which allowed structure validation by mutagenesis and disulfide crosslinking in E. coli. Furthermore, the interface is consistent with previously reported mutations that impair BamA-BamD binding. The structure serves as a linchpin to generate a BAM model where POTRA domains and BamD form an elongated periplasmic ring adjacent to the membrane with a central cavity approximately 30 × 60 Å wide. We propose that nascent OMPs bind this periplasmic ring prior to insertion and folding by BAM. Copyright © 2016 Elsevier Ltd. All rights reserved.

β-Amylase–Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development[C][W][OA

PubMed Central

Reinhold, Heike; Soyk, Sebastian; Šimková, Klára; Hostettler, Carmen; Marafino, John; Mainiero, Samantha; Vaughan, Cara K.; Monroe, Jonathan D.; Zeeman, Samuel C.

2011-01-01

Plants contain β-amylase–like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast. They possess BRASSINAZOLE RESISTANT1 (BZR1)-type DNA binding domains—also found in transcription factors mediating brassinosteroid (BR) responses. The two Arabidopsis thaliana BZR1-BAM proteins (BAM7 and BAM8) bind a cis-regulatory element that both contains a G box and resembles a BR-responsive element. In protoplast transactivation assays, these BZR1-BAMs activate gene expression. Structural modeling suggests that the BAM domain’s glucan binding cleft is intact, but the recombinant proteins are at least 1000 times less active than chloroplastic β-amylases. Deregulation of BZR1-BAMs (the bam7bam8 double mutant and BAM8-overexpressing plants) causes altered leaf growth and development. Of the genes upregulated in plants overexpressing BAM8 and downregulated in bam7bam8 plants, many carry the cis-regulatory element in their promoters. Many genes that respond to BRs are inversely regulated by BZR1-BAMs. We propose a role for BZR1-BAMs in controlling plant growth and development through crosstalk with BR signaling. Furthermore, we speculate that BZR1-BAMs may transmit metabolic signals by binding a ligand in their BAM domain, although diurnal changes in the concentration of maltose, a candidate ligand produced by chloroplastic β-amylases, do not influence their transcription factor function. PMID:21487098

β-amylase-like proteins function as transcription factors in Arabidopsis, controlling shoot growth and development.

PubMed

Reinhold, Heike; Soyk, Sebastian; Simková, Klára; Hostettler, Carmen; Marafino, John; Mainiero, Samantha; Vaughan, Cara K; Monroe, Jonathan D; Zeeman, Samuel C

2011-04-01

Plants contain β-amylase-like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast. They possess BRASSINAZOLE RESISTANT1 (BZR1)-type DNA binding domains--also found in transcription factors mediating brassinosteroid (BR) responses. The two Arabidopsis thaliana BZR1-BAM proteins (BAM7 and BAM8) bind a cis-regulatory element that both contains a G box and resembles a BR-responsive element. In protoplast transactivation assays, these BZR1-BAMs activate gene expression. Structural modeling suggests that the BAM domain's glucan binding cleft is intact, but the recombinant proteins are at least 1000 times less active than chloroplastic β-amylases. Deregulation of BZR1-BAMs (the bam7bam8 double mutant and BAM8-overexpressing plants) causes altered leaf growth and development. Of the genes upregulated in plants overexpressing BAM8 and downregulated in bam7bam8 plants, many carry the cis-regulatory element in their promoters. Many genes that respond to BRs are inversely regulated by BZR1-BAMs. We propose a role for BZR1-BAMs in controlling plant growth and development through crosstalk with BR signaling. Furthermore, we speculate that BZR1-BAMs may transmit metabolic signals by binding a ligand in their BAM domain, although diurnal changes in the concentration of maltose, a candidate ligand produced by chloroplastic β-amylases, do not influence their transcription factor function.

The gene encoding the catalytically inactive beta-amylase BAM4 involved in starch breakdown in Arabidopsis leaves is expressed preferentially in vascular tissues in source and sink organs.

PubMed

Francisco, Perigio; Li, Jing; Smith, Steven M

2010-07-15

Genetic studies in Arabidopsis thaliana have shown that two members of the beta-amylase (BAM) family BAM3 and BAM4 are required for leaf starch breakdown at night. Both are plastid proteins and while BAM3 encodes an active BAM, BAM4 is not an active alpha-1,4-glucan hydrolase. To gain further insight into the possible function of BAM4 we constructed reporter genes using promoters for both BAM3 and BAM4 genes, driving beta-glucuronidase (GUS) and luciferase (LUC) expression in transgenic Arabidopsis plants. Both promoters directed expression in vascular tissue throughout the plant including cotyledons, leaves, petioles, stems, petals, siliques and roots. Tissue sections showed expression to be focused in phloem cells in stem and petiole. The BAM3 promoter was also expressed strongly throughout the photosynthetic tissues of leaves, sepals and siliques, whereas the BAM4 promoter was not. Conversely, the BAM4 promoter was active in root tip but the BAM3 promoter was not. To confirm these expression patterns and to compare with expression of other starch genes we carried-out RT-PCR analysis on RNA from vascular (replum) and non-vascular (valve) tissues of siliques. This confirmed that BAM4 expression together with RAM1 (BAM5) and GWD2 genes is stronger in the replum than the valve, whereas BAM3 is strong in both tissues. These results show that even though BAM3 and BAM4 genes apparently interact genetically in leaf starch metabolism, BAM4 is preferentially expressed in non-photosynthetic vascular tissue, so revealing a potentially greater level of complexity in the control of starch breakdown than had previously been recognised. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

Assembly and relaxation behaviours of phosphatidylethanolamine monolayers investigated by polarization and frequency resolved SFG-VS.

PubMed

Wei, Feng; Xiong, Wei; Li, Wenhui; Lu, Wangting; Allen, Heather C; Zheng, Wanquan

2015-10-14

The assembly conformation and kinetics of phosphatidylethanolamine (PE) lipids are the key to their membrane curvatures and activities, such as exocytosis, endocytosis and Golgi membrane fusion. In the current study, a polarization and frequency resolved (bandwidth ≈ 1 cm(-1)) picosecond sum frequency generation (SFG) system was developed to characterize phosphatidylethanolamine monolayers. In addition to obtaining π-A isotherms and Brewster angle microscopy (BAM) images, the conformational changes and assembly behaviors of phosphatidylethanolamine molecules are investigated by analyzing the SFG spectra collected at various surface pressures (SPs). The compression kinetics and relaxation kinetics of phosphatidylethanolamine monolayers are also reported. The conformational changes of PE molecules during the monolayer compression are separated into several stages: reorientation of the head group PO2(-) in the beginning of the liquid-expanded (LE) phase, conformational changes of head group alkyl chains in the LE phase, and conformational changes of tail group alkyl chains in the LE-liquid condensed (LE-LC) phase. Such an understanding may help researchers to effectively control the lipid molecular conformation and membrane curvatures during the exocytosis/endocytosis processes.

Bovine insulin-phosphatidylcholine mixed Langmuir monolayers: behavior at the air-water interface.

PubMed

Pérez-López, S; Blanco-Vila, N M; Vila-Romeu, N

2011-08-04

The behavior of the binary mixed Langmuir monolayers of bovine insulin (INS) and phosphatidylcholine (PC) spread at the air-water interface was investigated under various subphase conditions. Pure and mixed monolayers were spread on water, on NaOH and phosphate-buffered solutions of pH 7.4, and on Zn(2+)-containing solutions. Miscibility and interactions between the components were studied on the basis of the analysis of the surface pressure (π)-mean molecular area (A) isotherms, surface compression modulus (C(s)(-1))-π curves, and plots of A versus mole fraction of INS (X(INS)). Our results indicate that intermolecular interactions between INS and PC depend on both the monolayer state and the structural characteristics of INS at the interface, which are strongly influenced by the subphase pH and salt content. Brewster angle microscopy (BAM) was applied to investigate the peptide aggregation pattern at the air-water interface in the presence of the studied lipid under any experimental condition investigated. The influence of the lipid on the INS behavior at the interface strongly depends on the subphase conditions.

An ellipsometric approach towards the description of inhomogeneous polymer-based Langmuir layers

PubMed Central

Rottke, Falko O; Schulz, Burkhard; Richau, Klaus; Kratz, Karl

2016-01-01

Summary The applicability of nulling-based ellipsometric mapping as a complementary method next to Brewster angle microscopy (BAM) and imaging ellipsometry (IE) is presented for the characterization of ultrathin films at the air–water interface. First, the methodology is demonstrated for a vertically nonmoving Langmuir layer of star-shaped, 4-arm poly(ω-pentadecalactone) (PPDL-D4). Using nulling-based ellipsometric mapping, PPDL-D4-based inhomogeneously structured morphologies with a vertical dimension in the lower nm range could be mapped. In addition to the identification of these structures, the differentiation between a monolayer and bare water was possible. Second, the potential and limitations of this method were verified by applying it to more versatile Langmuir layers of telechelic poly[(rac-lactide)-co-glycolide]-diol (PLGA). All ellipsometric maps were converted into thickness maps by introduction of the refractive index that was derived from independent ellipsometric experiments, and the result was additionally evaluated in terms of the root mean square roughness, R q. Thereby, a three-dimensional view into the layers was enabled and morphological inhomogeneity could be quantified. PMID:27826490

Gaia: focus, straylight and basic angle

NASA Astrophysics Data System (ADS)

Mora, A.; Biermann, M.; Bombrun, A.; Boyadjian, J.; Chassat, F.; Corberand, P.; Davidson, M.; Doyle, D.; Escolar, D.; Gielesen, W. L. M.; Guilpain, T.; Hernandez, J.; Kirschner, V.; Klioner, S. A.; Koeck, C.; Laine, B.; Lindegren, L.; Serpell, E.; Tatry, P.; Thoral, P.

2016-07-01

The Gaia all-sky astrometric survey is challenged by several issues affecting the spacecraft stability. Amongst them, we find the focus evolution, straylight and basic angle variations Contrary to pre-launch expectations, the image quality is continuously evolving, during commissioning and the nominal mission. Payload decontaminations and wavefront sensor assisted refocuses have been carried out to recover optimum performance. An ESA-Airbus DS working group analysed the straylight and basic angle issues and worked on a detailed root cause analysis. In parallel, the Gaia scientists have also analysed the data, most notably comparing the BAM signal to global astrometric solutions, with remarkable agreement. In this contribution, a status review of these issues will be provided, with emphasis on the mitigation schemes and the lessons learned for future space missions where extreme stability is a key requirement.

BamA β16C strand and periplasmic turns are critical for outer membrane protein insertion and assembly.

PubMed

Gu, Yinghong; Zeng, Yi; Wang, Zhongshan; Dong, Changjiang

2017-11-21

Outer membrane (OM) β-barrel proteins play important roles in importing nutrients, exporting wastes and conducting signals in Gram-negative bacteria, mitochondria and chloroplasts. The outer membrane proteins (OMPs) are inserted and assembled into the OM by OMP85 family proteins. In Escherichia coli , the β-barrel assembly machinery (BAM) contains four lipoproteins such as BamB, BamC, BamD and BamE, and one OMP BamA, forming a 'top hat'-like structure. Structural and functional studies of the E. coli BAM machinery have revealed that the rotation of periplasmic ring may trigger the barrel β1C-β6C scissor-like movement that promote the unfolded OMP insertion without using ATP. Here, we report the BamA C-terminal barrel structure of Salmonella enterica Typhimurium str. LT2 and functional assays, which reveal that the BamA's C-terminal residue Trp, the β16C strand of the barrel and the periplasmic turns are critical for the functionality of BamA. These findings indicate that the unique β16C strand and the periplasmic turns of BamA are important for the outer membrane insertion and assembly. The periplasmic turns might mediate the rotation of the periplasmic ring to the scissor-like movement of BamA β1C-β6C, triggering the OMP insertion. These results are important for understanding the OMP insertion in Gram-negative bacteria, as well as in mitochondria and chloroplasts. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Charge and pressure-tuned surface patterning of surfactant-encapsulated polyoxometalate complexes at the air-water interface.

PubMed

Xu, Miao; Li, Haolong; Zhang, Liying; Wang, Yizhan; Yuan, Yuan; Zhang, Jianming; Wu, Lixin

2012-10-16

In this paper, four organic-inorganic hybrid complexes were prepared using a cationic surfactant dimethyldioctadecylammonium (DODA) to replace the counter cations of four Keggin-type polyoxometalate (POM) clusters with gradually increased negative charges, PW(12)O(40)(3-), SiW(12)O(40)(4-), BW(12)O(40)(5-), and CoW(12)O(40)(6-). The formed surfactant-encapsulated POM (SEP) complexes showed typical amphiphilic properties and can be spread onto the air-water interface to form Langmuir monolayers. The interfacial behavior of the SEP monolayer films was systemically studied by multiple in situ and ex situ characterization methods including Brewster angle microscopy (BAM), atomic force microscopy (AFM), reflection-absorption infrared (RAIR), and X-ray photoelectron spectroscopy (XPS). We found that the increasing alkyl chain density of SEPs leads to an enhanced stability and a higher collapse pressure of SEP Langmuir monolayers. Moreover, a second layer evolved as patterns from the initial monolayers of all the SEPs, when the surface pressures approached the collapse values. The rational combination of alkyl chain density and surface pressure can precisely control the size and the morphology of SEP patterns transforming from disk-like to leaf-like structures on a micrometer scale. The pattern formation was demonstrated to be driven by the self-optimized surface energy of SEP monolayers. This finding can direct a new strategy for the fabrication of POM-hybrid films with controllable patterns, which should be instructive for designing POM-based thin film devices.

Morphogenesis of the Bacillus anthracis Spore

DTIC Science & Technology

2007-02-01

product and plasmid pEO-3 (53) with BamHI and HindIII and ligated the resulting DNA fragments to build pRG23. We passaged pRG23 through E. coli GM1684...to remove debris. The removal of the exosporium was confirmed by elec- tron microscopy (data not shown). Antibody production . To produce a...O. Henriques, and S. M. Cutting (ed.), Bacterial spore formers: probiotics and emerging applications. Horizon Bioscience, Norfolk, United Kingdom

Interfacial binding of divalent cations to calixarene-based Langmuir monolayers

DOE PAGES

Tulli, Ludovico G.; Wang, Wenjie; Lindemann, William R.; ...

2015-02-20

The interactions of Langmuir monolayers produced through the self-assembly of an amphiphilic p-carboxycalix[4]arene with a series of divalent, fourth-period transition metals, at the air-water interface, were investigated. Changes in the interfacial behavior of 1 in response to the presence of CuCl 2, CoCl 2, MnCl 2, and NiCl 2 were studied by means of Langmuir compression isotherms and Brewster angle microscopy (BAM). The measurements revealed that the self-assembly properties of 1 are significantly affected by Cu 2+ ions. The interactions of 1-based monolayers with Co 2+ and Cu 2+ ions were further investigated by means of synchrotron radiation-based X-ray reflectivitymore » (XRR), X-ray near-total-reflection fluorescence (XNTRF), and grazing incidence X-ray diffraction (GIXD). XNTRF and XRR analyses revealed that the monolayer of 1 binds more strongly to Cu 2+ than Co 2+ ions. In the presence of relatively high concentrations of Cu 2+ ions in the subphase (1.4 × 10 -3 M), XNTRF exhibited anomalous depth profile behavior and GIXD measurements showed considerably strong diffuse scattering. Furthermore, both measurements suggest the formation of Cu 2+ clusters contiguous to the monolayer of 1.« less

The interaction of an antiparasitic peptide active against African sleeping sickness with cell membrane models.

PubMed

Pascholati, Cauê P; Lopera, Esteban Parra; Pavinatto, Felippe J; Caseli, Luciano; Nobre, Thatyane M; Zaniquelli, Maria E D; Viitala, Tapani; D'Silva, Claudius; Oliveira, Osvaldo N

2009-12-01

Zwitterionic peptides with trypanocidal activity are promising lead compounds for the treatment of African Sleeping Sickness, and have motivated research into the design of compounds capable of disrupting the protozoan membrane. In this study, we use the Langmuir monolayer technique to investigate the surface properties of an antiparasitic peptide, namely S-(2,4-dinitrophenyl)glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer. The drug formed stable Langmuir monolayers, whose main feature was a phase transition accompanied by a negative surface elasticity. This was attributed to aggregation upon compression due to intermolecular bond associations of the molecules, inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, infrared spectroscopy and dynamic elasticity measurements. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

PubMed

Fleming, Patrick J; Patel, Dhilon S; Wu, Emilia L; Qi, Yifei; Yeom, Min Sun; Sousa, Marcelo Carlos; Fleming, Karen G; Im, Wonpil

2016-06-21

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Does cholesterol preferentially pack in lipid domains with saturated sphingomyelin over phosphatidylcholine? A comprehensive monolayer study combined with grazing incidence X-ray diffraction and Brewster angle microscopy experiments.

PubMed

Wydro, Paweł; Flasiński, Michał; Broniatowski, Marcin

2013-05-01

In this work, the Langmuir monolayers were used as a model for the analysis of the influence of cholesterol on 1,2-distearoyl-sn-glycero-3-phosphocholine - DSPC and stearoyl sphingomyelin - SSM, as well as their equimolar mixture. The aim of these studies was to compare the affinity of cholesterol to sphingomyelin and phosphatidylcholine and discuss the effectiveness of cholesterol packing with these phospholipids. The experiments involved the registration of the surface pressure-area isotherms combined with the application of Brewster angle microscopy (BAM) images and grazing incidence X-ray diffraction methods. We have performed a thorough analysis of the properties of both one-component DSPC and SSM films as well as their 1:1 mixture. Next, the effect of cholesterol on these systems was verified based on the results for 2:1 SSM/Chol, 2:1 DSPC/Chol, and 1:1:1 DSPC/SSM/Chol mixtures. It was found that both phospholipids form highly condensed monolayers, however, they differ in the orientation of acyl chains, namely the acyl chains are more tilted in DSPC film as compared to SSM monolayer as well as DSPC/SSM mixture. Furthermore, the area contraction provoked by the addition of cholesterol was found to be more pronounced for DSPC monolayer than in DSPC/SSM and SSM films. However, all the collected results allow one to postulate that the ability of cholesterol to form ordered domains with DSPC and SSM is similar and is predominantly driven by hydrophobic forces between molecules. The differences in the area condensation induced by cholesterol on the studied phospholipids films results from differences in molecular organization of pure phospholipids films rather than specific cholesterol-phospholipid interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.

PubMed

Wala, Jeremiah; Zhang, Cheng-Zhong; Meyerson, Matthew; Beroukhim, Rameen

2016-07-01

We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis. VariantBam and full documentation are available at github.com/jwalabroad/VariantBam rameen@broadinstitute.org Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effect of Powder Grain Size on Microstructure and Magnetic Properties of Hexagonal Barium Ferrite Ceramic

NASA Astrophysics Data System (ADS)

Shao, Li-Huan; Shen, Si-Yun; Zheng, Hui; Zheng, Peng; Wu, Qiong; Zheng, Liang

2018-05-01

Compact hexagonal barium ferrite (BaFe12O19, BaM) ceramics with excellent magnetic properties have been prepared from powder with the optimal grain size. The dependence of the microstructure and magnetic properties of the ceramics on powder grain size was studied in detail. Single-phase hexagonal barium ferrite powder with grain size of 177 nm, 256 nm, 327 nm, and 454 nm was obtained by calcination under different conditions. Scanning electron microscopy revealed that 327-nm powder was beneficial for obtaining homogeneous grain size and compact ceramic. In addition, magnetic hysteresis loops and complex permeability spectra demonstrated that the highest saturation magnetization (67.2 emu/g) and real part of the permeability (1.11) at 1 GHz were also obtained using powder with grain size of 327 nm. This relationship between the powder grain size and the properties of the resulting BaM ceramic could be significant for development of microwave devices.

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud

PubMed Central

Niemenmaa, Matti; Kallio, Aleksi; Schumacher, André; Klemelä, Petri; Korpelainen, Eija; Heljanko, Keijo

2012-01-01

Summary: Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps. Availability: Available under the open-source MIT license at http://sourceforge.net/projects/hadoop-bam/ Contact: matti.niemenmaa@aalto.fi Supplementary information: Supplementary material is available at Bioinformatics online. PMID:22302568

Genetic (In)stability of 2,6-Dichlorobenzamide Catabolism in Aminobacter sp. Strain MSH1 Biofilms under Carbon Starvation Conditions

PubMed Central

Raes, Bart; Brocatus, Hannelore; T'Syen, Jeroen; Rombouts, Caroline; Vanhaecke, Lynn; Hofkens, Johan; Springael, Dirk

2017-01-01

ABSTRACT Aminobacter sp. strain MSH1 grows on and mineralizes the groundwater micropollutant 2,6-dichlorobenzamide (BAM) and is of interest for BAM removal in drinking water treatment plants (DWTPs). The BAM-catabolic genes in MSH1 are located on plasmid pBAM1, carrying bbdA, which encodes the conversion of BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) (BbdA+ phenotype), and plasmid pBAM2, carrying gene clusters encoding the conversion of 2,6-DCBA to tricarboxylic acid (TCA) cycle intermediates (Dcba+ phenotype). There are indications that MSH1 easily loses its BAM-catabolic phenotype. We obtained evidence that MSH1 rapidly develops a population that lacks the ability to mineralize BAM when grown on nonselective (R2B medium) and semiselective (R2B medium with BAM) media. Lack of mineralization was explained by loss of the Dcba+ phenotype and corresponding genes. The ecological significance of this instability for the use of MSH1 for BAM removal in the oligotrophic environment of DWTPs was explored in lab and pilot systems. A higher incidence of BbdA+ Dcba− MSH1 cells was also observed when MSH1 was grown as a biofilm in flow chambers under C and N starvation conditions due to growth on nonselective residual assimilable organic carbon. Similar observations were made in experiments with a pilot sand filter reactor bioaugmented with MSH1. BAM conversion to 2,6-DCBA was not affected by loss of the DCBA-catabolic genes. Our results show that MSH1 is prone to BAM-catabolic instability under the conditions occurring in a DWTP. While conversion of BAM to 2,6-DCBA remains unaffected, BAM mineralization activity is at risk, and monitoring of metabolites is warranted. IMPORTANCE Bioaugmentation of dedicated biofiltration units with bacterial strains that grow on and mineralize micropollutants was suggested as an alternative for treating micropollutant-contaminated water in drinking water treatment plants (DWTPs). Organic-pollutant-catabolic genes in bacteria are often easily lost, especially under nonselective conditions, which affects the bioaugmentation success. In this study, we provide evidence that Aminobacter sp. strain MSH1, which uses the common groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C source, shows a high frequency of loss of its BAM-mineralizing phenotype due to the loss of genes that convert 2,6-DCBA to Krebs cycle intermediates when nonselective conditions occur. Moreover, we show that catabolic-gene loss also occurs in the oligotrophic environment of DWTPs, where growth of MSH1 depends mainly on the high fluxes of low concentrations of assimilable organic carbon, and hence show the ecological relevance of catabolic instability for using strain MSH1 for BAM removal in DWTPs. PMID:28363960

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.

PubMed

Niemenmaa, Matti; Kallio, Aleksi; Schumacher, André; Klemelä, Petri; Korpelainen, Eija; Heljanko, Keijo

2012-03-15

Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.

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

Bidlack, J.M.; Frey, D.K.; Seyed-Mozaffari, A.

The binding properties of 14{beta}-(bromoacetamido)morphine (BAM) and the ability of BAM to irreversibly inhibit opioid binding to rat brain membranes were examined to characterize the affinity and selectivity of BAM as an irreversible affinity ligand for opioid receptors. BAM had the same receptor selectivity as morphine, with a 3-5-fold decrease in affinity for the different types of opioid receptors. When brain membranes were incubated with BAM, followed by extensive washing, opioid binding was restored to control levels. However, when membranes were incubated with dithiothreitol (DTT), followed by BAM, and subsequently washed, 90% of the 0.25 nM ({sup 3}H)(D-Ala{sup 2},(Me)Phe{sup 4},Gly(ol){supmore » 5})enkephalin (DAGO) binding was irreversibly inhibited as a result of the specific alkylation of a sulfhydryl group at the {mu} binding site. This inhibition was dependent on the concentrations of both DTT and BAM. The {mu} receptor specificity of BAM alkylation was demonstrated by the ability of BAM alkylated membranes to still bind the {delta}-selective peptide ({sup 3}H)(D-penicillamine{sup 2},D-penicillamine{sup 5})enkephalin (DPDPE) and (-)-({sup 3}H)bremazocine in the presence of {mu} and {delta} blockers, selective for {kappa} binding sites. Morphine and naloxone partially protected the binding site from alkylation with BAM, while ligands that did not bind to the {mu}s site did not afford protection. These studies have demonstrated that when a disulfide bond at or near {mu} opioid binding sites was reduced, BAM could then alkylate this site, resulting in the specific irreversible labeling of {mu} opioid receptors.« less

The caBIG® Life Science Business Architecture Model.

PubMed

Boyd, Lauren Becnel; Hunicke-Smith, Scott P; Stafford, Grace A; Freund, Elaine T; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D

2011-05-15

Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

[SeHCAT scanning in bile acid malabsorption].

PubMed

Thomsen, L H; Arveschough, A K; Gustenhoff, P; Qvist, P

1998-09-07

Chronic diarrhea caused by bile acid malabsorption (BAM) is usually divided into three groups. Type 1 is associated with ileal disease or ileal resection; type 2 is idiopathic, and type 3 is BAM associated with certain predisposing conditions. We evaluated the applicability of the SeHCAT test as a routine investigation of different types of suspected BAM. Detailed information about 298 patients were obtained from retrospective review of patient records. All 68 patients with ileal resections had abnormal SeHCAT retention (median 0.6%; range 0-13%). Of 42 patients with non-resected Crohn's disease or radiation injury, BAM was found in 28 cases. A diagnosis of BAM type 2 was established in 33 of 150 patients with unexplained chronic diarrhoea. For patients tested for possible BAM type 3, the SeHCAT values were significantly lower compared to type 2 patients. For BAM type 1, the SeHCAT test is only recommended in non-resected patients. Idiopathic BAM seems to be more common than recognized. The presence of certain predisposing conditions might strengthen the indication for SeHCAT testing.

Poly(2,5-bis(N-Methyl-N-Hexylamino)Phenylene Vinylene) (BAM-PPV) as Pretreatment Coating for Aerospace Applications: Laboratory and Field Studies

PubMed Central

Zarras, Peter; Buhrmaster, Diane; Webber, Cindy; Anderson, Nicole; Stenger-Smith, John D.; Goodman, Paul A.

2014-01-01

In this study, an electroactive polymer (EAP), poly(2,5-bis(N-methyl-N-hexylamino)phenylene vinylene) (BAM-PPV) was investigated as a potential alternative surface pretreatment for hexavalent chromium (Cr(VI))-based aerospace coatings. BAM-PPV was tested as a pretreatment coating on an aerospace aluminum alloy (AA2024-T3) substrate in combination with a non-Cr(VI) epoxy primer and a polyurethane Advanced Performance Coating (APC) topcoat. This testing was undertaken to determine BAM-PPV’s adhesion, corrosion-inhibition, compatibility and survivability in laboratory testing and during outdoor field-testing. BAM-PPV showed excellent adhesion and acceptable corrosion performance in laboratory testing. The BAM-PPV aerospace coating system (BAM-PPV, non-Cr(VI) epoxy primer and polyurethane APC topcoat) was field tested for one year on the rear hatch door of the United States Air Force C-5 cargo plane. After one year of field testing there was no evidence of delamination or corrosion of the BAM-PPV aerospace coating system. PMID:28788292

Poly(2,5-bis(N-Methyl-N-Hexylamino)Phenylene Vinylene) (BAM-PPV) as Pretreatment Coating for Aerospace Applications: Laboratory and Field Studies.

PubMed

Zarras, Peter; Buhrmaster, Diane; Webber, Cindy; Anderson, Nicole; Stenger-Smith, John D; Goodman, Paul A

2014-12-17

In this study, an electroactive polymer (EAP), poly(2,5-bis( N -methyl- N -hexylamino)phenylene vinylene) (BAM-PPV) was investigated as a potential alternative surface pretreatment for hexavalent chromium (Cr(VI))-based aerospace coatings. BAM-PPV was tested as a pretreatment coating on an aerospace aluminum alloy (AA2024-T3) substrate in combination with a non-Cr(VI) epoxy primer and a polyurethane Advanced Performance Coating (APC) topcoat. This testing was undertaken to determine BAM-PPV's adhesion, corrosion-inhibition, compatibility and survivability in laboratory testing and during outdoor field-testing. BAM-PPV showed excellent adhesion and acceptable corrosion performance in laboratory testing. The BAM-PPV aerospace coating system (BAM-PPV, non-Cr(VI) epoxy primer and polyurethane APC topcoat) was field tested for one year on the rear hatch door of the United States Air Force C-5 cargo plane. After one year of field testing there was no evidence of delamination or corrosion of the BAM-PPV aerospace coating system.

C and N isotope fractionation during biodegradation of the pesticide metabolite 2,6-dichlorobenzamide (BAM): potential for environmental assessments.

PubMed

Reinnicke, Sandra; Simonsen, Allan; Sørensen, Sebastian R; Aamand, Jens; Elsner, Martin

2012-02-07

2,6-Dichlorobenzamide (BAM) is a metabolite of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), and a prominent groundwater contaminant. Observable compound-specific isotope fractionation during BAM formation-through transformation of dichlobenil by Rhodococcus erythropolis DSM 9685-was small. In contrast, isotope fractionation during BAM degradation-with Aminobacter sp. MSH1 and ASI1, the only known bacterial strains capable of mineralizing BAM-was large, with pronounced carbon (ε(C) = -7.5‰ to -7.8‰) and nitrogen (ε(N) = -10.7‰ to -13.5‰) isotopic enrichment factors. BAM isotope values in natural samples are therefore expected to be dominated by the effects of its degradation rather than formation. Dual isotope slopes Δ (=Δδ(15)N/Δδ(13)C ≈ ε(N)/ε(C)) showed only small differences for MSH1 (1.75 ± 0.03) and ASI1 (1.45 ± 0.03) suggesting similar transformation mechanisms of BAM hydrolysis. Observations are in agreement with either a tetrahedral intermediate promoted by OH(-) or H(3)O(+) catalysis, or a concerted reaction mechanism. Therefore, owing to consistent carbon isotopic fractionation, isotope shifts of BAM can be linked to BAM biodegradation, and may even be used to quantify degradation of this persistent metabolite. In contrast, nitrogen isotope values may be rather indicative of different sources. Our results delineate a new approach to assessing the fate of BAM in the environment.

Recombinant proteins secreted from tissue-engineered bioartificial muscle improve cardiac dysfunction and suppress cardiomyocyte apoptosis in rats with heart failure.

PubMed

Rong, Shu-Ling; Wang, Yong-Jin; Wang, Xiao-Lin; Lu, Yong-Xin; Wu, Yin; Liu, Qi-Yun; Mi, Shao-Hua; Xu, Yu-Lan

2010-12-01

Tissue-engineered bioartificial muscle-based gene therapy represents a promising approach for the treatment of heart diseases. Experimental and clinical studies suggest that systemic administration of insulin-like growth factor-1 (IGF-1) protein or overexpression of IGF-1 in the heart exerts a favorable effect on cardiovascular function. This study aimed to investigate a chronic stage after myocardial infarction (MI) and the potential therapeutic effects of delivering a human IGF-1 gene by tissue-engineered bioartificial muscles (BAMs) following coronary artery ligation in Sprague-Dawley rats. Ligation of the left coronary artery or sham operation was performed. Primary skeletal myoblasts were retrovirally transduced to synthesize and secrete recombinant human insulin-like growth factor-1 (rhIGF-1), and green fluorescent protein (GFP), and tissue-engineered into implantable BAMs. The rats that underwent ligation were randomly assigned to 2 groups: MI-IGF group (n = 6) and MI-GFP group (n = 6). The MI-IGF group received rhIGF-secreting BAM (IGF-BAMs) transplantation, and the MI-GFP group received GFP-secreting BAM (GFP-BAMs) transplantation. Another group of rats served as the sham operation group, which was also randomly assigned to 2 subgroups: S-IGF group (n = 6) and S-GFP group (n = 6). The S-IGF group underwent IGF-1-BAM transplantation, and S-GFP group underwent GFP-BAM transplantation. IGF-1-BAMs and GFP-BAMs were implanted subcutaneously into syngeneic rats after two weeks of operation was performed. Four weeks after the treatment, hemodynamics was performed. IGF-1 was measured by radioimmunoassay, and then the rats were sacrificed and ventricular samples were subjected to immunohistochemistry. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to examine the mRNA expression of bax and Bcl-2. TNF-α and caspase 3 expression in myocardium was examined by Western blotting. Primary rat myoblasts were retrovirally transduced to secrete rhIGF-1 and tissue-engineered into implantable BAMs containing parallel arrays of postmitotic myofibers. In vitro, they secreted consistent levels of hIGF (0.4 - 1.2 µg×BAM(-1)×d(-1)). When implanted into syngeneic rat, IGF-BAMs secreted and delivered rhIGF. Four weeks after therapy, the hemodynamics was improved significantly in MI rats treated with IGF-BAMs compared with those treated with GFP-BAMs. The levels of serum IGF-1 were increased significantly in both MI and sham rats treated with IGF-BAM. The mRNA expression of bax was lower and Bcl-2 expression was higher in MI-IGF group than MI-GFP group (P < 0.05). Western blotting assay showed TNF-α and caspase 3 expression was lower in MI-IGF group than MI-GFP group after therapy. rhIGF-1 significantly improves left ventricular function and suppresses cardiomyocyte apoptosis in rats with chronic heart failure. Genetically modified tissue-engineered BAMs provide a method delivering recombinant protein for the treatment of heart failure.

Extent and Durability of Contamination of Groundwater and Water Works With The Pesticide Metabolite Bam (2,6 -dichlorbenzamide) Evaluated For Representative Aquifers In Denmark

NASA Astrophysics Data System (ADS)

Jørgensen, Peter R.; Clausen, Liselotte; Larsen, Flemming

The pesticide metabolite BAM (2,6-dichlorbenzamide) is the most frequently found pesticide contaminant in Danish groundwater. In 1999 BAM was found in 26% of Danish water supply wells and the drinking water standard (0.1 µg/L) was exceeded in 11% of the wells. BAM is a metabolite from the active ingredient dichlobenil (DCB), which was used for non-agricultural total weed protection during 1966 ­ 1997. By using the numerical codes FRAC3Dvs and MODFLOW/MT3D it is the aim of the study to evaluate the extent and durability of the BAM pollution in Danish groundwater and to recommend planning strategies to avoid or minimize BAM in future water supply. The modeling was based on the total amount sold of the DCB (29.000 ton/year) combined with data for sorption and degradation of the DCB and BAM measured from comprehensive laboratory experiments with soil material representing root zone and main aquifer soil types in Denmark. As a main result the laboratory experiments revealed that BAM was only very slowly degraded in the root zone, while no degradation was observed in the sub-soil environments. Combining these model in-put data with representative data for the main aquifer types and overriding fractured clay aquitards, the modeling indicates that more than 99% of infiltrated dichlobenile has been transformed to its metabolite BAM (approximately 500 tons in total), and that currently (year 2001) approximately 100% of this compound appears widely in the groundwater and/or in the above aquitards. The modeling shows that the BAM pollution will appear in the groundwater with a high frequency in extensive parts of Denmark during the following 20 years to more than 100 years. The highest current BAM concentrations, but however also the shortest durability of the BAM pollution, will occur in contaminated aquifers, which are not covered with clay layers. Short durability in such areas is furthermore dependent on the lack of further up-stream BAM sources. The modeling moreover indicates that aquifers will be less vulnerable in contaminated areas with high run-of in the surface layers and small groundwater recharge. In contrast to the current vulnerability of the free water table aquifers, BAM contamination underneath thick clay layers (30 m or more) will not break through to the aquifers before year 2050 to 2070. However, hereafter the BAM concentration will increase until approximately year 2150. Hence, the modeling indicates that water extraction may proceed without influence of the BAM pollution from aquifers underneath thick clay aquitards until the middle or late end of the current century, and hereafter, may be moved to areas with no clay layers above aquifers, since such aquifers will have no measurable concentrations of BAM after approximately year 2050. The modeling moreover show that the extent and future evolution of the BAM pollution is a strong function of local geological and hydrological conditions, which indicates a promising potential for minimizing problems for the water supply through planning and management. The project was funded by the Danish Environmental Protection Agency and the EU-project "PEGASE".

Quantifying bile acid malabsorption helps predict response and tailor sequestrant therapy.

PubMed

Orekoya, Oluwafikunayo; McLaughlin, John; Leitao, Eugenia; Johns, Wendy; Lal, Simon; Paine, Peter

2015-06-01

Although recognised as a cause of chronic diarrhoea for over forty years, diagnostic tests and treatments for bile acid malabsorption (BAM) remain controversial. Recent National Institute for Health and Care Excellence (NICE) guidelines highlighted the lack of evidence in the field, and called for further research. This retrospective study explores the BAM subtype and severity, the use and response to bile acid sequestrants (BAS) and the prevalence of abnormal colonic histology. 264 selenium-75-labelled homocholic acid conjugated taurine (SeHCAT)-tested patient records were reviewed and the severity and subtype of BAM, presence of colonic histopathology and response to BAS were recorded. 53% of patients tested had BAM, with type-2 BAM in 45% of patients with presumed irritable bowel syndrome. Colonic histological abnormalities were similar overall between patients with (29%) or without (23%) BAM (p = 0.46) and between BAM subtypes, with no significant presence of inflammatory changes. 63% of patients with BAM had a successful BAS response which showed a trend to decreased response with reduced severity. Colestyramine was unsuccessful in 44% (38/87) and 45% of these (17/38) were related to medication intolerance, despite a positive SeHCAT. 47% (7/15) of colestyramine failures had a successful colesevelam response. No patient reported colesevelam intolerance. Quantifying severity of BAM appears to be useful in predicting BAS response. Colesevelam was better tolerated than colestyramine and showed some efficacy in colestyramine failures. Colestyramine failure should not be used to exclude BAM. Colonic histology is of no relevance. © Royal College of Physicians 2015. All rights reserved.

The caBIG® Life Science Business Architecture Model

PubMed Central

Boyd, Lauren Becnel; Hunicke-Smith, Scott P.; Stafford, Grace A.; Freund, Elaine T.; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T.; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D.

2011-01-01

Motivation: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. Results: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ). Contact: lbboyd@bcm.edu; laurenbboyd@gmail.com Supplementary information: Supplementary data) are avaliable at Bioinformatics online. PMID:21450709

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

PubMed

Barnett, Derek W; Garrison, Erik K; Quinlan, Aaron R; Strömberg, Michael P; Marth, Gabor T

2011-06-15

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification.

PubMed

Sanosyan, Armen; Fayd'herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load.

The impact of targeting repetitive BamHI-W sequences on the sensitivity and precision of EBV DNA quantification

PubMed Central

Fayd’herbe de Maudave, Alexis; Bollore, Karine; Zimmermann, Valérie; Foulongne, Vincent; Van de Perre, Philippe; Tuaillon, Edouard

2017-01-01

Background Viral load monitoring and early Epstein-Barr virus (EBV) DNA detection are essential in routine laboratory testing, especially in preemptive management of Post-transplant Lymphoproliferative Disorder. Targeting the repetitive BamHI-W sequence was shown to increase the sensitivity of EBV DNA quantification, but the variability of BamHI-W reiterations was suggested to be a source of quantification bias. We aimed to assess the extent of variability associated with BamHI-W PCR and its impact on the sensitivity of EBV DNA quantification using the 1st WHO international standard, EBV strains and clinical samples. Methods Repetitive BamHI-W- and LMP2 single- sequences were amplified by in-house qPCRs and BXLF-1 sequence by a commercial assay (EBV R-gene™, BioMerieux). Linearity and limits of detection of in-house methods were assessed. The impact of repeated versus single target sequences on EBV DNA quantification precision was tested on B95.8 and Raji cell lines, possessing 11 and 7 copies of the BamHI-W sequence, respectively, and on clinical samples. Results BamHI-W qPCR demonstrated a lower limit of detection compared to LMP2 qPCR (2.33 log10 versus 3.08 log10 IU/mL; P = 0.0002). BamHI-W qPCR underestimated the EBV DNA load on Raji strain which contained fewer BamHI-W copies than the WHO standard derived from the B95.8 EBV strain (mean bias: - 0.21 log10; 95% CI, -0.54 to 0.12). Comparison of BamHI-W qPCR versus LMP2 and BXLF-1 qPCR showed an acceptable variability between EBV DNA levels in clinical samples with the mean bias being within 0.5 log10 IU/mL EBV DNA, whereas a better quantitative concordance was observed between LMP2 and BXLF-1 assays. Conclusions Targeting BamHI-W resulted to a higher sensitivity compared to LMP2 but the variable reiterations of BamHI-W segment are associated with higher quantification variability. BamHI-W can be considered for clinical and therapeutic monitoring to detect an early EBV DNA and a dynamic change in viral load. PMID:28850597

Ames Lab 101: BAM (Boron-Aluminum-Magnesium)

ScienceCinema

Cook, Bruce

2017-12-13

Materials scientist, Bruce Cook, discusses the super hard, low friction, and lubricious alloy know as BAM (Boron-Aluminum-Magnesium). BAM was discovered by Bruce Cook and his team at the Ames Laboratory.

Bile acid malabsorption in chronic diarrhea: Pathophysiology and treatment

PubMed Central

Barkun, Alan; Love, Jonathan; Gould, Michael; Pluta, Henryk; Steinhart, A Hillary

2013-01-01

BACKGROUND: Bile acid malabsorption (BAM) is a common but frequently under-recognized cause of chronic diarrhea, with an estimated prevalence of 4% to 5%. METHODS: The published literature for the period 1965 to 2012 was examined for articles regarding the pathophysiology and treatment of BAM to provide an overview of the management of BAM in gastroenterology practice. RESULTS: BAM is classified as type 1 (secondary to ileal dysfunction), type 2 (idiopathic) or type 3 (secondary to gastrointestinal disorders not associated with ileal dysfunction). The estimated prevalence of BAM is >90% in patients with resected Crohn disease (CD) and 11% to 52% of unresected CD patients (type 1); 33% in diarrhea-predominant irritable bowel syndrome (type 2); and is a frequent finding postcholecystectomy or postvagotomy (type 3). Investigations include BAM fecal bile acid assay, 23-seleno-25-homo-tauro-cholic acid (SeHCAT) testing and high-performance liquid chromatography of serum 7-α-OH-4-cholesten-3-one (C4), to determine the level of bile acid synthesis. A less time-consuming and expensive alternative in practice is an empirical trial of the bile acid sequestering agent cholestyramine. An estimated 70% to 96% of chronic diarrhea patients with BAM respond to short-course cholestyramine. Adverse effects include constipation, nausea, borborygmi, flatulence, bloating and abdominal pain. Other bile acid sequestering agents, such as colestipol and colesevelam, are currently being investigated for the treatment of BAM-associated diarrhea. CONCLUSIONS: BAM is a common cause of chronic diarrhea presenting in gastroenterology practice. In accordance with current guidelines, an empirical trial of a bile acid sequestering agent is warranted as part of the clinical workup to rule out BAM. PMID:24199211

BamTools: a C++ API and toolkit for analyzing and managing BAM files

PubMed Central

Barnett, Derek W.; Garrison, Erik K.; Quinlan, Aaron R.; Strömberg, Michael P.; Marth, Gabor T.

2011-01-01

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools. Contact: barnetde@bc.edu PMID:21493652

The structure of the β-barrel assembly machinery complex

DOE PAGES

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

2016-01-08

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

The structure of the β-barrel assembly machinery complex

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

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

PubMed Central

Cheng, Yinhe; Tzeng, Tzy-Hwa Kathy

2016-01-01

This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156–186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory. PMID:27861637

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

Epitaxial growth of 100-μm thick M-type hexaferrite crystals on wide bandgap semiconductor GaN/Al{sub 2}O{sub 3} substrates

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

Hu, Bolin; Su, Zhijuan; Bennett, Steve

2014-05-07

Thick barium hexaferrite BaFe{sub 12}O{sub 19} (BaM) films having thicknesses of ∼100 μm were epitaxially grown on GaN/Al{sub 2}O{sub 3} substrates from a molten-salt solution by vaporizing the solvent. X-ray diffraction measurement verified the growth of BaM (001) textured growth of thick films. Saturation magnetization, 4πM{sub s}, was measured for as-grown films to be 4.6 ± 0.2 kG and ferromagnetic resonance measurements revealed a microwave linewidth of ∼100 Oe at X-band. Scanning electron microscopy indicated clear hexagonal crystals distributed on the semiconductor substrate. These results demonstrate feasibility of growing M-type hexaferrite crystal films on wide bandgap semiconductor substrates by using a simplemore » powder melting method. It also presents a potential pathway for the integration of ferrite microwave passive devices with active semiconductor circuit elements creating system-on-a-wafer architectures.« less

Anti-synchronization control of BAM memristive neural networks with multiple proportional delays and stochastic perturbations

NASA Astrophysics Data System (ADS)

Wang, Weiping; Yuan, Manman; Luo, Xiong; Liu, Linlin; Zhang, Yao

2018-01-01

Proportional delay is a class of unbounded time-varying delay. A class of bidirectional associative memory (BAM) memristive neural networks with multiple proportional delays is concerned in this paper. First, we propose the model of BAM memristive neural networks with multiple proportional delays and stochastic perturbations. Furthermore, by choosing suitable nonlinear variable transformations, the BAM memristive neural networks with multiple proportional delays can be transformed into the BAM memristive neural networks with constant delays. Based on the drive-response system concept, differential inclusions theory and Lyapunov stability theory, some anti-synchronization criteria are obtained. Finally, the effectiveness of proposed criteria are demonstrated through numerical examples.

biobambam: tools for read pair collation based algorithms on BAM files

PubMed Central

2014-01-01

Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

The Microstructure Analysis of Barium M- Hexaferrite Particles Coated by Pani Conducting Material with In Situ Polymerization Process

NASA Astrophysics Data System (ADS)

Zainuri, M.; Amalia, L.

2017-05-01

Barium M-Hexaferrite (BaM) was synthesized by coprecipitation method and doped with Zn. Polyaniline (PANI) was synthesized by chemically and doped DBSA. The composite of PANI/BaM was synthesized by in situ polymerization method. The phase identification of the sample was performed by XRD, FTIR and SEM. Based on XRD data, the phase composition of BaM and hematite are 85.52 % and 14.48%. The characteristic peaks of PANI occur at 3435, 1637, 1473, 1298, 1127, 1009, and 799 cm-1. The characteristic metal oxide stretching peaks of BaM occurs at 575 and 437 cm-1. There is no phase changing in PANI/BaM composite. Based on SEM photography, the shape of BaM is hexagonal. The particle size of BaM powder ranges from 400-700 nm. The qualitative interfacial bonding between PANI and BaM particles are conducted very well and the both materials have good wettability.

Discrete-time BAM neural networks with variable delays

NASA Astrophysics Data System (ADS)

Liu, Xin-Ge; Tang, Mei-Lan; Martin, Ralph; Liu, Xin-Bi

2007-07-01

This Letter deals with the global exponential stability of discrete-time bidirectional associative memory (BAM) neural networks with variable delays. Using a Lyapunov functional, and linear matrix inequality techniques (LMI), we derive a new delay-dependent exponential stability criterion for BAM neural networks with variable delays. As this criterion has no extra constraints on the variable delay functions, it can be applied to quite general BAM neural networks with a broad range of time delay functions. It is also easy to use in practice. An example is provided to illustrate the theoretical development.

A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies.

PubMed

Vij, Rajesh; Lin, Zhonghua; Chiang, Nancy; Vernes, Jean-Michel; Storek, Kelly M; Park, Summer; Chan, Joyce; Meng, Y Gloria; Comps-Agrar, Laetitia; Luan, Peng; Lee, Sophia; Schneider, Kellen; Bevers, Jack; Zilberleyb, Inna; Tam, Christine; Koth, Christopher M; Xu, Min; Gill, Avinash; Auerbach, Marcy R; Smith, Peter A; Rutherford, Steven T; Nakamura, Gerald; Seshasayee, Dhaya; Payandeh, Jian; Koerber, James T

2018-05-08

Outer membrane proteins (OMPs) in Gram-negative bacteria are essential for a number of cellular functions including nutrient transport and drug efflux. Escherichia coli BamA is an essential component of the OMP β-barrel assembly machinery and a potential novel antibacterial target that has been proposed to undergo large (~15 Å) conformational changes. Here, we explored methods to isolate anti-BamA monoclonal antibodies (mAbs) that might alter the function of this OMP and ultimately lead to bacterial growth inhibition. We first optimized traditional immunization approaches but failed to identify mAbs that altered cell growth after screening >3000 hybridomas. We then developed a "targeted boost-and-sort" strategy that combines bacterial cell immunizations, purified BamA protein boosts, and single hybridoma cell sorting using amphipol-reconstituted BamA antigen. This unique workflow improves the discovery efficiency of FACS + mAbs by >600-fold and enabled the identification of rare anti-BamA mAbs with bacterial growth inhibitory activity in the presence of a truncated lipopolysaccharide layer. These mAbs represent novel tools for dissecting the BamA-mediated mechanism of β-barrel folding and our workflow establishes a new template for the efficient discovery of novel mAbs against other highly dynamic membrane proteins.

Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water.

PubMed

Horemans, Benjamin; Raes, Bart; Vandermaesen, Johanna; Simanjuntak, Yanti; Brocatus, Hannelore; T'Syen, Jeroen; Degryse, Julie; Boonen, Jos; Wittebol, Janneke; Lapanje, Ales; Sørensen, Sebastian R; Springael, Dirk

2017-02-07

Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 μg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units.

Stress induced magnetic-domain evolution in magnetoelectric composites

NASA Astrophysics Data System (ADS)

Trivedi, Harsh; Shvartsman, Vladimir V.; Lupascu, Doru C.; Medeiros, Marco S. A.; Pullar, Robert C.

2018-06-01

Local observation of the stress mediated magnetoelectric (ME) effect in composites has gained a great deal of interest over the last decades. However, there is an apparent lack of rigorous methods for a quantitative characterization of the ME effect at the local scale, especially in polycrystalline microstructures. In the present work, we address this issue by locally probing the surface magnetic state of barium titante–hexagonal barium ferrite (BaTiO3–BaFe12O19) ceramic composites using magnetic force microscopy (MFM). The effect of the piezoelectrically induced local stress on the magnetostrictive component (BaFe12O19, BaM) was observed in the form of the evolution of the magnetic domains. The local piezoelectric stress was induced by applying a voltage to the neighboring BaTiO3 grains, using a conductive atomic force microscopy tip. The resulting stochastic evolution of magnetic domains was studied in the context of the induced magnetoelastic anisotropy. In order to overcome the ambiguity in the domain changes observed by MFM, certain generalizations about the observed MFM contrast are put forward, followed by application of an algorithm for extracting the average micromagnetic changes. An average change in domain wall thickness of 50 nm was extracted, giving a lower limit on the corresponding induced magnetoelastic anisotropy energy. Furthermore, we demonstrate that this induced magnetomechanical energy is approximately equal to the K1 magnetocrystalline anisotropy constant of BaM, and compare it with a modeled value of applied elastic energy density. The comparison allowed us to judge the quality of the interfaces in the composite system, by roughly gauging the energy conversion ratio.

Bile acid malabsorption after pelvic and prostate intensity modulated radiation therapy: an uncommon but treatable condition.

PubMed

Harris, Victoria; Benton, Barbara; Sohaib, Aslam; Dearnaley, David; Andreyev, H Jervoise N

2012-12-01

Intensity modulated radiation therapy (IMRT) is a significant therapeutic advance in prostate cancer, allowing increased tumor dose delivery and increased sparing of normal tissues. IMRT planning uses strict dose constraints to nearby organs to limit toxicity. Bile acid malabsorption (BAM) is a treatable disorder of the terminal ileum (TI) that presents with symptoms similar to radiation therapy toxicity. It has not been described in patients receiving RT for prostate cancer in the contemporary era. We describe new-onset BAM in men after IMRT for prostate cancer. Diagnosis of new-onset BAM was established after typical symptoms developed, selenium-75 homocholic acid taurine (SeHCAT) scanning showed 7-day retention of <15%, and patients' symptoms unequivocally responded to a bile acid sequestrant. The TI was identified on the original radiation therapy plan, and the radiation dose delivered was calculated and compared with accepted dose-volume constraints. Five of 423 men treated in a prospective series of high-dose prostate and pelvic IMRT were identified with new onset BAM (median age, 65 years old). All reported having normal bowel habits before RT. The volume of TI ranged from 26-141 cc. The radiation dose received by the TI varied between 11.4 Gy and 62.1 Gy (uncorrected). Three of 5 patients had TI treated in excess of 45 Gy (equivalent dose calculated in 2-Gy fractions, using an α/β ratio of 3) with volumes ranging from 1.6 cc-49.0 cc. One patient had mild BAM (SeHCAT retention, 10%-15%), 2 had moderate BAM (SeHCAT retention, 5%-10%), and 2 had severe BAM (SeHCAT retention, <5%). The 3 patients whose TI received ≥45 Gy developed moderate to severe BAM, whereas those whose TI received <45 Gy had only mild to moderate BAM. Radiation delivered to the TI during IMRT may cause BAM. Identification of the TI from unenhanced RT planning computed tomography scans is difficult and may impede accurate dosimetric evaluation. Thorough toxicity assessment and close liaison between oncologist and gastroenterologist allow timely diagnosis and treatment. Copyright © 2012 Elsevier Inc. All rights reserved.

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

Harris, Victoria; Benton, Barbara; Sohaib, Aslam

Purpose: Intensity modulated radiation therapy (IMRT) is a significant therapeutic advance in prostate cancer, allowing increased tumor dose delivery and increased sparing of normal tissues. IMRT planning uses strict dose constraints to nearby organs to limit toxicity. Bile acid malabsorption (BAM) is a treatable disorder of the terminal ileum (TI) that presents with symptoms similar to radiation therapy toxicity. It has not been described in patients receiving RT for prostate cancer in the contemporary era. We describe new-onset BAM in men after IMRT for prostate cancer. Methods and Materials: Diagnosis of new-onset BAM was established after typical symptoms developed, selenium-75more » homocholic acid taurine (SeHCAT) scanning showed 7-day retention of <15%, and patients' symptoms unequivocally responded to a bile acid sequestrant. The TI was identified on the original radiation therapy plan, and the radiation dose delivered was calculated and compared with accepted dose-volume constraints. Results: Five of 423 men treated in a prospective series of high-dose prostate and pelvic IMRT were identified with new onset BAM (median age, 65 years old). All reported having normal bowel habits before RT. The volume of TI ranged from 26-141 cc. The radiation dose received by the TI varied between 11.4 Gy and 62.1 Gy (uncorrected). Three of 5 patients had TI treated in excess of 45 Gy (equivalent dose calculated in 2-Gy fractions, using an {alpha}/{beta} ratio of 3) with volumes ranging from 1.6 cc-49.0 cc. One patient had mild BAM (SeHCAT retention, 10%-15%), 2 had moderate BAM (SeHCAT retention, 5%-10%), and 2 had severe BAM (SeHCAT retention, <5%). The 3 patients whose TI received {>=}45 Gy developed moderate to severe BAM, whereas those whose TI received <45 Gy had only mild to moderate BAM. Conclusions: Radiation delivered to the TI during IMRT may cause BAM. Identification of the TI from unenhanced RT planning computed tomography scans is difficult and may impede accurate dosimetric evaluation. Thorough toxicity assessment and close liaison between oncologist and gastroenterologist allow timely diagnosis and treatment.« less

Formulation and characterization of boanmycin-loaded liposomes prepared by pH gradient experimental design.

PubMed

Liu, Yu; Yoo, Sun Dong; Li, Li; Fang, Liang; Wen, Ziyi; Li, Tiefu

2012-02-01

This study reports the development of a novel liposomal formulation containing boanmycin (BAM) by the pH-gradient, spherical symmetric experimental design. DSC was used to elucidate the thermotropic transition of the soybean egg phosphatidylcholine (EPCS) bilayers. The DSC analysis showed that the incorporation of cholesterol into the EPCS bilayers caused a reduction in the cooperativity of the bilayer phase transition, leading to a dense and more stable structure. To further explore the possibility of the facilitated molecular interaction between BAM and lipids, the effective chemical shift anisotropy (Δδ) of EPCS was measured by (31)P-NMR spectroscopy in the presence and absence of BAM at 25 °C. The results revealed that the amino group of BAM interacted with the hydrophilic head group of EPCS by electrostatic attraction. Effects of the lipid concentration, pH of the outside buffer and incubation temperature on the encapsulation efficiency of the liposomes were investigated by the spherical symmetric design. Multiple nonlinear regression and second-order polynomial model were fitted to the data, and the resulting equations were used to produce the three dimensional response graphs. The actual response values were in good agreement with the predicted values calculated by the visual FoxPro software. To determine the plasma pharmacokinetics and tissue distribution characteristics of BAM, mice were i.v. injected with BAM-loaded liposomes and the commercial injection solution. The BAM-loaded liposomes exhibited significantly different t(1/2), CL and AUC in plasma and tissues. The MTT assay showed that the BAM-loaded liposomes effectively inhibited the cell proliferation by inducing apoptosis of HepG2 cells in a dose- and time-dependent manner. Compared to the control group, the BAM-loaded liposomes induced marked apoptotic morphologic alterations, including cell shrinkage and granular apoptotic bodies. © 2012 Informa Healthcare USA, Inc.

An investigation of cell growth and detachment from thermoresponsive physically crosslinked networks.

PubMed

Healy, Deirdre; Nash, Maria; Gorleov, Alexander; Thompson, Kerry; Dockery, Peter; Rochev, Yury

2017-11-01

The primary aim of this investigation was to determine the biocompatibility and cell culture potential of a newly designed class of thermoresponsive polymers. The attractiveness of these polymers lies in the fact that they swell rather than dissolve when the temperature is reduced below their respective lower critical solution temperature, due to the incorporation of octadecyl methacrylate (ODMA). The ODMA monomer acts as a physical crosslinker, preventing polymer dissolution upon temperature reduction. Two polymers were studied in this investigation poly(N isorpoylacrylamide (NIPAm)(99.25%)-co-ODMA(0.75%)) and poly(NIPAm(65%)-co-N-tert-butylacrylamide (NtBAm)(34.25%)-co-ODMA(0.75%)). Thin thermoresponsive films of the polymers were prepared via spin coating. 3T3 cells were then seeded on the prepared films and cell viability was assessed quantitatively through cell viability and activity assays and qualitatively by light microscopy. Cells were successfully seeded and grown on the poly(NIPAm-co-ODMA) and poly(NIPAm-co-NtBAm-co-ODMA) copolymer films after film modification with cell adhesion promoters (CAPs). Cell sheets successfully detached from the CAP coated poly(NIPAm-co-ODMA) platforms upon temperature reduction. Copyright © 2017 Elsevier B.V. All rights reserved.

Bile acid malabsorption in patients with chronic diarrhoea: clinical value of SeHCAT test.

PubMed

Wildt, S; Nørby Rasmussen, S; Lysgård Madsen, J; Rumessen, J J

2003-08-01

Bile acid malabsorption (BAM), a cause of chronic diarrhoea, can be diagnosed by the SeHCAT test. The purpose of this study was to evaluate the usefulness of SeHCAT testing by assessing the extent of BAM and describing the clinical characteristics in a group of patients with chronic diarrhoea. Clinical outcome after treatment with cholestyramine was also evaluated. During a 5-year period (1997-2001) the SeHCAT test was performed in 135 patients in whom a primary programme for diagnostic evaluation of chronic diarrhoea had not revealed a cause. File data from 133 patients could be evaluated. In 44% of patients, bile acid absorption was normal with SeHCAT retention > or = 15%. Impaired SeHCAT retention was found in 56%. All patients with ileocaecal resections had retention values < 10%. Patients with microscopic colitis presented with BAM in 39%. Only one patient with idiopathic BAM presented with steatorrhoea as opposed to 11 patients with type 1 and 3 BAM. Patients with idiopathic BAM and/or SeHCAT retention values < 5% had the best response to treatment with cholestyramine. The SeHCAT test is of value in evaluation of patients with chronic diarrhoea as a second-line investigation with a high diagnostic yield. The only a priori parameter to predict BAM was the existence of ileocaecal resections. The result of the SeHCAT test seems to predict the benefit of treatment with cholestyramine.

Are bile acid malabsorption and bile acid diarrhoea important causes of loose stool complicating cancer therapy?

PubMed

Phillips, F; Muls, A C G; Lalji, A; Andreyev, H J N

2015-08-01

Gastrointestinal (GI) symptoms during and after cancer therapy can significantly affect quality of life and interfere with treatment. This study assessed whether bile acid malabsorption (BAM) or bile acid diarrhoea (BAD) are important causes of diarrhoea associated with cancer treatment. A retrospective analysis was carried out of consecutive patients assessed for BAM using ((75) Se) Selenium homocholic acid taurocholate (SeHCAT) scanning, after reporting any episodes of loose stool, attending a gastroenterology clinic in a cancer centre. Between 2009 and 2013, 506 consecutive patients (54.5% male; age range: 20-91 years), were scanned. BAM/BAD was diagnosed in 215 (42.5%). It was mild in 25.6%, moderate in 29.3% and severe in 45.1%. Pelvic chemoradiation had induced BAM in > 50% of patients. BAM was also frequent after treatment for conditions not previously associated with BAM, such as anal and colorectal cancer, and was present in > 75% of patients referred after pancreatic surgery. It was also unexpectedly frequent in patients who were treated for malignancy outside the GI tract, such as breast cancer and haematological malignancy. BAM/BAD are very common and under-appreciated causes of GI symptoms after cancer treatment. Health professionals should have a low threshold in suspecting this condition, as diagnosis and treatment can significantly improve quality of life. Colorectal Disease © 2015 The Association of Coloproctology of Great Britain and Ireland.

Effect of Novel Starter Culture on Reduction of Biogenic Amines, Quality Improvement, and Sensory Properties of Doenjang, a Traditional Korean Soybean Fermented Sauce Variety.

PubMed

Shukla, Shruti; Lee, Jong Suk; Park, Hae-Kyong; Yoo, Jung-Ah; Hong, Sung-Yong; Kim, Jong-Kyu; Kim, Myunghee

2015-08-01

To select appropriate microorganisms as starter cultures for the reliable and reproducible fermentation of soybean fermented products of Korean Doenjang, various ratios of fungi (Aspergillus oryzae J, Mucor racemosus 15, M. racemosus 42) combined with Bacillus subtilis TKSP 24 were selected as either single, double, or multiple Meju strains for commercial mass production of Doenjang, followed by analysis of sensory characteristics. In the sensory evaluation, Doenjang BAM15-1 and BAM42-1, which were fermented with multiple strains (1:1:1), showed the highest sensory scores as compared to control. Based on sensory characteristics, 6 Doenjang samples were subjected to quantitative determination of amino acids, free sugars, and organic acids (volatile and nonvolatile) contents, followed by determination of biogenic amines. Total sweet taste amino acid contents were highest in BAM15-1 and BAM42-1 samples (333.7 and 295.8 mg/100 g, respectively) and similar that of control (391.1 mg/100 g). Samples BAM15-1 and BAM42-1 showed the relatively high volatile and nonvolatile organic acid contents (154.24, 192.26, and 71.31, 82.42 mg/100 g, respectively). In addition, BAM15-1 and BAM42-1 showed negligible biogenic amine formation, ranging from 0.00 to 1.02 and 0.00 to 3.92 mg/100 g, respectively. These findings indicate that determination of food components along with sensory and quality attributes using multiple microbial Meju strains as a starter culture may provide substantial results on improved quality fermented Doenjang products. © 2015 Institute of Food Technologists®

Existence and global exponential stability of periodic solution of memristor-based BAM neural networks with time-varying delays.

PubMed

Li, Hongfei; Jiang, Haijun; Hu, Cheng

2016-03-01

In this paper, we investigate a class of memristor-based BAM neural networks with time-varying delays. Under the framework of Filippov solutions, boundedness and ultimate boundedness of solutions of memristor-based BAM neural networks are guaranteed by Chain rule and inequalities technique. Moreover, a new method involving Yoshizawa-like theorem is favorably employed to acquire the existence of periodic solution. By applying the theory of set-valued maps and functional differential inclusions, an available Lyapunov functional and some new testable algebraic criteria are derived for ensuring the uniqueness and global exponential stability of periodic solution of memristor-based BAM neural networks. The obtained results expand and complement some previous work on memristor-based BAM neural networks. Finally, a numerical example is provided to show the applicability and effectiveness of our theoretical results. Copyright © 2015 Elsevier Ltd. All rights reserved.

Post-cholecystectomy diarrhea: evidence of bile acid malabsorption assessed by SeHCAT test.

PubMed

Sciarretta, G; Furno, A; Mazzoni, M; Malaguti, P

1992-12-01

Although bile acid malabsorption (BAM) in post-cholecystectomy diarrhea (PCD) is a well-known clinical condition, its true etiopathogenetic role is not entirely clear. The SeHCAT (23-selena-25-homotaurocholic acid) test, a simple and reliable BAM test, was performed in 33 cholecystectomized patients, 26 with chronic diarrhea. The test revealed a marked degree of BAM in 25/26 cases. Cholestyramine in doses of 2-12 g/day was effective in 23/25, ineffective in two, and was not tolerated in one patient. When treatment was suspended, diarrhea recurred in nine, whereas bowel habit remained regular in 60%, with brief sporadic episodes of diarrhea in the other cases. The SeHCAT test was repeated in 11 cases after cholestyramine treatment interruption, and revealed the normalization of parameters in two patients and an improvement in three. We conclude that BAM is an important etiopathogenetic factor in PCD that responds favorably to cholestyramine. In 60% of the cases, it resolved diarrhea definitively, although without eliminating BAM in all cases: this suggests that existence of other factors associated with BAM. The SeHCAT test is essential for a differential diagnosis between PCD and the irritable bowel syndrome.

A Boresight Adjustment Mechanism for use on Laser Altimeters

NASA Technical Reports Server (NTRS)

Hakun, Claef; Budinoff, Jason; Brown, Gary; Parong, Fil; Morell, Armando

2004-01-01

This paper describes the development of the Boresight Adjustment Mechanism (BAM) for the Geoscience Laser Altimeter System (GLAS) Instrument. The BAM was developed late in the integration and test phase of the GLAS instrument flight program. Thermal vacuum tests of the GLAS instrument indicated that the instrument boresight alignment stability over temperature may be marginal. To reduce the risk that GLAS may not be able to meet the boresight alignment requirements, an intensive effort was started to develop a BAM. Observatory-level testing and further evaluation of the boresight alignment data indicated that sufficient margin could be obtained utilizing existing instrument resources and therefore the BAM was never integrated onto the GLAS Instrument. However, the BAM was designed fabricated and fully qualified over a 4 month timeframe to be capable of precisely steering (< 1 arcsec over 300 arcsec) the output of three independent lasers to ensure the alignment between the transmit and receive paths of the GLAS instrument. The short timeline for the development of the mechanism resulted in several interesting design solutions. This paper discusses the requirement definition, design, and testing processes of the BAM development effort, how the design was affected by the extremely tight development schedule, and the lessons learned throughout the process.

Impact of breathing awareness meditation on ambulatory blood pressure and sodium handling in prehypertensive African American adolescents.

PubMed

Barnes, Vernon A; Pendergrast, Robert A; Harshfield, Gregory A; Treiber, Frank A

2008-01-01

This study evaluated the impact of a breathing awareness meditation (BAM) program on ambulatory blood pressure and sodium handling in African American adolescents with high-normal systolic blood pressure (SBP) levels. Following three consecutive days of SBP screenings, 66 eligible ninth graders were randomly assigned by school to either BAM (n = 20) or health education control (n = 46) groups. The BAM group engaged in 10-minute BAM sessions at school and at home each day for three months. Teachers conducted sessions at school during health classes. Before and after the intervention, overnight urine samples were collected, and ambulatory SBP, diastolic blood pressure, and heart rate were recorded periodically for 24 hours. Significant changes before and after the intervention were observed between BAM and control groups for SBP during school hours (-4.7 vs .9 mm Hg, P < .05), SBP at night (-4.8 vs -.6 mm Hg, P < .01), and heart rate during school hours (-6.7 vs -2.3 bpm, P < .02), adjusted for their respective preintervention levels. The overnight urinary sodium excretion rate decreased in the BAM group but increased in the control group (-.3 +/- 4.9 vs 1.1 +/- 4.0 mEq/hour, P < .03). These findings demonstrate the potential beneficial impact of BAM taught by school health teachers on blood pressure control in the natural environment in African American youth at risk for development of hypertension.

Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants[OPEN

PubMed Central

Thalmann, Matthias; Pazmino, Diana; Seung, David; Horrer, Daniel; Nigro, Arianna; Meier, Tiago; Zeeman, Samuel C.; Santelia, Diana

2016-01-01

Starch serves functions that range over a timescale of minutes to years, according to the cell type from which it is derived. In guard cells, starch is rapidly mobilized by the synergistic action of β-AMYLASE1 (BAM1) and α-AMYLASE3 (AMY3) to promote stomatal opening. In the leaves, starch typically accumulates gradually during the day and is degraded at night by BAM3 to support heterotrophic metabolism. During osmotic stress, starch is degraded in the light by stress-activated BAM1 to release sugar and sugar-derived osmolytes. Here, we report that AMY3 is also involved in stress-induced starch degradation. Recently isolated Arabidopsis thaliana amy3 bam1 double mutants are hypersensitive to osmotic stress, showing impaired root growth. amy3 bam1 plants close their stomata under osmotic stress at similar rates as the wild type but fail to mobilize starch in the leaves. 14C labeling showed that amy3 bam1 plants have reduced carbon export to the root, affecting osmolyte accumulation and root growth during stress. Using genetic approaches, we further demonstrate that abscisic acid controls the activity of BAM1 and AMY3 in leaves under osmotic stress through the AREB/ABF-SnRK2 kinase-signaling pathway. We propose that differential regulation and isoform subfunctionalization define starch-adaptive plasticity, ensuring an optimal carbon supply for continued growth under an ever-changing environment. PMID:27436713

Impulsive effect on global exponential stability of BAM fuzzy cellular neural networks with time-varying delays

NASA Astrophysics Data System (ADS)

Li, Kelin

2010-02-01

In this article, a class of impulsive bidirectional associative memory (BAM) fuzzy cellular neural networks (FCNNs) with time-varying delays is formulated and investigated. By employing delay differential inequality and M-matrix theory, some sufficient conditions ensuring the existence, uniqueness and global exponential stability of equilibrium point for impulsive BAM FCNNs with time-varying delays are obtained. In particular, a precise estimate of the exponential convergence rate is also provided, which depends on system parameters and impulsive perturbation intention. It is believed that these results are significant and useful for the design and applications of BAM FCNNs. An example is given to show the effectiveness of the results obtained here.

The Drosophila nuclear lamina protein otefin is required for germline stem cell survival.

PubMed

Barton, Lacy J; Pinto, Belinda S; Wallrath, Lori L; Geyer, Pamela K

2013-06-24

LEM domain (LEM-D) proteins are components of an extensive protein network that assembles beneath the inner nuclear envelope. Defects in LEM-D proteins cause tissue-restricted human diseases associated with altered stem cell homeostasis. Otefin (Ote) is a Drosophila LEM-D protein that is intrinsically required for female germline stem cell (GSC) maintenance. Previous studies linked Ote loss with transcriptional activation of the key differentiation gene bag-of-marbles (bam), leading to the model in which Ote tethers the bam gene to the nuclear periphery for gene silencing. Using genetic and phenotypic analyses of multiple ote(-/-) backgrounds, we obtained evidence that is inconsistent with this model. We show that bam repression is maintained in ote(-/-) GSCs and that germ cell loss persists in ote(-/-), bam(-/-) mutants, together demonstrating that GSC loss is independent of bam transcription. We show that the primary defect in ote(-/-) GSCs is a block of differentiation, which ultimately leads to germ cell death. Copyright © 2013 Elsevier Inc. All rights reserved.

The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence

PubMed Central

Flores, Heather A.; Bubnell, Jaclyn E.; Aquadro, Charles F.; Barbash, Daniel A.

2015-01-01

Many reproductive proteins from diverse taxa evolve rapidly and adaptively. These proteins are typically involved in late stages of reproduction such as sperm development and fertilization, and are more often functional in males than females. Surprisingly, many germline stem cell (GSC) regulatory genes, which are essential for the earliest stages of reproduction, also evolve adaptively in Drosophila. One example is the bag of marbles (bam) gene, which is required for GSC differentiation and germline cyst development in females and for regulating mitotic divisions and entry to spermatocyte differentiation in males. Here we show that the extensive divergence of bam between Drosophila melanogaster and D. simulans affects bam function in females but has no apparent effect in males. We further find that infection with Wolbachia pipientis, an endosymbiotic bacterium that can affect host reproduction through various mechanisms, partially suppresses female sterility caused by bam mutations in D. melanogaster and interacts differentially with bam orthologs from D. melanogaster and D. simulans. We propose that the adaptive evolution of bam has been driven at least in part by the long-term interactions between Drosophila species and Wolbachia. More generally, we suggest that microbial infections of the germline may explain the unexpected pattern of evolution of several GSC regulatory genes. PMID:26291077

Measuring recovery: An adapted Brief Assessment of Mood (BAM+) compared to biochemical and power output alterations.

PubMed

Shearer, David A; Sparkes, William; Northeast, Jonny; Cunningham, Daniel J; Cook, Christian J; Kilduff, Liam P

2017-05-01

Biochemical (e.g. creatine kinase (CK)) and neuromuscular (e.g. peak power output (PPO)) markers of recovery are expensive and require specialist equipment. Perceptual measures are an effective alternative, yet most validated scales are too long for daily use. This study utilises a longitudinal multi-level design to test an adapted Brief Assessment of Mood (BAM+), with four extra items and a 100mm visual analogue scale to measure recovery. Elite under-21 academy soccer players (N=11) were monitored across five games with data (BAM+, CK and PPO) collected for each game at 24h pre, 24h and 48h post-match. Match activity data for each participant was also collected using GPS monitors on players. BAM+, CK and PPO had significant (p<.05) linear and quadratic growth curves across time and games that matched the known time reports of fatigue and recovery. Multi-level linear modelling (MLM) with random intercepts for 'participant' and 'game' indicated only CK significantly contributed to the variance of BAM+ scores (p<.05). Significant correlations (p<.01) were found between changes in BAM+ scores from baseline at 24 and 48h post-match for total distance covered per minute, high intensity distance covered per minute, and total number of sprints per minute. Visual and inferential results indicate that the BAM+ appears effective for monitoring longitudinal recovery cycles in elite level athletes. Future research is needed to confirm both the scales reliability and validity. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli*

PubMed Central

Urfer, Matthias; Bogdanovic, Jasmina; Lo Monte, Fabio; Moehle, Kerstin; Zerbe, Katja; Omasits, Ulrich; Ahrens, Christian H.; Pessi, Gabriella; Eberl, Leo; Robinson, John A.

2016-01-01

Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses, such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptide JB-95 with potent antimicrobial activity against Escherichia coli. This peptide exhibits no cellular lytic activity, but electron microscopy and fluorescence studies reveal an ability to selectively disrupt the OM but not the inner membrane of E. coli. The selective targeting of the OM probably occurs through interactions of JB-95 with selected β-barrel OM proteins, including BamA and LptD as shown by photolabeling experiments. Membrane proteomic studies reveal rapid depletion of many β-barrel OM proteins from JB-95-treated E. coli, consistent with induction of a membrane stress response and/or direct inhibition of the Bam folding machine. The results suggest that lethal disruption of the OM by JB-95 occurs through a novel mechanism of action at key interaction sites within clusters of β-barrel proteins in the OM. These findings open new avenues for developing antibiotics that specifically target β-barrel proteins and the integrity of the Gram-negative OM. PMID:26627837

Experimental and computational study of the effect of breath-actuated mechanism built in the NEXThaler® dry powder inhaler.

PubMed

Farkas, Árpád; Lewis, David; Church, Tanya; Tweedie, Alan; Mason, Francesca; Haddrell, Allen E; Reid, Jonathan P; Horváth, Alpár; Balásházy, Imre

2017-11-25

The breath-actuated mechanism (BAM) is a mechanical unit included in NEXThaler ® with the role of delaying the emission of the drug until the inhalation flow rate of the patient is sufficiently high to detach the drug particles from their carriers. The main objective of this work was to analyse the effect of the presence of BAM on the size distribution of the emitted drug and its airway deposition efficiency and distribution. Study of the hygroscopic growth of the emitted drug particles and its effect on the deposition was another goal of this study. Size distributions of Foster ® NEXThaler ® drug particles emitted by dry powder inhalers with and without BAM have been measured by a Next Generation Impactor. Three characteristic inhalation profiles of asthmatic patients (low, moderate and high flow rates) were used for both experimental and modelling purposes. Particle hygroscopic growth was determined by a new method, where experimental measurements are combined with simulations. Upper airway and lung deposition fractions were computed assuming 5s and 10s breath-hold times. By the inclusion of BAM the fine particle fraction of the steroid component increased from 24 to 30% to 47-51%, while that of bronchodilator from 25-34% to 52-55%. The predicted upper airway steroid and bronchodilator doses decreased from about 60% to 35-40% due to BAM. At the same time, predicted lung doses increased from about 20%-35% (steroid) and from 22% to 38% (bronchodilator) for the moderate flow profile and from about 25% to 40% (steroid) and from 29% to 47% (bronchodilator) for the high inhalation flow profile. Although BDP and FF upper airway doses decreased by a factor of about two when BAM was present, lung doses of both components were about the same in the BAM and no-BAM configurations at the weakest flow profile. However, lung dose increased by 2-3% even for this profile when hygroscopic growth was taken into account. In conclusion, the NEXThaler ® BAM mechanism is a unique feature enabling high emitted fine particle fraction and enhanced drug delivery to the lungs. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

A new mechanism for bile acid diarrhea: defective feedback inhibition of bile acid biosynthesis.

PubMed

Walters, Julian R F; Tasleem, Ali M; Omer, Omer S; Brydon, W Gordon; Dew, Tracy; le Roux, Carel W

2009-11-01

Primary (idiopathic) bile acid malabsorption (BAM) is a common, yet underrecognized, chronic diarrheal syndrome. Diagnosis is difficult without selenium homocholic acid taurine (SeHCAT) testing. The diarrhea results from excess colonic bile acids, but the pathogenesis is unclear. Fibroblast growth factor 19 (FGF19), produced in the ileum in response to bile acid absorption, regulates hepatic bile acid synthesis. We proposed that FGF19 is involved in bile acid diarrhea and measured its levels in patients with BAM. Blood was collected from fasting patients with chronic diarrhea; BAM was diagnosed by SeHCAT. Serum FGF19 was measured by enzyme-linked immunosorbent assay. Serum 7alpha-hydroxy-4-cholesten-3-one (C4) was determined using high-performance liquid chromatography, to quantify bile acid synthesis. Data were compared between patients and subjects without diarrhea (controls). Samples were taken repeatedly after meals from several subjects. The median C4 level was significantly higher in patients with primary BAM than in controls (51 vs 18 ng/mL; P < .0001). The median FGF19 level was significantly lower in patients with BAM (120 vs 231 pg/mL; P < .0005). There was a significant inverse relationship between FGF19 and C4 levels (P < .0004). Low levels of FGF19 were also found in patients with postcholecystectomy and secondary bile acid diarrhea. Abnormal patterns of FGF19 levels were observed throughout the day in some patients with primary BAM. Patients with BAM have reduced serum FGF19 which may be useful in diagnosis. We propose a mechanism whereby impaired FGF19 feedback inhibition causes excessive bile acid synthesis that exceeds the normal capacity for ileal reabsorption, producing bile acid diarrhea.

Pasteurella haemolytica leukotoxin and endotoxin induced cytokine gene expression in bovine alveolar macrophages requires NF-kappaB activation and calcium elevation.

PubMed

Hsuan, S L; Kannan, M S; Jeyaseelan, S; Prakash, Y S; Malazdrewich, C; Abrahamsen, M S; Sieck, G C; Maheswaran, S K

1999-05-01

In bovine alveolar macrophages (BAMs), exposure to leukotoxin (Lkt) and endotoxin (LPS) from Pasteurella haemolytica results in expression of inflammatory cytokine genes and intracellular calcium ([Ca2+]i) elevation. Leukotoxin from P. haemolytica interacts only with leukocytes and platelets from ruminant species. Upregulation of cytokine genes in different cells by LPS involves activation of the transcription factor NF-kappaB (NF-kappaB), resulting in its translocation from the cytoplasm to the nucleus. Using immunocytochemical staining and confocal imaging, we studied whether NF-kappaB activation represents a common mechanism for the expression of multiple cytokine genes in BAMs (Lkt-susceptible cells) stimulated with Lkt and LPS. Bovine pulmonary artery endothelial cells and porcine alveolar macrophages were used as nonsusceptible cells. The role of Ca2+ and tyrosine kinases in NF-kappaB activation and inflammatory cytokine gene expression was studied, since an inhibitor of tyrosine kinases attenuates LPS-induced [Ca2+]i elevation in BAMs. The results are summarized as follows: (a) Lkt induced NF-kappaB activation and [Ca2+]i elevation only in BAMs, while LPS effects were demonstrable in all cell types; (b) chelation of [Ca2+]i blocked NF-kappaB activation and IL-1beta, TNFalpha, and IL-8 mRNA expression; and (c) tyrosine kinase inhibitor herbimycin A blocked expression of all three cytokine genes in BAMs stimulated with Lkt, while only the expression of IL-1beta was blocked in BAMs stimulated with LPS. We conclude that cytokine gene expression in BAMs requires NF-kappaB activation and [Ca2+]i elevation, and Lkt effects exhibit cell type- and species specificity. Copyright 1999 Academic Press.

Auto-calibrated scanning-angle prism-type total internal reflection microscopy for nanometer-precision axial position determination and optional variable-illumination-depth pseudo total internal reflection microscopy

DOEpatents

Fang, Ning; Sun, Wei

2015-04-21

A method, apparatus, and system for improved VA-TIRFM microscopy. The method comprises automatically controlled calibration of one or more laser sources by precise control of presentation of each laser relative a sample for small incremental changes of incident angle over a range of critical TIR angles. The calibration then allows precise scanning of the sample for any of those calibrated angles for higher and more accurate resolution, and better reconstruction of the scans for super resolution reconstruction of the sample. Optionally the system can be controlled for incident angles of the excitation laser at sub-critical angles for pseudo TIRFM. Optionally both above-critical angle and sub critical angle measurements can be accomplished with the same system.

BAM 1 and RECEPTOR-LIKE PROTEIN KINASE 2 constitute a signaling pathway and modulate CLE peptide-triggered growth inhibition in Arabidopsis root.

PubMed

Shimizu, Noriko; Ishida, Takashi; Yamada, Masashi; Shigenobu, Shuji; Tabata, Ryo; Kinoshita, Atsuko; Yamaguchi, Katsushi; Hasebe, Mitsuyasu; Mitsumasu, Kanako; Sawa, Shinichiro

2015-12-01

Ligand receptor-based signaling is a means of cell-to-cell communication for coordinating developmental and physiological processes in multicellular organisms. In plants, cell-producing meristems utilize this signaling to regulate their activities and ensure for proper development. Shoot and root systems share common requirements for carrying out this process; however, its molecular basis is largely unclear. It has been suggested that synthetic CLV3/EMBRYO SURROUNDING REGION (CLE) peptide shrinks the root meristem through the actions of CLAVATA2 (CLV2) and the RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) pathway in Arabidopsis thaliana. Our genetic screening for mutations that resist CLE peptide signaling in roots determined that BAM1, which is a member of the leucine-rich repeat receptor-like kinase (LRR-RLK) family, is also involved in this pathway. BAM1 is preferentially expressed in the root tip, including the quiescent center and its surrounding stem cells. Our genetic analysis revealed that BAM1 functions together with RPK2. Using coimmunoprecipitation assay, we showed that BAM1 is capable of forming heteromeric complexes with RPK2. These findings suggest that the BAM1 and RPK2 receptors constitute a signaling pathway that modulates cell proliferation in the root meristem and that related molecules are employed in root and shoot meristems. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The effect of BaM/PANI composition with epoxy paint matrix on single and double layers coating with spray coating method for radar absorbing materials applications

NASA Astrophysics Data System (ADS)

Widyastuti, Fajarin, Rindang; Pratiwi, Vania Mitha; Kholid, Rifki Rachman; Habib, Abdulloh

2018-04-01

In this study, RAM composite has been succesfully synthesized by mixing BaM as magnetic materials and PANI as conductive materials. BaM and PANI materials were prepared separately by solid state method and polymerization method, respectively. To investigated the presence of BaM phase and magnetic property of the as prepared BaM, XRD pert PAN analytical and VSM 250 Dexing Magnet were employed. Inductance Capacitance Resistance technique was carried out to measure electrical conductivity of the synthesized PANI materials. In order to further characterized the structural features of BaM and PANI, SEM-EDX FEI 850 and FTIR characterizations were conducted. RAM composite was prepared by mixing BaM and PANI powders with ultrasonic cleaner. Afterwards, VNA (Vector Network Analyzer) characterization was carried out to determine reflection loss value of RAM by applying mixed RAM composite and epoxy paint on aluminum plate using spray gun. Microscopic characterization was employed to investigated the distribution of RAM particles on the substrate. It was found that reflection loss value as low as -27.153 dB was achieved when applied 15 wt% BaM/PANi composite at 100.6 µm thickness. In addition, the absorption of electromagnetic waves value increase as the addition of RAM composite composition increases.

Tissue Engineered Skeletal Myofibers can Directly "Sense" Gravitational Force Changes

NASA Technical Reports Server (NTRS)

Vandenburgh, Herman H.; Shansky, J.; DelTatto, M.; Lee, Peter; Meir, J.

1999-01-01

Long-term manned space flight requires a better understanding of skeletal muscle atrophy resulting from microgravity. Atrophy most likely results from changes at both the systemic level (e.g. decreased circulating growth hormone, increased circulating glucocorticoids) and locally (e.g. decreased myofiber resting tension). Differentiated skeletal myofibers in tissue culture have provided a model system over the last decade for gaining a better understanding of the interactions of exogenous growth factors, endogenous growth factors, and muscle fiber tension in regulating protein turnover rates and muscle cell growth. Tissue engineering these cells into three dimensional bioartificial muscle (BAM) constructs has allowed us to extend their use to Space flight studies for the potential future development of countermeasures. Embryonic avian muscle cells were isolated and BAMs tissue engineered as described previously. The myoblasts proliferate and fuse into aligned postmitotic myofibers after ten to fourteen days in vitro. A cylindrical muscle-like structure containing several thousand myofibers is formed which is approximately 30 mm in length, 2-3 mm in diameter, and attached at each end. For the Space Shuttle experiments, the BAMs were transferred to 55 mL bioreactor cartridges (6 BAMs/cartridge). At Kennedy Space Center, the cartridges were mounted in two Space Tissue Loss (STL) Modules (three to four cartridges per Module) and either maintained as ground controls or loaded in a Mid-Deck locker of the Space Shuttle. The BAM cartridges were continuously perfused during the experiment at 1.5 mL/ min with tissue culture medium. Eighteen BAMs were flown for nine days on Mission STS66 while eighteen BAMs served as ground controls. The complete experiment was repeated on Mission STS77 with twenty four BAMs in each group. BAMs could be maintained in a healthy state for at least 30 days in the perfusion bioreactor cartridges. The BAM muscle fibers directly detected both the loss of gravity and the reloading effects of 1 x g. While total cellular metabolism and total protein degradation rates were not altered during 9 to 10 days in Space, protein synthesis rates were significantly reduced and resulted in significant myofiber atrophy compared to ground controls. One g reloading of the flight muscle cells post-flight significantly increased protein synthesis rates and the synthesis rates of myosin heavy chain, fibronectin, and collagen. Tissue cultured muscle cells can directly "sense" changes in gravity and provide a valid model to begin the study of countermeasures. Based on our ground based experiments, and the experiments of others, growth hormone and/or insulin-like growth factors are attractive protein therapeutics which may assisting attenuating skeletal muscle wasting in space. Our laboratory is developing a new cell-based delivery system for this and other potential therapeutic factors for attenuating muscle and bone wasting.

Phases, line tension and pattern formation in molecularly thin films at the air-water interface

NASA Astrophysics Data System (ADS)

Mandal, Pritam

A Langmuir film, which is a molecularly thin insoluble film on a liquid substrate, is one practical realization of a quasi-two dimensional matter. The major advantages of this system for the study of phase separation and phase co-existence are (a) it allows accurate control of the components and molecular area of the film and (b) it can be studied by various methods that require very flat films. Phase separation in molecularly thin films plays an important role in a range of systems from biomembranes to biosensors. For example, phase-separated lipid nano-domains in biomembranes are thought to play crucial roles in membrane function. I use Brewster Angel Microscopy (BAM) coupled with Fluorescence Microscopy (FM) and static Light Scattering Microscopy (LSM) to image phases and patterns within Langmuir films. The three microscopic techniques --- BAM, FM and LSM --- are complimentary to each other, providing distinct sets of information. They allow direct comparison with literature results in lipid systems. I have quantitatively validated the use of detailed hydrodynamic simulations to determine line tension in monolayers. Line tension decreases as temperature rises. This decrease gives us information on the entropy associated with the line, and thus about line structure. I carefully consider the thermodynamics of line energy and entropy to make this connection. In the longer run, LSM will be exploited to give us further information about line structure. I have also extended the technique by testing it on domains within the curved surface of a bilayer vesicle. I also note that in the same way that the presence of surface-active agents, known as surfactants, affects surface energy, the addiction of line active agents alters the inter-phase line energy. Thus my results set to stage to systematically study the influence of line active agents ---'linactants' --- on the inter-phase line energy. Hierarchal self-assembled chiral patterns were observed as a function of temperature. I found that the appearance of these domains could be explained with a simple uniaxial optical axis in the underlying structure, which is the first critical step to understanding the origin of these patterns.

Global exponential stability of BAM neural networks with time-varying delays: The discrete-time case

NASA Astrophysics Data System (ADS)

Raja, R.; Marshal Anthoni, S.

2011-02-01

This paper deals with the problem of stability analysis for a class of discrete-time bidirectional associative memory (BAM) neural networks with time-varying delays. By employing the Lyapunov functional and linear matrix inequality (LMI) approach, a new sufficient conditions is proposed for the global exponential stability of discrete-time BAM neural networks. The proposed LMI based results can be easily checked by LMI control toolbox. Moreover, an example is also provided to demonstrate the effectiveness of the proposed method.

Anti-scratch AlMgB14 Gorilla® Glass coating

NASA Astrophysics Data System (ADS)

Putrolaynen, V. V.; Grishin, A. M.; Rigoev, I. V.

2017-10-01

Hard aluminum-magnesium boride (BAM) films were fabricated onto Corning® Gorilla® Glass by radio-frequency magnetron sputtering of a single stoichiometric AlMgB14 target. BAM films exhibit a Vickers hardness from 10 to 30 GPa and a Young's modulus from 80 to 160 GPa depending on applied loading forces. Deposited hard coating increases the critical load at which glass substrate cracks. The adhesion energy of BAM films on Gorilla® Glass is 6.4 J/m2.

Surface phase behavior of di-n-tetradecyl hydrogen phosphate in Langmuir monolayers at the air-water interface.

PubMed

Hossain, Md Mufazzal; Iimura, Ken-Ichi; Kato, Teiji

2006-10-01

Surface phase behavior of di-n-tetradecyl hydrogen phosphate, DTP, has been studied by measuring pi-A isotherms with a film balance and observing monolayer morphology with a Brewster angle microscopy (BAM) at different temperatures. A generalized phase diagram, which shows a triple point for gas (G), liquid-expanded (LE) and liquid-condensed (LC) phases at about 32 degrees C, is constructed for the amphiphile. Below the triple point, a first-order G-LC phase transition has been shown to occur, whereas a first-order G-LE phase transition followed by another first-order LE-LC transition has been found to take place at a temperature above the triple point. The amphiphile shows the fingering LC domains with uniform brightness indicating the presence of untilted molecules. The domain shapes are independent of the change in temperature and compression rate. The existence of similar fingering domains over a wide range of temperature is rather uncommon in the monolayer systems and is considered to be due to the restricted movement of the molecules incorporating into the LC phase. Because the two-alkyl chains are directly attached to two covalent bonds of the phosphate head group, the rearrangement of the molecules, which is an essential condition for the circular domain formation, needs the movement of the whole molecules including the hydration sphere. The difficulty related to such a movement of the molecules causes fingering domains, which are independent of external variables.

Langmuir and Langmuir-Blodgett films of multifunctional, amphiphilic polyethers with cholesterol moieties.

PubMed

Reuter, Sascha; Hofmann, Anna M; Busse, Karsten; Frey, Holger; Kressler, Jörg

2011-03-01

Langmuir films of multifunctional, hydrophilic polyethers containing a hydrophobic cholesterol group (Ch) were studied by surface pressure-mean molecular area (π-mmA) measurements and Brewster angle microscopy (BAM). The polyethers were either homopolymers or diblock copolymers of linear poly(glycerol) (lPG), linear poly(glyceryl glycidyl ether) (lPGG), linear poly(ethylene glycol) (lPEG), or hyperbranched poly(glycerol) (hbPG). Surface pressure measurements revealed that the homopolymers lPG and hbPG did not stay at the water surface after spreading and solvent evaporation, in contrast to lPEG. Because of the incorporation of the Ch group in the polymer structure, stable Langmuir films were formed by Ch-lPG(n), Ch-lPGG(n), and Ch-hbPG(n). The Ch-hbPG(n), Ch-lPEG(n), Ch-lPEG(n)-b-lPG(m), Ch-lPEG(n)-b-lPGG(m), and Ch-lPEG(n)-b-hbPG(m) systems showed an extended plateau region assigned to a phase transition involving the Ch groups. Typical hierarchically ordered morphologies of the LB films on hydrophilic substrates were observed for all Ch-initiated polymers. All LB films showed that Ch of the Ch-initiated homopolymers is able to crystallize. This strong tendency of self-aggregation then triggers further dewetting effects of the respective polyether entities. Fingerlike morphologies are observed for Ch-lPEG(69), since the lPEG(69) entity is able to undergo crystallization after transfer onto the silicon substrate.

75SeHCAT scan in bile acid malabsorption in chronic diarrhoea.

PubMed

Mena Bares, L M; Carmona Asenjo, E; García Sánchez, M V; Moreno Ortega, E; Maza Muret, F R; Guiote Moreno, M V; Santos Bueno, A M; Iglesias Flores, E; Benítez Cantero, J M; Vallejo Casas, J A

Chronic diarrhoea is a common entity in daily clinical practice and it leads to a loss in these patients quality of life. It may be the main symptom of multiple ethiologies including bile acid malabsorption (BAM) which has a comparable prevalence to celiac disease. The BAM results from imbalances in the homeostasis of bile acids in the enterohepatic circulation. It can be a consequence of ileal disease or ileal dysfunction (BAM type i), it can be considered idiopathic or primary (BAM type ii) or associated with other gastrointestinal entities (BAM type iii). Among the different diagnostic methods available, 75 SeHCAT study is the primary current method due to its sensitivity, specificity, safety and low cost. The main disadvantage is that it's not available in all countries, so other diagnostic methods have appeared, such as serum measurement of FGF19 and C4, however they are significantly more complex and costly. The first-line treatment of bile acid diarrhoea is bile acid sequestrant, such as cholestyramine, which can be difficult to administer due to its poor tolerability and gastrointestinal side effects. These are less prominent with newer agents such as colesevelam. In summary, the BAM is a common entity underdiagnosed and undertreated, so it is essential to establish a diagnosis algorithm of chronic diarrhoea in which the 75 SeHCAT study would be first or second line in the differential diagnosis of these patients. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

Challenging current views on bile acid diarrhoea and malabsorption.

PubMed

Kurien, Matthew; Thurgar, Elizabeth; Davies, Ashley; Akehurst, Ron; Andreyev, Jervoise

2018-04-01

In 2012, the National Institute for Health and Care Excellence (NICE) assessed guidance (DG7) on the use of tauroselcholic ( 75 selenium) acid (also known as SeHCAT) for the investigation of diarrhoea due to bile acid malabsorption (BAM) in patients with IBS-D and in patients with Crohn's disease who have not had an ileal resection. NICE concluded that tauroselcholic ( 75 selenium) acid was recommended for use in research only. NICE will be reviewing the decision to update the guidance for tauroselcholic ( 75 selenium) acid, for these populations, in March 2017. Our aim is to summarise advances in BAM, also known as bile acid diarrhoea (BAD), and encourage clinicians to re-evaluate their understanding of this disorder. We review the prevalence, diagnosis and treatment of BAD/BAM. We describe the new evidence available since the original NICE review in 2012, and discuss the economic issues associated with failure to diagnose or to treat BAD/BAM accurately. There is new and compelling evidence available since DG7, which shows that tauroselcholic ( 75 selenium) acid scanning is a powerful tool in the diagnosis of BAD/BAM. We summarise published prevalence data (approximately 1% prevalence in the UK, as suggested by clinical practice diagnosis rates), and highlight that the true prevalence of BAD/BAM could be far greater than this. We present evidence that challenges current opinion about this disorder, and we commend both clinicians and health technology assessment (HTA) agencies for being open to arguments and new evidence in any future HTAs.

Measuring Recovery in Elite Rugby Players: The Brief Assessment of Mood, Endocrine Changes, and Power.

PubMed

Shearer, David A; Kilduff, Liam P; Finn, Charlotte; Jones, Rhys M; Bracken, Richard M; Mellalieu, Stephen D; Owen, Nic; Crewther, Blair T; Cook, Christian J

2015-01-01

There is demand in applied sport settings to measure recovery briefly and accurately. Research indicates mood disturbance as the strongest psychological predictor of mental and physical recovery. The Brief Assessment of Mood (BAM) is a shortened version of the Profile of Mood States that can be completed in less than 30 s. The purpose of this study was to examine the BAM as a quick measure of mood in relation to recovery status in elite rugby players alongside established physiological markers of recovery. Using elite rugby union players (N = 12), this study examined the utility of BAM as an indicator of mental and physical recovery in elite athletes by exploring pattern change in mood disturbance, energy index, power output, cortisol, and testosterone 36 hr before and 12 hr, 36 hr, and 60 hr after a competitive rugby match. Repeated-measures multivariate analysis of variance indicated significant changes in all variables across the 4 time points (p < .05, η(2) range = .20-.48), concurrent with previous study findings. Although visual inspection of the graphs indicated that the pattern of change for mood disturbance and energy index mapped changes in all physiological variables, only a low correlation was observed for power output (r = - .34). Although BAM scores changed significantly over time in accordance with the hypotheses, further testing is required to confirm the utility of the BAM as a measure of recovery. The results indicate that the BAM could be used as 1 indicator of recovery status alongside other measures.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica.

PubMed

Sampaio, Dayanna Souza; Almeida, Juliana Rodrigues Barboza; de Jesus, Hugo E; Rosado, Alexandre S; Seldin, Lucy; Jurelevicius, Diogo

2017-11-01

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Crisis management aspects of bam catastrophic earthquake: review article.

PubMed

Sadeghi-Bazargani, Homayoun; Azami-Aghdash, Saber; Kazemi, Abdolhassan; Ziapour, Behrad

2015-01-01

Bam earthquake was the most catastrophic natural disasters in recent years. The aim of this study was to review different aspects of crisis management during and after the catastrophic earthquake in Bam City, Iran. Data needed for this systematic review were collected through searching PubMed, EMBASE and SID databases, for the period from 2003 to 2011. Keywords included earthquake, Iran and Bam earthquake. The data were summarized and were analyzed using Content Analysis. Out of 422 articles, 25 articles were included in the study. Crisis Management aspects and existing pitfalls were classified into seven categories including planning and organization, human resource management, management of logistics, international humanitarian aids, field performance of the military and security forces, health and medical service provision, and information management. Positive aspects and major pitfalls of crisis management have been introduced in all the mentioned categories. The available evidence indicated poor crisis management during Bam earthquake that resulted in aggravating the losses as well as diminishing the effect of interventions. Thus, concerning the importance of different aspects of the crisis management and the high prevalence of disasters in Iran, the observed vulnerability in disaster management process should be addressed.

New Passivity Criteria for Fuzzy Bam Neural Networks with Markovian Jumping Parameters and Time-Varying Delays

NASA Astrophysics Data System (ADS)

Vadivel, P.; Sakthivel, R.; Mathiyalagan, K.; Thangaraj, P.

2013-02-01

This paper addresses the problem of passivity analysis issue for a class of fuzzy bidirectional associative memory (BAM) neural networks with Markovian jumping parameters and time varying delays. A set of sufficient conditions for the passiveness of the considered fuzzy BAM neural network model is derived in terms of linear matrix inequalities by using the delay fractioning technique together with the Lyapunov function approach. In addition, the uncertainties are inevitable in neural networks because of the existence of modeling errors and external disturbance. Further, this result is extended to study the robust passivity criteria for uncertain fuzzy BAM neural networks with time varying delays and uncertainties. These criteria are expressed in the form of linear matrix inequalities (LMIs), which can be efficiently solved via standard numerical software. Two numerical examples are provided to demonstrate the effectiveness of the obtained results.

Quenching and annealing in the minority game

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P. J.

2001-05-01

We study the bar attendance model (BAM) and a generalized version of the minority game (MG) in which a number of agents self organize to match an attendance that is fixed externally as a control parameter. We compare the probabilistic dynamics used in the MG with one that we introduce for the BAM that makes better use of the same available information. The relaxation dynamics of the MG leads the system to long lived, metastable (quenched) configurations in which adaptive evolution stops in spite of being far from equilibrium. On the contrary, the BAM relaxation dynamics avoids the MG glassy state, leading to an equilibrium configuration. Finally, we introduce in the MG model the concept of annealing by defining a new procedure with which one can gradually overcome the metastable MG states, bringing the system to an equilibrium that coincides with the one obtained with the BAM.

Investigating the Magneto Electric Coupling of [90 wt%Na0.5Bi0.5TiO3 (NBT)-10 wt% BaFe12O19 (BaM)] novel multiferroiccomposite system by increasing of BaM grain size

NASA Astrophysics Data System (ADS)

Pattanayak, Ranjit; Raut, Subhajit; Kuila, Sourav; Chandrasekhar, Mallam; Panigrahi, Simanchala

2017-02-01

Polycrystalline three novel [90 wt%Na0.5Bi0.5TiO3 (NBT)-10 wt% BaFe12O19 (BaM)] magnetoelctricmultiferroic composite systems were fabricated by considering the variation (increasing) of BaM grain size. The desired formation of composites was confirmed by X-ray diffraction study. The FESEM and SEM study were verified the variation of grain size and 0-3 type connectivity of composite systems. To predict the room temperature multiferroicbehaviour of theses composite systems we were taken PE and MH loop. For investigating the extrinsic and intrinsic magnetoelctric effect magneto impedance spectroscopy was considered for theses composite systems. The variation of intrinsic magnetoelctric coupling was predicted by proposing a simple mechanical model.

A simple process to obtain anisotropic self-biased magnets constituted of stacked barium ferrite single domain particles

NASA Astrophysics Data System (ADS)

Mattei, Jean-Luc; Le, Cong Nha; Chevalier, Alexis; Maalouf, Azar; Noutehou, Nathan; Queffelec, Patrick; Laur, Vincent

2018-04-01

An efficient and inexpensive process is presented that produces highly oriented bulk compacts made of BaM particles. Barium hexaferrite particles (BaM, nominal composition BaFe11O19) were prepared by a chemical coprecipitation method, using different rates and types of precipitating agents (NaOH and Na2CO3). It was demonstrated that when a large excess of Na2CO3 is used, a noteworthy packing of hexagonal BaM platelets is obtained, after mechanical compaction and firing at moderate temperature (1140 °C), without including any more steps than those required for a conventional sintering process. The hysteresis loop displays a very competitive squareness of 0.88 (normalized remanent magnetization) and a coercivity of 215 kA/m, which make this BaM bulk ferrite suitable for self-biased applications.

Spectroscopic study and enhanced thermostability of combustion-derived BaMgAl10O17:Eu2+ blue phosphors for solid-state lighting

NASA Astrophysics Data System (ADS)

Pradal, Nathalie; Potdevin, Audrey; Chadeyron, Geneviève; Bonville, Pierre; Caillier, Bruno; Mahiou, Rachid

2017-02-01

Blue-emitting BaMgAl10O17:Eu2+ (BAM:Eu), suitable for applications in a next generation of Hg-free lamps based on UV LEDs, was prepared by a microwave induced solution combustion synthesis, using urea as combustion fuel and nitrates as oxidizers. Purity control of the as-synthesized blue phosphor was undertaken by a washing step followed by a reduction one. Structural and morphological properties of the outcoming phosphors have been considered. Synthesis process allows producing a well-crystallized and nanostructured BAM phase within only few minutes. The influence of reduction treatment on the relative amounts of Eu2+/Eu3+ in our samples has been investigated through an original study by magnetization and Mössbauer spectroscopy. Furthermore, a complete optical study has been carried out and allowed us to determine the europium localization in the three possible sites in BAM matrix. The percentage of Eu2+ increased twofold after the reduction treatment, entailing an increase in the luminescence efficiency upon UV excitation. Finally, temperature-dependent luminescence of combustion-derived powders has been studied till 170 °C and compared to that of commercial BAM:Eu. MISCS-derived phosphors present a higher thermal stability than commercial one: whereas the emission efficiency of this last was reduced by 64%, the one of combustion-derived BAM:Eu experienced an only 12% decline. Furthermore, while commercial BAM suffered from a severe blue-shift with increasing temperature, our phosphors keep its color quality with a good stability of the photometric parameters.

Breathing awareness meditation and LifeSkills Training programs influence upon ambulatory blood pressure and sodium excretion among African American adolescents.

PubMed

Gregoski, Mathew J; Barnes, Vernon A; Tingen, Martha S; Harshfield, Gregory A; Treiber, Frank A

2011-01-01

To evaluate the effect of breathing awareness meditation (BAM), Botvin LifeSkills Training (LST), and health education control (HEC) on ambulatory blood pressure and sodium excretion in African American adolescents. Following 3 consecutive days of systolic blood pressure (SBP) screenings, 166 eligible participants (i.e., SBP >50th-95th percentile) were randomized by school to either BAM (n = 53), LST (n = 69), or HEC (n = 44). In-school intervention sessions were administered for 3 months by health education teachers. Before and after the intervention, overnight urine samples and 24-hour ambulatory SBP, diastolic blood pressure, and heart rate were obtained. Significant group differences were found for changes in overnight SBP and SBP, diastolic blood pressure, and heart rate over the 24-hour period and during school hours. The BAM treatment exhibited the greatest overall decreases on these measures (Bonferroni adjusted, ps < .05). For example, for school-time SBP, BAM showed a change of -3.7 mmHg compared with no change for LST and a change of -.1 mmHg for HEC. There was a nonsignificant trend for overnight urinary sodium excretion (p = .07), with the BAM group displaying a reduction of -.92 ± 1.1 mEq/hr compared with increases of .89 ± 1.2 mEq/hr for LST and .58 ± .9 mEq/hr for HEC group. BAM appears to improve hemodynamic function and may affect sodium handling among African American adolescents who are at increased risk for development of cardiovascular disease. Published by Elsevier Inc.

Nutrient removal using biosorption activated media: preliminary biogeochemical assessment of an innovative stormwater infiltration basin

USGS Publications Warehouse

O'Reilly, Andrew M.; Wanielista, Martin P.; Chang, Ni-Bin; Xuan, Zhemin; Harris, Willie G.

2012-01-01

Soil beneath a stormwater infiltration basin receiving runoff from a 22.7 ha predominantly residential watershed in central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop a prototype stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO3-/Cl-) ratios for the shallow groundwater indicate that prior to using BAM, NO3- concentrations were substantially influenced by nitrification or variations in NO3- input. In contrast, for the prototype basin utilizing BAM, NO3-/Cl- ratios indicate minor nitrification and NO3- losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest NO3- losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO43-) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO43-/Cl- ratios for shallow groundwater indicate predominantly minor increases and decreases in PO43- with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had not undergone significant chemical changes. Observed nitrogen and phosphorus losses demonstrate the potential, as well as future research needs to improve performance, of the prototype stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure.

Bam, Iran, Radar Interferometry -- Earthquake

NASA Image and Video Library

2004-06-25

A magnitude 6.5 earthquake devastated the small city of Bam in southeast Iran on December 26, 2003. The two images from ESA Envisat show similar measures of the radar interferometric correlation in grayscale on the left and in false colors on the right.

Multistability in bidirectional associative memory neural networks

NASA Astrophysics Data System (ADS)

Huang, Gan; Cao, Jinde

2008-04-01

In this Letter, the multistability issue is studied for Bidirectional Associative Memory (BAM) neural networks. Based on the existence and stability analysis of the neural networks with or without delay, it is found that the 2 n-dimensional networks can have 3 equilibria and 2 equilibria of them are locally exponentially stable, where each layer of the BAM network has n neurons. Furthermore, the results has been extended to (n+m)-dimensional BAM neural networks, where there are n and m neurons on the two layers respectively. Finally, two numerical examples are presented to illustrate the validity of our results.

The 2003 Bam (Iran) earthquake: Rupture of a blind strike-slip fault

NASA Technical Reports Server (NTRS)

Talebian, M.; Fielding, E. J.; Funning, G. J.; Ghorashi, M.; Jackson, J.; Nazari, H.; Parsons, B.; Priestley, K.; Rosen, P. A.; Walker, R.;

Thin films sputtered from Ba{sub 2}NdFeNb{sub 4}O{sub 15} multiferroic targets on BaFe{sub 12}O{sub 19} coated substrates

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

Bodeux, Romain; Univ. Bordeaux, ICMCB, UPR 9048, F-33600 Pessac; Michau, Dominique, E-mail: dominique.michau@icmcb.cnrs.fr

2016-09-15

Highlights: • Synthesis of Ba{sub 2}NdFeNb{sub 4}O{sub 15}/BaFe{sub 12}O{sub 19} (BaM) heterostructures by RF magnetron sputtering. • Growth of TTB layer were retained regardless of the underlayer (Pt bottom electrode or BaM). • Dielectric and magnetic properties were obtained from the Pt/TTB/BaM/Pt stacks. - Abstract: Ba{sub 2}NdFeNb{sub 4}O{sub 15} tetragonal tungsten bronze (TTB)/BaFe{sub 12}O{sub 19} (BaM) hexaferrite bilayers have been grown by RF magnetron sputtering on Pt/TiO{sub 2}/SiO{sub 2}/Si (PtS) substrates. The BaM layer is textured along (0 0 1) while the TTB layer is multioriented regardless of the PtS or BaM/PtS substrate. Dielectric properties of TTB films are similarmore » to those of bulk, i.e., ε ∼ 150 and a magnetic hysteresis loop is obtained from TTB/BaM bilayers, thanks to the BaM component. This demonstrates the possibility of transferring to 2 dimensional structures the composite multiferroic system TTB/BaM previously identified in 3 dimensional bulk ceramics.« less

Magnetic properties of in-plane oriented barium hexaferrite thin films prepared by direct current magnetron sputtering

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

Zhang, Xiaozhi; Yue, Zhenxing, E-mail: yuezhx@mail.tsinghua.edu.cn; Meng, Siqin

2014-12-28

In-plane c-axis oriented Ba-hexaferrite (BaM) thin films were prepared on a-plane (112{sup ¯}0) sapphire (Al{sub 2}O{sub 3}) substrates by DC magnetron sputtering followed by ex-situ annealing. The DC magnetron sputtering was demonstrated to have obvious advantages over the traditionally used RF magnetron sputtering in sputtering rate and operation simplicity. The sputtering power had a remarkable influence on the Ba/Fe ratio, the hematite secondary phase, and the grain morphology of the as-prepared BaM films. Under 80 W of sputtering power, in-plane c-axis highly oriented BaM films were obtained. These films had strong magnetic anisotropy with high hysteresis loop squareness (M{sub r}/M{sub s}more » of 0.96) along the in-plane easy axis and low M{sub r}/M{sub s} of 0.03 along the in-plane hard axis. X-ray diffraction patterns and pole figures revealed that the oriented BaM films grew via an epitaxy-like growth process with the crystallographic relationship BaM (101{sup ¯}0)//α-Fe{sub 2}O{sub 3}(112{sup ¯}0)//Al{sub 2}O{sub 3}(112{sup ¯}0)« less

Evolution of the Translocation and Assembly Module (TAM)

PubMed Central

Heinz, Eva; Selkrig, Joel; Belousoff, Matthew J.; Lithgow, Trevor

2015-01-01

Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function. The central component of this machinery is BamA, an Omp85 protein that is essential and found in all Gram-negative bacteria. An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB. We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages. A comprehensive phylogenetic and secondary structure analysis of the TamB protein family revealed that TamB was present very early in the evolution of bacteria. Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands. Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi. PMID:25994932

Effect of clay in controlling the non-fluorescence H-dimeric states of a cationic dye Nile Blue Chloride (NBC) in hybrid Langmuir-Blodgett (LB) film

NASA Astrophysics Data System (ADS)

Debnath, Chandan; Shil, Ashis; Hussain, S. A.; Bhattacharjee, D.

2018-01-01

Present communication reports the effect of amphiphilic matrices and nano-clay platelets on the aggregation properties of a water soluble cationic fluorescent dye Nile Blue Chloride (NBC) in Langmuir-Blodgett (LB) films. In-situ Brewster Angle Microscopic (BAM) studies showed distinct domain structures of complex and hybrid Langmuir monolayer at the air-water interface. UV-vis absorption spectra showed non-fluorescent H-dimeric band in concentrated aqueous solution of NBC and in complex LB film of NBC with stearic acid. By changing various parameters, a great control over H-dimeric states has been achieved in clay incorporated hybrid LB films. These films can act as efficient fluorescence probe.

An evaluation of the use of serum 7-alpha-hydroxycholestenone as a diagnostic test of bile acid malabsorption causing watery diarrhea

PubMed Central

Brydon, W Gordon; Culbert, Pearl; Kingstone, Kathleen; Jarvie, Ann; Iacucci, Marietta; Tenhage, Merel; Ghosh, Subrata

2011-01-01

BACKGROUND: Bile acid malabsorption (BAM) is a recognized cause of watery diarrhea, often diagnosed empirically based on clinical response to cholestyramine. The radionuclide selenium-labelled homocholic acid-taurine whole body retention test is expensive, labour intensive and of limited availability. OBJECTIVE: To report on the clinical performance of serum 7-alpha-hydroxy-4-cholesten-3-one (7HCO) as a test of BAM in adult patients with unexplained diarrhea. METHODS: Patients with unexplained diarrhea were investigated over a three-year period. Final diagnosis was determined based on medical history and investigations, serum levels of 7HCO and response to cholestyramine. ROC analysis was used to determine the ideal upper reference range cut-off value to optimize sensitivity/specificity for BAM. Time of blood specimen collection was recorded to investigate possible variation in results throughout the working day. RESULTS: ROC analysis yielded a sensitivity/specificity of 90%/77% for type 1 BAM (ileal disease/resection) and 97%/74% for type 2 BAM (idiopathic) using 30 ng/mL as the upper limit of normal for serum 7HCO when compared with all other patients. Of 813 patients, 196 tested positive. Serum 7HCO levels were significantly higher in blood specimens that were collected between 12:00 and 13:00 (median 24 ng/mL) than in specimens collected between 09:00 and 10:00 (median 17 ng/mL) (P<0.05). CONCLUSION: Serum 7HCO testing is a simple, sensitive, noninvasive, inexpensive alternative to other more commonly used tests for BAM. Time of specimen collection, however, resulted in small but significant result variations and, although unlikely to have much impact on test value, it should ideally be standardized. PMID:21766092

Systematic review with meta-analysis: the prevalence of bile acid malabsorption in the irritable bowel syndrome with diarrhoea.

PubMed

Slattery, S A; Niaz, O; Aziz, Q; Ford, A C; Farmer, A D

2015-07-01

Irritable bowel syndrome is a widespread disorder with a marked socioeconomic burden. Previous studies support the proposal that a subset of patients with features compatible with diarrhoea-predominant IBS (IBS-D) have bile acid malabsorption (BAM). To perform a systematic review and meta-analysis to assess the prevalence of BAM in patients meeting the accepted criteria for IBS-D. MEDLINE and EMBASE were searched up to March 2015. Studies recruiting adults with IBS-D, defined by the Manning, Kruis, Rome I, II or III criteria and which used 23-seleno-25-homotaurocholic acid (SeHCAT) testing for the assessment of BAM were included. BAM was defined as 7 day SeHCAT retention of <10%. We calculated the rate of BAM and 95% confidence intervals (CI) using a random effects model. The methodological quality of included studies was evaluated using the Quality Assessment for Diagnostic Accuracy Studies (QUADAS-2). The search strategy identified six relevant studies comprising 908 individuals. The rate of BAM ranged from 16.9% to 35.3%. The pooled rate was 28.1% (95% CI: 22.6-34%). There was significant heterogeneity in effect sizes (Q-test χ(2)  = 17.9, P < 0.004; I(2)  = 72.1%). The type of diagnostic criteria used or study country did not significantly modify the effect. These data provide evidence that in excess of one quarter of patients meeting accepted criteria for IBS-D have bile acid malabsorption. This distinction has implications for the interpretation of previous studies, as well as contemporaneous clinical practice and future guideline development. © 2015 John Wiley & Sons Ltd.

Robust stability of interval bidirectional associative memory neural network with time delays.

PubMed

Liao, Xiaofeng; Wong, Kwok-wo

2004-04-01

In this paper, the conventional bidirectional associative memory (BAM) neural network with signal transmission delay is intervalized in order to study the bounded effect of deviations in network parameters and external perturbations. The resultant model is referred to as a novel interval dynamic BAM (IDBAM) model. By combining a number of different Lyapunov functionals with the Razumikhin technique, some sufficient conditions for the existence of unique equilibrium and robust stability are derived. These results are fairly general and can be verified easily. To go further, we extend our investigation to the time-varying delay case. Some robust stability criteria for BAM with perturbations of time-varying delays are derived. Besides, our approach for the analysis allows us to consider several different types of activation functions, including piecewise linear sigmoids with bounded activations as well as the usual C1-smooth sigmoids. We believe that the results obtained have leading significance in the design and application of BAM neural networks.

Fungal hyphae stimulate bacterial degradation of 2,6-dichlorobenzamide (BAM).

PubMed

Knudsen, Berith Elkær; Ellegaard-Jensen, Lea; Albers, Christian Nyrop; Rosendahl, Søren; Aamand, Jens

2013-10-01

Introduction of specific degrading microorganisms into polluted soil or aquifers is a promising remediation technology provided that the organisms survive and spread in the environment. We suggest that consortia, rather than single strains, may be better suited to overcome these challenges. Here we introduced a fungal-bacterial consortium consisting of Mortierella sp. LEJ702 and the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 into small sand columns. A more rapid mineralisation of BAM was obtained by the consortium compared to MSH1 alone especially at lower moisture contents. Results from quantitative real-time polymerase chain reaction (qPCR) demonstrated better spreading of Aminobacter when Mortierella was present suggesting that fungal hyphae may stimulate bacterial dispersal. Extraction and analysis of BAM indicated that translocation of the compound was also affected by the fungal hyphae in the sand. This suggests that fungal-bacterial consortia are promising for successful bioremediation of pesticide contamination. Copyright © 2013 Elsevier Ltd. All rights reserved.

Using the Mixed Rasch Model to analyze data from the beliefs and attitudes about memory survey.

PubMed

Smith, Everett V; Ying, Yuping; Brown, Scott W

2012-01-01

In this study, we used the Mixed Rasch Model (MRM) to analyze data from the Beliefs and Attitudes About Memory Survey (BAMS; Brown, Garry, Silver, and Loftus, 1997). We used the original 5-point BAMS data to investigate the functioning of the "Neutral" category via threshold analysis under a 2-class MRM solution. The "Neutral" category was identified as not eliciting the model expected responses and observations in the "Neutral" category were subsequently treated as missing data. For the BAMS data without the "Neutral" category, exploratory MRM analyses specifying up to 5 latent classes were conducted to evaluate data-model fit using the consistent Akaike information criterion (CAIC). For each of three BAMS subscales, a two latent class solution was identified as fitting the mixed Rasch rating scale model the best. Results regarding threshold analysis, person parameters, and item fit based on the final models are presented and discussed as well as the implications of this study.

Three-dimensional deformation caused by the Bam, Iran, earthquake and the origin of shallow slip deficit.

PubMed

Fialko, Yuri; Sandwell, David; Simons, Mark; Rosen, Paul

2005-05-19

Our understanding of the earthquake process requires detailed insights into how the tectonic stresses are accumulated and released on seismogenic faults. We derive the full vector displacement field due to the Bam, Iran, earthquake of moment magnitude 6.5 using radar data from the Envisat satellite of the European Space Agency. Analysis of surface deformation indicates that most of the seismic moment release along the 20-km-long strike-slip rupture occurred at a shallow depth of 4-5 km, yet the rupture did not break the surface. The Bam event may therefore represent an end-member case of the 'shallow slip deficit' model, which postulates that coseismic slip in the uppermost crust is systematically less than that at seismogenic depths (4-10 km). The InSAR-derived surface displacement data from the Bam and other large shallow earthquakes suggest that the uppermost section of the seismogenic crust around young and developing faults may undergo a distributed failure in the interseismic period, thereby accumulating little elastic strain.

BAMS2 Workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections

PubMed Central

Bota, Mihail; Talpalaru, Ştefan; Hintiryan, Houri; Dong, Hong-Wei; Swanson, Larry W.

2014-01-01

We present in this paper a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information about gray matter region axonal connections. This de novo constructed module allows registered users to directly collate their data by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats, and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail, and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions. PMID:24668342

Fixed-time stabilization of impulsive Cohen-Grossberg BAM neural networks.

PubMed

Li, Hongfei; Li, Chuandong; Huang, Tingwen; Zhang, Wanli

2018-02-01

This article is concerned with the fixed-time stabilization for impulsive Cohen-Grossberg BAM neural networks via two different controllers. By using a novel constructive approach based on some comparison techniques for differential inequalities, an improvement theorem of fixed-time stability for impulsive dynamical systems is established. In addition, based on the fixed-time stability theorem of impulsive dynamical systems, two different control protocols are designed to ensure the fixed-time stabilization of impulsive Cohen-Grossberg BAM neural networks, which include and extend the earlier works. Finally, two simulations examples are provided to illustrate the validity of the proposed theoretical results. Copyright © 2017 Elsevier Ltd. All rights reserved.

76 FR 22045 - Fluopicolide; Pesticide Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-20

... increased quantitative susceptibility of rat or rabbit fetuses to in utero or postnatal exposure to... is identified as docket ID number EPA-HQ-OPP-2006-0481. A quantitative reassessment of the BAM risk... fluopicolide and separately, its metabolite, BAM in food as follows: i. Acute exposure. Quantitative acute...

Nutrient removal using biosorption activated media: preliminary biogeochemical assessment of an innovative stormwater infiltration basin.

PubMed

O'Reilly, Andrew M; Wanielista, Martin P; Chang, Ni-Bin; Xuan, Zhemin; Harris, Willie G

2012-08-15

Soil beneath a stormwater infiltration basin receiving runoff from a 23 ha predominantly residential watershed in north-central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop an innovative stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO(3)(-)/Cl(-)) ratios for the shallow groundwater indicates that prior to using BAM, NO(3)(-) concentrations were substantially influenced by nitrification or variations in NO(3)(-) input. In contrast, for the new basin utilizing BAM, NO(3)(-)/Cl(-) ratios indicate minor nitrification and NO(3)(-) losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest that NO(3)(-) losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by the increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO(4)(3-)) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO(4)(3-)/Cl(-) ratios for shallow groundwater indicate predominantly minor increases and decreases in PO(4)(3-) with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had undergone little biogeochemical transformation. Observed nitrogen and phosphorus losses demonstrate the potential, as well as the future research needs to improve performance, of the innovative stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure. Copyright © 2012 Elsevier B.V. All rights reserved.

Reliability and Validity of the Behavioral Addiction Measure for Video Gaming.

PubMed

Sanders, James L; Williams, Robert J

2016-01-01

Most tests of video game addiction have weak construct validity and limited ability to correctly identify people in denial. The purpose of the present research was to investigate the reliability and validity of a new test of video game addiction (Behavioral Addiction Measure-Video Gaming [BAM-VG]) that was developed in part to address these deficiencies. Regular adult video gamers (n = 506) were recruited from a Canadian online panel and completed a survey containing three measures of excessive video gaming (BAM-VG; DSM-5 criteria for Internet Gaming Disorder [IGD]; and the IGD-20), as well as questions concerning extensiveness of video game involvement and self-report of problems associated with video gaming. One month later, they were reassessed for the purposes of establishing test-retest reliability. The BAM-VG demonstrated good internal consistency as well as 1 month test-retest reliability. Criterion-related validity was demonstrated by significant correlations with the following: time spent playing, self-identification of video game problems, and scores on other instruments designed to assess video game addiction (DSM-5 IGD, IGD-20). Consistent with the theory, principal component analysis identified two components underlying the BAM-VG that roughly correspond with impaired control and significant negative consequences deriving from this impaired control. Together with its excellent construct validity and other technical features, the BAM-VG represents a reliable and valid test of video game addiction.

Oligoclonal T cell receptor gene rearrangements in blood lymphocytes of patients with acute Epstein-Barr virus-induced infectious mononucleosis.

PubMed Central

Strickler, J G; Movahed, L A; Gajl-Peczalska, K J; Horwitz, C A; Brunning, R D; Weiss, L M

1990-01-01

Gene rearrangement studies were performed on blood lymphocytes from eight patients with acute Epstein-Barr virus-induced infectious mononucleosis. The diagnosis in each case was based on characteristic clinical, hematologic, and serologic findings. The blood lymphocytes in each patient consisted predominantly of CD8+ T cells. EBV DNA was detected in seven patients by Southern blot analysis (EBV Bam HI W probe, Bam HI). A germline configuration was found for the immunoglobulin heavy and light chain genes (JH probe, Bam HI and Eco RI; C kappa probe, Bam HI; and C lambda probe, Eco RI). T cell receptor gene rearrangements were detected with J gamma and J beta 1 + 2 probes. Using a J gamma probe with two different restriction enzymes (Bgl II and Eco RI), the blood from each patient showed several bands corresponding to the polyclonal pattern previously described in the blood of normal individuals. Using J beta 1 + 2 probes with two different restriction enzymes (Bgl II and Bam HI), each case showed from 3 to about 12 extragermline bands of varying intensity and in different locations from case to case. In addition, each case showed relative deletion of the J beta 1 germline band. This oligoclonal pattern of T cell receptor gene rearrangements has not been previously reported in benign or malignant T cell populations. Images PMID:2170451

Kinetics of adsorption of whey proteins and hydroxypropyl-methyl-cellulose mixtures at the air-water interface.

PubMed

Pérez, Oscar E; Carrera Sánchez, Cecilio; Pilosof, Ana M R; Rodríguez Patino, Juan M

2009-08-15

The aim of this research is to quantify the competitive adsorption of a whey protein concentrate (WPC) and hydroxypropyl-methyl-cellulose (HPMC so called E4M, E50LV and F4M) at the air-water interface by means of dynamic surface tensiometry and Brewster angle microscopy (BAM). These biopolymers are often used together in many food applications. The concentration of both protein and HPMC, and the WPC/HPMC ratio in the aqueous bulk phase were variables, while pH (7), the ionic strength (0.05 M) and temperature (20 degrees C) were kept constant. The differences observed between mixed systems were in accordance with the relative bulk concentration of these biopolymers (C(HPMC) and C(WPC)) and the molecular structure of HPMC. At short adsorption times, the results show that under conditions where both WPC and HPMC could saturate the air-water interface on their own or when C(HPMC) > or = C(WPC), the polysaccharide dominates the surface. At concentrations where none of the biopolymers was able to saturate the interface, a synergistic behavior was observed for HPMC with lower surface activity (E50LV and F4M), while a competitive adsorption was observed for E4M (the HPMC with the highest surface activity). At long-term adsorption the rate of penetration controls the adsorption of mixed components. The results reflect complex competitive/synergistic phenomena under conditions of thermodynamic compatibility or in the presence of a "depletion mechanism". Finally, the order in which the different components reach the interface will influence the surface composition and the film properties.

Characterization of poly(2-hydroxyethyl methacrylate) (PHEMA) contact lens using the Langmuir monolayer technique.

PubMed

Nogueira, N; Conde, O; Miñones, M; Trillo, J M; Miñones, J

2012-11-01

The behavior of poly(2-hydroxyethyl methacrylate) (PHEMA) polymer monolayer spread on water was studied under various experimental conditions. The influence of subphase pH and temperature, compression speed, elapsed time from the deposit of the monolayer and the recording of the surface pressure-area (π-A) isotherms, as well as the number of polymer molecules deposited at the air/water surface (surface concentration) was studied. The obtained results show that PHEMA exhibits a very stable monolayer given that it is unaffected by modifications in the majority of these variables. Only the elapsed time between the spreading of the monolayer and the beginning of compression causes a small change in the π-A isotherms that consists in an increase in the area occupied by the film. This is attributed to the greater unfolding with time of the polymer's monomers at the air/water interface. The plateau that appears on π-A curves of the PHEMA monolayer is attributed to the reorientation of their hydroxyethyl polar groups through their C-O-C bonds, as well as to the reorientation of the ethylene (CH(2)) groups that link the monomers, which provokes a folding of the polymer's chains causing an accordion configuration. The existence of this structure is confirmed by the presence of numerous noise peaks in the relative thickness versus time curve corresponding to this region. In the same fashion, the images observed from Brewster angle microscopy (BAM) reveal the existence of light-dark "bands" relative to the different regions of this particular structure. Copyright © 2012 Elsevier Inc. All rights reserved.

Development of a Nonionic Azobenzene Amphiphile for Remote Photocontrol of a Model Biomembrane.

PubMed

Benedini, Luciano A; Sequeira, M Alejandra; Fanani, Maria Laura; Maggio, Bruno; Dodero, Verónica I

2016-05-05

We report the synthesis and characterization of a simple nonionic azoamphiphile, C12OazoE3OH, which behaves as an optically controlled molecule alone and in a biomembrane environment. First, Langmuir monolayer and Brewster angle microscopy (BAM) experiments showed that pure C12OazoE3OH enriched in the (E) isomer was able to form solidlike mesophase even at low surface pressure associated with supramolecular organization of the azobenzene derivative at the interface. On the other hand, pure C12OazoE3OH enriched in the (Z) isomer formed a less solidlike monolayer due to the bent geometry around the azobenzene moiety. Second, C12OazoE3OH is well-mixed in a biological membrane model, Lipoid s75 (up to 20%mol), and photoisomerization among the lipids proceeded smoothly depending on light conditions. It is proposed that the cross-sectional area of the hydroxyl triethylenglycol head of C12OazoE3OH inhibits azobenzenes H-aggregation in the model membrane; thus, the tails conformation change due to photoisomerization is transferred efficiently to the lipid membrane. We showed that the lipid membrane effectively senses the azobenzene geometrical change photomodulating some properties, like compressibility modulus, transition temperature, and morphology. In addition, photomodulation proceeds with a color change from yellow to orange, providing the possibility to externally monitor the system. Finally, Gibbs monolayers showed that C12OazoE3OH is able to penetrate the highly packing biomembrane model; thus, C12OazoE3OH might be used as photoswitchable molecular probe in real systems.

Development of Thin Films as Potential Structural Cathodes to Enable Multifunctional Energy-Storage Structural Composite Batteries for the U.S. Army’s Future Force

DTIC Science & Technology

2011-09-01

glancing angle X - ray diffraction (GAXRD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and electrochemical...Emission SEM FWHM full width at half maximum GAXRD glancing angle X - ray diffraction H3COCH2CH2OH 2-methoxyethanol LiMn2O4 lithium manganese oxide...were characterized by scanning electron microscopy (SEM), X - ray diffraction (XRD), and atomic force microscopy (AFM). In addition,

Characterization of a New Type of Human Papillomavirus That Causes Skin Warts

PubMed Central

Orth, Gérard; Favre, Michel; Croissant, Odile

1977-01-01

A human papillomavirus (HPV) was isolated from the lesions of a patient (ML) bearing numerous hand common warts. This virus was compared with the well-characterized HPV found in typical plantar warts (plantar HPV). ML and plantar HPV DNAs have similar molecular weights (5.26 × 106 and 5.23 × 106, respectively) but were shown to be different by restriction enzyme analysis. When the cleavage products of both DNAs by endonuclease EcoRI, BamI, HpaI, or Hind were analyzed by electron microscopy, one, two, one, and four fragments were detected for ML HPV DNA instead of the two, one, two, and six fragments, respectively, detected for plantar HPV DNA. In contrast to plantar HPV DNA, a high proportion of ML HPV DNA molecules were resistant to these restriction enzymes. Most, if not all, of the molecules were either resistant to BamI and sensitive to EcoRI or sensitive to BamI and resistant to EcoRI. After denaturation and renaturation of the cleavage products of ML HPV DNA by a mixture of the two enzymes, the circular “heteroduplexes” formed showed one to three heterology loops corresponding to about 4 to 8% of the genome length. No sequence homology was detected between ML and plantar HPV DNAs by cRNA-DNA filter hybridization, by measuring the reassociation kinetics of an iodinated plantar HPV DNA in the presence of a 25-fold excess of ML HPV DNA, or by the heteroduplex technique. The two viruses had distinct electrophoretic polypeptide patterns and showed no antigenic cross-reaction by immunodiffusion or immunofluorescence techniques. Preliminary cRNA-DNA hybridization experiments, using viral DNAs from single or pooled plantar or hand warts, suggest that hand common warts are associated with viruses similar or related to ML HPV. The existence of at least two distinct types of HPVs that cause skin warts was demonstrated; they were provisionally called HPV type 1 and HPV type 2, with plantar HPV and ML HPV as prototypical viruses, respectively. Images PMID:198572

Robust stability for uncertain stochastic fuzzy BAM neural networks with time-varying delays

NASA Astrophysics Data System (ADS)

Syed Ali, M.; Balasubramaniam, P.

2008-07-01

In this Letter, by utilizing the Lyapunov functional and combining with the linear matrix inequality (LMI) approach, we analyze the global asymptotic stability of uncertain stochastic fuzzy Bidirectional Associative Memory (BAM) neural networks with time-varying delays which are represented by the Takagi-Sugeno (TS) fuzzy models. A new class of uncertain stochastic fuzzy BAM neural networks with time varying delays has been studied and sufficient conditions have been derived to obtain conservative result in stochastic settings. The developed results are more general than those reported in the earlier literatures. In addition, the numerical examples are provided to illustrate the applicability of the result using LMI toolbox in MATLAB.

ABL and BAM Friction Analysis Comparison

DOE PAGES

Warner, Kirstin F.; Sandstrom, Mary M.; Brown, Geoffrey W.; ...

2014-12-29

Here, the Integrated Data Collection Analysis (IDCA) program has conducted a proficiency study for Small-Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here is a comparison of the Alleghany Ballistic Laboratory (ABL) friction data and Bundesanstalt fur Materialforschung und -prufung (BAM) friction data for 19 HEM and military standard explosives.

Optimization of rotational speed for growing BaFe12O19 thin films using spin coating

NASA Astrophysics Data System (ADS)

Budiawanti, S.; Soegijono, B.; Mudzakir, I.; Suharno, Fadillah, L.

2017-07-01

Barium ferrite (BaFe12O19, BaM) thin films were fabricated by the spin coating of precursors obtained by using a sol-gel method. The effects of the rotational speed on the spin-coating process for growing a BaM thin film were investigated in this study. Coated films were heat-deposited at different rotational speeds ranging from 2000 to 4000 rpm, while the number of layers was set to nine. Further, the effect of the number of layers on the growth of BaM thin films was discussed. For this purpose, we take the layers number 1 to 12 and take the constant rotational speed of 3000 rpm. All the film were characterized using X-Ray diffraction, Scanning Electron microscope, and Energy-dispersive X-Ray spectroscopy and Vibrating Sample Magnetometer. It was found that by increasing the rotational speed the amount of material deposited on the Si substrate decreased. The measured grain size of the BaM thin film was nearly similar for three three different rotational speeds. However, the grain size was found to increase the number of layers.

Bioaugmentation potential of free and formulated 2,6-dichlorobenzamide (BAM) degrading Aminobacter sp. MSH1 in soil, sand and water.

PubMed

Schultz-Jensen, Nadja; Aamand, Jens; Sørensen, Sebastian R

2016-12-01

Pesticides are used extensively worldwide, which has led to the unwanted contamination of soil and water resources. Former use of the herbicide 2,6-dichlorobenzonitrile (dichlobenil) has caused pollution of ground and surface water resources by the stable degradation product 2,6-dichlorobenzamide (BAM) in several parts of Europe, which has resulted in the costly closure of several drinking water wells. One strategy for preventing this in future is bioaugmentation using bacterial degraders. BAM-degrading Aminobacter sp. MSH1 was therefore formulated into dried beads and tests undertaken to establish their potential for use in the remediation of polluted soil, sand and water. The formulation procedure included freeze drying, combined with trehalose addition for cell wall protection, thus ensuring a high amount of viable cells following prolonged storage at room temperature. The beads were round-shaped pellets with a diameter of about 1.25 mm, a dry matter content of approximately 95 % and an average viable cell content of 4.4 × 10(9) cells/g bead. Formulated MSH1 cells led to a similar, and frequently even faster, BAM mineralisation (20-65 % (14)CO2 produced from (14)C-labelled BAM) in batch tests conducted with sand, water and different soil moisture contents compared to adding free cells. Furthermore, the beads were easy to handle and had a shelf life of several months.

Deterministic transfection drives efficient nonviral reprogramming and uncovers reprogramming barriers.

PubMed

Gallego-Perez, Daniel; Otero, Jose J; Czeisler, Catherine; Ma, Junyu; Ortiz, Cristina; Gygli, Patrick; Catacutan, Fay Patsy; Gokozan, Hamza Numan; Cowgill, Aaron; Sherwood, Thomas; Ghatak, Subhadip; Malkoc, Veysi; Zhao, Xi; Liao, Wei-Ching; Gnyawali, Surya; Wang, Xinmei; Adler, Andrew F; Leong, Kam; Wulff, Brian; Wilgus, Traci A; Askwith, Candice; Khanna, Savita; Rink, Cameron; Sen, Chandan K; Lee, L James

2016-02-01

Safety concerns and/or the stochastic nature of current transduction approaches have hampered nuclear reprogramming's clinical translation. We report a novel non-viral nanotechnology-based platform permitting deterministic large-scale transfection with single-cell resolution. The superior capabilities of our technology are demonstrated by modification of the well-established direct neuronal reprogramming paradigm using overexpression of the transcription factors Brn2, Ascl1, and Myt1l (BAM). Reprogramming efficiencies were comparable to viral methodologies (up to ~9-12%) without the constraints of capsid size and with the ability to control plasmid dosage, in addition to showing superior performance relative to existing non-viral methods. Furthermore, increased neuronal complexity could be tailored by varying BAM ratio and by including additional proneural genes to the BAM cocktail. Furthermore, high-throughput NEP allowed easy interrogation of the reprogramming process. We discovered that BAM-mediated reprogramming is regulated by AsclI dosage, the S-phase cyclin CCNA2, and that some induced neurons passed through a nestin-positive cell stage. In the field of regenerative medicine, the ability to direct cell fate by nuclear reprogramming is an important facet in terms of clinical application. In this article, the authors described their novel technique of cell reprogramming through overexpression of the transcription factors Brn2, Ascl1, and Myt1l (BAM) by in situ electroporation through nanochannels. This new technique could provide a platform for further future designs. Copyright © 2016 Elsevier Inc. All rights reserved.

Backscatter Mossbauer Spectrometer (BaMS) for extraterrestrial applications

NASA Technical Reports Server (NTRS)

Agresti, D. G.; Shelfer, T. D.; Pimperl, M. M.; Wills, E. L.; Shen, M. H.; Morris, R. V.

1993-01-01

Mossbauer spectroscopy is a nuclear gamma resonance technique particularly well suited to the study of materials that contain iron (Fe-57). It can provide information on the oxidation state of iron as well as the type and proportion of iron-containing mineral species in a sample of interest. Iron Mossbauer spectroscopy (FeMS) has been applied to samples believed to have come from Mars (SNC meteorites) and has been helpful in refining the choice among putative Martian surface materials by suggesting a likely nanophase component of the Martian regolity. FeMS spectrum of a Martial analogue material (Hawaiian palagonite) is shown; it is dominated by ferric-bearing phases and shows evidence of a nanophase component. FeMS has also been applied to lunar materials. It can be used to measure the maturity of lunar surface material and has been proposed as a prospector for lunar ilmenite, an oxygen resource mineral. Several years ago we suggested a backscatter Mossbauer spectrometer (BaMS) for a Mars rover mission. Backscatter design was selected as most appropriate for in-situ application because no sample preparation is required. Since that time, we have continued to develop the BaMS instrument in anticipation that it would eventually find a home on a NASA planetary mission. Gooding proposed BaMS as a geochemistry instrument on MESUR. More recently, an LPI workshop has recommended that BaMS be included in a three-instrument payload on the next (1996?) lunar lander.

THE USE OF KETAMINE-XYLAZINE OR BUTORPHANOL-AZAPERONE-MEDETOMIDINE TO IMMOBILIZE AMERICAN BLACK BEARS ( URSUS AMERICANUS).

PubMed

Williamson, Ryan H; Muller, Lisa L; Blair, Coy

2018-04-04

  Wildlife anesthetic protocols must offer rapid inductions and recoveries, be physiologically safe, and be minimally regulated. With this in mind, we evaluated differences in induction and recovery times and physiological parameters in 33 American black bears ( Ursus americanus) anesthetized with ketamine-xylazine (KX) or immobilized with a commercial drug combination of butorphanol, azaperone, and medetomidine (BAM). Dose was based on mass estimated from field observations. Bears were housed at Appalachian Bear Rescue, Townsend, Tennessee, US, or free-ranging within the Great Smoky Mountains National Park (Tennessee and North Carolina, US) and chemically immobilized for management purposes. From 11 April to 29 June 2016, we immobilized bears with injection via pole syringe or disposable dart projected from an air-powered dart rifle. Once immobilized, we measured each bear's temperature, respiration (breaths/min), heart rate (beats/min), hemoglobin oxygen saturation (via pulse oximetry), arterial blood gases, and mass (kg). We found no differences in the induction parameters, partial pressures of CO 2 , and rectal temperatures. The BAM-treated bears had lower heart and respiratory rates that led to lower hemoglobin oxygen saturation levels (from blood gas analysis, SaO 2 ). The SaO 2 after treatment with BAM (91.1±0.8%) was lower than with KX (93.4±0.9%). After handling, we reversed KX-treated bears with a x̄=0.2±0.02 mg/kg yohimbine and BAM-treated bears with x̄=1.5±0.1 mg/kg atipamezole and 0.8±0.1 mg/kg naltrexone. We found no differences in the recovery times to increased respiration and to the bear assuming a head-up position. The BAM-treated bears stood and recovered quicker than did KX-treated animals. Based on our observations, BAM appears to offer safe, predictable immobilizations with fewer drawbacks and faster recovery times than KX-treated bears.

Evaluation of Apoptosis and Autophagy Inducing Potential of Berberis aristata, Azadirachta indica, and Their Synergistic Combinations in Parental and Resistant Human Osteosarcoma Cells

PubMed Central

Sengupta, Pracheta; Raman, Sukanya; Chowdhury, Rajdeep; Lohitesh, K.; Saini, Heena; Mukherjee, Sudeshna; Paul, Atish

2017-01-01

Cancer is a multifactorial disease and hence can be effectively overcome by a multi-constituently therapeutic strategy. Medicinal plant extracts represent a perfect example of such stratagem. However, minimal studies have been done till date that portray the effect of extraction techniques on the phyto-constituent profile of plant extracts and its impact on anticancer activity. In the present study, we have evaluated the anticancer potential of methanolic extracts of Berberis aristata root and Azadirachta indica seeds prepared by various extraction techniques in human osteosarcoma (HOS) cells. Soxhlation extract of B. aristata (BAM-SX) and sonication extract of A. indica (AIM-SO) were most effective in inducing apoptosis in parental drug sensitive, as well as resistant cell type developed by repeated drug exposure. Generation of reactive oxygen species and cell cycle arrest preceded caspase-mediated apoptosis in HOS cells. Interestingly, inhibition of autophagy enhanced cell death suggesting the cytoprotective role of autophagy. Combination studies of different methanolic extracts of BAM and AIM were performed, among which, the combination of BAM-SO and AIM-SO (BAAISO) was found to show synergism (IC50 10.27 µg/ml) followed by combination of BAM-MC and AIM-MC (BAAIMC) with respect to other combinations in the ratio of 1:1. BAAISO also showed synergism when it was added to cisplatin-resistant HOS cells (HCR). Chromatographic profiling of BAM-SX and AIM-SO by high performance thin layer chromatography resulted in identification of berberine (Rf 0.55), palmitine (Rf 0.50) in BAM-SX and azadirachtin A (Rf 0.36), azadirachtin B (Rf 0.56), nimbin (Rf 0.80), and nimbolide (Rf 0.43) in AIM-SO. The cytotoxic sensitivity obtained can be attributed to the above compounds. Our results highlight the importance of extraction technique and subsequent mechanism of action of multi-constituential B. aristata and A. indica against both sensitive and drug refractory HOS cells. PMID:29312880

Evaluation of Apoptosis and Autophagy Inducing Potential of Berberis aristata, Azadirachta indica, and Their Synergistic Combinations in Parental and Resistant Human Osteosarcoma Cells.

PubMed

Sengupta, Pracheta; Raman, Sukanya; Chowdhury, Rajdeep; Lohitesh, K; Saini, Heena; Mukherjee, Sudeshna; Paul, Atish

2017-01-01

Cancer is a multifactorial disease and hence can be effectively overcome by a multi-constituently therapeutic strategy. Medicinal plant extracts represent a perfect example of such stratagem. However, minimal studies have been done till date that portray the effect of extraction techniques on the phyto-constituent profile of plant extracts and its impact on anticancer activity. In the present study, we have evaluated the anticancer potential of methanolic extracts of Berberis aristata root and Azadirachta indica seeds prepared by various extraction techniques in human osteosarcoma (HOS) cells. Soxhlation extract of B. aristata (BAM-SX) and sonication extract of A. indica (AIM-SO) were most effective in inducing apoptosis in parental drug sensitive, as well as resistant cell type developed by repeated drug exposure. Generation of reactive oxygen species and cell cycle arrest preceded caspase-mediated apoptosis in HOS cells. Interestingly, inhibition of autophagy enhanced cell death suggesting the cytoprotective role of autophagy. Combination studies of different methanolic extracts of BAM and AIM were performed, among which, the combination of BAM-SO and AIM-SO (BAAISO) was found to show synergism (IC 50 10.27 µg/ml) followed by combination of BAM-MC and AIM-MC (BAAIMC) with respect to other combinations in the ratio of 1:1. BAAISO also showed synergism when it was added to cisplatin-resistant HOS cells (HCR). Chromatographic profiling of BAM-SX and AIM-SO by high performance thin layer chromatography resulted in identification of berberine (R f 0.55), palmitine (R f 0.50) in BAM-SX and azadirachtin A (R f 0.36), azadirachtin B (R f 0.56), nimbin (R f 0.80), and nimbolide (R f 0.43) in AIM-SO. The cytotoxic sensitivity obtained can be attributed to the above compounds. Our results highlight the importance of extraction technique and subsequent mechanism of action of multi-constituential B. aristata and A. indica against both sensitive and drug refractory HOS cells.

Puzzling with online games (BAM-COG): reliability, validity, and feasibility of an online self-monitor for cognitive performance in aging adults.

PubMed

Aalbers, Teun; Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-12-03

Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. This study examines a new instrument called the Brain Aging Monitor-Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory ("Conveyer Belt"), visuospatial short-term memory ("Sunshine"), episodic recognition memory ("Viewpoint"), and planning ("Papyrinth"). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=-.029 (P=.44), rho=-.029 (P=.45), and rho=-.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=-.162 (P=.21). This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity.

Complex-valued Multidirectional Associative Memory

NASA Astrophysics Data System (ADS)

Kobayashi, Masaki; Yamazaki, Haruaki

Hopfield model is a representative associative memory. It was improved to Bidirectional Associative Memory(BAM) by Kosko and Multidirectional Associative Memory(MAM) by Hagiwara. They have two layers or multilayers. Since they have symmetric connections between layers, they ensure to converge. MAM can deal with multiples of many patterns, such as (x1, x2,…), where xm is the pattern on layer-m. Noest, Hirose and Nemoto proposed complex-valued Hopfield model. Lee proposed complex-valued Bidirectional Associative Memory. Zemel proved the rotation invariance of complex-valued Hopfield model. It means that the rotated pattern also stored. In this paper, the complex-valued Multidirectional Associative Memory is proposed. The rotation invariance is also proved. Moreover it is shown by computer simulation that the differences of angles of given patterns are automatically reduced. At first we define complex-valued Multidirectional Associative Memory. Then we define the energy function of network. By using energy function, we prove that the network ensures to converge. Next, we define the learning law and show the characteristic of recall process. The characteristic means that the differences of angles of given patterns are automatically reduced. Especially we prove the following theorem. In case that only a multiple of patterns is stored, if patterns with different angles are given to each layer, the differences are automatically reduced. Finally, we invest that the differences of angles influence the noise robustness. It reduce the noise robustness, because input to each layer become small. We show that by computer simulations.

Global exponential stability of BAM neural networks with time-varying delays and diffusion terms

NASA Astrophysics Data System (ADS)

Wan, Li; Zhou, Qinghua

2007-11-01

The stability property of bidirectional associate memory (BAM) neural networks with time-varying delays and diffusion terms are considered. By using the method of variation parameter and inequality technique, the delay-independent sufficient conditions to guarantee the uniqueness and global exponential stability of the equilibrium solution of such networks are established.

Learning Systematically from Experience through a Research-to-Practice Pipeline in Chicago

ERIC Educational Resources Information Center

Fine, Wendy; Lansing, Jiffy; Bacon, Marshaun

2018-01-01

The Becoming A Man (BAM) program is a school-based group counseling and mentoring program run by Youth Guidance (YG), a community organization that serves children in Chicago schools who are at risk. BAM guides young men to learn, internalize, and practice social cognitive skills, make responsible decisions for their future, and become positive…

Mei-P26 Cooperates with Bam, Bgcn and Sxl to Promote Early Germline Development in the Drosophila Ovary

PubMed Central

Li, Yun; Zhang, Qiao; Carreira-Rosario, Arnaldo; Maines, Jean Z.; McKearin, Dennis M.; Buszczak, Michael

2013-01-01

In the Drosophila female germline, spatially and temporally specific translation of mRNAs governs both stem cell maintenance and the differentiation of their progeny. However, the mechanisms that control and coordinate different modes of translational repression within this lineage remain incompletely understood. Here we present data showing that Mei-P26 associates with Bam, Bgcn and Sxl and nanos mRNA during early cyst development, suggesting that this protein helps to repress the translation of nanos mRNA. Together with recently published studies, these data suggest that Mei-P26 mediates both GSC self-renewal and germline differentiation through distinct modes of translational repression depending on the presence of Bam. PMID:23526974

Comparison of the Reveal 20-hour method and the BAM culture method for the detection of Escherichia coli O157:H7 in selected foods and environmental swabs: collaborative study.

PubMed

Bird, C B; Hoerner, R J; Restaino, L

2001-01-01

Four different food types along with environmental swabs were analyzed by the Reveal for E. coli O157:H7 test (Reveal) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli O157:H7. Twenty-seven laboratories representing academia and private industry in the United States and Canada participated. Sample types were inoculated with E. coli O157:H7 at 2 different levels. Of the 1,095 samples and controls analyzed and confirmed, 459 were positive and 557 were negative by both methods. No statistical differences (p <0.05) were observed between the Reveal and BAM methods.

Surface Ruptures and Building Damage of the 2003 Bam, Iran, Earthquake Mapped by Satellite Synthetic Aperture Radar Interferometric Correlation

NASA Technical Reports Server (NTRS)

Fielding, Eric J.; Talebian, M.; Rosen, P. A.; Nazari, H.; Jackson, J. A.; Ghorashi, M.; Walker, R.

2005-01-01

We use the interferometric correlation from Envisat synthetic aperture radar (SAR) images to map the details of the surface ruptures related to the 26 December 2003 earthquake that devastated Bam, Iran. The main strike-slip fault rupture south of the city of Bam has a series of four segments with left steps shown by a narrow line of low correlation in the coseismic interferogram. This also has a clear expression in the field because of the net extension across the fault. Just south of the city limits, the surface strain becomes distributed over a width of about 500 m, probably because of a thicker layer of soft sedimentary material.

Epitaxial Growth and Electronic Structure of Half Heuslers Co1-xNixTiSb (001), Ni1-xCoxTiSn, and PtLuSb

DTIC Science & Technology

2016-01-09

studied in detail using scanning tunneling microscopy and angle resolved photoemission. For the doping levels achieved in cobalt titanium antimony, the...angle resolved photoemission. For the doping levels achieved in cobalt titanium antimony, the electron mobility at room temperature was comparable...scanning tunneling microscopy and angle resolved photoemission. For the doping levels achieved in cobalt titanium antimony, the electron mobility at room

Bile acid malabsorption in persistent diarrhoea.

PubMed

Smith, M J; Cherian, P; Raju, G S; Dawson, B F; Mahon, S; Bardhan, K D

2000-01-01

We have investigated bile acid malabsorption (BAM), and its response to treatment, in patients seen in this district general hospital with chronic continuous or recurrent diarrhoea. Seven-day retention of 75-SeHCAT was measured (normal: > 10%). Patients were initially given conventional therapy (prednisolone +/- ASA drugs in Crohn's disease, and antidiarrhoeals in the others). If this therapy failed, bile acid sequestrants (BAS) were prescribed. The definition of successful response was based on the patient's perception of sustained improvement. The 304 patients were categorised as follows: Group 1: Crohn's disease patients with ileal resection, in clinical remission (n = 37). Group 2: Crohn's disease, unoperated and in clinical remission (n = 44). Group 3: vagotomy and pyloroplasty, with/without cholecystectomy (n = 26). Group 4: diarrhoea predominant 'irritable bowel syndrome' (IBS) (n = 197). BAM was found in 97% (36/37), 54% (24/44) and 58% (15/26) of patients in groups 1, 2 and 3 respectively. One third (65/197) of patients with IBS had BAM. The outcome of treatment was available in 96 patients with BAM: of the patients with ileal resection 32% responded to antidiarrhoeals, 60% to BAS. Of the unoperated Crohn's patients 55% responded to disease-specific therapy, 40% to BAS. Of the gastric surgery patients 18% responded to conventional treatment, 64% to BAS. Of the IBS patients 15% of responded to conventional therapy, 70% to BAS. This observational study indicates that BAM is common in patients with chronic diarrhoea, and is frequently found in IBS. The results of open treatment suggest that, where antidiarrhoeal drugs fail in such patients, BAS are often effective.

USDA FSIS, FDA BAM, and ISO culture methods BD BBL CHROMagar O157 media.

PubMed

Ritter, Vicki; Kircher, Susan; Dick, Nancy

2009-01-01

BBL CHROMagar O157 media (CO) was evaluated for detection of Escherichia coli O157:H7 in raw ground beef and unpasteurized apple cider. The recovery of E. coli O157:H7 on CO was compared to the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM), U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS), and International Organization for Standardization (ISO) reference-plated media using the recommended enrichment broths. Of the 180 food samples tested, 45 were tested using BAM, 45 using the USDA method, and 90 using the ISO method. CO produced comparable results with the reference methods on all matrixes with a sensitivity of 100% and a specificity of 100%. No false negatives were found in testing the food matrixes. There was no statistical difference in recovery based on Chi-square analysis. Method agreement for raw ground beef was 85% for the USDAFSIS method and 95% for the ISO method. Method agreement for unpasteurized apple cider was 100% for the ISO and FDA BAM methods. In all cases where method agreement was <100%, CO detected more positives than the reference method media. Evaluation of known isolates on CO in inclusivity and exclusivity testing had a sensitivity and specificity of 100%. The results of this study demonstrate that CO is an effective medium for the recovery and detection of E. coli O157:H7 in raw ground beef and unpasteurized apple cider using FDA BAM, USDA FSIS, and ISO methods.

Induced formation and maturation of acetylcholine receptor clusters in a defined 3D bio-artificial muscle.

PubMed

Wang, Lin; Shansky, Janet; Vandenburgh, Herman

2013-12-01

Dysfunction of the neuromuscular junction is involved in a wide range of muscular diseases. The development of neuromuscular junction through which skeletal muscle is innervated requires the functional modulation of acetylcholine receptor (AchR) clustering on myofibers. However, studies on AchR clustering in vitro are mostly done on monolayer muscle cell culture, which lacks a three-dimensional (3D) structure, a prominent limitation of the two-dimensional (2D) system. To enable a better understanding on the structure-function correlation underlying skeletal muscle innervation, a muscle system with a well-defined geometry mimicking the in vivo muscular setting is needed. Here, we report a 3D bio-artificial muscle (BAM) bioengineered from green fluorescent protein-transduced C3H murine myoblasts as a novel in vitro tissue-based model for muscle innervation studies. Our cell biological and molecular analysis showed that this BAM is structurally similar to in vivo muscle tissue and can reach the perinatal differentiation stage, higher than does 2D culture. Effective clustering and morphological maturation of AchRs on BAMs induced by agrin and laminin indicate the functional activity and plasticity of this BAM system toward innervation. Taken together, our results show that the BAM provides a favorable 3D environment that at least partially recapitulates real physiological skeletal muscle with regard to innervation. With a convenience of fabrication and manipulation, this 3D in vitro system offers a novel model for studying mechanisms underlying skeletal muscle innervation and testing therapeutic strategies for relevant nervous and muscular diseases.

Assessment of butorphanol-azaperone-medetomidine combination as anesthesia for semen collection and evaluation of semen quality in white-tailed deer (Odocoileus virginianus).

PubMed

Kirschner, S M; Rodenkirch, R

2017-09-01

The aim of this current study was to evaluate the level of anesthesia produced by a combination of butorphanol-azaperone-medetomidine (BAM) for semen collection by electroejaculation on captive white-tailed bucks (Odocoileus virginianus). Ten male white-tailed deer, weighing 68.2-115.9kg, ranging in age from one to four years were randomly selected from housing pens and anesthetized with the BAM drug combination at a dose volume of 2.0mL each. Semen was collected from each animal using a standard cervid electroejaculation protocol while under BAM anesthesia. Physiological data was recorded following induction of anesthesia and during semen collection. Collected ejaculates were prepared for analysis using a standard extender protocol for cryopreservation. Eleven sperm viability parameters were quantified for each sample using a Computerized Assisted Sperm Analysis system, including total seminal volume; sperm concentration and total sperm number. kinematic parameters of motile spermatozoa were also assessed. Results demonstrated that BAM provided an effective plane of anesthesia for successful collection of viable sperm. Measured physiological variables of heart rate, respiration and body temperature all remained within safe, normal limits. Data recorded on semen characteristics from all collected ejaculates correlated well with key traits determined to be important for successful fertilization through measurement of total semen volume; sperm concentration; total sperm number; and kinematic parameters of motile spermatozoa. There were no serious adverse events. This field study indicates that BAM anesthesia is suitable for semen collection in white-tailed deer. Copyright © 2017 Elsevier B.V. All rights reserved.

Fault Mechanics and Post-seismic Deformation at Bam, SE Iran

NASA Astrophysics Data System (ADS)

Wimpenny, S. E.; Copley, A.

2017-12-01

The extent to which aseismic deformation relaxes co-seismic stress changes on a fault zone is fundamental to assessing the future seismic hazard following any earthquake, and in understanding the mechanical behaviour of faults. We used models of stress-driven afterslip and visco-elastic relaxation, in conjunction with a dense time series of post-seismic InSAR measurements, to show that there has been minimal release of co-seismic stress changes through post-seismic deformation following the 2003 Mw 6.6 Bam earthquake. Our modelling indicates that the faults at Bam may remain predominantly locked, and that the co- plus inter-seismically accumulated elastic strain stored down-dip of the 2003 rupture patch may be released in a future Mw 6 earthquake. Modelling also suggests parts of the fault that experienced post-seismic creep between 2003-2009 overlapped with areas that also slipped co-seismically. Our observations and models also provide an opportunity to probe how aseismic fault slip leads to the growth of topography at Bam. We find that, for our modelled afterslip distribution to be consistent with forming the sharp step in the local topography at Bam over repeated earthquake cycles, and also to be consistent with the geodetic observations, requires either (1) far-field tectonic loading equivalent to a 2-10 MPa deviatoric stress acting across the fault system, which suggests it supports stresses 60-100 times less than classical views of static fault strength, or (2) that the fault surface has some form of mechanical anisotropy, potentially related to corrugations on the fault plane, that controls the sense of slip.

Fluorescence microscopy for measuring fibril angles in pine tracheids

Treesearch

Ralph O. Marts

1955-01-01

Observation and measurement of fibril angles in increment cores or similar small samples from living pine trees was facilitated by the use of fluorescence microscopy. Although some autofluorescence was present, brighter images could be obtained by staining the specimens with a 0.1% aqueous solution of a fluorochrome (Calcozine flavine TG extra concentrated, Calcozine...

Global Hopf bifurcation analysis on a BAM neural network with delays

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Han, Maoan; Pang, Xiaoming

2007-01-01

A delayed differential equation that models a bidirectional associative memory (BAM) neural network with four neurons is considered. By using a global Hopf bifurcation theorem for FDE and a Bendixon's criterion for high-dimensional ODE, a group of sufficient conditions for the system to have multiple periodic solutions are obtained when the sum of delays is sufficiently large.

Impact of Stress Reduction Interventions on Hostility and Ambulatory Systolic Blood Pressure in African American Adolescents

ERIC Educational Resources Information Center

Wright, Lynda Brown; Gregoski, Mathew J.; Tingen, Martha S.; Barnes, Vernon A.; Treiber, Frank A.

2011-01-01

This study examined the impact of breathing awareness meditation (BAM), life skills (LS) training, and health education (HE) interventions on self-reported hostility and 24-hour ambulatory blood pressure (ABP) in 121 African American (AA) ninth graders at increased risk for development of essential hypertension. They were randomly assigned to BAM,…

Recent advances in the understanding of bile acid malabsorption.

PubMed

Pattni, Sanjeev; Walters, Julian R F

2009-01-01

Bile acid malabsorption (BAM) is a syndrome of chronic watery diarrhoea with excess faecal bile acids. Disruption of the enterohepatic circulation of bile acids following surgical resection is a common cause of BAM. The condition is easily diagnosed by the selenium homocholic acid taurine (SeHCAT) test and responds to bile acid sequestrants. Idiopathic BAM (IBAM, primary bile acid diarrhoea) is the condition where no definitive cause for low SeHCAT retention can be identified. Review of PubMed and major journals. Evidence is accumulating that BAM is more prevalent than first thought. Management of chronic diarrhoea involves excluding secondary causes. Treatment of the condition is with bile acid binders. SeHCAT testing is not widely performed, limiting awareness of how common this condition can be. The underlying mechanism for IBAM has been unclear. Increasing awareness of the condition is important. Alternative mechanisms of IBAM have been suggested which involve an increased bile acid pool size and reduced negative feedback regulation of bile acid synthesis by FGF19. New sequestrants are available. Further research into the precise mechanism of IBAM is needed. Improvements in the recognition of the condition and optimization of treatment are required.

Colonoscopy and SeHCAT for investigation of chronic diarrhea.

PubMed

Müller, Marcella; Willén, Roger; Stotzer, Per-Ove

2004-01-01

Chronic diarrhea is a common problem. Colonoscopy is the investigation of choice for diagnosis. Even a macroscopically normal mucosa on endoscopy can have abnormalities such as microscopic colitis and bile acid malabsorption (BAM). The aim of this study was to establish the value of colonoscopy with biopsies in patients with chronic diarrhea and to evaluate the additive value of a SeHCAT test for diagnosing BAM in these patients. All patients who underwent a colonoscopy between November 1999 and December 2000 were included. Patient files, colonoscopy and pathology reports and SeHCAT test results were reviewed. 205 patients were included. The most common diagnoses were diarrhea-predominant IBS (n = 76) and IBD (n = 38). 158 patients had non-bloody diarrhea, 113 (72%) of them had a macroscopically normal appearing mucosa. In 40 (35%) of these patients, a histological diagnosis could be made and microscopic colitis was the most common diagnosis (n = 27). SeHCAT test was performed in 36 patients and 15 (42%) of them had BAM. In the 47 patients with bloody diarrhea, IBD was the main diagnosis (n = 23). Colonoscopy with biopsies must be performed when investigating chronic diarrhea and BAM should be excluded.

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Dimension dependence of clustering dynamics in models of ballistic aggregation and freely cooling granular gas

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2018-03-01

Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation. In addition, in the high packing fraction limit the behavior of these quantities become consistent with a scaling theory that predicts an inverse relation between energy and mass. On the other hand, in the case of the GGM we do not find any evidence for such a picture. In this case, even though the energy decay, irrespective of packing fraction, matches quantitatively with that for the high packing fraction picture of the BAM, it is inversely proportional to the growth of mass only in one dimension, and the growth appears to be rather insensitive to the choice of the dimension, unlike the BAM.

proBAMconvert: A Conversion Tool for proBAM/proBed.

PubMed

Olexiouk, Volodimir; Menschaert, Gerben

2017-07-07

The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at http://probam.biobix.be .

Global asymptotic stability to a generalized Cohen-Grossberg BAM neural networks of neutral type delays.

PubMed

Zhang, Zhengqiu; Liu, Wenbin; Zhou, Dongming

2012-01-01

In this paper, we first discuss the existence of a unique equilibrium point of a generalized Cohen-Grossberg BAM neural networks of neutral type delays by means of the Homeomorphism theory and inequality technique. Then, by applying the existence result of an equilibrium point and constructing a Lyapunov functional, we study the global asymptotic stability of the equilibrium solution to the above Cohen-Grossberg BAM neural networks of neutral type. In our results, the hypothesis for boundedness in the existing paper, which discussed Cohen-Grossberg neural networks of neutral type on the activation functions, are removed. Finally, we give an example to demonstrate the validity of our global asymptotic stability result for the above neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Multicenter Prospective Study to Investigate the Diagnostic Accuracy of the SeHCAT Test in Measuring Bile Acid Malabsorption: Research Protocol

PubMed Central

Peacock, Janet; Coker, Bola; McMillan, Viktoria; Lewis, Cornelius; Keevil, Stephen; Sherwood, Roy; Vivian, Gill; Logan, Robert; Summers, Jennifer

2016-01-01

Background Bile acid malabsorption (BAM) is one possible explanation for chronic diarrhea. BAM may be idiopathic, or result from ileal resection or inflammation including Crohn’s disease, or may be secondary to other conditions, including cholecystectomy, peptic ulcer surgery, and chronic pancreatitis. No “gold standard” exists for clinical diagnosis of BAM, but response to treatment with a bile acid sequestrant (BAS) is often accepted as confirmation. The SeHCAT (tauroselcholic [selenium-75] acid) test uses a radiolabeled synthetic bile acid and provides a diagnostic test for BAM, but its performance against “trial of treatment” is unknown. Fibroblast growth factor 19 (FGF-19) and 7-alpha-hydroxy-4-cholesten-3-one (C4) also offer potential new biomarkers of BAM. Objective This protocol describes a multicenter prospective study to evaluate the diagnostic accuracy of SeHCAT and 2 biomarkers in predicting BAM as assessed by trial of treatment. Methods Participating gastroenterology centers should have a minimum workload of 30 SeHCAT patients per annum. Patients should not be pregnant, on medication that could confound follow-up, or have any severe comorbidity. All eligible patients attending a gastrointestinal appointment will be invited to participate. On attending the SeHCAT test, blood and fecal samples will be collected for analysis of FGF-19 by enzyme-linked immunosorbent assay and for C4 and fractionated bile acids by liquid chromatography–mass spectrometry. A capsule containing radiolabeled SeHCAT will be administered orally and a scan performed to measure SeHCAT activity. Patients will return on day 7 to undergo a second scan to measure percentage SeHCAT retention. The test result will be concealed from clinicians and patients. BAS will be dispensed to all patients, with a follow-up gastroenterologist appointment at 2 weeks for clinical assessment of treatment response and adherence. Patients responding positively will continue treatment for a further 2 weeks and all patients will have a final follow-up at 8 weeks. The diagnostic accuracy of the SeHCAT test and biomarkers will be analyzed at different thresholds using sensitivity, specificity, positive and negative predictive value, likelihood ratios, and area under the curve in a sample of 600 patients. Multivariable logistic regression models will be used to assess the association between presence of BAM and continuous SeHCAT retention levels after adjustment for confounders. Results Funding is being sought to conduct this research. Conclusions The SeHCAT test for diagnosis of BAM has been in common use in the United Kingdom for more than 30 years and an evidence-based assessment of its accuracy is overdue. The proposed study has some challenges. Some forms of BAS treatment are unpleasant due to the texture and taste of the resin powder, which may negatively affect recruitment and treatment adherence. Trial of treatment is not as “golden” a standard as would be ideal, and itself warrants further study. PMID:26832436

A Multicenter Prospective Study to Investigate the Diagnostic Accuracy of the SeHCAT Test in Measuring Bile Acid Malabsorption: Research Protocol.

PubMed

Reid, Fiona; Peacock, Janet; Coker, Bola; McMillan, Viktoria; Lewis, Cornelius; Keevil, Stephen; Sherwood, Roy; Vivian, Gill; Logan, Robert; Summers, Jennifer

2016-02-01

Bile acid malabsorption (BAM) is one possible explanation for chronic diarrhea. BAM may be idiopathic, or result from ileal resection or inflammation including Crohn's disease, or may be secondary to other conditions, including cholecystectomy, peptic ulcer surgery, and chronic pancreatitis. No "gold standard" exists for clinical diagnosis of BAM, but response to treatment with a bile acid sequestrant (BAS) is often accepted as confirmation. The SeHCAT (tauroselcholic [selenium-75] acid) test uses a radiolabeled synthetic bile acid and provides a diagnostic test for BAM, but its performance against "trial of treatment" is unknown. Fibroblast growth factor 19 (FGF-19) and 7-alpha-hydroxy-4-cholesten-3-one (C4) also offer potential new biomarkers of BAM. This protocol describes a multicenter prospective study to evaluate the diagnostic accuracy of SeHCAT and 2 biomarkers in predicting BAM as assessed by trial of treatment. Participating gastroenterology centers should have a minimum workload of 30 SeHCAT patients per annum. Patients should not be pregnant, on medication that could confound follow-up, or have any severe comorbidity. All eligible patients attending a gastrointestinal appointment will be invited to participate. On attending the SeHCAT test, blood and fecal samples will be collected for analysis of FGF-19 by enzyme-linked immunosorbent assay and for C4 and fractionated bile acids by liquid chromatography-mass spectrometry. A capsule containing radiolabeled SeHCAT will be administered orally and a scan performed to measure SeHCAT activity. Patients will return on day 7 to undergo a second scan to measure percentage SeHCAT retention. The test result will be concealed from clinicians and patients. BAS will be dispensed to all patients, with a follow-up gastroenterologist appointment at 2 weeks for clinical assessment of treatment response and adherence. Patients responding positively will continue treatment for a further 2 weeks and all patients will have a final follow-up at 8 weeks. The diagnostic accuracy of the SeHCAT test and biomarkers will be analyzed at different thresholds using sensitivity, specificity, positive and negative predictive value, likelihood ratios, and area under the curve in a sample of 600 patients. Multivariable logistic regression models will be used to assess the association between presence of BAM and continuous SeHCAT retention levels after adjustment for confounders. Funding is being sought to conduct this research. The SeHCAT test for diagnosis of BAM has been in common use in the United Kingdom for more than 30 years and an evidence-based assessment of its accuracy is overdue. The proposed study has some challenges. Some forms of BAS treatment are unpleasant due to the texture and taste of the resin powder, which may negatively affect recruitment and treatment adherence. Trial of treatment is not as "golden" a standard as would be ideal, and itself warrants further study.

The effect of repeated lateral compression and expansions mimicking blinking on selected tear film polar lipid monofilms.

PubMed

Patterson, Matthew; Vogel, Hans J; Prenner, Elmar J

2017-03-01

The tear film lipid layer is formed on the anterior surface of the eye, functioning as a barrier to excess evaporation and foreign particles, while also providing stability to the tear film. The lipid layer is organized into a polar lipid layer consisting of phospholipids, ceramides, and free fatty acids that act as a surfactant to a non-polar multilayer of wax and cholesterol esters. Due to shear forces from eye movement and the compression and expansion of blinking, the tear lipids are under constant stress. However, tear film is able to resist immediate rupture and remains intact over multiple blinks. This work aimed to better understand the lateral organization of selected tear film polar lipids. The polar lipid biomimetic studied here consisted of dipalmitoyl phosphatidylcholine (DPPC), dipalmitoyl phosphatidylethanolamine (DPPE), palmitoyl glucosylceramide (PGC), and palmitoyl sphingomyelin (PSM). Surface pressure-area isocycles mimicked blinking and films were visualized by Brewster angle microscopy (BAM). All lipid systems formed relatively reversible films as indicated by limited hysteresis. However, pure DPPC and PSM films experienced greater changes in lipid packing upon compression and expansion compared to pure PGC and DPPE. This suggests that the driving force behind maintaining the lateral organization of the polar lipids from tear film may be the hydrogen bonding propensities of the head groups. Additionally, isocycles of films containing DPPC, DPPE, and PGC mixtures exhibited evidence for reversible multilayer formation or folding. This was supported by 3D analysis of structures that formed during compression but reintegrated back into the bulk lipid film during expansion near the in vitro tear film surface pressure of the open eye. Therefore, the polar lipids of tear film may be directly involved in preventing film rupture during a blink. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of calcium on ceramide-1-phosphate monolayers

PubMed Central

Brezesinski, Gerald; Hill, Alexandra; Gericke, Arne

2016-01-01

Summary Ceramide-1-phosphate (C1P) plays an important role in several biological processes, being identified as a key regulator of many protein functions. For instance, it acts as a mediator of inflammatory responses. The mediation of the inflammation process happens due to the interaction of C1P with the C2 domain of cPLA2α, an effector protein that needs the presence of submicromolar concentrations of calcium ions. The aim of this study was to determine the phase behaviour and structural properties of C1P in the presence and absence of millimolar quantities of calcium in a well-defined pH environment. For that purpose, we used monomolecular films of C1P at the soft air/liquid interface with calcium ions in the subphase. The pH was varied to change the protonation degree of the C1P head group. We used surface pressure versus molecular area isotherms coupled with other monolayer techniques as Brewster angle microscopy (BAM), infrared reflection–absorption spectroscopy (IRRAS) and grazing incidence X-ray diffraction (GIXD). The isotherms indicate that C1P monolayers are in a condensed state in the presence of calcium ions, regardless of the pH. At higher pH without calcium ions, the monolayer is in a liquid-expanded state due to repulsion between the negatively charged phosphate groups of the C1P molecules. When divalent calcium ions are added, they are able to bridge the highly charged phosphate groups, enhancing the regular arrangement of the head groups. Similar solidification of the monolayer structure can be seen in the presence of a 150 times larger concentration of monovalent sodium ions. Therefore, calcium ions have clearly a strong affinity for the phosphomonoester of C1P. PMID:26977381

Thermodynamic versus non-equilibrium stability of palmitic acid monolayers in calcium-enriched sea spray aerosol proxy systems.

PubMed

Wellen Rudd, Bethany A; Vidalis, Andrew S; Allen, Heather C

2018-04-16

Of the major cations in seawater (Na+, Mg2+, Ca2+, K+), Ca2+ is found to be the most enriched in fine sea spray aerosols (SSA). In this work, we investigate the binding of Ca2+ to the carboxylic acid headgroup of palmitic acid (PA), a marine-abundant fatty acid, and the impact such binding has on the stability of PA monolayers in both equilibrium and non-equilibrium systems. A range of Ca2+ conditions from 10 μM to 300 mM was utilized to represent the relative concentration of Ca2+ in high and low relative humidity aerosol environments. The CO2- stretching modes of PA detected by surface-sensitive infrared reflection-absorption spectroscopy (IRRAS) reveal ionic binding motifs of the Ca2+ ion to the carboxylate group with varying degrees of hydration. Surface tensiometry was used to determine the thermodynamic equilibrium spreading pressure (ESP) of PA on the various aqueous CaCl2 subphases. Up to concentrations of 1 mM Ca2+, each system reached equilibrium, and Ca2+:PA surface complexation gave rise to a lower energy state revealed by elevated surface pressures relative to water. We show that PA films are not thermodynamically stable at marine aerosol-relevant Ca2+ concentrations ([Ca2+] ≥ 10 mM). IRRAS and vibrational sum frequency generation (VSFG) spectroscopy were used to investigate the surface presence of PA on high concentration Ca2+ aqueous subphases. Non-equilibrium relaxation (NER) experiments were also conducted and monitored by Brewster angle microscopy (BAM) to determine the effect of the Ca2+ ions on PA stability. At high surface pressures, the relaxation mechanisms of PA varied among the systems and were dependent on Ca2+ concentration.

Puzzling With Online Games (BAM-COG): Reliability, Validity, and Feasibility of an Online Self-Monitor for Cognitive Performance in Aging Adults

PubMed Central

Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-01-01

Background Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. Objective This study examines a new instrument called the Brain Aging Monitor–Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. Methods The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory (“Conveyer Belt”), visuospatial short-term memory (“Sunshine”), episodic recognition memory (“Viewpoint”), and planning (“Papyrinth”). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Results Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=−.029 (P=.44), rho=−.029 (P=.45), and rho=−.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=−.162 (P=.21). Conclusions This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity. PMID:24300212

Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

PubMed

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

2017-07-26

Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function.Comprehensive protein-protein interaction (PPI) analysis among viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins using multi-vector yeast two-hybrid screening that was further supported by co-immunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize on the biological role localization within the viral particle of some viral ORFan proteins that will be helpful for understanding the biology of Gram-positive tectivirus. Copyright © 2017 American Society for Microbiology.

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

PubMed Central

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter

2017-01-01

ABSTRACT The family Tectiviridae comprises a group of tailless, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria. In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing knowledge about the viral proteome, we carried out a comprehensive yeast two-hybrid analysis of all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprised 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggest that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, with the latter finding also being supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving nonstructural proteins, such as the DNA-binding protein P1 and the genome terminal protein (P4), which was confirmed by coimmunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tailless viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function. Comprehensive protein-protein interaction (PPI) analysis of viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins determined using multivector yeast two-hybrid screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological role of the localization of some viral ORFan proteins within the viral particle that will be helpful for understanding the biology of tectiviruses infecting Gram-positive bacteria. PMID:28747494

Chemical modification of Nafion membranes by protic ionic liquids: the key role of ionomer-cation interactions.

PubMed

Lu, Fei; Gao, Xinpei; Xie, Shuting; Sun, Nan; Zheng, Liqiang

2014-10-21

Chemically modified Nafion composite membranes were successfully fabricated using five kinds of protic ionic liquids (PILs) with different cations, 1-butylammonium methanesulfonate (BA-MS), tributylammonium methanesulfonate (TBA-MS), 2,4,6-trimethylphenylammonium methanesulfonate (TMA-MS), butane-1,4-diammonium methanesulfonate (BDA-MS), and N-(2-aminoethyl)ethane-1,2-diammonium methanesulfonate (DETA-MS). The PIL incorporated Nafion composite membranes were characterized by impedance spectroscopy, small-angle X-ray scattering (SAXS), dynamic-mechanical analysis (DMA) and thermogravimetric analysis (TGA). In general, the Nafion/PIL composite membranes exhibit a significant increase in the ionic conductivities than Nafion under anhydrous conditions. The interactions between the Nafion ionomer and different geometric cations of PILs were also discussed by the comparison of nanostructures, dynamic-mechanical properties and thermal stabilities of the Nafion/PIL composite membranes.

An ABC of Drumming: Children's Narratives about Beat, Rhythm and Groove in a Primary Classroom

ERIC Educational Resources Information Center

Mackinlay, Elizabeth

2014-01-01

In this paper, I use a bricolage of arts-based research and writing practices to explore narratives by Grade 4 children about their experiences in a drumming circle called "Bam Bam" as represented in a text they created with me called An ABC of drumming. The term "narrative" is used here in a contemporary sense to…

Transcriptional activity across the Epstein-Barr virus genome in Raji cells during latency and after induction of an abortive lytic cycle.

PubMed

Kirchner, E A; Bornkamm, G W; Polack, A

1991-10-01

We have studied the relative rate of transcription across the Epstein-Barr virus genome in the Burkitt's lymphoma cell line Raji by nuclear run-on analysis during latency and after induction of an abortive lytic cycle with 12-0-tetradecanoylphorbol 13-acetate (TPA) and 5-iodo-2'-deoxyuridine (IUdR). During latency the entire, or almost the entire, viral genome was found to be transcriptionally active to a low or intermediate extent, with some variation in activity along the genome. The fragment with the highest transcriptional activity was EcoRI J, which contains the genes encoding the small nuclear RNAs EBER1 and -2, transcribed predominantly by RNA polymerase III. An intermediate level of transcription was observed between positions 10 and 138 (kb), with areas of slightly higher activity on the large internal repeats and the left duplicated region (DL). The remaining part of the viral genome, between position 138 and the termini, and the termini and position 10 (kb) (with the exception of the EcoRI J fragment), showed very little transcriptional activity, except for the intermediately active regions carrying the righthand oriLyt (DR) and the terminal repeats. Upon induction of the viral genome with TPA and IUdR, the viral genome was transcriptionally active at a rate at least tenfold that seen during latency. Polymerases were not equally distributed along the genome after induction; the highest density was found in regions 48 to 58 kb, 82 to 84 kb, 102 to 104 kb, 118 to 122 kb and 142 to 145 kb of the viral genome. High transcriptional activity correlated with distinct transcription units in some cases, i.e. BamHI H1LF1 (DL), BamHI MLF1, BamHI ZLF1/BamHI RLF1 and BamHI X (thymidine kinase), but not in others (BamHI H2). Besides initiation of transcription, other regulatory processes such as stabilization and processing of primary transcripts may also contribute to regulation of virus gene expression. Addition of cycloheximide completely abolished the transcriptional activation of the genome mediated by TPA and IUdR.

Methods for diagnosis of bile acid malabsorption in clinical practice.

PubMed

Vijayvargiya, Priya; Camilleri, Michael; Shin, Andrea; Saenger, Amy

2013-10-01

Altered concentrations of bile acid (BA) in the colon can cause diarrhea or constipation. More than 25% of patients with irritable bowel syndrome with diarrhea or chronic diarrhea in Western countries have BA malabsorption (BAM). As BAM is increasingly recognized, proper diagnostic methods are needed to help direct the most effective course of treatment for the chronic bowel dysfunction. We review the methodologies, advantages, and disadvantages of tools that directly measure BAM: the (14)C-glycocholate breath and stool test, the (75)selenium homotaurocholic acid test (SeHCAT), and measurements of 7 α-hydroxy-4-cholesten-3-one (C4) and fecal BAs. The (14)C-glycocholate test is laborious and no longer widely used. The (75)SeHCAT has been validated but is not available in the United States. Measurement of serum C4 is a simple and accurate method that can be used for most patients but requires further clinical validation. Assays to quantify fecal BA (total and individual levels) are technically cumbersome and not widely available. Regrettably, none of these tests are routinely available in the United States; assessment of the therapeutic effects of a BA binder is used as a surrogate for diagnosis of BAM. Recent data indicate the advantages to studying fecal excretion of individual BAs and their role in BAM; these could support the use of the fecal BA assay, compared with other tests. Measurement of fecal BA levels could become a routine addition to the measurement of fecal fat in patients with unexplained diarrhea. Availability ultimately determines whether the C4, SeHCAT, or fecal BA test is used; more widespread availability of such tests would enhance clinical management of these patients. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

Diagnostic Methods for Bile Acid Malabsorption in Clinical Practice

PubMed Central

Vijayvargiya, Priya; Camilleri, Michael; Shin, Andrea; Saenger, Amy

2013-01-01

Altered bile acid (BA) concentrations in the colon may cause diarrhea or constipation. BA malabsorption (BAM) accounts for >25% of patients with irritable bowel syndrome (IBS) with diarrhea and chronic diarrhea in Western countries. As BAM is increasingly recognized, proper diagnostic methods are desired in clinical practice to help direct the most effective treatment course for the chronic bowel dysfunction. This review appraises the methodology, advantages and disadvantages of 4 tools that directly measure BAM: 14C-glycocholate breath and stool test, 75Selenium HomotauroCholic Acid Test (SeHCAT), 7 α-hydroxy-4-cholesten-3-one (C4) and fecal BAs. 14C-glycocholate is a laborious test no longer widely utilized. 75SeHCAT is validated, but not available in the United States. Serum C4 is a simple, accurate method that is applicable to a majority of patients, but requires further clinical validation. Fecal measurements to quantify total and individual fecal BAs are technically cumbersome and not widely available. Regrettably, none of these tests are routinely available in the U.S., and a therapeutic trial with a BA binder is used as a surrogate for diagnosis of BAM. Recent data suggest there is an advantage to studying fecal excretion of the individual BAs and their role in BAM; this may constitute a significant advantage of the fecal BA method over the other tests. Fecal BA test could become a routine addition to fecal fat measurement in patients with unexplained diarrhea. In summary, availability determines the choice of test among C4, SeHCAT and fecal BA; more widespread availability of such tests would enhance clinical management of these patients. PMID:23644387

Comparing rapid methods for detecting Listeria in seafood and environmental samples using the most probably number (MPN) technique.

PubMed

Cruz, Cristina D; Win, Jessicah K; Chantarachoti, Jiraporn; Mutukumira, Anthony N; Fletcher, Graham C

2012-02-15

The standard Bacteriological Analytical Manual (BAM) protocol for detecting Listeria in food and on environmental surfaces takes about 96 h. Some studies indicate that rapid methods, which produce results within 48 h, may be as sensitive and accurate as the culture protocol. As they only give presence/absence results, it can be difficult to compare the accuracy of results generated. We used the Most Probable Number (MPN) technique to evaluate the performance and detection limits of six rapid kits for detecting Listeria in seafood and on an environmental surface compared with the standard protocol. Three seafood products and an environmental surface were inoculated with similar known cell concentrations of Listeria and analyzed according to the manufacturers' instructions. The MPN was estimated using the MPN-BAM spreadsheet. For the seafood products no differences were observed among the rapid kits and efficiency was similar to the BAM method. On the environmental surface the BAM protocol had a higher recovery rate (sensitivity) than any of the rapid kits tested. Clearview™, Reveal®, TECRA® and VIDAS® LDUO detected the cells but only at high concentrations (>10(2) CFU/10 cm(2)). Two kits (VIP™ and Petrifilm™) failed to detect 10(4) CFU/10 cm(2). The MPN method was a useful tool for comparing the results generated by these presence/absence test kits. There remains a need to develop a rapid and sensitive method for detecting Listeria in environmental samples that performs as well as the BAM protocol, since none of the rapid tests used in this study achieved a satisfactory result. Copyright © 2011 Elsevier B.V. All rights reserved.

pth moment exponential stability of stochastic memristor-based bidirectional associative memory (BAM) neural networks with time delays.

PubMed

Wang, Fen; Chen, Yuanlong; Liu, Meichun

2018-02-01

Stochastic memristor-based bidirectional associative memory (BAM) neural networks with time delays play an increasingly important role in the design and implementation of neural network systems. Under the framework of Filippov solutions, the issues of the pth moment exponential stability of stochastic memristor-based BAM neural networks are investigated. By using the stochastic stability theory, Itô's differential formula and Young inequality, the criteria are derived. Meanwhile, with Lyapunov approach and Cauchy-Schwarz inequality, we derive some sufficient conditions for the mean square exponential stability of the above systems. The obtained results improve and extend previous works on memristor-based or usual neural networks dynamical systems. Four numerical examples are provided to illustrate the effectiveness of the proposed results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermal treatment of the minority game

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P.

2002-03-01

We study a cost function for the aggregate behavior of all the agents involved in the minority game (MG) or the bar attendance model (BAM). The cost function allows us to define a deterministic, synchronous dynamic that yields results that have the main relevant features than those of the probabilistic, sequential dynamics used for the MG or the BAM. We define a temperature through a Langevin approach in terms of the fluctuations of the average attendance. We prove that the cost function is an extensive quantity that can play the role of an internal energy of the many-agent system while the temperature so defined is an intensive parameter. We compare the results of the thermal perturbation to the deterministic dynamics and prove that they agree with those obtained with the MG or BAM in the limit of very low temperature.

Thermal treatment of the minority game.

PubMed

Burgos, E; Ceva, Horacio; Perazzo, R P J

2002-03-01

We study a cost function for the aggregate behavior of all the agents involved in the minority game (MG) or the bar attendance model (BAM). The cost function allows us to define a deterministic, synchronous dynamic that yields results that have the main relevant features than those of the probabilistic, sequential dynamics used for the MG or the BAM. We define a temperature through a Langevin approach in terms of the fluctuations of the average attendance. We prove that the cost function is an extensive quantity that can play the role of an internal energy of the many-agent system while the temperature so defined is an intensive parameter. We compare the results of the thermal perturbation to the deterministic dynamics and prove that they agree with those obtained with the MG or BAM in the limit of very low temperature.

A Decadal Regional and Global Trend Analysis of the Aerosol Optical Depth using a Data-Assimilation Grade Over-Water MODIS and Level 2 MISR Aerosol Products

DTIC Science & Technology

2010-01-01

and seasonal sensitivities to clear sky fraction and emissions (e.g., see annual state of the climate summaries in the BAMS, http://www.ncdc.noaa...gov/bams- state - of - the - climate /). Long term changes are as- sumed to be attributable to more background changes of en- ergy use and economic development

The EP-3E vs. the BAMS UAS: An Operating and Support Cost Comparison

DTIC Science & Technology

2012-09-01

Accountability Office HALE High Altitude Long Endurance ISR Intelligence, Surveillance and Reconnaissance JCC Joint Architecture...others are very complex high altitude long endurance (HALE) aircraft. However, most share the common need for satellite bandwidth. The DoD plan is...collection sites, and risks as they apply to the BAMS UAS. These factors were not adequately considered in the original O&S analysis . Once the analysis

Removal and retention of phosphorus by periphyton from wastewater with high organic load.

PubMed

Cao, Jinxiang; Hong, Xiaoxing; Pei, Guofeng

2014-01-01

The total phosphorus (TP) removal efficiency from organic wastewater (pig farm and distillery wastewater) were estimated by using filamentous green algae (FGA) and benthic algal mats (BAM) treatment systems under laboratory conditions, and the contents of periphyton phosphorus fractions were determined by using a sequential extraction. The removal rates of TP reached 59-78% within the first 8 days of all treatment systems and could achieve average 80% during 30 day period, and the phosphorus removal rates by using BAM was higher than that of FGA. The ability of retention TP of periphyton enhanced gradually, the BAM TP contents were higher than that of FGA, the highest TP concentrations of BAM and FGA were 26.24 and 10.52 mg P g(-1)·dry weight. Inorganic phosphorus (IP) always exceeded 67.5% of TP, but the organic phosphorus fraction only made up less than 20% of TP. The calcium-binding phosphorus (Ca-P) was the dominant fraction and its relative contribution to TP was more than 40%. The TP was also strongly and positively correlated with the IP and Ca-P (p < 0.01) in periphyton. It showed that the periphyton had a potential ability of rapid phosphorus removing and remarkable retention from wastewater with high load phosphorus.

Identification of a conjunctivitis-associated gene locus from the virulence plasmid of Yersinia enterocolitica.

PubMed

Miliotis, M D; Morris, J G; Cianciosi, S; Wright, A C; Wood, P K; Robins-Browne, R M

1990-08-01

The virulence plasmid (pYV) of Yersinia enterocolitica is necessary for production of conjunctivitis in guinea pigs and for mouse lethality. To identify the genes responsible for production of conjunctivitis in guinea pigs, we subcloned the BamHI and SalI restriction fragments of the virulence plasmid of Y. enterocolitica A2635 (serotype O:8) into derivatives of the broad-host-range plasmid pRK290 and introduced the constructions into plasmid-negative Y. enterocolitica strains. A mild, transient conjunctivitis was evident 24 h after inoculation with strains containing a 2.8-kilobase (kb) BamHI fragment of pYV. These strains were cytotoxic to HEp-2 cells but did not cause death in iron-loaded adult mice. When the 2.8- and adjacent 0.5-kb BamHI fragments were deleted from the virulence plasmid of a fully virulent Y. enterocolitica isolate, the resultant strain did not cause conjunctivitis in guinea pigs and was not cytotoxic to HEp-2 cells. However, the strain with the deletion appeared to be more virulent for mice, with more rapid dissemination after orogastric inoculation, compared with that of the parent strain. When the deletion was complemented by introduction of a plasmid containing the 2.8-kb BamHI fragment, the strain again caused conjunctivitis but had decreased virulence for mice.

Fabrication and characterization of magnetically tunable metal-semiconductor schottky diode using barium hexaferrite thin film on gold

NASA Astrophysics Data System (ADS)

Kaur, Jotinder; Sharma, Vinay; Sharma, Vipul; Veerakumar, V.; Kuanr, Bijoy K.

2016-05-01

Barium Hexaferrite (BaM) is an extensively studied magnetic material due to its potential device application. In this paper, we study Schottky junction diodes fabricated using gold and BaM and demonstrate the function of a spintronic device. Gold (50 nm)/silicon substrate was used to grow the BaM thin films (100-150 nm) using pulsed laser deposition. I-V characteristics were measured on the Au/BaM structure sweeping the voltage from ±5 volts. The forward and reverse bias current-voltage curves show diode like rectifying characteristics. The threshold voltage decreases while the output current increases with increase in the applied external magnetic field showing that the I-V characteristics of the BaM based Schottky junction diodes can be tuned by external magnetic field. It is also demonstrated that, the fabricated Schottky diode can be used as a half-wave rectifier, which could operate at high frequencies in the range of 1 MHz compared to the regular p-n junction diodes, which rectify below 10 kHz. In addition, it is found that above 1 MHz, Au/BaM diode can work as a rectifier as well as a capacitor filter, making the average (dc) voltage much larger.

Profile-Based LC-MS Data Alignment—A Bayesian Approach

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2014-01-01

A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets. PMID:23929872

Skeletal muscle atrophy in bioengineered skeletal muscle: a new model system.

PubMed

Lee, Peter H U; Vandenburgh, Herman H

2013-10-01

Skeletal muscle atrophy has been well characterized in various animal models, and while certain pathways that lead to disuse atrophy and its associated functional deficits have been well studied, available drugs to counteract these deficiencies are limited. An ex vivo tissue-engineered skeletal muscle offers a unique opportunity to study skeletal muscle physiology in a controlled in vitro setting. Primary mouse myoblasts isolated from adult muscle were tissue engineered into bioartificial muscles (BAMs) containing hundreds of aligned postmitotic muscle fibers expressing sarcomeric proteins. When electrically stimulated, BAMs generated measureable active forces within 2-3 days of formation. The maximum isometric tetanic force (Po) increased for ∼3 weeks to 2587±502 μN/BAM and was maintained at this level for greater than 80 days. When BAMs were reduced in length by 25% to 50%, muscle atrophy occurred in as little as 6 days. Length reduction resulted in significant decreases in Po (50.4%), mean myofiber cross-sectional area (21.7%), total protein synthesis rate (22.0%), and noncollagenous protein content (6.9%). No significant changes occurred in either the total metabolic activity or protein degradation rates. This study is the first in vitro demonstration that length reduction alone can induce skeletal muscle atrophy, and establishes a novel in vitro model for the study of skeletal muscle atrophy.

Integrated Data Collection and Analysis Project: Friction Correlation Study

DTIC Science & Technology

2015-08-01

methods authorized in AOP-7 include Pendulum Friction, Rotary Friction, Sliding Friction (ABL), BAM Friction and Steel/Fiber Shoe Methods. The...sensitivity can be obtained by Pendulum Friction, Rotary Friction, Sliding Friction (such as the ABL), BAM Friction and Steel/Fiber Shoe Methods.3, 4 Within...Figure 4.16 A variable compressive force is applied downward through the wheel hydraulically (50-1995 psi). The 5 kg pendulum impacts (8 ft/sec is the

Exponential stability preservation in semi-discretisations of BAM networks with nonlinear impulses

NASA Astrophysics Data System (ADS)

Mohamad, Sannay; Gopalsamy, K.

2009-01-01

This paper demonstrates the reliability of a discrete-time analogue in preserving the exponential convergence of a bidirectional associative memory (BAM) network that is subject to nonlinear impulses. The analogue derived from a semi-discretisation technique with the value of the time-step fixed is treated as a discrete-time dynamical system while its exponential convergence towards an equilibrium state is studied. Thereby, a family of sufficiency conditions governing the network parameters and the impulse magnitude and frequency is obtained for the convergence. As special cases, one can obtain from our results, those corresponding to the non-impulsive discrete-time BAM networks and also those corresponding to continuous-time (impulsive and non-impulsive) systems. A relation between the Lyapunov exponent of the non-impulsive system and that of the impulsive system involving the size of the impulses and the inter-impulse intervals is obtained.

Dynamical quenching and annealing in self-organization multiagent models.

PubMed

Burgos, E; Ceva, H; Perazzo, R P

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Dynamical quenching and annealing in self-organization multiagent models

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P.

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Investigations on antibody binding to a micro-cantilever coated with a BAM pesticide residue.

PubMed

Bache, Michael; Taboryski, Rafael; Schmid, Silvan; Aamand, Jens; Jakobsen, Mogens Havsteen

2011-05-16

The attachment of an antibody to an antigen-coated cantilever has been investigated by repeated experiments, using a cantilever-based detection system by Cantion A/S. The stress induced by the binding of a pesticide residue BAM (2,6 dichlorobenzamide) immobilized on a cantilever surface to anti-BAM antibody is measured using the CantiLab4© system from Cantion A/S with four gold-coated cantilevers and piezo resistive readout. The detection mechanism is in principle label-free, but fluorescent-marked antibodies have been used to subsequently verify the binding on the cantilever surface. The bending and increase in mass of each cantilever has also been investigated using a light interferometer and a Doppler Vibrometer. The system has been analyzed during repeated measurements to investigate whether the CantiLab4© system is a suited platform for a pesticide assay system.

Enhanced robust finite-time passivity for Markovian jumping discrete-time BAM neural networks with leakage delay.

PubMed

Sowmiya, C; Raja, R; Cao, Jinde; Rajchakit, G; Alsaedi, Ahmed

2017-01-01

This paper is concerned with the problem of enhanced results on robust finite-time passivity for uncertain discrete-time Markovian jumping BAM delayed neural networks with leakage delay. By implementing a proper Lyapunov-Krasovskii functional candidate, the reciprocally convex combination method together with linear matrix inequality technique, several sufficient conditions are derived for varying the passivity of discrete-time BAM neural networks. An important feature presented in our paper is that we utilize the reciprocally convex combination lemma in the main section and the relevance of that lemma arises from the derivation of stability by using Jensen's inequality. Further, the zero inequalities help to propose the sufficient conditions for finite-time boundedness and passivity for uncertainties. Finally, the enhancement of the feasible region of the proposed criteria is shown via numerical examples with simulation to illustrate the applicability and usefulness of the proposed method.

Small angle neutron scattering study of nano sized microstructure in Fe-Cr ODS steels for gen IV in-core applications.

PubMed

Han, Young-Soo; Mao, Xiadong; Jang, Jinsung

2013-11-01

The nano-sized microstructures in Fe-Cr oxide dispersion strengthened steel for Gen IV in-core applications were studied using small angle neutron scattering. The oxide dispersion strengthened steel was manufactured through hot isostatic pressing with various chemical compositions and fabrication conditions. Small angle neutron scattering experiments were performed using a 40 m small angle neutron scattering instrument at HANARO. Nano sized microstructures, namely, yttrium oxides and Cr-oxides were quantitatively analyzed by small angle neutron scattering. The yttrium oxides and Cr-oxides were also observed by transmission electron microscopy. The microstructural analysis results from small angle neutron scattering were compared with those obtained by transmission electron microscopy. The effects of the chemical compositions and fabrication conditions on the microstructure were investigated in relation to the quantitative microstructural analysis results obtained by small angle neutron scattering. The volume fraction of Y-oxide increases after fabrication, and this result is considered to be due to the formation of non-stochiometric Y-Ti-oxides.

A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326

PubMed Central

Luthra, Amit; Anand, Arvind; Hawley, Kelly L.; LeDoyt, Morgan; La Vake, Carson J.; Caimano, Melissa J.; Cruz, Adriana R.; Salazar, Juan C.

2015-01-01

ABSTRACT We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu593 → Gln593) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a “structure-to-pathogenesis” approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. IMPORTANCE Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog. Using a homology model as a guide, we found that TP_0326 displays unique features which presumably relate to its function(s) in the biogenesis of T. pallidum's unorthodox OM. The model also enabled us to identify an immunodominant epitope in a large extracellular loop that is both an opsonic target and subject to immune pressure in a human population. Ours is the first study to follow a structure-to-pathogenesis approach to map the surface topology of a T. pallidum rare OMP within the context of syphilitic infection. PMID:25825429

Concurrent segregation and erosion effects in medium-energy iron beam patterning of silicon surfaces

NASA Astrophysics Data System (ADS)

Redondo-Cubero, A.; Lorenz, K.; Palomares, F. J.; Muñoz, A.; Castro, M.; Muñoz-García, J.; Cuerno, R.; Vázquez, L.

2018-07-01

We have bombarded crystalline silicon targets with a 40 keV Fe+ ion beam at different incidence angles. The resulting surfaces have been characterized by atomic force, current-sensing and magnetic force microscopies, scanning electron microscopy, and x-ray photoelectron spectroscopy. We have found that there is a threshold angle smaller than 40° for the formation of ripple patterns, which is definitely lower than those frequently reported for noble gas ion beams. We compare our observations with estimates of the value of the critical angle and of additional basic properties of the patterning process, which are based on a continuum model whose parameters are obtained from binary collision simulations. We have further studied experimentally the ripple structures and measured how the surface slopes change with the ion incidence angle. We explore in particular detail the fluence dependence of the pattern for an incidence angle value (40°) close to the threshold. Initially, rimmed holes appear randomly scattered on the surface, which evolve into large, bug-like structures. Further increasing the ion fluence induces a smooth, rippled background morphology. By means of microscopy techniques, a correlation between the morphology of these structures and their metal content can be unambiguously established.

NAMRU-3 Reprint Accession List 1982. Number 12.

DTIC Science & Technology

1983-01-01

1316 * VETERINARY MEDICINE Canine parvovirus infection 1288 Congenital osteopetrosis in o/op mouse 1317 History of rabies vaccination 1278 Liver biopsy...Entomol., 19(2):209- 210, 1982. _ 1288 8UCCIO T.J., BOTROS, B.A.-M. and EL tiOLLA, M.: Canine Parvovirus Infe~tion: A Brief Review and Report of First...1278 BOTROS, B.A.M.: History of Rabies Vaccination . Review and Comments. J. Egypt. Public Health Assoc., 55(566):309-318, 1980. 1279 KLOOS, H

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

NASA Astrophysics Data System (ADS)

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng; Xie, Xiaoxun; Wang, Hongli; Li, Jiandong; Shi, Zhengguo; Liu, Yangang

2018-01-01

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments reveals that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10 m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution, and size distribution.

Bile acid malabsorption: an under-investigated differential diagnosis in patients presenting with diarrhea predominant irritable bowel syndrome type symptoms.

PubMed

Kurien, Matthew; Evans, Kate E; Leeds, John S; Hopper, Andy D; Harris, Andrew; Sanders, David S

2011-07-01

Bile acid malabsorption (BAM) has been reported as a possible cause of diarrhea predominant irritable bowel syndrome (D-IBS) type symptoms. We aimed to determine how commonly patients with D-IBS type symptoms had a diagnosis of BAM as demonstrated by a positive SeHCAT (75 Selenium-homocholic acid taurine) test (retention <10% at seven days). A retrospective analysis was undertaken of patient's records for all patients who underwent a SeHCAT test between 2001 and 2009 in a tertiary hospital (Group A). Concurrently, a cohort of patients with Rome II D-IBS type symptoms was examined to determine the potential utility of SeHCAT test (Group B). In Group A 39.2% (n = 107/273) of patients had a positive SeHCAT result. The median time from first hospital visit to SeHCAT result was 30 weeks. Predictive factors for BAM: terminal ileal Crohn's disease (p < 0.01), terminal ileal resection (p < 0.01), and previous cholecystectomy (p < 0.01). 33.6% of patients who had a positive SeHCAT also had Rome II D-IBS. In Group B the D-IBS control cohort only 1.9% of patients had undergone a SeHCAT scan (p < 0.001 compared to Group A). BAM is common and should be considered earlier when investigating unselected patients with D-IBS type symptoms.

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria.

PubMed

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-08-05

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria*

PubMed Central

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-01-01

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. PMID:27298319

Toward a Better Nutritional Aiding in Disasters: Relying on Lessons Learned during the Bam Earthquake.

PubMed

Nekouie Moghadam, Mahmoud; Amiresmaieli, Mohammadreza; Hassibi, Mohammad; Doostan, Farideh; Khosravi, Sajad

2017-08-01

Introduction Examining various problems in the aftermath of disasters is very important to the disaster victims. Managing and coordinating food supply and its distribution among the victims is one of the most important problems after an earthquake. Therefore, the purpose of this study was to recognize problems and experiences in the field of nutritional aiding during an earthquake. This qualitative study was of phenomenological type. Using the purposive sampling method, 10 people who had experienced nutritional aiding during the Bam Earthquake (Iran; 2003) were interviewed. Colaizzi's method of analysis was used to analyze interview data. The findings of this study identified four main categories and 19 sub-categories concerning challenges in the nutritional aiding during the Bam Earthquake. The main topics included managerial, aiding, infrastructural, and administrative problems. The major problems in nutritional aiding include lack of prediction and development of a specific program of suitable nutritional pattern and nutritional assessment of the victims in critical conditions. Forming specialized teams, educating team members about nutrition, and making use of experts' knowledge are the most important steps to resolve these problems in the critical conditions; these measures are the duties of the relevant authorities. Nekouie Moghadam M , Amiresmaieli M , Hassibi M , Doostan F , Khosravi S . Toward a better nutritional aiding in disasters: relying on lessons learned during the Bam Earthquake. Prehosp Disaster Med. 2017;32(4):382-386.

Delivery of CdiA Nuclease Toxins into Target Cells during Contact-Dependent Growth Inhibition

PubMed Central

Webb, Julia S.; Nikolakakis, Kiel C.; Willett, Julia L. E.; Aoki, Stephanie K.

2013-01-01

Bacterial contact-dependent growth inhibition (CDI) is mediated by the CdiB/CdiA family of two-partner secretion proteins. CDI systems deploy a variety of distinct toxins, which are contained within the polymorphic C-terminal region (CdiA-CT) of CdiA proteins. Several CdiA-CTs are nucleases, suggesting that the toxins are transported into the target cell cytoplasm to interact with their substrates. To analyze CdiA transfer to target bacteria, we used the CDI system of uropathogenic Escherichia coli 536 (UPEC536) as a model. Antibodies recognizing the amino- and carboxyl-termini of CdiAUPEC536 were used to visualize transfer of CdiA from CDIUPEC536+ inhibitor cells to target cells using fluorescence microscopy. The results indicate that the entire CdiAUPEC536 protein is deposited onto the surface of target bacteria. CdiAUPEC536 transfer to bamA101 mutants is reduced, consistent with low expression of the CDI receptor BamA on these cells. Notably, our results indicate that the C-terminal CdiA-CT toxin region of CdiAUPEC536 is translocated into target cells, but the N-terminal region remains at the cell surface based on protease sensitivity. These results suggest that the CdiA-CT toxin domain is cleaved from CdiAUPEC536 prior to translocation. Delivery of a heterologous Dickeya dadantii CdiA-CT toxin, which has DNase activity, was also visualized. Following incubation with CDI+ inhibitor cells targets became anucleate, showing that the D.dadantii CdiA-CT was delivered intracellularly. Together, these results demonstrate that diverse CDI toxins are efficiently translocated across target cell envelopes. PMID:23469034

Psychological distress among Bam earthquake survivors in Iran: a population-based study.

PubMed

Montazeri, Ali; Baradaran, Hamid; Omidvari, Sepideh; Azin, Seyed Ali; Ebadi, Mehdi; Garmaroudi, Gholamreza; Harirchi, Amir Mahmood; Shariati, Mohammad

2005-01-11

An earthquake measuring 6.3 on the Richter scale struck the city of Bam in Iran on the 26th of December 2003 at 5.26 A.M. It was devastating, and left over 40,000 dead and around 30,000 injured. The profound tragedy of thousands killed has caused emotional and psychological trauma for tens of thousands of people who have survived. A study was carried out to assess psychological distress among Bam earthquake survivors and factors associated with severe mental health in those who survived the tragedy. This was a population-based study measuring psychological distress among the survivors of Bam earthquake in Iran. Using a multi-stage stratified sampling method a random sample of individuals aged 15 years and over living in Bam were interviewed. Psychological distress was measured using the 12-item General Health Questionnaire (GHQ-12). In all 916 survivors were interviewed. The mean age of the respondents was 32.9 years (SD = 12.4), mostly were males (53%), married (66%) and had secondary school education (50%). Forty-one percent reported they lost 3 to 5 members of their family in the earthquake. In addition the findings showed that 58% of the respondents suffered from severe mental health as measured by the GHQ-12 and this was three times higher than reported psychological distress among the general population. There were significant differences between sub-groups of the study sample with regard to their psychological distress. The results of the logistic regression analysis also indicated that female gender; lower education, unemployment, and loss of family members were associated with severe psychological distress among earthquake victims. The study findings indicated that the amount of psychological distress among earthquake survivors was high and there is an urgent need to deliver mental health care to disaster victims in local medical settings and to reduce negative health impacts of the earthquake adequate psychological counseling is needed for those who survived the tragedy.

Psychological distress among Bam earthquake survivors in Iran: a population-based study

PubMed Central

Montazeri, Ali; Baradaran, Hamid; Omidvari, Sepideh; Azin, Seyed Ali; Ebadi, Mehdi; Garmaroudi, Gholamreza; Harirchi, Amir Mahmood; Shariati, Mohammad

2005-01-01

Background An earthquake measuring 6.3 on the Richter scale struck the city of Bam in Iran on the 26th of December 2003 at 5.26 A.M. It was devastating, and left over 40,000 dead and around 30,000 injured. The profound tragedy of thousands killed has caused emotional and psychological trauma for tens of thousands of people who have survived. A study was carried out to assess psychological distress among Bam earthquake survivors and factors associated with severe mental health in those who survived the tragedy. Methods This was a population-based study measuring psychological distress among the survivors of Bam earthquake in Iran. Using a multi-stage stratified sampling method a random sample of individuals aged 15 years and over living in Bam were interviewed. Psychological distress was measured using the 12-item General Health Questionnaire (GHQ-12). Results In all 916 survivors were interviewed. The mean age of the respondents was 32.9 years (SD = 12.4), mostly were males (53%), married (66%) and had secondary school education (50%). Forty-one percent reported they lost 3 to 5 members of their family in the earthquake. In addition the findings showed that 58% of the respondents suffered from severe mental health as measured by the GHQ-12 and this was three times higher than reported psychological distress among the general population. There were significant differences between sub-groups of the study sample with regard to their psychological distress. The results of the logistic regression analysis also indicated that female gender; lower education, unemployment, and loss of family members were associated with severe psychological distress among earthquake victims. Conclusion The study findings indicated that the amount of psychological distress among earthquake survivors was high and there is an urgent need to deliver mental health care to disaster victims in local medical settings and to reduce negative health impacts of the earthquake adequate psychological counseling is needed for those who survived the tragedy. PMID:15644145

Distinctive Roles for Periplasmic Proteases in the Maintenance of Essential Outer Membrane Protein Assembly.

PubMed

Soltes, Garner R; Martin, Nicholas R; Park, Eunhae; Sutterlin, Holly A; Silhavy, Thomas J

2017-10-15

Outer membrane protein (OMP) biogenesis in Escherichia coli is a robust process essential to the life of the organism. It is catalyzed by the β-barrel assembly machine (Bam) complex, and a number of quality control factors, including periplasmic chaperones and proteases, maintain the integrity of this trafficking pathway. Little is known, however, about how periplasmic proteases recognize and degrade OMP substrates when assembly is compromised or whether different proteases recognize the same substrate at distinct points in the assembly pathway. In this work, we use well-defined assembly-defective mutants of LptD, the essential lipopolysaccharide assembly translocon, to show that the periplasmic protease DegP degrades substrates with assembly defects that prevent or impair initial contact with Bam, causing the mutant protein to accumulate in the periplasm. In contrast, another periplasmic protease, BepA, degrades a LptD mutant substrate that has engaged the Bam complex and formed a nearly complete barrel. Furthermore, we describe the role of the outer membrane lipoprotein YcaL, a protease of heretofore unknown function, in the degradation of a LptD substrate that has engaged the Bam complex but is stalled at an earlier step in the assembly process that is not accessible to BepA. Our results demonstrate that multiple periplasmic proteases monitor OMPs at distinct points in the assembly process. IMPORTANCE OMP assembly is catalyzed by the essential Bam complex and occurs in a cellular environment devoid of energy sources. Assembly intermediates that misfold can compromise this essential molecular machine. Here we demonstrate distinctive roles for three different periplasmic proteases that can clear OMP substrates with folding defects that compromise assembly at three different stages. These quality control factors help ensure the integrity of the permeability barrier that contributes to the intrinsic resistance of Gram-negative organisms to many antibiotics. Copyright © 2017 American Society for Microbiology.

BioAerosol Mass Spectrometry: Reagentless Detection of Individual Airborne Spores and Other Bioagent Particles Based on Laser Desorption/Ionization Mass Spectrometry

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

Steele, Paul Thomas

2004-09-01

Better devices are needed for the detection of aerosolized biological warfare agents. Advances in the ongoing development of one such device, the BioAerosol Mass Spectrometry (BAMS) system, are described here in detail. The system samples individual, micrometer-sized particles directly from the air and analyzes them in real-time without sample preparation or use of reagents. At the core of the BAMS system is a dual-polarity, single-particle mass spectrometer with a laser based desorption and ionization (DI) system. The mass spectra produced by early proof-of-concept instruments were highly variable and contained limited information to differentiate certain types of similar biological particles. Themore » investigation of this variability and subsequent changes to the DI laser system are described. The modifications have reduced the observed variability and thereby increased the usable information content in the spectra. These improvements would have little value without software to analyze and identify the mass spectra. Important improvements have been made to the algorithms that initially processed and analyzed the data. Single particles can be identified with an impressive level of accuracy, but to obtain significant reductions in the overall false alarm rate of the BAMS instrument, alarm decisions must be made dynamically on the basis of multiple analyzed particles. A statistical model has been developed to make these decisions and the resulting performance of a hypothetical BAMS system is quantitatively predicted. The predictions indicate that a BAMS system, with reasonably attainable characteristics, can operate with a very low false alarm rate (orders of magnitude lower than some currently fielded biodetectors) while still being sensitive to small concentrations of biological particles in a large range of environments. Proof-of-concept instruments, incorporating some of the modifications described here, have already performed well in independent testing.« less

Oxidation-state sensitive imaging of cerium dioxide by atomic-resolution low-angle annular dark field scanning transmission electron microscopy.

PubMed

Johnston-Peck, Aaron C; Winterstein, Jonathan P; Roberts, Alan D; DuChene, Joseph S; Qian, Kun; Sweeny, Brendan C; Wei, Wei David; Sharma, Renu; Stach, Eric A; Herzing, Andrew A

2016-03-01

Low-angle annular dark field (LAADF) scanning transmission electron microscopy (STEM) imaging is presented as a method that is sensitive to the oxidation state of cerium ions in CeO2 nanoparticles. This relationship was validated through electron energy loss spectroscopy (EELS), in situ measurements, as well as multislice image simulations. Static displacements caused by the increased ionic radius of Ce(3+) influence the electron channeling process and increase electron scattering to low angles while reducing scatter to high angles. This process manifests itself by reducing the high-angle annular dark field (HAADF) signal intensity while increasing the LAADF signal intensity in close proximity to Ce(3+) ions. This technique can supplement STEM-EELS and in so doing, relax the experimental challenges associated with acquiring oxidation state information at high spatial resolutions. Published by Elsevier B.V.

High resolution quantitative phase imaging of live cells with constrained optimization approach

NASA Astrophysics Data System (ADS)

Pandiyan, Vimal Prabhu; Khare, Kedar; John, Renu

2016-03-01

Quantitative phase imaging (QPI) aims at studying weakly scattering and absorbing biological specimens with subwavelength accuracy without any external staining mechanisms. Use of a reference beam at an angle is one of the necessary criteria for recording of high resolution holograms in most of the interferometric methods used for quantitative phase imaging. The spatial separation of the dc and twin images is decided by the reference beam angle and Fourier-filtered reconstructed image will have a very poor resolution if hologram is recorded below a minimum reference angle condition. However, it is always inconvenient to have a large reference beam angle while performing high resolution microscopy of live cells and biological specimens with nanometric features. In this paper, we treat reconstruction of digital holographic microscopy images as a constrained optimization problem with smoothness constraint in order to recover only complex object field in hologram plane even with overlapping dc and twin image terms. We solve this optimization problem by gradient descent approach iteratively and the smoothness constraint is implemented by spatial averaging with appropriate size. This approach will give excellent high resolution image recovery compared to Fourier filtering while keeping a very small reference angle. We demonstrate this approach on digital holographic microscopy of live cells by recovering the quantitative phase of live cells from a hologram recorded with nearly zero reference angle.

Design and fabrication of highly hydrophobic Mn nano-sculptured thin films and evaluation of surface properties on hydrophobicity

NASA Astrophysics Data System (ADS)

Hosseini, Somaye; Savaloni, Hadi; Gholipour-Shahraki, Mehran

2017-03-01

The wettability of solid surfaces is important from the aspects of both science and technology. The Mn nano-sculptured thin films were designed and fabricated by oblique angle deposition of Mn on glass substrates at room temperature. The obtained structure was characterized by field emission scanning electron microscopy and atomic force microscopy. The wettability of thin films samples was investigated by water contact angle (WCA). The 4-pointed helical star-shaped structure exhibits hydrophobicity with static WCAs of more than 133° for a 10-mg distilled water droplet. This sample also shows the rose petal effect with the additional property of high adhesion. The Mn nano-sculptured thin films also act as a sticky surface which is confirmed by hysteresis of the contact angle obtained from advancing and receding contact angles measurements. Physicochemical property of liquid phase could effectively change the contact angle, and polar solvents in contact with hydrophobic solid surfaces do not necessarily show high contact angle value.

Experimental Study of Static Contact-angle on Peak-like Microstructural Surfaces Produced by PIII Technology

NASA Astrophysics Data System (ADS)

Yang, Runhua; Yang, Lixin

2018-06-01

Plasma immersion ion implantation (PIII) was used to fabricate micro/nano structures on monocrystalline Si surfaces with different ratios of mixed gases (SF6/O2). The micro/nano structures on the surfaces of the sample were characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The results showed that with increasing ratio of mixed gases (SF6/O2), the height of the micro/nano structures first increased and then decreased. Contact-angle measurements indicated that the surfaces' micro/nano structures have an obvious effect on the contact-angle, and could cause a change in surface wettability. The theoretical analysis of contact-angle showed that the Wenzel and Cassie theories cannot predict the contact-angle of a roughened surface accurately, and should be corrected for practical applications using an actual model. Moreover, the contact-angle first increased and then decreased with increasing ratio of mixed gases (SF6/O2), which is in accordance with the change of the height of micro/nano structures.

Periodic bidirectional associative memory neural networks with distributed delays

NASA Astrophysics Data System (ADS)

Chen, Anping; Huang, Lihong; Liu, Zhigang; Cao, Jinde

2006-05-01

Some sufficient conditions are obtained for the existence and global exponential stability of a periodic solution to the general bidirectional associative memory (BAM) neural networks with distributed delays by using the continuation theorem of Mawhin's coincidence degree theory and the Lyapunov functional method and the Young's inequality technique. These results are helpful for designing a globally exponentially stable and periodic oscillatory BAM neural network, and the conditions can be easily verified and be applied in practice. An example is also given to illustrate our results.

Passivity analysis for uncertain BAM neural networks with time delays and reaction-diffusions

NASA Astrophysics Data System (ADS)

Zhou, Jianping; Xu, Shengyuan; Shen, Hao; Zhang, Baoyong

2013-08-01

This article deals with the problem of passivity analysis for delayed reaction-diffusion bidirectional associative memory (BAM) neural networks with weight uncertainties. By using a new integral inequality, we first present a passivity condition for the nominal networks, and then extend the result to the case with linear fractional weight uncertainties. The proposed conditions are expressed in terms of linear matrix inequalities, and thus can be checked easily. Examples are provided to demonstrate the effectiveness of the proposed results.

Developing new optical imaging techniques for single particle and molecule tracking in live cells

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

Sun, Wei

Differential interference contrast (DIC) microscopy is a far-field as well as wide-field optical imaging technique. Since it is non-invasive and requires no sample staining, DIC microscopy is suitable for tracking the motion of target molecules in live cells without interfering their functions. In addition, high numerical aperture objectives and condensers can be used in DIC microscopy. The depth of focus of DIC is shallow, which gives DIC much better optical sectioning ability than those of phase contrast and dark field microscopies. In this work, DIC was utilized to study dynamic biological processes including endocytosis and intracellular transport in live cells.more » The suitability of DIC microscopy for single particle tracking in live cells was first demonstrated by using DIC to monitor the entire endocytosis process of one mesoporous silica nanoparticle (MSN) into a live mammalian cell. By taking advantage of the optical sectioning ability of DIC, we recorded the depth profile of the MSN during the endocytosis process. The shape change around the nanoparticle due to the formation of a vesicle was also captured. DIC microscopy was further modified that the sample can be illuminated and imaged at two wavelengths simultaneously. By using the new technique, noble metal nanoparticles with different shapes and sizes were selectively imaged. Among all the examined metal nanoparticles, gold nanoparticles in rod shapes were found to be especially useful. Due to their anisotropic optical properties, gold nanorods showed as diffraction-limited spots with disproportionate bright and dark parts that are strongly dependent on their orientation in the 3D space. Gold nanorods were developed as orientation nanoprobes and were successfully used to report the self-rotation of gliding microtubules on kinesin coated substrates. Gold nanorods were further used to study the rotational motions of cargoes during the endocytosis and intracellular transport processes in live mammalian cells. New rotational information was obtained: (1) during endocytosis, cargoes lost their rotation freedom at the late stage of internalization; (2) cargoes performed train-like motion when they were transported along the microtubule network by motor proteins inside live cells; (3) During the pause stage of fast axonal transport, cargoes were still bound to the microtubule tracks by motor proteins. Total internal reflection fluorescence microscopy (TIRFM) is another non-invasive and far-field optical imaging technique. Because of its near-field illumination mechanism, TIRFM has better axial resolution than epi-fluorescence microscopy and confocal microscopy. In this work, an auto-calibrated, prism type, angle-scanning TIRFM instrument was built. The incident angle can range from subcritical angles to nearly 90°, with an angle interval less than 0.2°. The angle precision of the new instrument was demonstrated through the finding of the surface plasmon resonance (SPR) angle of metal film coated glass slide. The new instrument improved significantly the precision in determining the axial position. As a result, the best obtained axial resolution was ~ 8 nm, which is better than current existing instruments similar in function. The instrument was further modified to function as a pseudo TIRF microscope. The illumination depth can be controlled by changing the incident angle of the excitation laser beam or adjusting the horizontal position of the illumination laser spot on the prism top surface. With the new technique, i.e., variable-illumination-depth pseudo TIRF microscopy, the whole cell body from bottom to top was scanned.« less

Imaging of high-angle annular dark-field scanning transmission electron microscopy and observations of GaN-based violet laser diodes.

PubMed

Shiojiri, M; Saijo, H

2006-09-01

The first part of this paper is devoted to physics, to explain high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) imaging and to interpret why HAADF-STEM imaging is incoherent, instructing a strict definition of interference and coherence of electron waves. Next, we present our recent investigations of InGaN/GaN multiple quantum wells and AlGaN/GaN strained-layer superlattice claddings in GaN-based violet laser diodes, which have been performed by HAADF-STEM and high-resolution field-emission gun scanning electron microscopy.

Bio-Aerosol Detection Using Mass Spectrometry: Public Health Applications

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

Ludvigson, Laura D.

2004-01-01

I recently spent a summer as an intern at the Lawrence Livermore National Laboratory. I worked on a project involving the real-time, reagentless, single cell detection of aerosolized pathogens using a novel mass spectrometry approach called Bio-Aerosol Mass Spectrometry (BAMS). Based upon preliminary results showing the differentiation capabilities of BAMS, I would like to explore the development and use of this novel detection system in the context of both environmental and clinical sample pathogen detection. I would also like to explore the broader public health applications that a system such as BAMS might have in terms of infectious disease preventionmore » and control. In order to appreciate the potential of this instrument, I will demonstrate the need for better pathogen detection methods, and outline the instrumentation, data analysis and preliminary results that lead me toward a desire to explore this technology further. I will also discuss potential experiments for the future along with possible problems that may be encountered along the way.« less

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

DOE PAGES

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng; ...

2018-01-18

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments revealsmore » that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10-m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Thus, mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution and size distribution.« less

Anti-tumor immunity of BAM-SiPc-mediated vascular photodynamic therapy in a BALB/c mouse model.

PubMed

Yeung, Hing-Yuen; Lo, Pui-Chi; Ng, Dennis K P; Fong, Wing-Ping

2017-02-01

In recent decades, accumulating evidence from both animal and clinical studies has suggested that a sufficiently activated immune system may strongly augment various types of cancer treatment, including photodynamic therapy (PDT). Through the generation of reactive oxygen species, PDT eradicates tumors by triggering localized tumor damage and inducing anti-tumor immunity. As the major component of anti-tumor immunity, the involvement of a cell-mediated immune response in PDT has been well investigated in the past decade, whereas the role of humoral immunity has remained relatively unexplored. In the present investigation, using the photosensitizer BAM-SiPc and the CT26 tumor-bearing BALB/c mouse model, it was demonstrated that both cell-mediated and humoral adaptive immune components could be involved in PDT. With a vascular PDT (VPDT) regimen, BAM-SiPc could eradicate the tumors of ∼70% of tumor-bearing mice and trigger an anti-tumor immune response that could last for more than 1 year. An elevation of Th2 cytokines was detected ex vivo after VPDT, indicating the potential involvement of a humoral response. An analysis of serum from the VPDT-cured mice also revealed elevated levels of tumor-specific antibodies. Moreover, this serum could effectively hinder tumor growth and protect the mice against further re-challenge in a T-cell-dependent manner. Taken together, these results show that the humoral components induced after BAM-SiPc-VPDT could assist the development of anti-tumor immunity.

Vestibular function assessment using the NIH Toolbox

PubMed Central

Schubert, Michael C.; Whitney, Susan L.; Roberts, Dale; Redfern, Mark S.; Musolino, Mark C.; Roche, Jennica L.; Steed, Daniel P.; Corbin, Bree; Lin, Chia-Cheng; Marchetti, Greg F.; Beaumont, Jennifer; Carey, John P.; Shepard, Neil P.; Jacobson, Gary P.; Wrisley, Diane M.; Hoffman, Howard J.; Furman, Gabriel; Slotkin, Jerry

2013-01-01

Objective: Development of an easy to administer, low-cost test of vestibular function. Methods: Members of the NIH Toolbox Sensory Domain Vestibular, Vision, and Motor subdomain teams collaborated to identify 2 tests: 1) Dynamic Visual Acuity (DVA), and 2) the Balance Accelerometry Measure (BAM). Extensive work was completed to identify and develop appropriate software and hardware. More than 300 subjects between the ages of 3 and 85 years, with and without vestibular dysfunction, were recruited and tested. Currently accepted gold standard measures of static visual acuity, vestibular function, dynamic visual acuity, and balance were performed to determine validity. Repeat testing was performed to examine reliability. Results: The DVA and BAM tests are affordable and appropriate for use for individuals 3 through 85 years of age. The DVA had fair to good reliability (0.41–0.94) and sensitivity and specificity (50%–73%), depending on age and optotype chosen. The BAM test was moderately correlated with center of pressure (r = 0.42–0.48) and dynamic posturography (r = −0.48), depending on age and test condition. Both tests differentiated those with and without vestibular impairment and the young from the old. Each test was reliable. Conclusion: The newly created DVA test provides a valid measure of visual acuity with the head still and moving quickly. The novel BAM is a valid measure of balance. Both tests are sensitive to age-related changes and are able to screen for impairment of the vestibular system. PMID:23479540

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

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

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments revealsmore » that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10-m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Thus, mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution and size distribution.« less

Creating a single twin boundary between two CdTe (111) wafers with controlled rotation angle by wafer bonding

NASA Astrophysics Data System (ADS)

Sun, Ce; Lu, Ning; Wang, Jinguo; Lee, Jihyung; Peng, Xin; Klie, Robert F.; Kim, Moon J.

2013-12-01

The single twin boundary with crystallographic orientation relationship (1¯1¯1¯)//(111) [01¯1]//[011¯] was created by wafer bonding. Electron diffraction patterns and high-resolution transmission electron microscopy images demonstrated the well control of the rotation angle between the bonded pair. At the twin boundary, one unit of wurtzite structure was found between two zinc-blende matrices. High-angle annular dark-field scanning transmission electron microscopy images showed Cd- and Te-terminated for the two bonded portions, respectively. The I-V curve across the twin boundary showed increasingly nonlinear behavior, indicating a potential barrier at the bonded twin boundary.

Discrete-time bidirectional associative memory neural networks with variable delays

NASA Astrophysics Data System (ADS)

Liang, variable delays [rapid communication] J.; Cao, J.; Ho, D. W. C.

2005-02-01

Based on the linear matrix inequality (LMI), some sufficient conditions are presented in this Letter for the existence, uniqueness and global exponential stability of the equilibrium point of discrete-time bidirectional associative memory (BAM) neural networks with variable delays. Some of the stability criteria obtained in this Letter are delay-dependent, and some of them are delay-independent, they are less conservative than the ones reported so far in the literature. Furthermore, the results provide one more set of easily verified criteria for determining the exponential stability of discrete-time BAM neural networks.

Characterization of a Laser-Generated Perturbation in High-Speed Flow for Receptivity Studies

DTIC Science & Technology

2014-01-01

to trip the boundary layer. Figure 1. Schematic of the Boeing/AFOSR Mach-6 Quiet Tunnel (BAM6QT) The BAM6QT is a Ludwieg tube with a double- burst ...reduced to a 4-mm beam diameter by an aperture. Although the PIV-400 is a double- pulse laser, only the first pulse is used to generate perturbations in the...also both seeded, and pulse at 10 Hz, with a pulse width of about 7 ns. 2. Forming Optics The laser-generated perturbation is created by focusing a

Nanoscale cellular imaging with scanning angle interference microscopy.

PubMed

DuFort, Christopher; Paszek, Matthew

2014-01-01

Fluorescence microscopy is among the most widely utilized tools in cell and molecular biology due to its ability to noninvasively obtain time-resolved images of live cells with molecule-specific contrast. In this chapter, we describe a simple high-resolution technique, scanning angle interference microscopy (SAIM), for the imaging and localization of fluorescent molecules with nanometer precision along the optical axis. In SAIM, samples above a reflective surface are sequentially scanned with an excitation laser at varying angles of incidence. Interference patterns generated between the incident and reflected lights result in an emission intensity that depends on the height of a fluorophore above the silicon surface and the angle of the incident radiation. The measured fluorescence intensities are then fit to an optical model to localize the labeled molecules along the z-axis with 5-10 nm precision and diffraction-limited lateral resolution. SAIM is easily implemented on widely available commercial total internal reflection fluorescence microscopes, offering potential for widespread use in cell biology. Here, we describe the setup of SAIM and its application for imaging cellular structures near (<1 μm) the sample substrate. © 2014 Elsevier Inc. All rights reserved.

Correlation of Cell Surface Biomarker Expression Levels with Adhesion Contact Angle Measured by Lateral Microscopy.

PubMed

Walz, Jenna A; Mace, Charles R

2018-06-05

Immunophenotyping is typically achieved using flow cytometry, but any influence a biomarker may have on adhesion or surface recognition cannot be determined concurrently. In this manuscript, we demonstrate the utility of lateral microscopy for correlating cell surface biomarker expression levels with quantitative descriptions of cell morphology. With our imaging system, we observed single cells from two T cell lines and two B cell lines adhere to antibody-coated substrates and quantified this adhesion using contact angle measurements. We found that SUP-T1 and CEM CD4+ cells, both of which express similar levels of CD4, experienced average changes in contact angle that were not statistically different from one another on surfaces coated in anti-CD4. However, MAVER-1 and BJAB K20 cells, both of which express different levels of CD20, underwent average changes in contact angle that were significantly different from one another on surfaces coated in anti-CD20. Our results indicate that changes in cell contact angles on antibody-coated substrates reflect the expression levels of corresponding antigens on the surfaces of cells as determined by flow cytometry. Our lateral microscopy approach offers a more reproducible and quantitative alternative to evaluate adhesion compared to commonly used wash assays and can be extended to many additional immunophenotyping applications to identify cells of interest within heterogeneous populations.

Formative evaluation on cultural tailoring breathing awareness meditation smartphone apps to reduce stress and blood pressure

PubMed Central

Adams, Zachary W.; Nemeth, Lynne; Brunner-Jackson, Brenda; Mueller, Martina; Anderson, Ashley; Patel, Sachin; Sox, Luke; Treiber, Frank A.

2017-01-01

Background Chronic stress is an independent risk factor for essential hypertension (EH), cardiovascular disease (CVD), and is sometimes confronted by mal-adaptive coping behaviors (e.g., stress eating, excessive alcohol consumption, etc.). Pre-essential hypertension (preEH) is the leading predictor of future EH status. Breathing awareness meditation (BAM) can result in clinically beneficial blood pressure (BP) reductions, though face-to-face sessions presents barriers to reach those in need. The purpose of this study was to identify if a culturally tailored approach is needed in the design and preferences between groups of preEH African American and White adults toward using a smartphone BAM app, the Tension Tamer (TT) app. Methods TT includes audio delivered BAM instructions, real-time heart rate, feedback graphs and motivational reinforcement text messaging. Questionnaires and two focus groups each of African American and White adults, [n=34, mean age =43.1 years, (SD 13.8 years), 44.1% African American] were conducted to understand stress, EH knowledge, app usage along with feedback from a hands-on demonstration of TT. Grounded theory using NVivo 10 was used to develop themes and combined with the questionnaires in the analysis. Results No racial differences were found in the analysis including app use scenarios, preferences, knowledge, technology use or the attitudes and acceptance toward mobile health (mHealth) programs. Reported stress was high for African Americans [PSS-4: mean 6.87 (SD 3.3) versus mean 4.56 (SD 2.6); P=0.03]. Four main themes were found: (I) stress was pervasive; (II) coping strategies were both positive and negative; (III) BAM training was easy to incorporated; and (IV) tracking stress responses was useful. Responses suggest that additional personalization of app interfaces may drive ownership and adherence to protocols. Measures and reports of heart rate monitoring while in session were favorably viewed with low issues with confidentiality or trust issues on collected session data. Conclusions Results suggest that a culturally tailored approach may be unnecessary in the design of BAM apps. Further investigation is warranted for other racial groups, age ranges, and disease conditions. PMID:29184896

Comparison of a novel strategy for the detection and isolation of Salmonella in shell eggs with the Food and Drug Administration Bacteriological Analytical Manual method.

PubMed

Zhang, Guodong; Thau, Eve; Brown, Eric W; Hammack, Thomas S

2013-12-01

The current FDA Bacteriological Analytical Manual (BAM) method for the detection of Salmonella in eggs requires 2 wk to complete. The objective of this project was to improve the BAM method for the detection and isolation of Salmonella in whole shell eggs. A novel protocol, using 1,000 g of liquid eggs for direct preenrichment with 2 L of tryptic soy broth (TSB) followed by enrichment using Rappaport-Vassiliadis and Tetrathionate broths, was compared with the standard BAM method, which requires 96 h room temperature incubation of whole shell egg samples followed by preenrichment in TSB supplemented with FeSO4. Four Salmonella ser. Enteritidis (4 phage types) and one Salmonella ser. Heidelberg isolates were used in the study. Bulk inoculated pooled liquid eggs, weighing 52 or 56 kg (approximately 1,100 eggs) were used in each trial. Twenty 1,000-g test portions were withdrawn from the pooled eggs for both the alternative and the reference methods. Test portions were inoculated with Salmonella at 1 to 5 cfu/1,000 g eggs. Two replicates were performed for each isolate. In the 8 trials conducted with Salmonella ser. Enteritidis, the alternative method was significantly (P < 0.05) more productive than the reference method in 3 trials, and significantly (P < 0.05) less productive than the reference method in 1 trial. There were no significant (P < 0.05) differences between the 2 methods for the other 4 trials. For Salmonella ser. Heidelberg, combined data from 2 trials showed the alternative method was significantly (P < 0.05) more efficient than the BAM method. We have concluded that the alternative method, described herein, has the potential to replace the current BAM culture method for detection and isolation of Salmonella from shell eggs based on the following factors: 1) the alternative method is 4 d shorter than the reference method; 2) it uses regular TSB instead of the more complicated TSB supplemented with FeSO4; and 3) it was equivalent or superior to the reference method in 9 out of 10 trials for the detection of Salmonella in shell eggs.

Implantation of In Vitro Tissue Engineered Muscle Repair Constructs and Bladder Acellular Matrices Partially Restore In Vivo Skeletal Muscle Function in a Rat Model of Volumetric Muscle Loss Injury

PubMed Central

Corona, Benjamin T.; Ward, Catherine L.; Baker, Hannah B.; Walters, Thomas J.

2014-01-01

The frank loss of a large volume of skeletal muscle (i.e., volumetric muscle loss [VML]) can lead to functional debilitation and presents a significant problem to civilian and military medicine. Current clinical treatment for VML involves the use of free muscle flaps and physical rehabilitation; however, neither are effective in promoting regeneration of skeletal muscle to replace the tissue that was lost. Toward this end, skeletal muscle tissue engineering therapies have recently shown great promise in offering an unprecedented treatment option for VML. In the current study, we further extend our recent progress (Machingal et al., 2011, Tissue Eng; Corona et al., 2012, Tissue Eng) in the development of tissue engineered muscle repair (TEMR) constructs (i.e., muscle-derived cells [MDCs] seeded on a bladder acellular matrix (BAM) preconditioned with uniaxial mechanical strain) for the treatment of VML. TEMR constructs were implanted into a VML defect in a tibialis anterior (TA) muscle of Lewis rats and observed up to 12 weeks postinjury. The salient findings of the study were (1) TEMR constructs exhibited a highly variable capacity to restore in vivo function of injured TA muscles, wherein TEMR-positive responders (n=6) promoted an ≈61% improvement, but negative responders (n=7) resulted in no improvement compared to nonrepaired controls, (2) TEMR-positive and -negative responders exhibited differential immune responses that may underlie these variant responses, (3) BAM scaffolds (n=7) without cells promoted an ≈26% functional improvement compared to uninjured muscles, (4) TEMR-positive responders promoted muscle fiber regeneration within the initial defect area, while BAM scaffolds did so only sparingly. These findings indicate that TEMR constructs can improve the in vivo functional capacity of the injured musculature at least, in part, by promoting generation of functional skeletal muscle fibers. In short, the degree of functional recovery observed following TEMR implantation (BAM+MDCs) was 2.3×-fold greater than that observed following implantation of BAM alone. As such, this finding further underscores the potential benefits of including a cellular component in the tissue engineering strategy for VML injury. PMID:24066899

Design of angle-resolved illumination optics using nonimaging bi-telecentricity for 193 nm scatterfield microscopy.

PubMed

Sohn, Martin Y; Barnes, Bryan M; Silver, Richard M

2018-03-01

Accurate optics-based dimensional measurements of features sized well-below the diffraction limit require a thorough understanding of the illumination within the optical column and of the three-dimensional scattered fields that contain the information required for quantitative metrology. Scatterfield microscopy can pair simulations with angle-resolved tool characterization to improve agreement between the experiment and calculated libraries, yielding sub-nanometer parametric uncertainties. Optimized angle-resolved illumination requires bi-telecentric optics in which a telecentric sample plane defined by a Köhler illumination configuration and a telecentric conjugate back focal plane (CBFP) of the objective lens; scanning an aperture or an aperture source at the CBFP allows control of the illumination beam angle at the sample plane with minimal distortion. A bi-telecentric illumination optics have been designed enabling angle-resolved illumination for both aperture and source scanning modes while yielding low distortion and chief ray parallelism. The optimized design features a maximum chief ray angle at the CBFP of 0.002° and maximum wavefront deviations of less than 0.06 λ for angle-resolved illumination beams at the sample plane, holding promise for high quality angle-resolved illumination for improved measurements of deep-subwavelength structures using deep-ultraviolet light.

Systematic review: the management of chronic diarrhoea due to bile acid malabsorption.

PubMed

Wilcox, C; Turner, J; Green, J

2014-05-01

Bile acid malabsorption (BAM) is a common, yet under-recognised, cause of chronic diarrhoea, with limited guidance available on the appropriate management of patients with BAM. To summarise the evidence supporting different treatments available for patients with bile acid malabsorption, noting their impact on clinical outcomes, tolerability and associated side effects. A literature search was conducted through PubMed, the Cochrane Database of Systematic Reviews and Scopus. Relevant articles studied patients who had been diagnosed with BAM and were clinically assessed before and after therapy. A total of 30 relevant publications (1241 adult patients) were identified, which investigated the clinical response to drugs, including colestyramine, colestipol, colesevelam, aluminium hydroxide and obeticholic acid. The most commonly used diagnostic test of bile acid malabsorption was the SeHCAT test (24 studies). Colestyramine treatment was by far the most studied of these agents, and was successful in 70% of 801 patients (range: 63-100%). Colestyramine and colestipol are generally effective treatments of gastrointestinal symptoms from BAM, but may be poorly tolerated and reduce the bioavailability of co-administered agents. Alternative therapies (including colesevelam and aluminium hydroxide) as well as dietary intervention may also have a role, and the promising results of the first proof-of-concept study of obeticholic acid suggest that its novel approach may have an exciting future in the treatment of this condition. Future trials should employ accurate diagnostic testing and be conducted over longer periods so that the long-term benefits and tolerability of these different approaches can be evaluated. © 2014 John Wiley & Sons Ltd.

Attenuation of skeletal muscle wasting with recombinant human growth hormone secreted from a tissue-engineered bioartificial muscle

NASA Technical Reports Server (NTRS)

Vandenburgh, H.; Del Tatto, M.; Shansky, J.; Goldstein, L.; Russell, K.; Genes, N.; Chromiak, J.; Yamada, S.

1998-01-01

Skeletal muscle wasting is a significant problem in elderly and debilitated patients. Growth hormone (GH) is an anabolic growth factor for skeletal muscle but is difficult to deliver in a therapeutic manner by injection owing to its in vivo instability. A novel method is presented for the sustained secretion of recombinant human GH (rhGH) from genetically modified skeletal muscle implants, which reduces host muscle wasting. Proliferating murine C2C12 skeletal myoblasts stably transduced with the rhGH gene were tissue engineered in vitro into bioartificial muscles (C2-BAMs) containing organized postmitotic myofibers secreting 3-5 microg of rhGH/day in vitro. When implanted subcutaneously into syngeneic mice, C2-BAMs delivered a sustained physiologic dose of 2.5 to 11.3 ng of rhGH per milliliter of serum. rhGH synthesized and secreted by the myofibers was in the 22-kDa monomeric form and was biologically active, based on downregulation of a GH-sensitive protein synthesized in the liver. Skeletal muscle disuse atrophy was induced in mice by hindlimb unloading, causing the fast plantaris and slow soleus muscles to atrophy by 21 to 35% ( < 0.02). This atrophy was significantly attenuated 41 to 55% (p < 0.02) in animals that received C2-BAM implants, but not in animals receiving daily injections of purified rhGH (1 mg/kg/day). These data support the concept that delivery of rhGH from BAMs may be efficacious in treating muscle-wasting disorders.

Synthesis and Characterization Materials M-Barium Hexaferrite Doping Ions Co-Mn Nano Particle

NASA Astrophysics Data System (ADS)

Susilawati; Doyan, A.; Sahlam

2017-05-01

This research has been success in the synthesis of M-Barium hexaferrite (BaM) doping Co-Mn ions using coprecipitation method are expected to be applied as a base material in the coating RADAR. M-Barium hexaferrite (BaM) are BaFe12-2xCoxMnxO19 synthesized with various concentrations (x = 0.0, 0.1, 0.2, 0.3) and the calcinations temperature (T = 400°C, 600°C, 800°C). The materials characterization using a X-Ray Diffraction (XRD), Transmission Electron Microscope (TEM), Inductance Capacitance and resistance (LCR) meter, and Vibrating Sample Magnetometer (VSM) Instruments. The measurement results using XRD shows the material has a hexagonal crystalline structure. The measurement results using a TEM show a sample of nano crystal materials with grain diameters up to 40 nm and spacing of the crystal lattice. The measurement results using a LCR-meter shows the electric conductivity of 1.15 × 10-6 S/cm to BaM without doping, 3.75 × 10-6 S/cm to 0.1 doping concentration calcination temperature of 400 °C, and 1,23 × 10-5 S/cm to 0.3 doping concentration calcination temperature of 800 °C, thus including semiconductor materials. The magnetic properties of materials using a VSM test results show the value of coercivity of 0.1 T; remanence value of 0.06 emu/g; and the saturation value of 0.42 emu/g. The results above show BaM Co-Mn metal doping potential as anti-radar material.

Molecularly imprinted phloroglucinol-formaldehyde-melamine resin prepared in a deep eutectic solvent for selective recognition of clorprenaline and bambuterol in urine.

PubMed

Liang, Shiru; Yan, Hongyuan; Cao, Jiankun; Han, Yehong; Shen, Shigang; Bai, Ligai

2017-01-25

A new molecularly imprinted phloroglucinol-formaldehyde-melamine resin (MIPFMR) was synthesized in a deep eutectic solvent (DES) using phenylephrine as a dummy template. The MIPFMR was used as a solid phase extraction (SPE) sorbent for the selective isolation and recognition of clorprenaline (CLP) and bambuterol (BAM) in urine. Phloroglucinol and melamine were used as double functional monomers that introduced abundant hydrophilic groups (such as hydroxyl groups, imino groups, and ether linkages) into the MIPFMR, making it compatible with aqueous solvents. In addition, the formation of DES by combining the quaternary ammonium salt of choline chloride with ethylene glycol as a hydrogen bond donor was an environmentally safe alternative to toxic organic solvents such as chloroform and dimethylsulfoxide that are typically used in the preparation of most molecularly imprinted polymers (MIPs). Moreover, MIPFMR-based SPE of CLP and BAM in urine resulted in higher recoveries and purer extracts than those obtained by using other SPE materials (e.g., SCX, C 18 , HLB, and non-imprinted phloroglucinol-formaldehyde-melamine resin (NIPFMR)). The optimized MIPFMR-SPE-HPLC-UV method had good linearity (r 2  ≥ 0.9996) ranging from 15.0 to 3000.0 ng mL -1 for CLP and BAM, and the recoveries at three spiked levels ranged from 91.7% to 100.1% with RSDs ≤7.6%. The novel MIPFMR-SPE-HPLC-UV method is simple, selective, and accurate, and can be used for the determination of CLP and BAM in urine samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Trends of Serum Electrolyte Changes in Crush syndrome patients of Bam Earthquake; a Cross sectional Study.

PubMed

Safari, Saeed; Eshaghzade, Mehdi; Najafi, Iraj; Baratloo, Alireza; Hashemi, Behrooz; Forouzanfar, Mohammad Mehdi; Rahmati, Farhad

2017-01-01

Electrolyte imbalances are very common among crushed earthquake victims but there is not enough data regarding their trend of changes. The present study was designed to evaluate the trend of changes in sodium, calcium, and phosphorus ions among crush syndrome patients. In this retrospective cross-sectional study, using the database of Bam earthquake victims, which was developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 10-day trend of sodium, calcium, and phosphorus ions changes in > 15 years old crush syndrome patients was evaluated. 118 patients with the mean age of 25.6 ± 6.9 years were studied (57.3 male). On the first day of admission, 52.5% (95% CI: 42.7 - 62.3) of the patients had hyponatremia, which reached 43.9% (95% CI: 28.5 - 59.3) on day 10. 100.0% of patients were hypocalcemic on admission and serum calcium level did not change dramatically during the 10 days of hospitalization. The prevalence of hyperphosphatemia on the first day was 90.5% (95% CI: 81.5 - 99.5) and on the 10 th day of hospitalization 66.7% (95% CI: 48.5 - 84.8) of the patients were still affected. The results of the present study shows the 52.5% prevalence of hyponatremia, 100% hypocalcemia, and 90.5% hyperphosphatemia among crush syndrome patients of Bam earthquake victims on the first day of admission. Evaluation of 10-day trend shows a slow decreasing pattern of these imbalances as after 10 days, 43.9% still remain hyponatremic, 92.3% hypocalcemic, and 66.7% hypophosphatemic.

Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

PubMed Central

Jourda, Cyril; Cardi, Céline; Gibert, Olivier; Giraldo Toro, Andrès; Ricci, Julien; Mbéguié-A-Mbéguié, Didier; Yahiaoui, Nabila

2016-01-01

Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage. PMID:27994606

Impact of leakage delay on bifurcation in high-order fractional BAM neural networks.

PubMed

Huang, Chengdai; Cao, Jinde

2018-02-01

The effects of leakage delay on the dynamics of neural networks with integer-order have lately been received considerable attention. It has been confirmed that fractional neural networks more appropriately uncover the dynamical properties of neural networks, but the results of fractional neural networks with leakage delay are relatively few. This paper primarily concentrates on the issue of bifurcation for high-order fractional bidirectional associative memory(BAM) neural networks involving leakage delay. The first attempt is made to tackle the stability and bifurcation of high-order fractional BAM neural networks with time delay in leakage terms in this paper. The conditions for the appearance of bifurcation for the proposed systems with leakage delay are firstly established by adopting time delay as a bifurcation parameter. Then, the bifurcation criteria of such system without leakage delay are successfully acquired. Comparative analysis wondrously detects that the stability performance of the proposed high-order fractional neural networks is critically weakened by leakage delay, they cannot be overlooked. Numerical examples are ultimately exhibited to attest the efficiency of the theoretical results. Copyright © 2017 Elsevier Ltd. All rights reserved.

In situ hybridisation of EBV DNA-DNA hybrids using wet heat in polypropylene containers.

PubMed Central

Labrecque, L G

1992-01-01

AIMS: To explore procedures designed to optimise DNA-DNA in situ hybridisation, using cells infected with Epstein-Barr virus (EBV) and tissues and subfragments of the EBV DNA as probes. METHODS: The denaturation step occurred in a polypropylene container, using wet heat generated by a hot water container, the pressure cooker, or the microwave oven, without coverslips, reaching a temperature of 121 degrees C or more in these two last systems. Two different visualisation systems were used. RESULTS: Fixed cells and tumours harbouring a high and medium to low copy number (a few hundreds to 33 copies per cell), were clearly labelled, using a simple reiterated subfragment (BamW) of the EBV DNA, and fresh frozen cells, harbouring a very low copy number (one to two on average) labelled using BamW as well as BamH (single non-reiterated 6 kilobase subfragment). CONCLUSION: This is a valuable alternative technique for DNA-DNA ISH that can be used in fresh frozen samples as well as fixed samples. Images PMID:1336018

Compositions and methods for detecting gene rearrangements and translocations

DOEpatents

Rowley, Janet D.; Diaz, Manuel O.

2000-01-01

Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.

A bat algorithm with mutation for UCAV path planning.

PubMed

Wang, Gaige; Guo, Lihong; Duan, Hong; Liu, Luo; Wang, Heqi

2012-01-01

Path planning for uninhabited combat air vehicle (UCAV) is a complicated high dimension optimization problem, which mainly centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. Original bat algorithm (BA) is used to solve the UCAV path planning problem. Furthermore, a new bat algorithm with mutation (BAM) is proposed to solve the UCAV path planning problem, and a modification is applied to mutate between bats during the process of the new solutions updating. Then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic BA. The realization procedure for original BA and this improved metaheuristic approach BAM is also presented. To prove the performance of this proposed metaheuristic method, BAM is compared with BA and other population-based optimization methods, such as ACO, BBO, DE, ES, GA, PBIL, PSO, and SGA. The experiment shows that the proposed approach is more effective and feasible in UCAV path planning than the other models.

Molecular cloning and physical mapping of the genome of fish lymphocystis disease virus.

PubMed

Darai, G; Delius, H; Clarke, J; Apfel, H; Schnitzler, P; Flügel, R M

1985-10-30

A defined and complete gene library of the fish lymphocystis disease virus (FLDV) genome was established. FLDV DNA was cleaved with EcoRI, BamHI, EcoRI/BamHI and EcoRI/HindIII and the resulting fragments were inserted into the corresponding sites of the pACYC184 or pAT153 plasmid vectors using T4 DNA ligase. Since FLDV DNA is highly methylated at CpG sequences (Darai et al., 1983; Wagner et al., 1985), an Escherichia coli GC-3 strain was required to amplify the recombinant plasmids harboring the FLDV DNA fragments. Bacterial colonies harboring recombinant plasmids were selected. All cloned fragments were individually identified by digestion of the recombinant plasmid DNA with different restriction enzymes and screened by hybridization of recombinant plasmid DNA to viral DNA. This analysis revealed that sequences representing 100% of the viral genome were cloned. Using these recombinant plasmids, the physical maps of the genome were constructed for BamHI, EcoRI, BestEII, and PstI restriction endonucleases. Although the FLDV genome is linear, due to circular permutation the restriction maps are circular.

Supramolecular architectures of iron phthalocyanine Langmuir-Blodgett films: The role played by the solution solvents

NASA Astrophysics Data System (ADS)

Rubira, Rafael Jesus Gonçalves; Aoki, Pedro Henrique Benites; Constantino, Carlos José Leopoldo; Alessio, Priscila

2017-09-01

The developing of organic-based devices has been widely explored using ultrathin films as the transducer element, whose supramolecular architecture plays a central role in the device performance. Here, Langmuir and Langmuir-Blodgett (LB) ultrathin films were fabricated from iron phthalocyanine (FePc) solutions in chloroform (CHCl3), dichloromethane (CH2Cl2), dimethylformamide (DMF), and tetrahydrofuran (THF) to determine the influence of different solvents on the supramolecular architecture of the ultrathin films. The UV-vis absorption spectroscopy shows a strong dependence of the FePc aggregation on these solvents. As a consequence, the surface pressure vs. mean molecular area (π-A) isotherms and Brewster angle microscopy (BAM) reveal a more homogeneous (surface morphology) Langmuir film at the air/water interface for FePc in DMF. The same morphological pattern observed for the Langmuir films is preserved upon LB deposition onto solid substrates. The Raman and FTIR analyses indicate the DMF-FePc interaction relies on coordination bonds between N atom (from DMF) and Fe atom (from FePc). Besides, the FePc molecular organization was also found to be affected by the DMF-FePc chemical interaction. It is interesting to note that, if the DMF-FePc leads to less aggregated FePc either in solution or ultrathin films (Langmuir and LB), with time (one week) the opposite trend is found. Taking into account the N-Fe interaction, the performance of the FePc ultrathin films with distinct supramolecular architectures composing sensing units was explored as proof-of-principle in the detection of trace amounts of atrazine herbicide in water using impedance spectroscopy. Further statistical and computational analysis reveal not only the role played by FePc supramolecular architecture but also the sensitivity of the system to detect atrazine solutions down to 10-10 mol/L, which is sufficient to monitor the quality of drinking water even according to the most stringent international regulations.

Global exponential stability analysis on impulsive BAM neural networks with distributed delays

NASA Astrophysics Data System (ADS)

Li, Yao-Tang; Yang, Chang-Bo

2006-12-01

Using M-matrix and topological degree tool, sufficient conditions are obtained for the existence, uniqueness and global exponential stability of the equilibrium point of bidirectional associative memory (BAM) neural networks with distributed delays and subjected to impulsive state displacements at fixed instants of time by constructing a suitable Lyapunov functional. The results remove the usual assumptions that the boundedness, monotonicity, and differentiability of the activation functions. It is shown that in some cases, the stability criteria can be easily checked. Finally, an illustrative example is given to show the effectiveness of the presented criteria.

Existence and global exponential stability of periodic solution to BAM neural networks with periodic coefficients and continuously distributed delays

NASA Astrophysics Data System (ADS)

Zhou, distributed delays [rapid communication] T.; Chen, A.; Zhou, Y.

2005-08-01

By using the continuation theorem of coincidence degree theory and Liapunov function, we obtain some sufficient criteria to ensure the existence and global exponential stability of periodic solution to the bidirectional associative memory (BAM) neural networks with periodic coefficients and continuously distributed delays. These results improve and generalize the works of papers [J. Cao, L. Wang, Phys. Rev. E 61 (2000) 1825] and [Z. Liu, A. Chen, J. Cao, L. Huang, IEEE Trans. Circuits Systems I 50 (2003) 1162]. An example is given to illustrate that the criteria are feasible.

Fundamental study of phosphor separation by controlling magnetic force

NASA Astrophysics Data System (ADS)

Wada, Kohei; Mishima, Fumihito; Akiyama, Yoko; Nishijima, Shigehiro

2013-11-01

The phosphor wastes consist of phosphors with different emission colors, green (LAP), red (YOX), blue (BAM) and white (HP). It is required to recover and reuse the rare earth phosphors with high market value. In this study, we tried to separate the phosphor using the magnetic separation by HTS bulk magnet utilizing the differences of magnetic susceptibility by the type of phosphors. We succeeded in the successive separation of HP with low market value from YOX and BAM including the rare earth using the magnetic Archimedes method. In this method, vertical and radial components of the magnetic force were used.

Comparison of Friction Characteristics on TN and VA Mode Alignment Films with Friction Force Microscopy

NASA Astrophysics Data System (ADS)

Kwak, Musun; Chung, Hanrok; Kwon, Hyukmin; Kim, Jehyun; Han, Daekyung; Yi, Yoonseon; Lee, Sangmun; Lee, Chulgu; Cha, Sooyoul

Using frictional force microscopy (FFM), the friction surface characteristics were compared between twisted nematic (TN) mode and vertical alignment (VA) mode alignment films (AFs). The friction asymmetry was detected depending on temperature conditions on TN mode AF, but not on VA mode AF. The difference between two modes was explained by leaning intermolecular repulsion caused by the pre-tilt angle uniformity and the density of side chain. No level difference according to temperature conditions appeared when the pre-tilt angle were measured after liquid crystal (LC) injection.

Morphology and crystallinity of ZnS nanocolumns prepared by glancing angle deposition.

PubMed

Lu, Lifang; Zhang, Fujun; Xu, Zheng; Zhao, Suling; Wang, Yongsheng

2010-03-01

ZnS films with different morphologies and nanometer structures were fabricated via high vacuum electron beam deposition by changing the oblique angle alpha between the incoming particle flux and the substrate normal. The morphology and crystallinity of ZnS nanocrystalline films prepared on the substrates at alpha = 0 degrees and 80 degrees were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray diffraction. These experimental results show that the ZnS nanocolumn structure was formed at the situation of alpha = 80 degrees. The incidence angle also strongly influenced the crystallinity of thin films. The most intensive diffraction peaks changed from (220) to (111) when the incidence angle was set to 0 degrees and 80 degrees. The dynamic growth process of ZnS films at alpha = 0 degrees and 80 degrees has been analyzed by shadow effect and atomic surface diffusion. The transmittance spectra of the ZnS thin films prepared at different oblique angles were measured, and the transmissivity of ZnS nanocolumn thin films was enhanced compared with ZnS thin films prepared by normal deposition in the visible light range.

Multicentre prospective survey of SeHCAT provision and practice in the UK.

PubMed

Summers, Jennifer A; Peacock, Janet; Coker, Bolaji; McMillan, Viktoria; Ofuya, Mercy; Lewis, Cornelius; Keevil, Stephen; Logan, Robert; McLaughlin, John; Reid, Fiona

2016-01-01

A clinical diagnosis of bile acid malabsorption (BAM) can be confirmed using SeHCAT (tauroselcholic ((75)selenium) acid), a radiolabelled synthetic bile acid. However, while BAM can be the cause of chronic diarrhoea, it is often overlooked as a potential diagnosis. Therefore, we investigated the use of SeHCAT for diagnosis of BAM in UK hospitals. A multicentre survey was conducted capturing centre and patient-level information detailing patient care-pathways, clinical history, SeHCAT results, treatment with bile acid sequestrants (BAS), and follow-up in clinics. Eligible data from 38 centres and 1036 patients were entered into a validated management system. SeHCAT protocol varied between centres, with no standardised patient positioning, and differing referral systems. Surveyed patients had a mean age of 50 years and predominantly women (65%). The mean SeHCAT retention score for all patients was 19% (95% CI 17.8% to 20.3%). However, this differed with suspected BAM type: type 1: 9% (95% CI 6.3% to 11.4%), type 2: 21% (95% CI 19.2% to 23.0%) and type 3: 22% (95% CI 19.6% to 24.2%). Centre-defined 'abnormal' and 'borderline' results represented over 50% of the survey population. BAS treatment was prescribed to only 73% of patients with abnormal results. The study identified a lack of consistent cut-off/threshold values, with differing centre criteria for defining an 'abnormal' SeHCAT result. BAS prescription was not related in a simple way to the SeHCAT result, nor to the centre-defined result, highlighting a lack of clear patient care-pathways. There is a clear need for a future diagnostic accuracy study and a better understanding of optimal management pathways.

Multicentre prospective survey of SeHCAT provision and practice in the UK

PubMed Central

Peacock, Janet; Coker, Bolaji; McMillan, Viktoria; Ofuya, Mercy; Lewis, Cornelius; Keevil, Stephen; Logan, Robert; McLaughlin, John; Reid, Fiona

2016-01-01

Objective A clinical diagnosis of bile acid malabsorption (BAM) can be confirmed using SeHCAT (tauroselcholic (75selenium) acid), a radiolabelled synthetic bile acid. However, while BAM can be the cause of chronic diarrhoea, it is often overlooked as a potential diagnosis. Therefore, we investigated the use of SeHCAT for diagnosis of BAM in UK hospitals. Design A multicentre survey was conducted capturing centre and patient-level information detailing patient care-pathways, clinical history, SeHCAT results, treatment with bile acid sequestrants (BAS), and follow-up in clinics. Eligible data from 38 centres and 1036 patients were entered into a validated management system. Results SeHCAT protocol varied between centres, with no standardised patient positioning, and differing referral systems. Surveyed patients had a mean age of 50 years and predominantly women (65%). The mean SeHCAT retention score for all patients was 19% (95% CI 17.8% to 20.3%). However, this differed with suspected BAM type: type 1: 9% (95% CI 6.3% to 11.4%), type 2: 21% (95% CI 19.2% to 23.0%) and type 3: 22% (95% CI 19.6% to 24.2%). Centre-defined ‘abnormal’ and ‘borderline’ results represented over 50% of the survey population. BAS treatment was prescribed to only 73% of patients with abnormal results. Conclusions The study identified a lack of consistent cut-off/threshold values, with differing centre criteria for defining an ‘abnormal’ SeHCAT result. BAS prescription was not related in a simple way to the SeHCAT result, nor to the centre-defined result, highlighting a lack of clear patient care-pathways. There is a clear need for a future diagnostic accuracy study and a better understanding of optimal management pathways. PMID:27252882

20-Day Trend of Serum Potassium Changes in Bam Earthquake Victims with Crush Syndrome; a Cross-sectional Study.

PubMed

Safari, Saeed; Najafi, Iraj; Hosseini, Mostafa; Baratloo, Alireza; Yousefifard, Mahmoud; Mohammadi, Hamidreza

2017-01-01

Many of those who survive following an earthquake die in the next phase due to preventable and treatable medical conditions such as hyperkalemia. The present study aimed to evaluate the trend of potassium changes in crush syndrome patients of Bam earthquake. In this retrospective cross-sectional study, using the database of Bam earthquake victims, which were developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 20-day trend of potassium changes in > 15 years old crush syndrome patients was evaluated. 135 crush syndrome patients with the mean age of 29.9 ± 9.91 years were evaluated (56.3% male). Mean potassium concentration during the first 3 days of admission was 5.6 ± 1.3 mEq/L. On the day of admission, 43.1% (95% CI: 34.0 - 52.2) had normal potassium concentration, 3.4% (95% CI: 0.1 - 6.8) had hypokalemia, and 53.4% (44.3 - 62.6) had hyperkalemia. During 20-day follow-up, 62.3% (95% CI: 66.7-71.9) of the patients had normal potassium. While, 11.5% (95% CI: 9.7-13.3) had hypokalemia and 19.2% (95% CI: 17.0-21.5) had hyperkalemia. As the days of hospitalization increased, prevalence of hyperkalemia decreased while hypokalemia increased. On the 17 th day 21.2% (95% CI: 2.2-39.9) had hypokalemia and 10.5% (95% CI: 0.1 - 24.7) had hyperkalemia. Findings of the present study showed that following urine alkalinization and fluid resuscitation, the prevalence of hyperkalemia reduced, but hypokalemia developed. It seems that the correction of serum potassium level should be accompanied by precise monitoring of intake and output of the patient and prescription of reasonable amount of intravenous fluid.

Motivating Latino caregivers of children with asthma to quit smoking: a randomized trial.

PubMed

Borrelli, Belinda; McQuaid, Elizabeth L; Novak, Scott P; Hammond, S Katharine; Becker, Bruce

2010-02-01

Secondhand smoke exposure is associated with asthma onset and exacerbation. Latino children have higher rates of asthma morbidity than other groups. The current study compared the effectiveness of a newly developed smoking cessation treatment with existing clinical guidelines for smoking cessation. Latino caregivers who smoked (N = 133; 72.9% female; mean age = 36.8 years) and had a child with asthma were randomly assigned to receive 1 of 2 smoking cessation counseling interventions during a home-based asthma program: (a) behavioral action model (BAM; modeled on clinical guidelines for smoking cessation) or (b) precaution adoption model (PAM; feedback on the caregiver's carbon monoxide level and child's secondhand smoke exposure using Motivational Interviewing). Counseling was delivered by a bilingual Latina health educator, and the content was tailored to Latino values and culture. It was not necessary for smokers to want to quit smoking to participate. Smoking cessation was biochemically verified and secondhand smoke exposure was objectively measured through passive nicotine monitors. Intent-to-treat analyses showed that 20.5% of participants in the PAM condition and 9.1% of those in the BAM condition were continuously abstinent at 2 months posttreatment (OR = 2.54; 95% CI = 0.91-7.10), whereas 19.1% of participants in the PAM condition and 12.3% of those in BAM condition were continuously abstinent at 3 months posttreatment (OR = 1.68; 95% CI = 0.64-4.37). Secondhand smoke exposure decreased only in the BAM condition (p < .001), an effect due to less smoking around the child among nonquitters in this condition. Asthma morbidity showed significant decreases in the posttreatment period for the PAM group only (p < .001). Results provide support for targeting specific populations with theory-based interventions.

Réalisation de couches minces magnétiques d'hexaferrite de baryum en vue de concevoir un isolateur coplanaire passif

NASA Astrophysics Data System (ADS)

Capraro, S.; Nader, C.; Chatelon, J. P.; Le Berre, M.; Rouiller, T.; Bayard, B.; Joisten, H.; Barbier, D.; Rousseau, J. J.

2005-05-01

Le développement des dispositifs intégrés employant un ferrite est un objectif majeur pour des applications électroniques dans la gamme hyperfréquence (circulateurs et isolateurs). Les ferrites hexagonaux, tel que l'hexaferrite de baryum (BaFe{12}O{19} ou BaM), présentent un grand intérêt pour de tels dispositifs en raison de leurs grandes résistivités et de leurs perméabilités élevées aux hautes fréquences. Dans cette étude, les couches minces de BaM, sont déposées et optimisées par pulvérisation cathodique RF sur des substrats d'alumine et de silicium. Après dépôt, les films sont amorphes et un recuit thermique à 800° C est nécessaire pour que les couches de BaM cristallisent et présentent des propriétés magnétiques. Les propriétés magnétiques des couches minces de BaM ont été déterminées par VSM, et on constate que le champ coercitif et l'aimantation à saturation atteignent respectivement 330 kA/m et 500 mT. Des isolateurs sont réalisés par dépôt d'une couche conductrice d'or en utilisant la technique du lift-off qui permet la mise en place du ruban signal ainsi que des plans de masse. Les premiers résultats de mesure en transmission ont montré un effet non réciproque qui atteint 8 dB/cm à 50 GHz.

Effect of Mas-related gene (Mrg) receptors on hyperalgesia in rats with CFA-induced inflammation via direct and indirect mechanisms.

PubMed

Jiang, Jianping; Wang, Dongmei; Zhou, Xiaolong; Huo, Yuping; Chen, Tingjun; Hu, Fenjuan; Quirion, Rémi; Hong, Yanguo

2013-11-01

Mas oncogene-related gene (Mrg) receptors are exclusively distributed in small-sized neurons in trigeminal and dorsal root ganglia (DRG). We investigated the effects of MrgC receptor activation on inflammatory hyperalgesia and its mechanisms. A selective MrgC receptor agonist, bovine adrenal medulla peptide 8-22 (BAM8-22) or melanocyte-stimulating hormone (MSH) or the μ-opioid receptor (MOR) antagonist CTAP was administered intrathecally (i.t.) in rats injected with complete Freund's adjuvant (CFA) in one hindpaw. Thermal and mechanical nociceptive responses were assessed. Neurochemicals were measured by immunocytochemistry, Western blot, ELISA and RT-PCR. CFA injection increased mRNA for MrgC receptors in lumbar DRG. BAM8-22 or MSH, given i.t., generated instant short and delayed long-lasting attenuations of CFA-induced thermal hyperalgesia, but not mechanical allodynia. These effects were associated with decreased up-regulation of neuronal NOS (nNOS), CGRP and c-Fos expression in the spinal dorsal horn and/or DRG. However, i.t. administration of CTAP blocked the induction by BAM8-22 of delayed anti-hyperalgesia and inhibition of nNOS and CGRP expression in DRG. BAM8-22 also increased mRNA for MORs and pro-opiomelanocortin, along with β-endorphin content in the lumbar spinal cord and/or DRG. MrgC receptors and nNOS were co-localized in DRG neurons. Activation of MrgC receptors suppressed up-regulation of pronociceptive mediators and consequently inhibited inflammatory pain, because of the activation of up-regulated MrgC receptors and subsequent endogenous activity at MORs. The uniquely distributed MrgC receptors could be a novel target for relieving inflammatory pain. © 2013 The British Pharmacological Society.

Evaluation of PCR detection of Salmonella in alfalfa sprouts and spent irrigation water collected during sprouting of naturally contaminated seed.

PubMed

Maks, Nicole; Fu, Tong-Jen

2013-02-01

This study evaluated the efficacy of a PCR-based system (DuPont Qualicon BAX) for detection of Salmonella in sprouts and spent irrigation water collected during sprouting of seeds naturally contaminated with Salmonella. Alfalfa seeds were grown in Mason jars at 20 and 30°C for 3 days. Levels of Salmonella present in the water and sprouts were determined by most-probable-number (MPN) analysis. Background microflora levels were also determined. Samples of spent irrigation water and sprouts were enriched overnight individually in tetrathionate broth and in buffered peptone water with novobiocin at 42°C and then run in the BAX system. Samples were also enriched according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA BAM) method for Salmonella as a comparison. Salmonella levels were lower at 20°C compared with 30°C for some trials, and background microflora levels ranged from 10(7) to 10(8) CFU/g or ml at 20°C and 10(8) to 10(9) CFU/g or ml at 30°C. In trials with a Salmonella level >1.1 MPN/g or ml, both the BAX and FDA BAM methods were able to detect Salmonella in all samples. In trials with lower levels (0.21 MPN/g or ml or lower) of Salmonella, BAX was able to detect more positive samples than FDA BAM. For one trial with <0.003 MPN/g or ml of Salmonella, the presence of the pathogen was not indicated by either the BAX or the FDA BAM method. The results suggest that PCR detected low levels of Salmonella in sprouts or spent irrigation water collected from sprouting of naturally contaminated seeds.

Topography of Cells Revealed by Variable-Angle Total Internal Reflection Fluorescence Microscopy.

PubMed

Cardoso Dos Santos, Marcelina; Déturche, Régis; Vézy, Cyrille; Jaffiol, Rodolphe

2016-09-20

We propose an improved version of variable-angle total internal reflection fluorescence microscopy (vaTIRFM) adapted to modern TIRF setup. This technique involves the recording of a stack of TIRF images, by gradually increasing the incident angle of the light beam on the sample. A comprehensive theory was developed to extract the membrane/substrate separation distance from fluorescently labeled cell membranes. A straightforward image processing was then established to compute the topography of cells with a nanometric axial resolution, typically 10-20 nm. To highlight the new opportunities offered by vaTIRFM to quantify adhesion process of motile cells, adhesion of MDA-MB-231 cancer cells on glass substrate coated with fibronectin was examined. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Self-organization of a wedge-shaped surfactant in monolayers and multilayers.

PubMed

Cain, Nicholas; Van Bogaert, Josh; Gin, Douglas L; Hammond, Scott R; Schwartz, Daniel K

2007-01-16

The self-organization behavior of a wedge-shaped surfactant, disodium-3,4,5-tris(dodecyloxy)phenylmethylphosphonate, was studied in Langmuir monolayers (at the air-water interface), Langmuir-Blodgett (LB) monolayers and multilayers, and films adsorbed spontaneously from isooctane solution onto a mica substrate (self-assembled films). This compound forms an inverted hexagonal lyotropic liquid crystal phase in the bulk and in thick adsorbed films. Surface pressure isotherm and Brewster angle microscope (BAM) studies of Langmuir monolayers revealed three phases: gas (G), liquid expanded (LE), and liquid condensed (LC). The surface pressure-temperature phase diagram was determined in detail; a triple point was found at approximately 10 degrees C. Atomic force microscope (AFM) images of LB monolayers transferred from various regions of the phase diagram were consistent with the BAM images and indicated that the LE regions are approximately 0.5 nm thinner than the LC regions. AFM images were also obtained of self-assembled films after various adsorption times. For short adsorption times, when monolayer self-assembly was incomplete, the film topography indicated the coexistence of two distinct monolayer phases. The height difference between these two phases was again 0.5 nm, suggesting a correspondence with the LE/LC coexistence observed in the Langmuir monolayers. For longer immersion times, adsorbed multilayers assembled into highly organized periodic arrays of inverse cylindrical micelles. Similar periodic structures, with the same repeat distance of 4.5 nm, were also observed in three-layer LB films. However, the regions of organized periodic structure were much smaller and more poorly correlated in the LB multilayers than in the films adsorbed from solution. Collectively, these observations indicate a high degree of similarity between the molecular organization in Langmuir layers/LB films and adsorbed self-assembled films. In both cases, monolayers progress through an LE phase, into LE/LC coexistence, and finally into LC phase as surface density increases. Following the deposition of an additional bilayer, the film reorganizes to form an array of inverted cylindrical micelles.

{l_angle}110{r_angle} dendrite growth in aluminum feathery grains

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

Henry, S.; Rappaz, M.; Jarry, P.

1998-11-01

Automatic indexing of electron backscattered diffraction patterns, scanning electron microscopy, and optical microscopy observations have been carried out on aluminum-magnesium-silicon, aluminum-copper, and aluminum-silicon alloys directionally solidified or semicontinuously cast using the direct chill casting process. From these combined observations, it is shown that the feathery grains are made of {l_angle}110{r_angle} primary dendrite trunks (e.g., [011{bar 1}]) split in their centers by a coherent (111) twin plane. The average spacing of the dendrite trunks in the twin plane (about 10 to 20 {micro}m) is typically one order of magnitude smaller than that separating successive rows of trunks (or twin planes). Themore » [011{bar 1}] orientation of these trunks is close to the thermal gradient direction (typically within 15 deg)--a feature probably resulting from a growth competition mechanism similar to that occurring during normal <100> columnar dendrite growth. On both sides of these trunks, secondary dendrite arms also grow along {l_angle}110{r_angle} directions. Their impingement creates wavy noncoherent twin boundaries between the coherent twin planes. In the twin plane, evidence is shown that {l_angle}110{r_angle} branching mechanisms lead to the propagation of the twinned regions, to the regular arrangement of the primary dendrite trunks along a [{bar 2}11] direction, and to coherent planar twin boundaries. From these observations, it is concluded that the feathery grains are probably the result of a change from a normal <100> to a {l_angle}110{r_angle} surface tension/attachment kinetics anisotropy growth mode. Finally, the proposed mechanisms of leathery grain growth are further supported by the observation of {l_angle}110{r_angle} dendrite growth morphologies in thin aluminum-zinc coatings.« less

Superhydrophobicity of hierarchical nanostructure of candle soot films

NASA Astrophysics Data System (ADS)

Hankhuntond, A.; Singjai, P.; Sakulsermsuk, S.

2017-09-01

Candle soot containing carbon nanoparticles can form hierarchical structure films. We prepared soot films by using glass slides blocking candle flame in the middle of the flame. The hierarchical nanostructures of the carbon nanoparticles films were confirmed by scanning electron microscopy and transmission electron microscopy. Carbon nanoparticle size was 49.2 ± 9.0 nm from SEM, which agrees to 37.9 ± 8.5 nm from TEM. The contact angles of water droplets on these films are more than 150°, indicating superhydrophobic surface. Decrease contact angles of water droplets were observed with an increase deposition time. The decrease of contact angle was saturated at about 150° when the deposition time reaches 180 s. Cassie-Baxter state was attributed to describe superhydrophobicity of carbon nanoparticles films because the hierarchical nanostructures of the surface provide a large fraction of hollows on the surface. We proposed that the contact angle dependence on deposition time was governed by the increase of the distance between nanopillars in carbon nanoparticles films.

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

PubMed Central

Wala, Jeremiah; Beroukhim, Rameen

2017-01-01

Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

A Bat Algorithm with Mutation for UCAV Path Planning

PubMed Central

Wang, Gaige; Guo, Lihong; Duan, Hong; Liu, Luo; Wang, Heqi

2012-01-01

Path planning for uninhabited combat air vehicle (UCAV) is a complicated high dimension optimization problem, which mainly centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. Original bat algorithm (BA) is used to solve the UCAV path planning problem. Furthermore, a new bat algorithm with mutation (BAM) is proposed to solve the UCAV path planning problem, and a modification is applied to mutate between bats during the process of the new solutions updating. Then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic BA. The realization procedure for original BA and this improved metaheuristic approach BAM is also presented. To prove the performance of this proposed metaheuristic method, BAM is compared with BA and other population-based optimization methods, such as ACO, BBO, DE, ES, GA, PBIL, PSO, and SGA. The experiment shows that the proposed approach is more effective and feasible in UCAV path planning than the other models. PMID:23365518

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

PubMed

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Optical metrology for DMD™ characterization

NASA Astrophysics Data System (ADS)

Miller, Seth A.; Mezenner, Rabah; Doane, Dennis

2001-01-01

The Digital Micromirror Device™ (DMD™) developed at Texas Instruments is a spatial light modulator composed of 500,000 to 1.3 million movable micromachined aluminum mirrors. The DMD™ serves as the engine for the current generation of computer-driven slide and video projectors, and for next generation devices in digital television and movie projectors. Because of the unique architecture and applications of the device, Texas Instruments has developed a series of customized optical testers for characterizing DMD™ performance. This paper provides a general overview of the MirrorMaster, a custom optical inspection tool. Particular attention is given to Bias Adhesion Mapping (BAM) as a device performance metric. BAM is an optical test that monitors the performance of the mirrors as a function of an applied voltage. This voltage drives the mirrors to the `on' or `off' position, and as the bias is stepped down the mirrors return to their neutral orientations. Important forces involved in this process include the electrostatic field applied, the compliance of the hinge, and static friction (stiction). BAM curves can help characterize device stiction and allow us to examine the efficacy of the lubrication system over the lifetime of the device.

Monohalogenated acetamide-induced cellular stress and genotoxicity are related to electrophilic softness and thiol/thiolate reactivity.

PubMed

Pals, Justin A; Wagner, Elizabeth D; Plewa, Michael J; Xia, Menghang; Attene-Ramos, Matias S

2017-08-01

Haloacetamides (HAMs) are cytotoxic, genotoxic, and mutagenic byproducts of drinking water disinfection. They are soft electrophilic compounds that form covalent bonds with the free thiol/thiolate in cysteine residues through an S N 2 reaction mechanism. Toxicity of the monohalogenated HAMs (iodoacetamide, IAM; bromoacetamide, BAM; or chloroacetamide, CAM) varied depending on the halogen substituent. The aim of this research was to investigate how the halogen atom affects the reactivity and toxicological properties of HAMs, measured as induction of oxidative/electrophilic stress response and genotoxicity. Additionally, we wanted to determine how well in silico estimates of electrophilic softness matched thiol/thiolate reactivity and in vitro toxicological endpoints. Each of the HAMs significantly induced nuclear Rad51 accumulation and ARE signaling activity compared to a negative control. The rank order of effect was IAM>BAM>CAM for Rad51, and BAM≈IAM>CAM for ARE. In general, electrophilic softness and in chemico thiol/thiolate reactivity provided a qualitative indicator of toxicity, as the softer electrophiles IAM and BAM were more thiol/thiolate reactive and were more toxic than CAM. Copyright © 2017. Published by Elsevier B.V.

Visually testing the dynamic character of a blazed-angle adjustable grating by digital holographic microscopy.

PubMed

Qin, Chuan; Zhao, Jianlin; Di, Jianglei; Wang, Le; Yu, Yiting; Yuan, Weizheng

2009-02-10

We employed digital holographic microscopy to visually test microoptoelectromechanical systems (MOEMS). The sample is a blazed-angle adjustable grating. Considering the periodic structure of the sample, a local area unwrapping method based on a binary template was adopted to demodulate the fringes obtained by referring to a reference hologram. A series of holograms at different deformation states due to different drive voltages were captured to analyze the dynamic character of the MOEMS, and the uniformity of different microcantilever beams was also inspected. The results show this testing method is effective for a periodic structure.

Three-dimensional imaging of individual point defects using selective detection angles in annular dark field scanning transmission electron microscopy.

PubMed

Johnson, Jared M; Im, Soohyun; Windl, Wolfgang; Hwang, Jinwoo

2017-01-01

We propose a new scanning transmission electron microscopy (STEM) technique that can realize the three-dimensional (3D) characterization of vacancies, lighter and heavier dopants with high precision. Using multislice STEM imaging and diffraction simulations of β-Ga 2 O 3 and SrTiO 3 , we show that selecting a small range of low scattering angles can make the contrast of the defect-containing atomic columns substantially more depth-dependent. The origin of the depth-dependence is the de-channeling of electrons due to the existence of a point defect in the atomic column, which creates extra "ripples" at low scattering angles. The highest contrast of the point defect can be achieved when the de-channeling signal is captured using the 20-40mrad detection angle range. The effect of sample thickness, crystal orientation, local strain, probe convergence angle, and experimental uncertainty to the depth-dependent contrast of the point defect will also be discussed. The proposed technique therefore opens new possibilities for highly precise 3D structural characterization of individual point defects in functional materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Formation mechanisms for the dominant kinks with different angles in InP nanowires.

PubMed

Zhang, Minghuan; Wang, Fengyun; Wang, Chao; Wang, Yiqian; Yip, SenPo; Ho, Johnny C

2014-01-01

The morphologies and microstructures of kinked InP nanowires (NWs) prepared by solid-source chemical vapor deposition method were examined using scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). Statistical analysis and structural characterization reveal that four different kinds of kinks are dominant in the grown InP NWs with a bending angle of approximately 70°, 90°, 110°, and 170°, respectively. The formation mechanisms of these kinks are discussed. Specifically, the existence of kinks with bending angles of approximately 70° and 110° are mainly attributed to the occurrence of stacking faults and nanotwins in the NWs, which could easily form by the glide of {111} planes, while approximately 90° kinks result from the local amorphorization of InP NWs. Also, approximately 170° kinks are mainly caused by small-angle boundaries, where the insertion of extra atomic planes could make the NWs slightly bent. In addition, multiple kinks with various angles are also observed. Importantly, all these results are beneficial to understand the formation mechanisms of kinks in compound semiconductor NWs, which could guide the design of nanostructured materials, morphologies, microstructures, and/or enhanced mechanical properties.

Formation mechanisms for the dominant kinks with different angles in InP nanowires

PubMed Central

2014-01-01

The morphologies and microstructures of kinked InP nanowires (NWs) prepared by solid-source chemical vapor deposition method were examined using scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). Statistical analysis and structural characterization reveal that four different kinds of kinks are dominant in the grown InP NWs with a bending angle of approximately 70°, 90°, 110°, and 170°, respectively. The formation mechanisms of these kinks are discussed. Specifically, the existence of kinks with bending angles of approximately 70° and 110° are mainly attributed to the occurrence of stacking faults and nanotwins in the NWs, which could easily form by the glide of {111} planes, while approximately 90° kinks result from the local amorphorization of InP NWs. Also, approximately 170° kinks are mainly caused by small-angle boundaries, where the insertion of extra atomic planes could make the NWs slightly bent. In addition, multiple kinks with various angles are also observed. Importantly, all these results are beneficial to understand the formation mechanisms of kinks in compound semiconductor NWs, which could guide the design of nanostructured materials, morphologies, microstructures, and/or enhanced mechanical properties. PMID:24910572

Two-photon microscopy for real-time monitoring of focused ultrasound-mediated drug delivery to the brain in a mouse model of Alzheimer's disease

NASA Astrophysics Data System (ADS)

Burgess, Alison; Eterman, Naomi; Aubert, Isabelle; Hynynen, Kullervo

2013-02-01

There is substantial evidence that focused ultrasound (FUS) in combination with microbubble contrast agent can cause disruption of the blood-brain barrier (BBB) to aid in drug delivery to the brain. We have previously demonstrated that FUS efficiently delivers antibodies against amyloid-β peptides (Aβ) through the BBB, leading to a reduction in amyloid pathology at 4 days in a mouse model of Alzheimer's disease. In the current study, we used two-photon microscopy to characterize the effect of FUS in real time on amyloid pathology in the mouse brain. Mice were anesthetized and a cranial window was made in the skull. A custom-built ultrasound transducer was fixed to a coverslip and attached to the skull, covering the cranial window. Methoxy-X04 [2-5mg/kg] delivered intravenously 1 hr prior to the experiment clearly labelled the Aβ surrounding the vessels and the amyloid plaques in the cortex. Dextran conjugated Texas Red (70kDa) administered intravenously, confirmed BBB disruption. BBB disruption occurred in transgenic and non-transgenic animals at similar ultrasound pressures tested. However, the time required for BBB closure following FUS was longer in the Tg mice. We have conjugated Aβ antibodies to the fluorescent molecule FITC for real time monitoring of the antibody distribution in the brain. Our current experiments are aimed at optimizing the parameters to achieve maximal fluorescent intensity of the BAM10 antibody at the plaque surface. Two-photon microscopy has proven to be a valuable tool for evaluating the efficacy of FUS mediated drug delivery, including antibodies, to the Alzheimer brain.

Paraconsistent Annotated Logic in Viability Analysis: an Approach to Product Launching

NASA Astrophysics Data System (ADS)

Romeu de Carvalho, Fábio; Brunstein, Israel; Abe, Jair Minoro

2004-08-01

In this paper we present an application of the Para-analyzer, a logical analyzer based on the Paraconsistent Annotated Logic Pτ, introduced by Da Silva Filho and Abe in the decision-making systems. An example is analyzed in detail showing how uncertainty, inconsistency and paracompleteness can be elegantly handled with this logical system. As application for the Para-analyzer in decision-making, we developed the BAM — Baricenter Analysis Method. In order to make the presentation easier, we present the BAM applied in the viability analysis of product launching. Some of the techniques of Paraconsistent Annotated Logic have been applied in Artificial Intelligence, Robotics, Information Technolgy (Computer Sciences), etc..

Indexcov: fast coverage quality control for whole-genome sequencing.

PubMed

Pedersen, Brent S; Collins, Ryan L; Talkowski, Michael E; Quinlan, Aaron R

2017-11-01

The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license. © The Authors 2017. Published by Oxford University Press.

High-angle annular dark field scanning transmission electron microscopy on carbon-based functional polymer systems.

PubMed

Sourty, Erwan; van Bavel, Svetlana; Lu, Kangbo; Guerra, Ralph; Bar, Georg; Loos, Joachim

2009-06-01

Two purely carbon-based functional polymer systems were investigated by bright-field conventional transmission electron microscopy (CTEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). For a carbon black (CB) filled polymer system, HAADF-STEM provides high contrast between the CB agglomerates and the polymer matrix so that details of the interface organization easily can be revealed and assignment of the CB phase is straightforward. For a second system, the functional polymer blend representing the photoactive layer of a polymer solar cell, details of its nanoscale organization could be observed that were not accessible with CTEM. By varying the camera length in HAADF-STEM imaging, the contrast can be enhanced between crystalline and amorphous compounds due to diffraction contrast so that nanoscale interconnections between domains are identified. In general, due to its incoherent imaging characteristics HAADF-STEM allows for reliable interpretation of the data obtained.

Nutrient analysis of the Beef Alternative Merchandising cuts.

PubMed

Desimone, T L; Acheson, R A; Woerner, D R; Engle, T E; Douglass, L W; Belk, K E

2013-03-01

The objective of this study was to generate raw and cooked nutrient composition data to identify Quality Grade differences in proximate values for eight Beef Alternative Merchandising (BAM) cuts. The data generated will be used to update the nutrient data in the USDA National Nutrient Database for Standard Reference (SR). Beef Rib, Oven-Prepared, Beef Loin, Strip Loin, and Beef Loin, Top Sirloin Butt subprimals were collected from a total of 24 carcasses from four packing plants. The carcasses were a combination of USDA Yield Grades 2 (n=12) and 3 (n=12), USDA Quality Grades upper two-thirds Choice (n=8), low Choice (n=8), and Select (n=8), and two genders, steer (n=16) and heifer (n=8). After aging, subprimals were fabricated into the BAM cuts, dissected, and nutrient analysis was performed. Sample homogenates from each animal were homogenized and composited for analysis of the following: proximate analysis, long chain and trans-fatty acids, conjugated linoleic acid, total cholesterol, vitamin B-12, and selenium. This study identified seven BAM cuts from all three Quality Grades that qualify for USDA Lean; seven Select cuts that qualify for USDA Extra Lean; and three Select cuts that qualify for the American Heart Association's Heart Healthy Check. Copyright © 2012 Elsevier Ltd. All rights reserved.

Maternal expectations and postpartum emotional adjustment in first-time mothers: results of a questionnaire survey.

PubMed

Henshaw, Erin J; Fried, Rachel; Teeters, Jenni Beth; Siskind, Emily E

2014-09-01

Several predictors of postpartum mood have been identified in the literature, but the role of maternal expectations in postpartum mental health remains unclear. The aim of this study was to identify whether maternal expectations during the postpartum hospital stay predict adjustment and depressive symptoms at 6 weeks postpartum. The sample included 233 first-time mothers recruited from the postpartum unit of a Midwestern hospital. Participants completed measures of maternal expectations and depressive symptoms (EPDS) at Time 1 (2 d postpartum) and completed EPDS and an Emotional Adjustment Scale (BaM-13) at Time 2 (6 weeks postpartum). A conditional relationship between the expectation that an infant's behavior will reflect maternal skill and Time 2 outcomes (BaM-13 and EPDS) was found, such that endorsing this belief predicted increased depression and poorer adjustment in those with higher (but not lower) Time 1 EPDS scores. Time 2 BaM-13 scores were also negatively predicted by expectations of self-sacrifice and positively predicted by expectations that parenthood would be naturally fulfilling. The expectations that new mothers hold about parenting soon after delivery are predictive of emotional adjustment in the early postpartum period, suggesting a role for discussion of expectations in future preventive strategies.

Targeting human Mas-related G protein-coupled receptor X1 to inhibit persistent pain

PubMed Central

Li, Zhe; Tseng, Pang-Yen; Tiwari, Vinod; Xu, Qian; He, Shao-Qiu; Wang, Yan; Zheng, Qin; Han, Liang; Wu, Zhiping; Blobaum, Anna L.; Cui, Yiyuan; Tiwari, Vineeta; Sun, Shuohao; Cheng, Yingying; Huang-Lionnet, Julie H. Y.; Geng, Yixun; Xiao, Bo; Peng, Junmin; Hopkins, Corey; Raja, Srinivasa N.; Guan, Yun; Dong, Xinzhong

2017-01-01

Human Mas-related G protein-coupled receptor X1 (MRGPRX1) is a promising target for pain inhibition, mainly because of its restricted expression in nociceptors within the peripheral nervous system. However, constrained by species differences across Mrgprs, drug candidates that activate MRGPRX1 do not activate rodent receptors, leaving no responsive animal model to test the effect on pain in vivo. Here, we generated a transgenic mouse line in which we replaced mouse Mrgprs with human MrgprX1. This humanized mouse allowed us to characterize an agonist [bovine adrenal medulla 8–22 (BAM8–22)] and a positive allosteric modulator (PAM), ML382, of MRGPRX1. Cellular studies suggested that ML382 enhances the ability of BAM8–22 to inhibit high-voltage-activated Ca2+ channels and attenuate spinal nociceptive transmission. Importantly, both BAM8–22 and ML382 effectively attenuated evoked, persistent, and spontaneous pain without causing obvious side effects. Notably, ML382 by itself attenuated both evoked pain hypersensitivity and spontaneous pain in MrgprX1 mice after nerve injury without acquiring coadministration of an exogenous agonist. Our findings suggest that humanized MrgprX1 mice provide a promising preclinical model and that activating MRGPRX1 is an effective way to treat persistent pain. PMID:28223516

Evaluation of BAM (butorphanol-azaperone-medetomidine) in captive African lion (Panthera leo) immobilization.

PubMed

Semjonov, Aleksandr; Andrianov, Vladimir; Raath, Jacobus P; Orro, Toomas; Venter, Derik; Laubscher, Liesel; Pfitzer, Silke

2017-07-01

The combination of butorphanol, azaperone and medetomidine (BAM) with subsequent antagonism by naltrexone-yohimbine or naltrexone-atipamezole was evaluated for reversible immobilization of captive African lions (Panthea leo). Prospective, clinical trial. Twenty lions, 11 males and nine females, weighing 38-284 kg were immobilized in South Africa. The BAM volume dose rate administered was 0.005-0.008 mL kg -1 (0.6 mL 100 kg -1 ). Physiologic variables were recorded every 5 minutes. Four arterial blood samples were collected from all animals at 20, 30, 40 and 50 minutes after immobilization for analysis of blood-gases and acid-base status. The actual doses administered were as follows: butorphanol, 0.18±0.03 mg kg -1 ; azaperone, 0.07±0.01 mg kg -1 ; and medetomidine, 0.07±0.01 mg kg -1 . The inductions were calm and smooth, and induction time ranged from 4 to 10 minutes (7±2 minutes). The amount of time needed to work with each lion was 70 minutes, and no additional drug doses were needed. Heart rate (40±8 beats minute -1 ) and respiratory frequency (15±4 breaths minute -1 ) were stable throughout immobilization. The mean arterial blood pressure of all animals was stable but elevated (142±16 mmHg). The rectal temperature slightly increased over time but remained within acceptable range. The recovery time was significantly shorter when using naltrexone and atipamezole (9±1 minutes) compared to using naltrexone and yohimbine (22±7 minutes). The BAM combination proved to be reliable for general veterinary anaesthesia in lions. During anaesthesia, minor veterinary procedures such a blood collection, intubation, vaccination and collaring could safely be performed with no additional dosing required. Copyright © 2017 Association of Veterinary Anaesthetists and American College of Veterinary Anesthesia and Analgesia. Published by Elsevier Ltd. All rights reserved.

Toxicological and biochemical characterizations of AChE in phosalone-susceptible and resistant populations of the common pistachio psyllid, Agonoscena pistaciae

PubMed Central

Alizadeh, Ali; Talebi-Jahromi, Khalil; Hosseininaveh, Vahid; Ghadamyari, Mohammad

2014-01-01

Abstract The toxicological and biochemical characteristics of acetylcholinesterases (AChE) in nine populations of the common pistachio psyllid, Agonoscena pistaciae Burckhardt and Lauterer (Hemiptera: Psyllidae), were investigated in Kerman Province, Iran. Nine A. pistaciae populations were collected from pistachio orchards, Pistacia vera L. (Sapindales: Anacardiaceae), located in Rafsanjan, Anar, Bam, Kerman, Shahrbabak, Herat, Sirjan, Pariz, and Paghaleh regions of Kerman province. The previous bioassay results showed these populations were susceptible or resistant to phosalone, and the Rafsanjan population was most resistant, with a resistance ratio of 11.3. The specific activity of AChE in the Rafsanjan population was significantly higher than in the susceptible population (Bam). The affinity ( KM ) and hydrolyzing efficiency ( Vmax ) of AChE on acetylthiocholine iodide, butyrylthiocholine iodide, and propionylthiocholine odide as artificial substrates were clearly lower in the Bam population than that in the Rafsanjan population. These results indicated that the AChE of the Rafsanjan population had lower affinity to these substrates than that of the susceptible population. The higher Vmax value in the Rafsanjan population compared to the susceptible population suggests a possible over expression of AChE in the Rafsanjan population. The in vitro inhibitory effect of several organophosphates and carbamates on AChE of the Rafsanjan and Bam populations was determined. Based on I50, the results showed that the ratios of AChE insensitivity of the resistant to susceptible populations were 23 and 21.7-fold to monocrotophos and phosphamidon, respectively. Whereas, the insensitivity ratios for Rafsanjan population were 0.86, 0.8, 0.78, 0.46, and 0.43 for carbaryl, eserine, propoxur, m-tolyl methyl carbamate, and carbofuran, respectively, suggesting negatively correlated sensitivity to organophosphate-insensitive AChE. Therefore, AChE from the Rafsanjan population showed negatively correlated sensitivity, being insensitive to phosphamidon and monocrotophos and sensitive to N -methyl carbamates. PMID:25373165

Three-dimensional image formation in fiber-optical second-harmonic-generation microscopy.

PubMed

Gu, Min; Fu, Ling

2006-02-06

Three-dimensional (3-D) image formation in fiber-optical second-harmonic-generation microscopy is revealed to be purely coherent and therefore can be described by a 3-D coherent transfer function (CTF) that exhibits the same spatial frequency passband as that of fiber-optical reflection-mode non-fluorescence microscopy. When the numerical aperture of the fiber is much larger than the angle of convergence of the illumination on the fiber aperture, the performance of fiber-optical second-harmonic-generation microscopy behaves as confocal second-harmonic-generation microscopy. The dependence of axial resolution on fiber coupling parameters shows an improvement of approximately 7%, compared with that in fiber-optical two-photon fluorescence microscopy.

Growth and high rate reactive ion etching of epitaxially grown barium hexaferrite films on single crystal silicon carbide substrates

NASA Astrophysics Data System (ADS)

Chen, Zhaohui

Ferrites are an invaluable group of insulating magnetic materials used for high frequency microwave applications in such passive electronic devices as isolators, phase shifters, and circulators. Because of their high permeability, non-reciprocal electromagnetic properties, and low eddy current losses, there are no other materials that serve such a broad range of applications. Until recently, they have been widely employed in bulk form, with little success in thin film-based applications in commercial or military microwave technologies. In today's technology, emerging electronic systems, such as high frequency, high power wireless and satellite communications (GPS, Bluetooth, WLAN, commercial radar, etc) thin film materials are in high demand. It is widely recognized that as high frequency devices shift to microwave frequencies the integration of passive devices with semiconductor electronics holds significant advantages in the realization of miniaturization, broader bandwidths, higher performance, speed, power and lower production costs. Thus, the primary objective of this thesis is to explore the integration of ferrite films with wide band gap semiconductor substrates for the realization of monolithic integrated circuits (MICs). This thesis focuses on two key steps for the integration of barium hexaferrite (Ba M-type or BaM) devices on semiconductor substrates. First, the development of high crystal quality ferrite film growth via pulsed laser deposition on wide band gap silicon carbide semiconductor substrates, and second, the effective patterning of BaM films using dry etching techniques. To address part one, BaM films were deposited on 6H silicon carbide (0001) substrates by Pulsed Laser Deposition. X-ray diffraction showed strong crystallographic alignment while pole figures exhibited reflections consistent with epitaxial growth. After optimized annealing, BaM films have a perpendicular magnetic anisotropy field of 16,900 Oe, magnetization (4piMs) of 4.4 kG, and ferromagnetic resonance peak-to-peak derivative linewidth at 53 GHz of 96 Oe. This combination of properties qualifies these films for microwave device applications. This marks the first growth of a microwave ferrite on SiC substrates and offers a new approach in the design and development of mu-wave and mm-wave monolithic integrated circuits. In part two, high-rate reactive ion etching using CHF3/SF6 gas mixtures was successfully demonstrated on BaM films, resulting in high aspect profile features of less than 50 nm in lateral dimension. These demonstrations enable the future integration of ferrites into MIC devices and technologies.

Molecular Beam Epitaxy Integration of Magnetic Ferrites with Wide Bandgap Semiconductor 6Hydrogen-Silicon carbide for Next-generation Microwave and Spintronic Devices

NASA Astrophysics Data System (ADS)

Cai, Zhuhua

Ferrite/ferroelectric heterostructures have attracted much attention in recent years because of their unique ability to potentially enable dual magnetic and electric field tunability. The simultaneous magnetic and electric tunability in such structures can be applied in a wide range of microwave planar devices (e.g., tunable phase shifters, resonators, and delay lines) and spintronics (e.g., magnetic tunneling junctions for magnetic sensors and nonvolatile magnetic memories). However, the attempts to engineer ferrite/ferroelectric heterostructures to operate at the frequencies higher than 5 GHz are limited. Barium hexaferrite (BaM, BaFe12O19) is an ideal candidate for high frequency microwave device applications because of its strong uniaxial anisotropy (HA ˜17 kOe) and can be tuned to ferromagnetic resonance (FMR) at frequencies higher than 40 GHz with relatively small applied magnetic fields. Spinel ferrite Fe3O4 has a high Curie temperature of 858 K and is predicted to possess ˜ 100% spin polarization, which can lead to ultrahigh tunneling magnetoresistence even at room temperature. The performance of today's ferrite-based microwave communication and spintronic devices would be enhanced and next-generation monolithic microwave integrated circuit (MMIC) would be possible if ferrite/ferroelectric heterostructures can be integrated with wide band gap semiconductors (e.g., SiC or GaN), which can function in high-temperature, high-power, and high-frequency environments. The goal of this work is to use molecular beam epitaxy (MBE) to understand nucleation and film growth mechanisms needed to integrate magnetic ferrites (BaM and Fe3O4) with SiC, and subsequently understand the material chemistry and structure influences on forming functional interfaces (i.e., interfaces that enable effective ferrite/ferroelectric coupling). The study of chemistry, structure, and magnetic properties of three generations of BaM films grown by pulsed laser deposition shows a MBE-grown single crystalline MgO template promotes the c-axis alignment through formation of an oxygen bridge at the interface and minimizes the interface mixing, which enables the effective heteroepitaxy of device quality BaM on 6H-SiC. Epitaxial single crystalline BaM film with strong c-axis perpendicular alignment, high H A (16.2 kOe) and magnetization (4.1 kG) was also successfully grown by MBE for the first time on 6H-SiC. Through MBE, further study of the chemistry and structure evolution at the BaM//SiC interface suggests the 10 nm MgO template not only functions as a diffusion barrier, but also forms a spinel transition layer that is structurally similar to BaM. The high quality BaM film on SiC is compatible with MMIC and can also function as a magnetic layer in BaM/ferroelectric multiferroic heterostructures for electrostatic FMR tuning. Through MBE, single crystalline, epitaxial Fe3O4 (111) films and Fe 3O4/BaTiO3/Fe3O4 heterostructures were successfully integrated with 6H-SiC. The Fe3O4 film exhibits high strucutrual order with sharp interfaces and an easy axis in-plane magnetization with a coercivity of 200 Oe. In the Fe3O 4/BaTiO3/Fe3O4 heterostructure, the magnetoeletric coupling is demonstrated at room-temperature by an electric field induced magnetic anisotropy field change. The Fe3O4 /BaTiO3/Fe3O4 heterostructure has the potential application in multiferroic tunneling junction used in novel information storage. Understanding the ferrite growth mechanisms and interface functions through this research, is an important contribution toward the realization of a next-generation, multifunctional device.

New exponential stability criteria for stochastic BAM neural networks with impulses

NASA Astrophysics Data System (ADS)

Sakthivel, R.; Samidurai, R.; Anthoni, S. M.

2010-10-01

In this paper, we study the global exponential stability of time-delayed stochastic bidirectional associative memory neural networks with impulses and Markovian jumping parameters. A generalized activation function is considered, and traditional assumptions on the boundedness, monotony and differentiability of activation functions are removed. We obtain a new set of sufficient conditions in terms of linear matrix inequalities, which ensures the global exponential stability of the unique equilibrium point for stochastic BAM neural networks with impulses. The Lyapunov function method with the Itô differential rule is employed for achieving the required result. Moreover, a numerical example is provided to show that the proposed result improves the allowable upper bound of delays over some existing results in the literature.

Global exponential stability and lag synchronization for delayed memristive fuzzy Cohen-Grossberg BAM neural networks with impulses.

PubMed

Yang, Wengui; Yu, Wenwu; Cao, Jinde; Alsaadi, Fuad E; Hayat, Tasawar

2018-02-01

This paper investigates the stability and lag synchronization for memristor-based fuzzy Cohen-Grossberg bidirectional associative memory (BAM) neural networks with mixed delays (asynchronous time delays and continuously distributed delays) and impulses. By applying the inequality analysis technique, homeomorphism theory and some suitable Lyapunov-Krasovskii functionals, some new sufficient conditions for the uniqueness and global exponential stability of equilibrium point are established. Furthermore, we obtain several sufficient criteria concerning globally exponential lag synchronization for the proposed system based on the framework of Filippov solution, differential inclusion theory and control theory. In addition, some examples with numerical simulations are given to illustrate the feasibility and validity of obtained results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption-Desorption Transition.

PubMed

Grebíková, Lucie; Whittington, Stuart G; Vancso, Julius G

2018-05-23

The adsorption-desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption-desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption-desorption transitions.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption–Desorption Transition

PubMed Central

2018-01-01

The adsorption–desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption–desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption–desorption transitions. PMID:29712430

Materials characterisation by angle-resolved scanning transmission electron microscopy.

PubMed

Müller-Caspary, Knut; Oppermann, Oliver; Grieb, Tim; Krause, Florian F; Rosenauer, Andreas; Schowalter, Marco; Mehrtens, Thorsten; Beyer, Andreas; Volz, Kerstin; Potapov, Pavel

2016-11-16

Solid-state properties such as strain or chemical composition often leave characteristic fingerprints in the angular dependence of electron scattering. Scanning transmission electron microscopy (STEM) is dedicated to probe scattered intensity with atomic resolution, but it drastically lacks angular resolution. Here we report both a setup to exploit the explicit angular dependence of scattered intensity and applications of angle-resolved STEM to semiconductor nanostructures. Our method is applied to measure nitrogen content and specimen thickness in a GaN x As 1-x layer independently at atomic resolution by evaluating two dedicated angular intervals. We demonstrate contrast formation due to strain and composition in a Si- based metal-oxide semiconductor field effect transistor (MOSFET) with Ge x Si 1-x stressors as a function of the angles used for imaging. To shed light on the validity of current theoretical approaches this data is compared with theory, namely the Rutherford approach and contemporary multislice simulations. Inconsistency is found for the Rutherford model in the whole angular range of 16-255 mrad. Contrary, the multislice simulations are applicable for angles larger than 35 mrad whereas a significant mismatch is observed at lower angles. This limitation of established simulations is discussed particularly on the basis of inelastic scattering.

Dynamic Measurement of Low Contact Angles by Optical Microscopy.

PubMed

Campbell, James M; Christenson, Hugo K

2018-05-16

Precise measurement of contact angles is an important challenge in surface science, in the design and characterization of materials and in many crystallization experiments. Here we present a novel technique for measuring the contact angles of droplets between about 2° and 30°, with the lowest experimental uncertainty at the lower end of this range, typically ±0.1°. The lensing effect of a droplet interface produces the appearance of bright circles in low-aperture light, whose diameter is related to the contact angle. The technique requires no specialized equipment beyond an ordinary optical microscope, and may be used to study the dynamic evolution of the contact angle in situ during an experiment.

Morphological study of polymer surfaces exposed to non-thermal plasma based on contact angle and the use of scaling laws

NASA Astrophysics Data System (ADS)

Felix, T.; Cassini, F. A.; Benetoli, L. O. B.; Dotto, M. E. R.; Debacher, N. A.

2017-05-01

The experiments presented in this communication have the purpose to elaborate an explanation for the morphological evolution of the growth of polymeric surfaces provided by the treatment of non-thermal plasma. According to the roughness analysis and the model proposed by scaling laws it is possible relate to a predictable or merely random effect. Polyethylene terephthalate (PET) and poly(etherether)ketone (PEEK) samples were exposed to a non-thermal plasma discharge and the resulting surfaces roughness were analyzed based on the measurements from contact angle, scanning electron microscopy and atomic force microscopy coupled with scaling laws analysis which can help to describe and understand the dynamic of formation of a wide variety of rough surfaces. The roughness, RRMS (RMS- Root Mean Square) values for polymer surface range between 19.8 nm and 110.9 nm. The contact angle and the AFM (Atomic Force Microscopy) measurements as a function of the plasma exposure time were in agreement with both polar and dispersive components according to the surface roughness and also with the morphology evaluated described by Wolf-Villain model, with proximate values of α between 0.91(PET) and 0.88(PEEK), β = 0.25(PET) and z = 3,64(PET).

Tomographic diffractive microscopy with agile illuminations for imaging targets in a noisy background.

PubMed

Zhang, T; Godavarthi, C; Chaumet, P C; Maire, G; Giovannini, H; Talneau, A; Prada, C; Sentenac, A; Belkebir, K

2015-02-15

Tomographic diffractive microscopy is a marker-free optical digital imaging technique in which three-dimensional samples are reconstructed from a set of holograms recorded under different angles of incidence. We show experimentally that, by processing the holograms with singular value decomposition, it is possible to image objects in a noisy background that are invisible with classical wide-field microscopy and conventional tomographic reconstruction procedure. The targets can be further characterized with a selective quantitative inversion.

Systematic review: the prevalence of idiopathic bile acid malabsorption as diagnosed by SeHCAT scanning in patients with diarrhoea-predominant irritable bowel syndrome.

PubMed

Wedlake, L; A'Hern, R; Russell, D; Thomas, K; Walters, J R F; Andreyev, H J N

2009-10-01

Recurrent, watery diarrhoea affects one-third of patients diagnosed with irritable bowel syndrome ('IBS-D'). Idiopathic bile acid malabsorption ('I-BAM') may be the cause. To determine the prevalence of I-BAM in patients suffering from IBS-D. A systematic search was performed of publications reporting patients presenting with IBS-D type symptoms, who were subsequently confirmed as having I-BAM by SeHCAT scanning. Eighteen relevant studies, 15 prospective, comprising 1223 patients were identified. Five studies (429 patients) indicated that 10% (CI: 7-13) patients had severe bile acid malabsorption (SeHCAT 7 day retention <5% of baseline value). 17 studies (1073 patients) indicated that 32% (CI: 29-35) patients had moderate bile acid malabsorption (SeHCAT <10%). 7 studies (618 patients) indicated that 26% (CI: 23-30) patients had mild (SeHCAT <15%) bile acid malabsorption. Pooled data from 15 studies showed a dose-response relationship according to severity of malabsorption to treatment with a bile acid binder: response to colestyramine occurred in 96% of patients with <5% retention, 80% at <10% retention and 70% at <15% retention. Idiopathic adult-onset bile acid malabsorption is not rare. International guidelines for the management of irritable bowel syndrome need to be revised so that clinicians become more aware of this possibility.

Evaluation and single-laboratory verification of a proposed modification to the U.S. Food and Drug Administration method for detection and identification of Campylobacter jejuni or Campylobacter coli from raw silo milk.

PubMed

Gharst, Greg; Bark, Don H; Newkirk, Robert; Guillen, Lacey; Wang, Qian; Abeyta, Carlos

2013-01-01

The current U.S. Food and Drug Administration (FDA) methodology for detection of Campylobacter, a leading source for foodborne illness, is outdated. The purpose of this study, therefore, was to improve and update the cultural and identification methods found in the FDA/Bacteriological Analytical Manual (BAM). Raw silo milk samples containing typical and atypical strains of Campylobacter jejuni and Campylobacter coli at different levels (5 CFU/25 g, 50 CFU/25 g, and 125 CFU/25 g) were analyzed. Valid results were obtained from 240 test portions. Six inoculated (at the levels described above) and two uninoculated samples were sent to a participating laboratory to mimic a "real-world" scenario. These combined data indicated that the use of sheep blood in combination with enrichment is not necessary. R & F Campylobacter jejuni/Campylobacter coli Chromogenic Plating Medium is significantly (P < 0.05) more sensitive for detection of C. jejuni or C. coli at low inoculation levels than the modified Cefoperazone Charcoal Deoxycholate Agar used in the BAM. The quantitative PCR method described demonstrated rapid confirmation and identification of C. jejuni or C. coli. It reduced the time to isolate C. jejuni or C. coli, and increased the sensitivity compared to the current BAM protocol.

BAM: Bayesian AMHG-Manning Inference of Discharge Using Remotely Sensed Stream Width, Slope, and Height

NASA Astrophysics Data System (ADS)

Hagemann, M. W.; Gleason, C. J.; Durand, M. T.

2017-11-01

The forthcoming Surface Water and Ocean Topography (SWOT) NASA satellite mission will measure water surface width, height, and slope of major rivers worldwide. The resulting data could provide an unprecedented account of river discharge at continental scales, but reliable methods need to be identified prior to launch. Here we present a novel algorithm for discharge estimation from only remotely sensed stream width, slope, and height at multiple locations along a mass-conserved river segment. The algorithm, termed the Bayesian AMHG-Manning (BAM) algorithm, implements a Bayesian formulation of streamflow uncertainty using a combination of Manning's equation and at-many-stations hydraulic geometry (AMHG). Bayesian methods provide a statistically defensible approach to generating discharge estimates in a physically underconstrained system but rely on prior distributions that quantify the a priori uncertainty of unknown quantities including discharge and hydraulic equation parameters. These were obtained from literature-reported values and from a USGS data set of acoustic Doppler current profiler (ADCP) measurements at USGS stream gauges. A data set of simulated widths, slopes, and heights from 19 rivers was used to evaluate the algorithms using a set of performance metrics. Results across the 19 rivers indicate an improvement in performance of BAM over previously tested methods and highlight a path forward in solving discharge estimation using solely satellite remote sensing.

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

Radigan, Jacqueline, E-mail: radigan@stsci.edu

Observations of variability can provide valuable information about the processes of cloud formation and dissipation in brown dwarf atmospheres. Here we report the results of an independent analysis of archival data from the Brown dwarf Atmosphere Monitoring (BAM) program. Time series data for 14 L and T dwarfs reported to be significantly variable over timescales of hours were analyzed. We confirm large-amplitude variability (amplitudes >2%) for 4 out of 13 targets and place upper limits of 0.7%-1.6% on variability in the remaining sample. For two targets we find evidence of weak variability at amplitudes of 1.3% and 1.6%. Based onmore » our revised classification of variable objects in the BAM study, we find strong variability outside the L/T transition to be rare at near infrared wavelengths. From a combined sample of 81 L0-T9 dwarfs from the revised BAM sample and the variability survey of Radigan et al., we infer an overall observed frequency for large-amplitude variability outside the L/T transition of 3.2{sub −1.8}{sup +2.8}%, in contrast to 24{sub −9}{sup +11}% for L9-T3.5 spectral types. We conclude that while strong variability is not limited to the L/T transition, it occurs more frequently in this spectral type range, indicative of larger or more highly contrasting cloud features at these spectral types.« less

Enhanced and broadband microwave absorption of flake-shaped Fe and FeNi composite with Ba ferrites

NASA Astrophysics Data System (ADS)

Li, Wangchang; Lv, Junjun; Zhou, Xiang; Zheng, Jingwu; Ying, Yao; Qiao, Liang; Yu, Jing; Che, Shenglei

2017-03-01

In order to achieve a broad bandwidth absorber at high frequency, the composites of M-type ferrite BaCo1.0Ti1.0Fe10O19 (BaM) with flaked carbonyl iron powders (CIP) and flaked Fe50Ni50 were prepared to optimize the surface impedance in broadband frequency, respectively. The diameter of the flaked carbonyl iron powders (CIP) and Fe50Ni50 is in the range of 5-10 μm and 10-20 μm and the thickness of the CIP and Fe50Ni50 is close to 200 nm and 400 nm, respectively. The complex permeability and permittivity show that the addition of BaM obviously reduces the values of real part of permittivity and imaginary part of the permeability which can enhance the matched-wave-impedance. The absorption bands less than -10 dB of CIP-BaM and FeNi-BaM absorber approach to 5.5 GHz (5.7-11.2 GHz) and 7 GHz (11-18 GHz) at 1.5 mm. However, the bands of CIP and FeNi are only 1.9 GHz (4.7-6.6 GHz) and 2.1 GHz (4.0-6.1 GHz). Hence, the electromagnetic match property is greatly improved by BaM ferrites, and this composite shows a broaden absorption band.

Innovative methodology for the synthesis of Ba-M hexaferrite BaFe{sub 12}O{sub 19} nanoparticles

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

Ahmed, M.A., E-mail: moala@47hotmail.com; Helmy, N.; El-Dek, S.I.

2013-09-01

Graphical abstract: Transmission electron microscope images for the BaFe12O19. - Highlights: • BaFe{sub 12}O{sub 19}nanoparticles were prepared in single-phase from organometallic precursors. • BaFe{sub 12}O{sub 19} possesses small size 65 nm, H{sub C} = 3695 Oe and M{sub s} = 58 emu/g. • This method of preparation could be extended in the synthesis of other metal oxide nanoparticles. - Abstract: In this piece of work, high quality and homogeneity, barium hexaferrite (BaM) BaFe{sub 12}O{sub 19} nanoparticles were prepared from organometallic precursors for the 1st time. This method is based on the formation of supramolecular crystal structure of Ba[Fe(H{sub 3}NCH{sub 2}CH{submore » 2}NH{sub 3})]Cl{sub 7}·8H{sub 2}O. The crystal structure, morphology and magnetic properties of BaFe{sub 12}O{sub 19} at two different annealing temperatures namely 1000 °C and 1200 °C were investigated using X-ray diffraction, transmission electron microscope TEM and vibrating sample magnetometry (VSM). The results show that monophasic nanoparticles of hexaferrites were obtained. Nanoparticles of crystallite size 40–50 nm distinguished by narrow distribution and excellent homogeneity were obtained with superior magnetic properties which suggested single-domain particles of Ba-M hexaferrite.« less

Compound-Specific Stable Isotope Fractionation of Pesticides and Pharmaceuticals in a Mesoscale Aquifer Model.

PubMed

Schürner, Heide K V; Maier, Michael P; Eckert, Dominik; Brejcha, Ramona; Neumann, Claudia-Constanze; Stumpp, Christine; Cirpka, Olaf A; Elsner, Martin

2016-06-07

Compound-specific isotope analysis (CSIA) receives increasing interest for its ability to detect natural degradation of pesticides and pharmaceuticals. Despite recent laboratory studies, CSIA investigations of such micropollutants in the environment are still rare. To explore the certainty of information obtainable by CSIA in a near-environmental setting, a pulse of the pesticide bentazone, the pesticide metabolite 2,6-dichlorobenzamide (BAM), and the pharmaceuticals diclofenac and ibuprofen was released into a mesoscale aquifer with quasi-two-dimensional flow. Concentration breakthrough curves (BTC) of BAM and ibuprofen demonstrated neither degradation nor sorption. Bentazone was transformed but did not sorb significantly, whereas diclofenac showed both degradation and sorption. Carbon and nitrogen CSIA could be accomplished in similar concentrations as for "traditional" priority pollutants (low μg/L range), however, at the cost of uncertainties (0.4-0.5‰ (carbon), 1‰ (nitrogen)). Nonetheless, invariant carbon and nitrogen isotope values confirmed that BAM was neither degraded nor sorbed, while significant enrichment of (13)C and in particular (15)N corroborated transformation of diclofenac and bentazone. Retardation of diclofenac was reflected in additional (15)N sorption isotope effects, whereas isotope fractionation of transverse dispersion could not be identified. These results provide a benchmark on the performance of CSIA to monitor the reactivity of micropollutants in aquifers and may guide future efforts to accomplish CSIA at even lower concentrations (ng/L range).

Contact angle distribution of particles at fluid interfaces.

PubMed

Snoeyink, Craig; Barman, Sourav; Christopher, Gordon F

2015-01-27

Recent measurements have implied a distribution of interfacially adsorbed particles' contact angles; however, it has been impossible to measure statistically significant numbers for these contact angles noninvasively in situ. Using a new microscopy method that allows nanometer-scale resolution of particle's 3D positions on an interface, we have measured the contact angles for thousands of latex particles at an oil/water interface. Furthermore, these measurements are dynamic, allowing the observation of the particle contact angle with high temporal resolution, resulting in hundreds of thousands of individual contact angle measurements. The contact angle has been found to fit a normal distribution with a standard deviation of 19.3°, which is much larger than previously recorded. Furthermore, the technique used allows the effect of measurement error, constrained interfacial diffusion, and particle property variation on the contact angle distribution to be individually evaluated. Because of the ability to measure the contact angle noninvasively, the results provide previously unobtainable, unique data on the dynamics and distribution of the adsorbed particles' contact angle.

Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

PubMed Central

Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

2016-01-01

The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation. PMID:27452115

Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

NASA Astrophysics Data System (ADS)

Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

2016-07-01

The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.

Effects of the environmental factors on the casein micelle structure studied by cryo transmission electron microscopy and small-angle x-ray scattering/ultrasmall-angle x-ray scattering

NASA Astrophysics Data System (ADS)

Marchin, Stéphane; Putaux, Jean-Luc; Pignon, Frédéric; Léonil, Joëlle

2007-01-01

Casein micelles are colloidal protein-calcium-transport complexes whose structure has not been unequivocally elucidated. This study used small-angle x-ray scattering (SAXS) and ultrasmall angle x-ray scattering (USAXS) as well as cryo transmission electron microscopy (cryo-TEM) to provide fine structural details on their structure. Cryo-TEM observations of native casein micelles fractionated by differential centrifugation showed that colloidal calcium phosphate appeared as nanoclusters with a diameter of about 2.5nm. They were uniformly distributed in a homogeneous tangled web of caseins and were primarily responsible for the intensity distribution in the SAXS profiles at the highest q vectors corresponding to the internal structure of the casein micelles. A specific demineralization of casein micelles by decreasing the pH from 6.7 to 5.2 resulted in a reduced granular aspect of the micelles observed by cryo-TEM and the existence of a characteristic point of inflection in SAXS profiles. This supports the hypothesis that the smaller substructures detected by SAXS are colloidal calcium phosphate nanoclusters rather than putative submicelles.

Full-angle tomographic phase microscopy of flowing quasi-spherical cells.

PubMed

Villone, Massimiliano M; Memmolo, Pasquale; Merola, Francesco; Mugnano, Martina; Miccio, Lisa; Maffettone, Pier Luca; Ferraro, Pietro

2017-12-19

We report a reliable full-angle tomographic phase microscopy (FA-TPM) method for flowing quasi-spherical cells along microfluidic channels. This method lies in a completely passive optical system, i.e. mechanical scanning or multi-direction probing of the sample is avoided. It exploits the engineered rolling of cells while they are flowing along a microfluidic channel. Here we demonstrate significant progress with respect to the state of the art of in-flow TPM by showing a general extension to cells having almost spherical shapes while they are flowing in suspension. In fact, the adopted strategy allows the accurate retrieval of rotation angles through a theoretical model of the cells' rotation in a dynamic microfluidic flow by matching it with phase-contrast images resulting from holographic reconstructions. So far, the proposed method is the first and the only one that permits to get in-flow TPM by probing the cells with full-angle, achieving accurate 3D refractive index mapping and the simplest optical setup, simultaneously. Proof of concept experiments were performed successfully on human breast adenocarcinoma MCF-7 cells, opening the way for the full characterization of circulating tumor cells (CTCs) in the new paradigm of liquid biopsy.

Determination of domain wall chirality using in situ Lorentz transmission electron microscopy

DOE PAGES

Chess, Jordan J.; Montoya, Sergio A.; Fullerton, Eric E.; ...

2017-02-23

Controlling domain wall chirality is increasingly seen in non-centrosymmetric materials. Mapping chiral magnetic domains requires knowledge about all the vector components of the magnetization, which poses a problem for conventional Lorentz transmission electron microscopy (LTEM) that is only sensitive to magnetic fields perpendicular to the electron beams direction of travel. The standard approach in LTEM for determining the third component of the magnetization is to tilt the sample to some angle and record a second image. Furthermore, this presents a problem for any domain structures that are stabilized by an applied external magnetic field (e.g. skyrmions), because the standard LTEMmore » setup does not allow independent control of the angle of an applied magnetic field, and sample tilt angle. Here we show that applying a modified transport of intensity equation analysis to LTEM images collected during an applied field sweep, we can determine the domain wall chirality of labyrinth domains in a perpendicularly magnetized material, avoiding the need to tilt the sample.« less

Determination of domain wall chirality using in situ Lorentz transmission electron microscopy

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

Chess, Jordan J.; Montoya, Sergio A.; Fullerton, Eric E.

Controlling domain wall chirality is increasingly seen in non-centrosymmetric materials. Mapping chiral magnetic domains requires knowledge about all the vector components of the magnetization, which poses a problem for conventional Lorentz transmission electron microscopy (LTEM) that is only sensitive to magnetic fields perpendicular to the electron beams direction of travel. The standard approach in LTEM for determining the third component of the magnetization is to tilt the sample to some angle and record a second image. Furthermore, this presents a problem for any domain structures that are stabilized by an applied external magnetic field (e.g. skyrmions), because the standard LTEMmore » setup does not allow independent control of the angle of an applied magnetic field, and sample tilt angle. Here we show that applying a modified transport of intensity equation analysis to LTEM images collected during an applied field sweep, we can determine the domain wall chirality of labyrinth domains in a perpendicularly magnetized material, avoiding the need to tilt the sample.« less

Linear Dichroism and Photoluminescence Microscopy Imaging of Grain Boundaries in Crystalline Metal-Free Phthalocyanine Thin Films

NASA Astrophysics Data System (ADS)

Pan, Zhenwen; Lamarche, Cody; Cour, Ishviene; Rawat, Naveen; Manning, Lane; Headrick, Randall; Furis, Madalina; Physics Dept.; Material Science Program, University of Vermont, Burlington, VT 05405 Team

2011-03-01

We employed a combination of linear dichroism and photoluminescence microscopy with spatial resolution of 5 μ m to study the excitonic properties of solution-processed metal-free phthalocyanine (H2Pc) crystalline thin films with millimeter-sized grains. We observe a highly-localized, sharp, monomer-like emission at the high angle grain boundaries, in contrast to samples with more uniform grain orientation where no such feature has been observed. The energy difference between the grain boundary luminescence and the HOMO-LUMO singlet exciton recombination of the crystalline H2Pc is measured to be 160meV. Our systematic survey of grain boundaries indicates this localized state is never present at low angle boundaries where the π -orbital overlap between adjacent grains is significant. It supports recent results which associated a decrease in carrier mobility with the presence of large angle boundaries in similar crystalline pentacene films. This project is supported by DMR- 0722451; DMR-0348354; DMR- 0821268.

Nanoscopic analysis of oxygen segregation at tilt boundaries in silicon ingots using atom probe tomography combined with TEM and ab initio calculations.

PubMed

Ohno, Y; Inoue, K; Fujiwara, K; Kutsukake, K; Deura, M; Yonenaga, I; Ebisawa, N; Shimizu, Y; Inoue, K; Nagai, Y; Yoshida, H; Takeda, S; Tanaka, S; Kohyama, M

2017-12-01

We have developed an analytical method to determine the segregation levels on the same tilt boundaries (TBs) at the same nanoscopic location by a joint use of atom probe tomography and scanning transmission electron microscopy, and discussed the mechanism of oxygen segregation at TBs in silicon ingots in terms of bond distortions around the TBs. The three-dimensional distribution of oxygen atoms was determined at the typical small- and large-angle TBs by atom probe tomography with a low impurity detection limit (0.01 at.% on a TB plane) simultaneously with high spatial resolution (about 0.4 nm). The three-dimensional distribution was correlated with the atomic stress around the TBs; the stress at large-angle TBs was estimated by ab initio calculations based on atomic resolution scanning transmission electron microscopy data and that at small-angle TBs were calculated with the elastic theory based on dark-field transmission electron microscopy data. Oxygen atoms would segregate at bond-centred sites under tensile stress above about 2 GPa, so as to attain a more stable bonding network by reducing the local stress. The number of oxygen atoms segregating in a unit TB area N GB (in atoms nm -2 ) was determined to be proportional to both the number of the atomic sites under tensile stress in a unit TB area n bc and the average concentration of oxygen atoms around the TB [O i ] (in at.%) with N GB ∼ 50 n bc [O i ]. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Adhesion of living cells revealed by variable-angle total internal reflection fluorescence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Cardoso Dos Santos, Marcelina; Vézy, Cyrille; Jaffiol, Rodolphe

2016-02-01

Total Internal Reflection Fluorescence Microscopy (TIRFM) is a widespread technique to study cellular process occurring near the contact region with the glass substrate. In this field, determination of the accurate distance from the surface to the plasma membrane constitutes a crucial issue to investigate the physical basis of cellular adhesion process. However, quantitative interpretation of TIRF pictures regarding the distance z between a labeled membrane and the substrate is not trivial. Indeed, the contrast of TIRF images depends on several parameters more and less well known (local concentration of dyes, absorption cross section, angular emission pattern…). The strategy to get around this problem is to exploit a series of TIRF pictures recorded at different incident angles in evanescent regime. This technique called variable-angle TIRF microscopy (vaTIRFM), allowing to map the membrane-substrate separation distance with a nanometric resolution (10-20 nm). vaTIRFM was developed by Burmeister, Truskey and Reichert in the early 1990s with a prism-based TIRF setup [Journal of Microscopy 173, 39-51 (1994)]. We propose a more convenient prismless setup, which uses only a rotatable mirror to adjust precisely the laser beam on the back focal plane of the oil immersion objective (no azimuthal scanning is needed). The series of TIRF images permit us to calculate accurately membrane-surface distances in each pixel. We demonstrate that vaTIRFM are useful to quantify the adhesion of living cells for specific and unspecific membrane-surface interactions, achieved on various functionalized substrates with polymers (BSA, poly-L-lysin) or extracellular matrix proteins (collagen and fibronectin).

Secondary structure of spiralin in solution, at the air/water interface, and in interaction with lipid monolayers.

PubMed

Castano, Sabine; Blaudez, Daniel; Desbat, Bernard; Dufourcq, Jean; Wróblewski, Henri

2002-05-03

The surface of spiroplasmas, helically shaped pathogenic bacteria related to the mycoplasmas, is crowded with the membrane-anchored lipoprotein spiralin whose structure and function are unknown. In this work, the secondary structure of spiralin under the form of detergent-free micelles (average Stokes radius, 87.5 A) in water and at the air/water interface, alone or in interaction with lipid monolayers was analyzed. FT-IR and circular dichroism (CD) spectroscopic data indicate that spiralin in solution contains about 25+/-3% of helices and 38+/-2% of beta sheets. These measurements are consistent with a consensus predictive analysis of the protein sequence suggesting about 28% of helices, 32% of beta sheets and 40% of irregular structure. Brewster angle microscopy (BAM) revealed that, in water, the micelles slowly disaggregate to form a stable and homogeneous layer at the air/water interface, exhibiting a surface pressure up to 10 mN/m. Polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) spectra of interfacial spiralin display a complex amide I band characteristic of a mixture of beta sheets and alpha helices, and an intense amide II band. Spectral simulations indicate a flat orientation for the beta sheets and a vertical orientation for the alpha helices with respect to the interface. The combination of tensiometric and PMIRRAS measurements show that, when spiroplasma lipids are used to form a monolayer at the air/water interface, spiralin is adsorbed under this monolayer and its antiparallel beta sheets are mainly parallel to the polar-head layer of the lipids without deep perturbation of the fatty acid chains organization. Based upon these results, we propose a 'carpet model' for spiralin organization at the spiroplasma cell surface. In this model, spiralin molecules anchored into the outer leaflet of the lipid bilayer by their N-terminal lipid moiety are composed of two colinear domains (instead of a single globular domain) situated at the lipid/water interface. Owing to the very high amount of spiralin in the membrane, such carpets would cover most if not all the lipids present in the outer leaflet of the bilayer.

Effect of pre-strain on precipitation and exfoliation corrosion resistance in an Al-Zn-Mg alloy

NASA Astrophysics Data System (ADS)

Lu, Xianghan; Du, Zhiwei; Han, Xiaolei; Li, Ting; Wang, Guojun; Lu, Liying; Bai, Xiaoxia; Zhou, Tietao

2017-12-01

To investigate the effect of pre-strain on behaviors in a specially developed Al-4.5Zn-1.2Mg alloy, transmission electron microscopy (TEM) bright field (BF) imaging combined with select area electron diffraction (SAED), Vickers-hardness tests and electrical conductivity tests was conducted for insight into precipitation in aluminum (Al) matrix during two step ageing, and standard exfoliation corrosion (EXCO) test combined with high-angle angular dark field scanning transmission electron microscopy (HAADF-STEM) and scanning electron microscopy (SEM) was carried out for corrosion behavior. Results showed that pre-strain accelerated precipitation during two step ageing as the sequence of: (i) supersaturated solid solution (SSS), GPI zones precipitations, GPI dissolution; (ii) SSS, fcc precipitates, η’ phases or η phases. And the precipitation hardening of the fcc precipitates was not effective as GPI zones. Pre-strain also accelerated EXCO developing, which was mainly attributed to the coverage ratio of η phases on high-angle grain boundaries (HAGBs) increasing as pre-strain increase.

Fixed-time synchronization of memristor-based BAM neural networks with time-varying discrete delay.

PubMed

Chen, Chuan; Li, Lixiang; Peng, Haipeng; Yang, Yixian

2017-12-01

This paper is devoted to studying the fixed-time synchronization of memristor-based BAM neural networks (MBAMNNs) with discrete delay. Fixed-time synchronization means that synchronization can be achieved in a fixed time for any initial values of the considered systems. In the light of the double-layer structure of MBAMNNs, we design two similar feedback controllers. Based on Lyapunov stability theories, several criteria are established to guarantee that the drive and response MBAMNNs can realize synchronization in a fixed time. In particular, by changing the parameters of controllers, this fixed time can be adjusted to some desired value in advance, irrespective of the initial values of MBAMNNs. Numerical simulations are included to validate the derived results. Copyright © 2017 Elsevier Ltd. All rights reserved.

LLNL Small-Scale Friction sensitivity (BAM) Test

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

Simpson, L.R.; Foltz, M.F.

1996-06-01

Small-scale safety testing of explosives, propellants and other energetic materials, is done to determine their sensitivity to various stimuli including friction, static spark, and impact. Testing is done to discover potential handling problems for either newly synthesized materials of unknown behavior, or materials that have been stored for long periods of time. This report describes the existing {open_quotes}BAM{close_quotes} Small-Scale Friction Test, and the methods used to determine the friction sensitivity pertinent to handling energetic materials. The accumulated data for the materials tested is not listed here - that information is in a database. Included is, however, a short list ofmore » (1) materials that had an unusual response, and (2), a few {open_quotes}standard{close_quotes} materials representing the range of typical responses usually seen.« less

Structural and optical properties of glancing angle deposited TiO2 nanowires array.

PubMed

Chinnamuthu, P; Mondal, A; Singh, N K; Dhar, J C; Das, S K; Chattopadhyay, K K

2012-08-01

TiO2 nanowires (NWs) have been synthesized by glancing angle deposition technique using e-beam evaporator. The average length 490 nm and diameter 80 nm of NWs were examined by field emission-scanning electron microscopy. Transmission electron microscopy emphasized that the NWs were widely dispersed at the top. X-ray diffraction has been carried out on the TiO2 thin film (TF) and NW array. A small blue shift of 0.03 eV was observed in Photoluminescence (PL) main band emission for TiO2 NW as compared to TiO2 TF. The high temperature annealing at 980 degrees C partially removed the oxygen vacancy from the sample, which was investigated by PL and optical absorption measurements.

Asymmetrical flow field-flow fractionation with multi-angle light scattering and quasi-elastic light scattering for characterization of polymersomes: comparison with classical techniques.

PubMed

Till, Ugo; Gaucher-Delmas, Mireille; Saint-Aguet, Pascale; Hamon, Glenn; Marty, Jean-Daniel; Chassenieux, Christophe; Payré, Bruno; Goudounèche, Dominique; Mingotaud, Anne-Françoise; Violleau, Frédéric

2014-12-01

Polymersomes formed from amphiphilic block copolymers, such as poly(ethyleneoxide-b-ε-caprolactone) (PEO-b-PCL) or poly(ethyleneoxide-b-methylmethacrylate), were characterized by asymmetrical flow field-flow fractionation coupled with quasi-elastic light scattering (QELS), multi-angle light scattering (MALS), and refractive index detection, leading to the determination of their size, shape, and molecular weight. The method was cross-examined with more classical ones, like batch dynamic and static light scattering, electron microscopy, and atomic force microscopy. The results show good complementarities between all the techniques; asymmetrical flow field-flow fractionation being the most pertinent one when the sample exhibits several different types of population.

Interaction of Elastic Waves with Corrosion Damage

DTIC Science & Technology

2010-08-01

Joachim Schneider -Gloetzl, Gloetzl GmbH, Rheinstetten, Germany Rainer Gloetzl, RG Research, Ettlingen, Germany...Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal Institute for Materials, Research and Testing, Berlin, Germany

Fabrication and characterization of optical-fiber nanoprobes for scanning near-field optical microscopy.

PubMed

Essaidi, N; Chen, Y; Kottler, V; Cambril, E; Mayeux, C; Ronarch, N; Vieu, C

1998-02-01

The current scanning near-field optical microscopy has been developed with optical-fiber probes obtained by use of either laser-heated pulling or chemical etching. For high-resolution near-field imaging, the detected signal is rapidly attenuated as the aperture size of the probe decreases. It is thus important to fabricate probes optimized for both spot size and optical transmission. We present a two-step fabrication that allowed us to achieve an improved performance of the optical-fiber probes. Initially, a CO(2) laser-heated pulling was used to produce a parabolic transitional taper ending with a top thin filament. Then, a rapid chemical etching with 50% buffered hydrofluoric acid was used to remove the thin filament and to result in a final conical tip on the top of the parabolic transitional taper. Systematically, we obtained optical-fiber nanoprobes with the apex size as small as 10 nm and the final cone angle varying from 15 degrees to 80 degrees . It was found that the optical transmission efficiency increases rapidly as the taper angle increases from 15 degrees to 50 degrees , but a further increase in the taper angle gives rise to important broadening of the spot size. Finally, the fabricated nanoprobes were used in photon-scanning tunneling microscopy, which allowed observation of etched double lines and grating structures with periods as small as 200 nm.

Electronic and Optical Properties of Twisted Bilayer Graphene

NASA Astrophysics Data System (ADS)

Huang, Shengqiang

The ability to isolate single atomic layers of van der Waals materials has led to renewed interest in the electronic and optical properties of these materials as they can be fundamentally different at the monolayer limit. Moreover, these 2D crystals can be assembled together layer by layer, with controllable sequence and orientation, to form artificial materials that exhibit new features that are not found in monolayers nor bulk. Twisted bilayer graphene is one such prototype system formed by two monolayer graphene layers placed on top of each other with a twist angle between their lattices, whose electronic band structure depends on the twist angle. This thesis presents the efforts to explore the electronic and optical properties of twisted bilayer graphene by Raman spectroscopy and scanning tunneling microscopy measurements. We first synthesize twisted bilayer graphene with various twist angles via chemical vapor deposition. Using a combination of scanning tunneling microscopy and Raman spectroscopy, the twist angles are determined. The strength of the Raman G peak is sensitive to the electronic band structure of twisted bilayer graphene and therefore we use this peak to monitor changes upon doping. Our results demonstrate the ability to modify the electronic and optical properties of twisted bilayer graphene with doping. We also fabricate twisted bilayer graphene by controllable stacking of two graphene monolayers with a dry transfer technique. For twist angles smaller than one degree, many body interactions play an important role. It requires eight electrons per moire unit cell to fill up each band instead of four electrons in the case of a larger twist angle. For twist angles smaller than 0.4 degree, a network of domain walls separating AB and BA stacking regions forms, which are predicted to host topologically protected helical states. Using scanning tunneling microscopy and spectroscopy, these states are confirmed to appear on the domain walls when inversion symmetry is broken with an external electric field. We observe a double-line profile of these states on the domain walls, only occurring when the AB and BA regions are gaped. These states give rise to channels that could transport charge in a dissipationless manner making twisted bilayer graphene a promising platform to realize controllable topological networks for future applications.

Experimental studies of contact angle hysteresis phenomena on polymer surfaces – Toward the understanding and control of wettability for different applications.

PubMed

Grundke, K; Pöschel, K; Synytska, A; Frenzel, R; Drechsler, A; Nitschke, M; Cordeiro, A L; Uhlmann, P; Welzel, P B

2015-08-01

Contact angle hysteresis phenomena on polymer surfaces have been studied by contact angle measurements using sessile liquid droplets and captive air bubbles in conjunction with a drop shape method known as Axisymmetric Drop Shape Analysis - Profile (ADSA-P). In addition, commercially available sessile drop goniometer techniques were used. The polymer surfaces were characterized with respect to their surface structure (morphology, roughness, swelling) and surface chemistry (elemental surface composition, acid-base characteristics) by scanning electron microscopy (SEM), scanning force microscopy (SFM), ellipsometry, X-ray photoelectron spectroscopy (XPS) and streaming potential measurements. Heterogeneous polymer surfaces with controlled roughness and chemical composition were prepared by different routes using plasma etching and subsequent dip coating or grafting of polymer brushes, anodic oxidation of aluminium substrates coated with thin polymer films, deposition techniques to create regular patterned and rough fractal surfaces from core-shell particles, and block copolymers. To reveal the effects of swelling and reorientation at the solid/liquid interface contact angle hysteresis phenomena on polyimide surfaces, cellulose membranes, and thermo-responsive hydrogels have been studied. The effect of different solutes in the liquid (electrolytes, surfactants) and their impact on contact angle hysteresis were characterized for solid polymers without and with ionizable functional surface groups in aqueous electrolyte solutions of different ion concentrations and pH and for photoresist surfaces in cationic aqueous surfactant solutions. The work is an attempt toward the understanding of contact angle hysteresis phenomena on polymer surfaces aimed at the control of wettability for different applications. Copyright © 2014 Elsevier B.V. All rights reserved.

BAM! Physical Activity

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

Application of high-angle annular dark field scanning transmission electron microscopy, scanning transmission electron microscopy-energy dispersive X-ray spectrometry, and energy-filtered transmission electron microscopy to the characterization of nanoparticles in the environment.

PubMed

Utsunomiya, Satoshi; Ewing, Rodney C

2003-02-15

A major challenge to the development of a fundamental understanding of transport and retardation mechanisms of trace metal contaminants (<10 ppm) is their identification and characterization at the nanoscale. Atomic-scale techniques, such as conventional transmission electron microscopy, although powerful, are limited by the extremely small amounts of material that are examined. However, recent advances in electron microscopy provide a number of new analytical techniques that expand its application in environmental studies, particularly those concerning heavy metals on airborne particulates or water-borne colloids. High-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), STEM-energy-dispersive X-ray spectrometry (EDX), and energy-filtered TEM (EFTEM) can be effectively used to identify and characterize nanoparticles. The image contrast in HAADF-STEM is strongly correlated to the atomic mass: heavier elements contribute to brighter contrast. Gold nanocrystals in pyrite and uranium nanocrystals in atmospheric aerosols have been identified by HAADF-STEM and STEM-EDX mapping and subsequently characterized by high-resolution TEM (HRTEM). EFTEM was used to identify U and Fe nanocrystals embedded in an aluminosilicate. A rare, As-bearing nanophase, westerveldite (FeAs), was identified by STEM-EDX and HRTEM. The combined use of these techniques greatly expands the effective application of electron microscopy in environmental studies, especially when applied to metals of very low concentrations. This paper describes examples of how these electron microbeam techniques can be used in combination to characterize a low concentration of heavy metals (a few ppm) on nanoscale particles.

An Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat.

PubMed

Kenney, S; Kamine, J; Markovitz, D; Fenrick, R; Pagano, J

1988-03-01

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, we demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.

The potato amylase inhibitor gene SbAI regulates cold-induced sweetening in potato tubers by modulating amylase activity.

PubMed

Zhang, Huiling; Liu, Jun; Hou, Juan; Yao, Ying; Lin, Yuan; Ou, Yongbin; Song, Botao; Xie, Conghua

2014-09-01

Potato cold-induced sweetening (CIS) is critical for the postharvest quality of potato tubers. Starch degradation is considered to be one of the key pathways in the CIS process. However, the functions of the genes that encode enzymes related to starch degradation in CIS and the activity regulation of these enzymes have received less attention. A potato amylase inhibitor gene known as SbAI was cloned from the wild potato species Solanum berthaultii. This genetic transformation confirmed that in contrast to the SbAI suppression in CIS-resistant potatoes, overexpressing SbAI in CIS-sensitive potatoes resulted in less amylase activity and a lower rate of starch degradation accompanied by a lower reducing sugar (RS) content in cold-stored tubers. This finding suggested that the SbAI gene may play crucial roles in potato CIS by modulating the amylase activity. Further investigations indicated that pairwise protein-protein interactions occurred between SbAI and α-amylase StAmy23, β-amylases StBAM1 and StBAM9. SbAI could inhibit the activities of both α-amylase and β-amylase in potato tubers primarily by repressing StAmy23 and StBAM1, respectively. These findings provide the first evidence that SbAI is a key regulator of the amylases that confer starch degradation and RS accumulation in cold-stored potato tubers. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran.

PubMed

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-07-03

Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1.

System dynamics modeling of nitrogen removal in a stormwater infiltration basin with biosorption-activated media.

PubMed

Xuan, Zhemin; Chang, Ni-Bin; Wanielista, Martin P; Williams, Evan Shane

2013-07-01

Stormwater infiltration basins, one of the typical stormwater best management practices, are commonly constructed for surface water pollution control, flood mitigation, and groundwater restoration in rural or residential areas. These basins have soils with better infiltration capacity than the native soil; however, the ever-increasing contribution of nutrients to groundwater from stormwater due to urban expansion makes existing infiltration basins unable to meet groundwater quality criteria related to environmental sustainability and public health. This issue requires retrofitting current infiltration basins for flood control as well as nutrient control before the stormwater enters the groundwater. An existing stormwater infiltration basin in north-central Florida was selected, retrofitted, and monitored to identify subsurface physiochemical and biological processes during 2007-2010 to investigate nutrient control processes. This implementation in the nexus of contaminant hydrology and ecological engineering adopted amended soil layers packed with biosorption activated media (BAM; tire crumb, silt, clay, and sand) to perform nutrient removal in a partitioned forebay using a berm. This study presents an infiltration basin-nitrogen removal (IBNR) model, a system dynamics model that simulates nitrogen cycling in this BAM-based stormwater infiltration basin with respect to changing hydrologic conditions and varying dissolved nitrogen concentrations. Modeling outputs of IBNR indicate that denitrification is the biogeochemical indicator in the BAM layer that accounted for a loss of about one third of the total dissolved nitrogen mass input. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Involvement of MrgprC in Electroacupuncture Analgesia for Attenuating CFA-Induced Thermal Hyperalgesia by Suppressing the TRPV1 Pathway.

PubMed

Liu, Ying-Jun; Lin, Xiao-Xi; Fang, Jian-Qiao; Fang, Fang

2018-01-01

Mas-related G-protein-coupled receptor C (MrgprC) plays an important role in modulating chronic inflammatory pain. Electroacupuncture (EA) has a satisfactory analgesic effect on chronic pain. This study aimed to investigate the involvement of MrgprC and its transient receptor potential vanilloid 1 (TRPV1) pathway in EA analgesia in chronic inflammatory pain. Chronic inflammatory pain was induced by subcutaneously injecting complete Freund's adjuvant (CFA) into the left hind paw. EA (2/100 Hz) stimulation was administered. MrgprC siRNAs were intrathecally administered to inhibit MrgprC expression, and bovine adrenal medulla 8-22 (BAM8-22) was used to activate MrgprC. The mechanical allodynia was decreased by EA significantly since day 3. The piled analgesic effect of EA was partially blocked by 6 intrathecal administrations of MrgprC siRNA. Both EA and BAM8-22 could downregulate the expression of TRPV1 and PKC in both the DRG and the SCDH. Both EA and BAM8-22 could also decrease the TRPV1 translocation and p-TRPV1 level in both the DRG and the SCDH. The effects of EA on PKC ε , TRPV1 translocation, and p-TRPV1 in both the DRG and the SCDH were reversed by MrgprC siRNA. The results indicated that MrgprC played crucial roles in chronic pain modulation and was involved in EA analgesia partially through the regulation of TRPV1 function at the DRG and SCDH levels.

StratBAM: A Discrete-Event Simulation Model to Support Strategic Hospital Bed Capacity Decisions.

PubMed

Devapriya, Priyantha; Strömblad, Christopher T B; Bailey, Matthew D; Frazier, Seth; Bulger, John; Kemberling, Sharon T; Wood, Kenneth E

2015-10-01

The ability to accurately measure and assess current and potential health care system capacities is an issue of local and national significance. Recent joint statements by the Institute of Medicine and the Agency for Healthcare Research and Quality have emphasized the need to apply industrial and systems engineering principles to improving health care quality and patient safety outcomes. To address this need, a decision support tool was developed for planning and budgeting of current and future bed capacity, and evaluating potential process improvement efforts. The Strategic Bed Analysis Model (StratBAM) is a discrete-event simulation model created after a thorough analysis of patient flow and data from Geisinger Health System's (GHS) electronic health records. Key inputs include: timing, quantity and category of patient arrivals and discharges; unit-level length of care; patient paths; and projected patient volume and length of stay. Key outputs include: admission wait time by arrival source and receiving unit, and occupancy rates. Electronic health records were used to estimate parameters for probability distributions and to build empirical distributions for unit-level length of care and for patient paths. Validation of the simulation model against GHS operational data confirmed its ability to model real-world data consistently and accurately. StratBAM was successfully used to evaluate the system impact of forecasted patient volumes and length of stay in terms of patient wait times, occupancy rates, and cost. The model is generalizable and can be appropriately scaled for larger and smaller health care settings.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran

PubMed Central

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-01-01

ABSTRACT Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1. PMID:27028760

Size-Dependent Grain-Boundary Structure with Improved Conductive and Mechanical Stabilities in Sub-10-nm Gold Crystals

NASA Astrophysics Data System (ADS)

Wang, Chunyang; Du, Kui; Song, Kepeng; Ye, Xinglong; Qi, Lu; He, Suyun; Tang, Daiming; Lu, Ning; Jin, Haijun; Li, Feng; Ye, Hengqiang

2018-05-01

Low-angle grain boundaries generally exist in the form of dislocation arrays, while high-angle grain boundaries (misorientation angle >15 ° ) exist in the form of structural units in bulk metals. Here, through in situ atomic resolution aberration corrected electron microscopy observations, we report size-dependent grain-boundary structures improving both stabilities of electrical conductivity and mechanical properties in sub-10-nm-sized gold crystals. With the diameter of a nanocrystal decreasing below 10 nm, the high-angle grain boundary in the crystal exists as an array of dislocations. This size effect may be of importance to a new generation of interconnects applications.

Anterior chamber configuration in patients with glaucoma: MR gonioscopy evaluation with half-Fourier single-shot RARE sequence and microscopy coil.

PubMed

Tanitame, Keizo; Sasaki, Ko; Sone, Takashi; Uyama, Shinji; Sumida, Masumi; Ichiki, Toshio; Ito, Katsuhide

2008-10-01

The purpose of the study was to determine the accuracy of half-Fourier single-shot rapid acquisition with relaxation enhancement high-spatial-resolution magnetic resonance (MR) imaging performed with a microscopy coil in the diagnosis of narrow anterior chamber angle in patients with glaucoma. Slit-lamp biomicroscopy served as the reference standard. The institutional review board approved this study, and written informed consent was obtained from the 20 recruited patients. There was excellent agreement between MR gonioscopy and slit-lamp biomicroscopy in the classification of anterior chamber angles as narrow or open (kappa = 0.89 [95% confidence interval: 0.69, 1.10]). MR gonioscopy has substantial potential as a technique used to evaluate glaucoma. (c) RSNA, 2008.

Glancing angle deposition of sculptured thin metal films at room temperature

NASA Astrophysics Data System (ADS)

Liedtke, S.; Grüner, Ch; Lotnyk, A.; Rauschenbach, B.

2017-09-01

Metallic thin films consisting of separated nanostructures are fabricated by evaporative glancing angle deposition at room temperature. The columnar microstructure of the Ti and Cr columns is investigated by high resolution transmission electron microscopy and selective area electron diffraction. The morphology of the sculptured metallic films is studied by scanning electron microscopy. It is found that tilted Ti and Cr columns grow with a single crystalline morphology, while upright Cr columns are polycrystalline. Further, the influence of continuous substrate rotation on the shaping of Al, Ti, Cr and Mo nanostructures is studied with view to surface diffusion and the shadowing effect. It is observed that sculptured metallic thin films deposited without substrate rotation grow faster compared to those grown with continuous substrate rotation. A theoretical model is provided to describe this effect.

Optical Interactions at Randomly Rough Surfaces

DTIC Science & Technology

2003-03-10

frequency range. The design of a random surface that acts as a Lambertian diffuser, especially in the infrared region of the optical spectrum, is...FTIR grazing angle microscopy. Recently, an experimental study was performed of the far-field scattering at small grazing angles, especially the enhanced...a specular component in the scattered light, in this frequency range. The design of a random surface that acts as a Lambertian diffuser, especially in

Tomographic diffractive microscopy with a wavefront sensor.

PubMed

Ruan, Y; Bon, P; Mudry, E; Maire, G; Chaumet, P C; Giovannini, H; Belkebir, K; Talneau, A; Wattellier, B; Monneret, S; Sentenac, A

2012-05-15

Tomographic diffractive microscopy is a recent imaging technique that reconstructs quantitatively the three-dimensional permittivity map of a sample with a resolution better than that of conventional wide-field microscopy. Its main drawbacks lie in the complexity of the setup and in the slowness of the image recording as both the amplitude and the phase of the field scattered by the sample need to be measured for hundreds of successive illumination angles. In this Letter, we show that, using a wavefront sensor, tomographic diffractive microscopy can be implemented easily on a conventional microscope. Moreover, the number of illuminations can be dramatically decreased if a constrained reconstruction algorithm is used to recover the sample map of permittivity.

A novel fibrous duct structure discovered in the brain meninges by using polarized light microscopy

NASA Astrophysics Data System (ADS)

Nam, Min-Ho; Jung, Sharon Jiyoon; Soh, Kwang-Sup; Lim, Jaekwan; Seo, Eunseok; Lim, Jun; Baek, Miok; Lee, Sang Joon

2016-05-01

We have previously reported the discovery of a novel fibrous structure (NFS) consisting of unidirectionally arranged collagen fibers in the spinal pia mater. Due to its unique structure, it was easily detected using polarized light microscopy. In the current study, we describe the discovery of a similar NFS in the brain meninges of rats by using polarized light microscopy. This NFS is located beneath the superior sagittal sinus. Initially, we systemically analyzed the polarization properties of the NFS. The change in the light intensity of the NFS, with respect to the polarization angle, was eight times greater than that of blood vessels, showing that the collagen fibers are oriented in a particular direction with almost perfect parallelism (0.99). The orientation angle of the polarization ellipse confirmed the orientation of the collagen fibers in the NFS. Histological studies further confirmed that the unidirectionally arranged collagen fibers were responsible for this distinct polarization property. Surprisingly, X-ray microtomography and 3D confocal imaging revealed that the NFS contains within it a duct structure, a putative primo vessel. In conclusion, we report a NFS in the brain meninges, detected by using polarized light microscopy, that provides space for a putative primo vessel, not a blood vessel.

High indium content homogenous InAlN layers grown by plasma-assisted molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kyle, Erin C. H.; Kaun, Stephen W.; Wu, Feng; Bonef, Bastien; Speck, James S.

2016-11-01

InAlN grown by plasma-assisted molecular beam epitaxy often contains a honeycomb microstructure. The honeycomb microstructure consists of 5-10 nm diameter aluminum-rich regions which are surrounded by indium-rich regions. Layers without this microstructure were previously developed for nominally lattice-matched InAlN and have been developed here for higher indium content InAlN. In this study, InAlN was grown in a nitrogen-rich environment with high indium to aluminum flux ratios at low growth temperatures. Samples were characterized by high-resolution x-ray diffraction, atomic force microscopy, high-angle annular dark-field scanning transmission electron microscopy, and atom probe tomography. Atomic force microscopy showed InAlN layers grown at temperatures below 450 °C under nitrogen-rich conditions were free of droplets. InAlN films with indium contents up to 81% were grown at temperatures between 410 and 440 °C. High-angle annular dark-field scanning transmission electron microscopy and atom probe tomography showed no evidence of honeycomb microstructure for samples with indium contents of 34% and 62%. These layers are homogeneous and follow a random alloy distribution. A growth diagram for InAlN of all indium contents is reported.

BAM! Guide to Getting Along

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

BAM! Body and Mind

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

Study of the composition, structure, and optical properties of a-Si{sub 1-x}C{sub x}:H Left-Pointing-Angle-Bracket Er Right-Pointing-Angle-Bracket films erbium doped from the Er(pd){sub 3} complex compound

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

Kudoyarova, V. Kh., E-mail: kudoyarova@mail.ioffe.ru; Tolmachev, V. A.; Gushchina, E. V.

2013-03-15

Rutherford backscattering, IR spectroscopy, ellipsometry, and atomic-force microscopy are used to perform an integrated study of the composition, structure and optical properties of a-Si{sub 1-x}C{sub x}:H Left-Pointing-Angle-Bracket Er Right-Pointing-Angle-Bracket amorphous films. The technique employed to obtain the a-Si{sub 1-x}C{sub x}:H Left-Pointing-Angle-Bracket Er Right-Pointing-Angle-Bracket amorphous films includes the high-frequency decomposition of a mixture of gases, (SiH{sub 4}){sub a} + (CH{sub 4}){sub b}, and the simultaneous thermal evaporation of a complex compound, Er(pd){sub 3}. It is demonstrated that raising the amount of CH{sub 4} in the gas mixture results in an increase in the carbon content of the films under study andmore » an increase in the optical gap E{sub g}{sup opt} from 1.75 to 2.2 eV. Changes in the composition of a-Si{sub 1-x}C{sub x}:H Left-Pointing-Angle-Bracket Er Right-Pointing-Angle-Bracket amorphous films, accompanied, in turn, by changes in the optical constants, are observed in the IR spectra. The ellipsometric spectra obtained are analyzed in terms of multiple-parameter models. The conclusion is made on the basis of this analysis that the experimental and calculated spectra coincide well when variation in the composition of the amorphous films with that of the gas mixture is taken into account. The existence of a thin (6-8 nm) silicon-oxide layer on the surface of the films under study and the validity of using the double-layer model in ellipsometric calculations is confirmed by the results of structural analyses by atomic-force microscopy.« less

A coating of silane modified silica nanoparticles on PET substrate film for inkjet printing

NASA Astrophysics Data System (ADS)

Wu, J.; Liu, L.; Jiang, B.; Hu, Z.; Wang, X. Q.; Huang, Y. D.; Lin, D. R.; Zhang, Q. H.

2012-04-01

The paper aims to design nanoporous coatings for inkjet printing and study its microstructure influence on the ink absorption. In the present work, two inkjet materials were prepared: one with unmodified nano-SiO2 (S_1), the other with silica coupling agent modified nano-SiO2 (S_2). The surface characteristic changing after modification was investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM). Wetting with contact angles was determined by the dynamic contact angle analysis test (DCAT). Through measurements, the dispersion of modified nano-SiO2 particles in the coating was superior to the dispersion of unmodified nano-SiO2 particles, surface roughness value (Ra) of S_1 was significantly higher than that of S_2, dynamic contact angle of S_2 is smaller than that of S_1 and ink droplet absorption in S_2 was much faster than in S_1. These results also reveal that the modification method is effective and offers a potential way to fabricate inkjet material with the advantages of microstructure and ink absorption over traditional methods.

Scanning tunneling microscopy and spectroscopy of twisted trilayer graphene

NASA Astrophysics Data System (ADS)

Zuo, Wei-Jie; Qiao, Jia-Bin; Ma, Dong-Lin; Yin, Long-Jing; Sun, Gan; Zhang, Jun-Yang; Guan, Li-Yang; He, Lin

2018-01-01

Twist, as a simple and unique degree of freedom, could lead to enormous novel quantum phenomena in bilayer graphene. A small rotation angle introduces low-energy van Hove singularities (VHSs) approaching the Fermi level, which result in unusual correlated states in the bilayer graphene. It is reasonable to expect that the twist could also affect the electronic properties of few-layer graphene dramatically. However, such an issue has remained experimentally elusive. Here, by using scanning tunneling microscopy/spectroscopy (STM/STS), we systematically studied a twisted trilayer graphene (TTG) with two different small twist angles between adjacent layers. Two sets of VHSs, originating from the two twist angles, were observed in the TTG, indicating that the TTG could be simply regarded as a combination of two different twisted bilayers of graphene. By using high-resolution STS, we observed a split of the VHSs and directly imaged the spatial symmetry breaking of electronic states around the VHSs. These results suggest that electron-electron interactions play an important role in affecting the electronic properties of graphene systems with low-energy VHSs.

Effect of ophthalmic solution components on acrylic intraocular lenses.

PubMed

Ayaki, Masahiko; Nishihara, Hitoshi; Yaguchi, Shigeo; Koide, Ryohei

2007-01-01

To investigate the effect of ophthalmic solution components on the surface of acrylic intraocular lenses (IOLs). Department of Opthalmology, Showa University School of Medicine. Measurement of the contact angles of ophthalmic solutions on 3 acrylic IOLs was performed. The solutions were diclofenac sodium (Diclod), bromfenac sodium (Bronuck), betamethasone phosphate (Rinderon), dibekacin sulfate (Panimycin), polysorbate 80 (Tween 20), benzalkonium chloride, chlorobutanol, methylparahydroxybenzoate, and propylparahydroxybenzoate. The IOLs were incubated at 35 degrees C for 2 weeks in undiluted ophthalmic solutions and in 1:10 dilutions of ophthalmic solution components. The IOLs were sectioned and observed by scanning electron microscopy. The contact angle of Diclod and Bronuck solutions was the smallest. The contact angle of Rinderon and Panimycin was similar to that of distilled water. Scanning electron microscopy examination of IOLs incubated in ophthalmic solution components showed intralenticular changes. The IOLs immersed in ophthalmic solutions did not show any change, even after extended incubation. The chemical components of ophthalmic solutions, such as surfactants and solvents, permeate acrylic IOLs, suggesting the potential for long-term adverse effects of eyedrops in pseudophakic eyes.

Effect of dielectric barrier discharge treatment on surface nanostructure and wettability of polylactic acid (PLA) nonwoven fabrics

NASA Astrophysics Data System (ADS)

Ren, Yu; Xu, Lin; Wang, Chunxia; Wang, Xiaona; Ding, Zhirong; Chen, Yuyue

2017-12-01

Polylactic acid (PLA) nonwoven fabrics are treated with atmospheric dielectric barrier discharge (DBD) plasma to improve surface wettability. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) show that micro- to nano-scale textures appear on the treated PLA surfaces dependent on the treatment time. X-ray photoelectron spectroscopy (XPS) analysis reveals that the DBD plasma treatments result in decreased carbon contents and increased oxygen contents as well as slightly increased nitrogen contents. The water contact angle decreases sharply with the increase of the DBD plasma treatment time. The super hydrophilic PLA surfaces (the water contact angle reached 0°) are obtained when the treatment time is longer than 90 s. Ninety days after the DBD plasma treatment, the XPS analysis shows that Csbnd O/Csbnd N and Cdbnd O/Osbnd Cdbnd O percentages decline for all treatment groups. However, the water contact angle is kept constant at 0° for the groups treated above 90 s, which could be due to the oxidized nano-structured layer on the DBD plasma treated PLA surfaces.

Reflective small angle electron scattering to characterize nanostructures on opaque substrates

NASA Astrophysics Data System (ADS)

Friedman, Lawrence H.; Wu, Wen-Li; Fu, Wei-En; Chien, Yunsan

2017-09-01

Feature sizes in integrated circuits (ICs) are often at the scale of 10 nm and are ever shrinking. ICs appearing in today's computers and hand held devices are perhaps the most prominent examples. These smaller feature sizes demand equivalent advances in fast and accurate dimensional metrology for both development and manufacturing. Techniques in use and continuing to be developed include X-ray based techniques, optical scattering, and of course the electron and scanning probe microscopy techniques. Each of these techniques has their advantages and limitations. Here, the use of small angle electron beam scattering measurements in a reflection mode (RSAES) to characterize the dimensions and the shape of nanostructures on flat and opaque substrates is demonstrated using both experimental and theoretical evidence. In RSAES, focused electrons are scattered at angles smaller than 1 ° with the assistance of electron optics typically used in transmission electron microscopy. A proof-of-concept experiment is combined with rigorous electron reflection simulations to demonstrate the efficiency and accuracy of RSAES as a method of non-destructive measurement of shapes of features less than 10 nm in size on flat and opaque substrates.

Reflective Small Angle Electron Scattering to Characterize Nanostructures on Opaque Substrates.

PubMed

Friedman, Lawrence H; Wu, Wen-Li; Fu, Wei-En; Chien, Yunsan

2017-09-01

Features sizes in integrated circuits (ICs) are often at the scale of 10 nm and are ever shrinking. ICs appearing in today's computers and hand held devices are perhaps the most prominent examples. These smaller feature sizes demand equivalent advances in fast and accurate dimensional metrology for both development and manufacturing. Techniques in use and continuing to be developed include X-ray based techniques, optical scattering and of course the electron and scanning probe microscopy techniques. Each of these techniques have their advantages and limitations. Here the use of small angle electron beam scattering measurements in a reflection mode (RSAES) to characterize the dimensions and the shape of nanostructures on flat and opaque substrates is demonstrated using both experimental and theoretical evidence. In RSAES, focused electrons are scattered at angles smaller than 1° with the assistance of electron optics typically used in transmission electron microscopy. A proof-of-concept experiment is combined with rigorous electron reflection simulations to demonstrate the efficiency and accuracy of RSAES as a method of non-destructive measurement of shapes of features less than 10 nm in size on flat and opaque substrates.

Frozen lattice and absorptive model for high angle annular dark field scanning transmission electron microscopy: A comparison study in terms of integrated intensity and atomic column position measurement.

PubMed

Alania, M; Lobato, I; Van Aert, S

2018-01-01

In this paper, both the frozen lattice (FL) and the absorptive potential (AP) approximation models are compared in terms of the integrated intensity and the precision with which atomic columns can be located from an image acquired using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM). The comparison is made for atoms of Cu, Ag, and Au. The integrated intensity is computed for both an isolated atomic column and an atomic column inside an FCC structure. The precision has been computed using the so-called Cramér-Rao Lower Bound (CRLB), which provides a theoretical lower bound on the variance with which parameters can be estimated. It is shown that the AP model results into accurate measurements for the integrated intensity only for small detector ranges under relatively low angles and for small thicknesses. In terms of the attainable precision, both methods show similar results indicating picometer range precision under realistic experimental conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-assembled monolayers of alkyl-thiols on InAs: A Kelvin probe force microscopy study

NASA Astrophysics Data System (ADS)

Szwajca, A.; Wei, J.; Schukfeh, M. I.; Tornow, M.

2015-03-01

We report on the preparation and characterization of self-assembled monolayers from aliphatic thiols with different chain length and termination on InAs (100) planar surfaces. This included as first step the development and investigation of a thorough chemical InAs surface preparation step using a dedicated bromine/NH4OH-based etching process. Ellipsometry, contact angle measurements and atomic force microscopy (AFM) indicated the formation of smooth, surface conforming monolayers. The molecular tilt angles were obtained as 30 ± 10° with respect to the surface normal. Kelvin probe force microscopy (KPFM) measurements in hand with Parameterized Model number 5 (PM5) calculations of the involved molecular dipoles allowed for an estimation of the molecular packing densities on the surface. We obtained values of up to n = 1014 cm- 2 for the SAMs under study. These are close to what is predicted from a simple geometrical model that would calculate a maximum density of about n = 2.7 × 1014 cm- 2. We take this as additional conformation of the substrate smoothness and quality of our InAs-SAM hybrid layer systems.

Analogous on-axis interference topographic phase microscopy (AOITPM).

PubMed

Xiu, P; Liu, Q; Zhou, X; Xu, Y; Kuang, C; Liu, X

2018-05-01

The refractive index (RI) of a sample as an endogenous contrast agent plays an important role in transparent live cell imaging. In tomographic phase microscopy (TPM), 3D quantitative RI maps can be reconstructed based on the measured projections of the RI in multiple directions. The resolution of the RI maps not only depends on the numerical aperture of the employed objective lens, but also is determined by the accuracy of the quantitative phase of the sample measured at multiple scanning illumination angles. This paper reports an analogous on-axis interference TPM, where the interference angle between the sample and reference beams is kept constant for projections in multiple directions to improve the accuracy of the phase maps and the resolution of RI tomograms. The system has been validated with both silica beads and red blood cells. Compared with conventional TPM, the proposed system acquires quantitative RI maps with higher resolution (420 nm @λ = 633 nm) and signal-to-noise ratio that can be beneficial for live cell imaging in biomedical applications. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Magnetic and microwave properties of U-type hexaferrite films with high remanence and low ferromagnetic resonance linewidth

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

Su, Zhijuan; Bennett, Steven; Hu, Bolin

2014-05-07

U-type barium hexaferrite films (Ba{sub 4}Ni{sub 1.4}Co{sub 0.6}Fe{sub 36}O{sub 60}) were deposited on (0001) sapphire substrates by pulsed laser deposition. Microstructure and magnetic properties of the films were characterized by X-ray diffraction, scanning electron microscopy and vibrating sample magnetometry. Ferromagnetic resonance (FMR) measurements were performed at X-band. The results indicate an anisotropy field of ∼8 kOe, and the saturation magnetization (4πM{sub s}) of ∼3.6 kG. An optimal post-deposition annealing of films results in a strong (0 0 n) crystallographic texture and a high hysteresis loop squareness (M{sub r}/M{sub s} = 92%) leading to self biased properties. Furthermore, the highly self-biased ferrite films exhibitedmore » an FMR linewidth of ∼200 Oe. The U-type hexaferrite films having low microwave loss, low magnetic anisotropy field, and high squareness are a suitable alternative to Sc or In doped BaM ferrites that have been the choice material for self-biased microwave devices at X-band frequencies.« less

Correcting sample drift using Fourier harmonics.

PubMed

Bárcena-González, G; Guerrero-Lebrero, M P; Guerrero, E; Reyes, D F; Braza, V; Yañez, A; Nuñez-Moraleda, B; González, D; Galindo, P L

2018-07-01

During image acquisition of crystalline materials by high-resolution scanning transmission electron microscopy, the sample drift could lead to distortions and shears that hinder their quantitative analysis and characterization. In order to measure and correct this effect, several authors have proposed different methodologies making use of series of images. In this work, we introduce a methodology to determine the drift angle via Fourier analysis by using a single image based on the measurements between the angles of the second Fourier harmonics in different quadrants. Two different approaches, that are independent of the angle of acquisition of the image, are evaluated. In addition, our results demonstrate that the determination of the drift angle is more accurate by using the measurements of non-consecutive quadrants when the angle of acquisition is an odd multiple of 45°. Copyright © 2018 Elsevier Ltd. All rights reserved.

Superhydrophobic coatings on wood substrate for self-cleaning and EMI shielding

NASA Astrophysics Data System (ADS)

Xing, Yingjie; Xue, Yaping; Song, Jinlong; Sun, Yankui; Huang, Liu; Liu, Xin; Sun, Jing

2018-04-01

A layer of superhydrophobic coating having good electromagnetic shielding and self-cleaning performance was fabricated on a wood surface through an electroless copper plated process. The superhydrophobic property of the wood surface was measured by contact angle (CA) and roll-off angle (RA) measurements. The microstructure and chemical composition of the superhydrophobic coating were analyzed by scanning electron microscopy (SEM), energy dispersive spectrometer (EDS) and X-ray diffraction (XRD). The analysis revealed that the microscale particles were uniformly distributed on the wood surface and the main component of the coating is metallic copper. The as-prepared Cu coatings on wood substrate exhibit a good superhydrophobicity with water contact angle about 160° and rolling angle less than 5°.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

In Situ Airborne Instrumentation: Addressing and Solving Measurement Problems in Ice Clouds

DOE PAGES

Baumgardner, Darrel; Kok, Greg; Avallone, L.; ...

2012-02-01

A meeting of 31 international experts on in situ measurements from aircraft was held to identify unresolved questions concerning ice formation and evolution in ice clouds, assess the current state of instrumentation that can address these problems, introduce emerging technology that may overcome current measurement issues and recommend future courses of action that can improve our understanding of ice cloud microphysical processes and their impact on the environment. The meeting proceedings and outcome has been described in detail in a manuscript submitted to the Bulletin of the American Meteorological Society (BAMS) on March 24, 2011. This paper is currently undermore » review. The remainder of this summary, in the following pages, is the text of the BAMS article. A technical note that will be published by the National Center for Atmospheric Research is currently underway and is expected to be published before the end of the year.« less

An Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat.

PubMed Central

Kenney, S; Kamine, J; Markovitz, D; Fenrick, R; Pagano, J

1988-01-01

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, we demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses. Images PMID:2830625

Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat

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

Kenney, S.; Kamine, J.; Markovitz, D.

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, the authors demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBVmore » gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.« less

Characterization of ambient aerosols at the San Francisco International Airport using BioAerosol Mass Spectrometry

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

Steele, P T; McJimpsey, E L; Coffee, K R

2006-03-16

The BioAerosol Mass Spectrometry (BAMS) system is a rapidly fieldable, fully autonomous instrument that can perform correlated measurements of multiple orthogonal properties of individual aerosol particles. The BAMS front end uses optical techniques to nondestructively measure a particle's aerodynamic diameter and fluorescence properties. Fluorescence can be excited at 266nm or 355nm and is detected in two broad wavelength bands. Individual particles with appropriate size and fluorescence properties can then be analyzed more thoroughly in a dual-polarity time-of-flight mass spectrometer. Over the course of two deployments to the San Francisco International Airport, more than 6.5 million individual aerosol particles were fullymore » analyzed by the system. Analysis of the resulting data has provided a number of important insights relevant to rapid bioaerosol detection, which are described here.« less

Biological nano-functionalization of titanium-based biomaterial surfaces: a flexible toolbox

PubMed Central

Beutner, René; Michael, Jan; Schwenzer, Bernd; Scharnweber, Dieter

2010-01-01

Surface functionalization with bioactive molecules (BAMs) on a nanometre scale is a main field in current biomaterial research. The immobilization of a vast number of substances and molecules, ranging from inorganic calcium phosphate phases up to peptides and proteins, has been investigated throughout recent decades. However, in vitro and in vivo results are heterogeneous. This may be at least partially attributed to the limits of the applied immobilization methods. Therefore, this paper highlights, in the first part, advantages and limits of the currently applied methods for the biological nano-functionalization of titanium-based biomaterial surfaces. The second part describes a new immobilization system recently developed in our groups. It uses the nanomechanical fixation of at least partially single-stranded nucleic acids (NAs) into an anodic titanium oxide layer as an immobilization principle and their hybridization ability for the functionalization of the surface with BAMs conjugated to the respective complementary NA strands. PMID:19889692

Viewing Angle Classification of Cryo-Electron Microscopy Images Using Eigenvectors

PubMed Central

Singer, A.; Zhao, Z.; Shkolnisky, Y.; Hadani, R.

2012-01-01

The cryo-electron microscopy (cryo-EM) reconstruction problem is to find the three-dimensional structure of a macromolecule given noisy versions of its two-dimensional projection images at unknown random directions. We introduce a new algorithm for identifying noisy cryo-EM images of nearby viewing angles. This identification is an important first step in three-dimensional structure determination of macromolecules from cryo-EM, because once identified, these images can be rotationally aligned and averaged to produce “class averages” of better quality. The main advantage of our algorithm is its extreme robustness to noise. The algorithm is also very efficient in terms of running time and memory requirements, because it is based on the computation of the top few eigenvectors of a specially designed sparse Hermitian matrix. These advantages are demonstrated in numerous numerical experiments. PMID:22506089

Effect of calcium concentration on the structure of casein micelles in thin films.

PubMed

Müller-Buschbaum, P; Gebhardt, R; Roth, S V; Metwalli, E; Doster, W

2007-08-01

The structure of thin casein films prepared with spin-coating is investigated as a function of the calcium concentration. Grazing incidence small-angle x-ray scattering and atomic force microscopy are used to probe the micelle structure. For comparison, the corresponding casein solutions are investigated with dynamic light-scattering experiments. In the thin films with added calcium three types of casein structures, aggregates, micelles, and mini-micelles, are observed in coexistence with atomic force microscopy and grazing incidence small-angle x-ray scattering. With increasing calcium concentration, the size of the aggregates strongly increases, while the size of micelles slightly decreases and the size of the mini-micelles increases. This effect is explained in the framework of the particle-stabilizing properties of the hairy layer of kappa-casein surrounding the casein micelles.

Effect of Calcium Concentration on the Structure of Casein Micelles in Thin Films

PubMed Central

Müller-Buschbaum, P.; Gebhardt, R.; Roth, S. V.; Metwalli, E.; Doster, W.

2007-01-01

The structure of thin casein films prepared with spin-coating is investigated as a function of the calcium concentration. Grazing incidence small-angle x-ray scattering and atomic force microscopy are used to probe the micelle structure. For comparison, the corresponding casein solutions are investigated with dynamic light-scattering experiments. In the thin films with added calcium three types of casein structures, aggregates, micelles, and mini-micelles, are observed in coexistence with atomic force microscopy and grazing incidence small-angle x-ray scattering. With increasing calcium concentration, the size of the aggregates strongly increases, while the size of micelles slightly decreases and the size of the mini-micelles increases. This effect is explained in the framework of the particle-stabilizing properties of the hairy layer of κ-casein surrounding the casein micelles. PMID:17496032

A privacy-preserving solution for compressed storage and selective retrieval of genomic data.

PubMed

Huang, Zhicong; Ayday, Erman; Lin, Huang; Aiyar, Raeka S; Molyneaux, Adam; Xu, Zhenyu; Fellay, Jacques; Steinmetz, Lars M; Hubaux, Jean-Pierre

2016-12-01

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data. © 2016 Huang et al.; Published by Cold Spring Harbor Laboratory Press.

Signal-on electrochemical assay for label-free detection of TdT and BamHI activity based on grown DNA nanowire-templated copper nanoclusters.

PubMed

Hu, Yufang; Zhang, Qingqing; Xu, Lihua; Wang, Jiao; Rao, Jiajia; Guo, Zhiyong; Wang, Sui

2017-11-01

Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient "signal-on" electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3'-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to H 2 O 2 reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3'-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery. Graphical Abstract Extraordinary TdT-generated DNA-CuNCs are synthesized and act as a novel electrochemical sensing platform for sensitive detection of TdT and BamHI activity in biological environments.

Facilitators and obstacles in pre-hospital medical response to earthquakes: a qualitative study.

PubMed

Djalali, Ahmadreza; Khankeh, Hamidreza; Öhlén, Gunnar; Castrén, Maaret; Kurland, Lisa

2011-05-16

Earthquakes are renowned as being amongst the most dangerous and destructive types of natural disasters. Iran, a developing country in Asia, is prone to earthquakes and is ranked as one of the most vulnerable countries in the world in this respect. The medical response in disasters is accompanied by managerial, logistic, technical, and medical challenges being also the case in the Bam earthquake in Iran. Our objective was to explore the medical response to the Bam earthquake with specific emphasis on pre-hospital medical management during the first days. The study was performed in 2008; an interview based qualitative study using content analysis. We conducted nineteen interviews with experts and managers responsible for responding to the Bam earthquake, including pre-hospital emergency medical services, the Red Crescent, and Universities of Medical Sciences. The selection of participants was determined by using a purposeful sampling method. Sample size was given by data saturation. The pre-hospital medical service was divided into three categories; triage, emergency medical care and transportation, each category in turn was identified into facilitators and obstacles. The obstacles identified were absence of a structured disaster plan, absence of standardized medical teams, and shortage of resources. The army and skilled medical volunteers were identified as facilitators. The most compelling, and at the same time amenable obstacle, was the lack of a disaster management plan. It was evident that implementing a comprehensive plan would not only save lives but decrease suffering and enable an effective praxis of the available resources at pre-hospital and hospital levels.

Facilitators and obstacles in pre-hospital medical response to earthquakes: a qualitative study

PubMed Central

2011-01-01

Background Earthquakes are renowned as being amongst the most dangerous and destructive types of natural disasters. Iran, a developing country in Asia, is prone to earthquakes and is ranked as one of the most vulnerable countries in the world in this respect. The medical response in disasters is accompanied by managerial, logistic, technical, and medical challenges being also the case in the Bam earthquake in Iran. Our objective was to explore the medical response to the Bam earthquake with specific emphasis on pre-hospital medical management during the first days. Methods The study was performed in 2008; an interview based qualitative study using content analysis. We conducted nineteen interviews with experts and managers responsible for responding to the Bam earthquake, including pre-hospital emergency medical services, the Red Crescent, and Universities of Medical Sciences. The selection of participants was determined by using a purposeful sampling method. Sample size was given by data saturation. Results The pre-hospital medical service was divided into three categories; triage, emergency medical care and transportation, each category in turn was identified into facilitators and obstacles. The obstacles identified were absence of a structured disaster plan, absence of standardized medical teams, and shortage of resources. The army and skilled medical volunteers were identified as facilitators. Conclusions The most compelling, and at the same time amenable obstacle, was the lack of a disaster management plan. It was evident that implementing a comprehensive plan would not only save lives but decrease suffering and enable an effective praxis of the available resources at pre-hospital and hospital levels. PMID:21575233

Synthesis and Characterization of BaFe12O19/Poly(aniline, pyrrole, ethylene terephthalate) Composites Coatings as Radar Absorbing Material (RAM)

NASA Astrophysics Data System (ADS)

Sasria, Nia; Ardhyananta, H.; Fajarin, R.; Widyastuti

2017-07-01

This research shows the processing and design of radar absorbing material (RAM) based on barium hexaferrite (BaM) and poly(aniline, pyrrole, ethylene terephthalate) (PAni,PPy,PET). BaM was prepared by sol gel method with Ni-Zn doping at mole fraction of 0. 4 to obtain soft magnetic material. BaM/(PAni,PPy) composites were synthesized by in-situ polymerization method at ˜0 °C. (BaM/PET) composite was prepared by melt compounding at 220°C. The composites were coated on A-grade AH36 steel using Dallenbach Layer, Salisbury Screen and Jaumann Layer methods with thickness of 2, 4, and 6 mm. The composites were evaluated using XRD, SEM, FTIR, VSM, LCM-meter and VNA. Results showed that doped BaM showed BaNixZnxFe12-2xO19 structure. BaM/(PAni,PPy,PET) composites possessed globular morphology with M-O and C-H bonds. BaNixZnxFe12-2xO19 exhibited the value of Ms and Hc, 56.6 emu/g and 60 Oe respectively. High electrical conductivity of 1.77744 × 10-5 S/cm was achieved of BaM/PAni composite. The maximum reflection loss (RL) was reached at - 48.720 dB and 8.1 GHz for BaM/PAni composite coating with 6 mm thickness at Jaumann Layer. These results indicated that BaM/PAni composite was a soft magnetic material with a high RL value that is suitable for RAM, which used in stealth technology on naval vessels.

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

PubMed Central

Huang, Zhicong; Ayday, Erman; Lin, Huang; Aiyar, Raeka S.; Molyneaux, Adam; Xu, Zhenyu; Hubaux, Jean-Pierre

2016-01-01

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients’ complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data. PMID:27789525

Ultra-hard amorphous AlMgB14 films RF sputtered onto curved substrates

NASA Astrophysics Data System (ADS)

Grishin, A. M.; Putrolaynen, V. V.; Yuzvyuk, M. H.

2017-03-01

Recently, hard AlMgB14 (BAM) coatings were deposited for the first time by RF magnetron sputtering using a single stoichiometric ceramic target. High target sputtering power and sufficiently short target-to-substrate distance were found to be critical processing conditions. They enabled fabrication of stoichiometric in-depth compositionally homogeneous films with the peak values of nanohardness 88 GPa and Young’s modulus 517 GPa at the penetration depth of 26 nm and, respectively, 35 GPa and 275 GPa at 200 nm depth in 2 µm thick film (Grishin et al 2014 JETP Lett. 100 680). The narrow range of sufficiently short target-to-substrate distance makes impossible to coat non flat specimens. To achieve ultimate BAM films’ characteristics onto curved surfaces we developed two-step sputtering process. The first thin layer is deposited as a template at low RF power that facilitates a layered Frank van der Merwe mode growth of smooth film occurs. The next layer is grown at high RF target sputtering power. The affinity of subsequent flow of sputtered atoms to already evenly condensed template fosters the development of smooth film surface. As an example, we made BAM coating onto hemispherical 5 mm in diameter ball made from a hard tool steel and used as a head of a special gauge. Very smooth (6.6 nm RMS surface roughness) and hard AlMgB14 films fabricated onto commercial ball-shaped items enhance hardness of tool steel specimens by a factor of four.

RGB-Switchable Porous Electrospun Nanofiber Chemoprobe-Filter Prepared from Multifunctional Copolymers for Versatile Sensing of pH and Heavy Metals.

PubMed

Liang, Fang-Cheng; Kuo, Chi-Ching; Chen, Bo-Yu; Cho, Chia-Jung; Hung, Chih-Chien; Chen, Wen-Chang; Borsali, Redouane

2017-05-17

Novel red-green-blue (RGB) switchable probes based on fluorescent porous electrospun (ES) nanofibers exhibiting high sensitivity to pH and mercury ions (Hg 2+ ) were prepared with one type of copolymer (poly(methyl methacrylatete-co-1,8-naphthalimide derivatives-co-rhodamine derivative); poly(MMA-co-BNPTU-co-RhBAM)) by using a single-capillary spinneret. The MMA, BNPTU, and RhBAM moieties were designed to (i) permit formation of porous fibers, (ii) fluoresce for Hg 2+ detection, and (iii) fluoresce for pH, respectively. The fluorescence emission of BNPTU (fluorescence resonance energy transfer (FRET) donor) changed from green to blue as it detected Hg 2+ . The fluorescence emission of RhBAM (FRET acceptor) was highly selective for pH, changing from nonfluorescent (pH 7) to exhibiting strong red fluorescence (pH 2). The full-color emission of the ES nanofibers included green, red, blue, purple, and white depending on the particular pH and Hg 2+ -concentration combination of the solution. The porous ES nanofibers with 30 nm pores were fabricated using hydrophobic MMA, low-boiling-point solvent, and at a high relative humidity (80%). These porous ES nanofibers had a higher surface-to-volume ratio than did the corresponding thin films, which enhanced their performance. The present study demonstrated that the FRET-based full-color-fluorescence porous nanofibrous membranes, which exhibit on-off switching and can be used as naked eye probes, have potential for application in water purification sensing filters.

Integrating smoking cessation into substance use disorder treatment for military veterans: measurement and treatment engagement efforts.

PubMed

Shealy, Suzanne E; Winn, Jaime L

2014-02-01

Military personnel and veterans smoke at higher rates than the general population, compromising physical performance readiness and health (Committee on Smoking Cessation in Military and Veteran Populations & Institute of Medicine, 2009). While efforts are being made within both the Department of Defense and the Veterans' Administration (VA) hospitals to prevent onset, change the smoking culture, and promote smoking cessation; smoking rates are increasing among combat deployed service members, and smoking rates are particularly high among veterans with mental health and other substance use disorders (McFall, 2006). Recent research supports making smoking cessation widely available and integrated with other forms of care (Gierisch et al., 2012; McFall et al., 2010). This paper describes the efforts of one VA substance use disorder (SUD) treatment program to integrate smoking cessation in routine care, including assessment of tobacco use and motivation and intention to quit via the proposed Nic-BAM assessment. Our team was 100% successful in incorporating the Nic-BAM into our regular assessment of treatment program participants. This suggests that staff members are amenable to assessing for tobacco addiction alongside other substance addictions. Although smoking did not decrease according to the Nic-BAM, an increase in the use of nicotine-replacement products suggests that participants are willing to initiate a quit attempt during SUD treatment. The availability of new evidence-based approaches for integration of tobacco cessation with mental health and SUD treatment may help to enhance programmatic efforts. Environmental changes are needed to fully incorporate tobacco recovery into SUD programming, and additional resources may include peer support specialists. © 2013.

Digital optical correlator x-ray telescope alignment monitoring system

NASA Astrophysics Data System (ADS)

Lis, Tomasz; Gaskin, Jessica; Jasper, John; Gregory, Don A.

2018-01-01

The High-Energy Replicated Optics to Explore the Sun (HEROES) program is a balloon-borne x-ray telescope mission to observe hard x-rays (˜20 to 70 keV) from the sun and multiple astrophysical targets. The payload consists of eight mirror modules with a total of 114 optics that are mounted on a 6-m-long optical bench. Each mirror module is complemented by a high-pressure xenon gas scintillation proportional counter. Attached to the payload is a camera that acquires star fields and then matches the acquired field to star maps to determine the pointing of the optical bench. Slight misalignments between the star camera, the optical bench, and the telescope elements attached to the optical bench may occur during flight due to mechanical shifts, thermal gradients, and gravitational effects. These misalignments can result in diminished imaging and reduced photon collection efficiency. To monitor these misalignments during flight, a supplementary Bench Alignment Monitoring System (BAMS) was added to the payload. BAMS hardware comprises two cameras mounted directly to the optical bench and rings of light-emitting diodes (LEDs) mounted onto the telescope components. The LEDs in these rings are mounted in a predefined, asymmetric pattern, and their positions are tracked using an optical/digital correlator. The BAMS analysis software is a digital adaption of an optical joint transform correlator. The aim is to enhance the observational proficiency of HEROES while providing insight into the magnitude of mechanically and thermally induced misalignments during flight. Results from a preflight test of the system are reported.

Sample holder for axial rotation of specimens in 3D microscopy.

PubMed

Bruns, T; Schickinger, S; Schneckenburger, H

2015-10-01

In common light microscopy, observation of samples is only possible from one perspective. However, especially for larger three-dimensional specimens observation from different views is desirable. Therefore, we are presenting a sample holder permitting rotation of the specimen around an axis perpendicular to the light path of the microscope. Thus, images can be put into a defined multidimensional context, enabling reliable three-dimensional reconstructions. The device can be easily adapted to a great variety of common light microscopes and is suitable for various applications in science, education and industry, where the observation of three-dimensional specimens is essential. Fluorescence z-projection images of copepods and ixodidae ticks at different rotation angles obtained by confocal laser scanning microscopy and light sheet fluorescence microscopy are reported as representative results. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Design Framework Validation for a Hot Spot on Complex Aircraft Structures

DTIC Science & Technology

2010-08-01

LEONARD, S. E. OLSON AND M. P. DESIMIO Joachim Schneider -Gloetzl, Gloetzl GmbH, Rh instetten, Germany...Rainer Gloetzl, RG Research, Ettlingen, Ger any Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal Institute for

Single Etch-Pit Shape on Off-Angled 4H-SiC(0001) Si-Face Formed by Chlorine Trifluoride

NASA Astrophysics Data System (ADS)

Hatayama, Tomoaki; Tamura, Tetsuya; Yano, Hiroshi; Fuyuki, Takashi

2012-07-01

The etch pit shape of an off-angled 4H-SiC Si-face formed by chlorine trifluoride (ClF3) in nitrogen (N2) ambient has been studied. One type of etch pit with a crooked hexagonal shape was formed at an etching temperature below 500 °C. The angle of the etch pit measured from a cross-sectional atomic force microscopy image was about 10° from the [11bar 20] view. The dislocation type of the etch pit was discussed in relation to the etch pit shape and an electron-beam-induced current image.

Superhydrophobic aluminum alloy surfaces by a novel one-step process.

PubMed

Saleema, N; Sarkar, D K; Paynter, R W; Chen, X-G

2010-09-01

A simple one-step process has been developed to render aluminum alloy surfaces superhydrophobic by immersing the aluminum alloy substrates in a solution containing NaOH and fluoroalkyl-silane (FAS-17) molecules. Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and water contact angle measurements have been performed to characterize the morphological features, chemical composition and superhydrophobicity of the surfaces. The resulting surfaces provided a water contact angle as high as ∼162° and a contact angle hysteresis as low as ∼4°. The study indicates that it is possible to fabricate superhydrophobic aluminum surfaces easily and effectively without involving the traditional two-step processes.

Superhydrophobic ceramic coating: Fabrication by solution precursor plasma spray and investigation of wetting behavior.

PubMed

Xu, Pengyun; Coyle, Thomas W; Pershin, Larry; Mostaghimi, Javad

2018-08-01

Superhydrophobic surfaces are often created by fabricating suitable surface structures from low-surface-energy organic materials using processes that are not suitable for large-scale fabrication. Rare earth oxides (REO) exhibit hydrophobic behavior that is unusual among oxides. Solution precursor plasma spray (SPPS) deposition is a rapid, one-step process that can produce ceramic coatings with fine scale columnar structures. Manipulation of the structure of REO coatings through variation in deposition conditions may allow the wetting behavior to be controlled. Yb 2 O 3 coatings were fabricated via SPPS. Coating structure was investigated by scanning electron microscopy, digital optical microscopy, and x-ray diffraction. The static water contact angle and roll-off angle were measured, and the dynamic impact of water droplets on the coating surface recorded. Superhydrophobic behavior was observed; the best coating exhibited a water contact angle of ∼163°, a roll-off angle of ∼6°, and complete droplet rebound behavior. All coatings were crystalline Yb 2 O 3 , with a nano-scale roughness superimposed on a micron-scale columnar structure. The wetting behaviors of coatings deposited at different standoff distances were correlated with the coating microstructures and surface topographies. The self-cleaning, water flushing and water jetting tests were conducted and further demonstrated the excellent and durable hydrophobicity of the coatings. Copyright © 2018 Elsevier Inc. All rights reserved.

New insights into microstructural evolution of epitaxial Ni-Mn-Ga films on MgO (1 0 0) substrate by high-resolution X-ray diffraction and orientation imaging investigations

NASA Astrophysics Data System (ADS)

Sharma, Amit; Mohan, Sangeneni; Suwas, Satyam

2018-04-01

In this work, a detailed investigation has been performed on hetero-epitaxial growth and microstructural evolution in highly oriented Ni-Mn-Ga (1 0 0) films grown on MgO (1 0 0) substrate using high-resolution X-ray diffraction and orientation imaging microscopy. Mosaicity of the films has been analysed in terms of tilt angle, twist angle, lateral and vertical coherence length and threading dislocation densities by performing rocking curve measurements and reciprocal space mapping. Density of edge dislocations is found to be an order of magnitude higher than the density of screw dislocations, irrespective of film thickness. X-ray pole figure measurements have revealed an orientation relationship of ? || (1 0 0)MgO; ? || [0 0 1]MgO between the film and substrate. Microstructure predicted by X-ray diffraction is in agreement with that obtained from electron microscopy and atomic force microscopy. The evolution of microstructure in the film with increasing thickness has been explained vis-à-vis dislocation generation and growth mechanisms. Orientation imaging microscopy observations indicate evolutionary growth of film by overgrowth mechanism. Decrease in coercivity with film thickness has been explained as an interplay between stress field developed due to crystal defects and magnetic domain pinning due to surface roughness.

Effect of angle of deposition on the Fractal properties of ZnO thin film surface

NASA Astrophysics Data System (ADS)

Yadav, R. P.; Agarwal, D. C.; Kumar, Manvendra; Rajput, Parasmani; Tomar, D. S.; Pandey, S. N.; Priya, P. K.; Mittal, A. K.

2017-09-01

Zinc oxide (ZnO) thin films were prepared by atom beam sputtering at various deposition angles in the range of 20-75°. The deposited thin films were examined by glancing angle X-ray diffraction and atomic force microscopy (AFM). Scaling law analysis was performed on AFM images to show that the thin film surfaces are self-affine. Fractal dimension of each of the 256 vertical sections along the fast scan direction of a discretized surface, obtained from the AFM height data, was estimated using the Higuchi's algorithm. Hurst exponent was computed from the fractal dimension. The grain sizes, as determined by applying self-correlation function on AFM micrographs, varied with the deposition angle in the same manner as the Hurst exponent.

Microwave Absorption Properties of Co@C Nanofiber Composite for Normal and Oblique Incidence

NASA Astrophysics Data System (ADS)

Zhang, Junming; Wang, Peng; Chen, Yuanwei; Wang, Guowu; Wang, Dian; Qiao, Liang; Wang, Tao; Li, Fashen

2018-05-01

Co@C nanofibers have been prepared by an electrospinning technique. Uniform morphology of the nanofibers and good dispersion of the magnetic cobalt nanoparticles in the carbon fiber frame were confirmed by field-emission scanning electron microscopy and high-resolution transmission electron microscopy. The electromagnetic parameters of a composite absorber composed of Co@C nanofibers/paraffin were measured from 2 GHz to 15 GHz. The electromagnetic wave absorption properties were simulated and investigated in the case of normal and oblique incidence. In the normal case, the absorber achieved absorption performance of - 40 dB at 7.1 GHz. When the angle of incidence was increased to 60°, the absorption effect with reflection loss (RL) exceeding - 10 dB could still be obtained. These results demonstrate that the reported Co@C nanofiber absorber exhibits excellent absorption performance over a wide range of angle of incidence.

Self-assembled biomimetic superhydrophobic CaCO3 coating inspired from fouling mineralization in geothermal water.

PubMed

Wang, Gong G; Zhu, Li Q; Liu, Hui C; Li, Wei P

2011-10-18

Inspired from fouling self-mineralization in geothermal water, a novel biomimetic cactuslike CaCO(3) coating with superhydrophobic features is reported in this letter. The structure, morphologies, and phases of the CaCO(3) coating were characterized by X-ray diffractometry, scanning electron microscopy, transmission electron microscopy, and infrared spectrophotometry. After prenucleation treatment, a continuous cactuslike CaCO(3) coating with hierarchical nano- and microstructures was self-assembled on stainless steel surfaces after immersion in simulated geothermal water at 50 °C for 48 h. After being modified with a low-surface-energy monolayer of sodium stearate, the as-prepared coating exhibited superhydrophobic properties with a water contact angle of 158.9° and a sliding angle of 2°. Therefore, this work might open up a new application field of geothermal resources and provide insight into designing multidimensional structures with functional applications, including superhydrophobic surfaces. © 2011 American Chemical Society

Determination of the size and phase composition of silver nanoparticles in a gel film of bacterial cellulose by small-angle X-ray scattering, electron diffraction, and electron microscopy

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

Volkov, V. V.; Klechkovskaya, V. V., E-mail: klechvv@ns.crys.ras.ru; Shtykova, E. V.

2009-03-15

The nanoscale structural features in a composite (gel film of Acetobacter Xylinum cellulose with adsorbed silver nanoparticles, stabilized by N-polyvinylpyrrolidone) have been investigated by small-angle X-ray scattering. The size distributions of inhomogeneities in the porous structure of the cellulose matrix and the size distributions of silver nanoparticles in the composite have been determined. It is shown that the sizes of synthesized nanoparticles correlate with the sizes of inhomogeneities in the gel film. Particles of larger size (with radii up to 100 nm) have also been found. Electron microscopy of thin cross sections of a dried composite layer showed that largemore » particles are located on the cellulose layer surface. Electron diffraction revealed a crystal structure of silver nanoparticles in the composite.« less

Nanostructural reorganization of bacterial cellulose by ultrasonic treatment.

PubMed

Tischer, Paula C S Faria; Sierakowski, Maria Rita; Westfahl, Harry; Tischer, Cesar Augusto

2010-05-10

In this work, bacterial cellulose was subjected to a high-power ultrasonic treatment for different time intervals. The morphological analysis, scanning electron microscopy, and atomic force microscopy revealed that this treatment changed the width and height of the microfibrillar ribbons and roughness of their surface, originating films with new nanostructures. Differential thermal analysis showed a higher thermal stability for ultrasonicated samples with a pyrolysis onset temperature of 208 degrees C for native bacterial cellulose and 250 and 268 degrees C for the modified samples. The small-angle X-ray scattering experiments demonstrated that the treatment with ultrasound increased the thickness of the ribbons, while wide-angle X-ray scattering experiments demonstrated that the average crystallite dimension and the degree of crystallinity also increased. A model is proposed where the thicker ribbons and crystallites result from the fusion of neighboring ribbons due to cavitation effects.

Study of structural and optical properties of ZnS zigzag nanostructured thin films

NASA Astrophysics Data System (ADS)

Rahchamani, Seyyed Zabihollah; Rezagholipour Dizaji, Hamid; Ehsani, Mohammad Hossein

2015-11-01

Zinc sulfide (ZnS) nanostructured thin films of different thicknesses with zigzag shapes have been deposited on glass substrates by glancing angle deposition (GLAD) technique. Employing a homemade accessory attached to the substrate holder enabled the authors to control the substrate temperature and substrate angle. The prepared samples were subjected to X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM) and UV-VIS. spectroscopy techniques. The structural studies revealed that the film deposited at room temperature crystallized in cubic structure. The FESEM images of the samples confirmed the formation of zigzag nano-columnar shape with mean diameter about 60-80 nm. By using the data obtained from optical studies, the real part of the refractive index (n), the absorption coefficient (α) and the band gap (Eg) of the samples were calculated. The results show that the refractive indices of the prepared films are very sensitive to deposition conditions.

Work Function Variations in Twisted Graphene Layers

DOE PAGES

Robinson, Jeremy T.; Culbertson, James; Berg, Morgann; ...

2018-01-31

By combining optical imaging, Raman spectroscopy, kelvin probe force microscopy (KFPM), and photoemission electron microscopy (PEEM), we show that graphene’s layer orientation, as well as layer thickness, measurably changes the surface potential (Φ). Detailed mapping of variable-thickness, rotationally-faulted graphene films allows us to correlate Φ with specific morphological features. Using KPFM and PEEM we measure ΔΦ up to 39 mV for layers with different twist angles, while ΔΦ ranges from 36–129 mV for different layer thicknesses. The surface potential between different twist angles or layer thicknesses is measured at the KPFM instrument resolution of ≤ 200 nm. The PEEM measuredmore » work function of 4.4 eV for graphene is consistent with doping levels on the order of 10 12cm -2. Here, we find that Φ scales linearly with Raman G-peak wavenumber shift (slope = 22.2 mV/cm -1) for all layers and twist angles, which is consistent with doping-dependent changes to graphene’s Fermi energy in the ‘high’ doping limit. Our results here emphasize that layer orientation is equally important as layer thickness when designing multilayer two-dimensional systems where surface potential is considered.« less

Scanning transmission electron microscopy through-focal tilt-series on biological specimens.

PubMed

Trepout, Sylvain; Messaoudi, Cédric; Perrot, Sylvie; Bastin, Philippe; Marco, Sergio

2015-10-01

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Variable-angle epifluorescence microscopy characterizes protein dynamics in the vicinity of plasma membrane in plant cells.

PubMed

Chen, Tong; Ji, Dongchao; Tian, Shiping

2018-03-14

The assembly of protein complexes and compositional lipid patterning act together to endow cells with the plasticity required to maintain compositional heterogeneity with respect to individual proteins. Hence, the applications for imaging protein localization and dynamics require high accuracy, particularly at high spatio-temporal level. We provided experimental data for the applications of Variable-Angle Epifluorescence Microscopy (VAEM) in dissecting protein dynamics in plant cells. The VAEM-based co-localization analysis took penetration depth and incident angle into consideration. Besides direct overlap of dual-color fluorescence signals, the co-localization analysis was carried out quantitatively in combination with the methodology for calculating puncta distance and protein proximity index. Besides, simultaneous VAEM tracking of cytoskeletal dynamics provided more insights into coordinated responses of actin filaments and microtubules. Moreover, lateral motility of membrane proteins was analyzed by calculating diffusion coefficients and kymograph analysis, which represented an alternative method for examining protein motility. The present study presented experimental evidence on illustrating the use of VAEM in tracking and dissecting protein dynamics, dissecting endosomal dynamics, cell structure assembly along with membrane microdomain and protein motility in intact plant cells.

Topography and surface free energy of DPPC layers deposited on a glass, mica, or PMMA support.

PubMed

Jurak, Malgorzata; Chibowski, Emil

2006-08-15

An investigation of energetic properties of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) layers deposited on glass, mica, and PMMA (poly(methyl methacrylate)) surfaces was carried out by means of contact angles measurements (advancing and receding) for three probe liquids (diiodomethane, water, and formamide). DPPC was deposited on the surfaces from water (on glass and mica) or methanol (on PMMA) solutions. The topography of the tested surfaces was determined with a help of scanning electron microscopy (SEM) and atomic force microscopy (AFM). Using the measured contact angles, the total apparent surface free energy and its components of the studied layers were determined from van Oss et al.'s (Lifshitz-van der Waals and acid-base components, LWAB) and contact angle hysteresis (CAH) approaches. It allowed us to learn about changes in the surface free energy of the layers (hydrophobicity/hydrophilicity) depending on their number and kind of support. It was found that the changes in the energy greatly depended on the surface properties of the substrate as well as the statistical number of monolayers of DPPC. However, principal changes took place for first three monolayers.

Highly exothermic and superhydrophobic Mg/fluorocarbon core/shell nanoenergetic arrays.

PubMed

Zhou, Xiang; Xu, Daguo; Yang, Guangcheng; Zhang, Qiaobao; Shen, Jinpeng; Lu, Jian; Zhang, Kaili

2014-07-09

Mg/fluorocarbon core/shell nanoenergetic arrays are prepared onto silicon substrate, with Mg nanorods as the core and fluorocarbon as the shell. Mg nanorods are deposited by the glancing angle deposition technique, and the fluorocarbon layer is then prepared as a shell to encase the Mg nanorods by the magnetron sputtering deposition process. Scanning electron microscopy and transmission electron microscopy show the core/shell structure of the Mg/fluorocarbon arrays. X-ray energy-dispersive spectroscopy, X-ray diffraction, and Fourier transform infrared spectroscopy are used to characterize the structural composition of the Mg/fluorocarbon. It is found that the as-prepared fluorocarbon layer consists of shorter molecular chains compared to that of bulk polytetrafluoroethylene, which is proven beneficial to the low onset reaction temperature of Mg/fluorocarbon. Water contact angle test demonstrates the superhydrophobicity of the Mg/fluorocarbon arrays, and a static contact angle as high as 162° is achieved. Thermal analysis shows that the Mg/fluorocarbon material exhibits a very low onset reaction temperature of about 270 °C as well as an ultrahigh heat of reaction approaching 9 kJ/g. A preliminary combustion test reveals rapid combustion wave propagation, and a convective mechanism is adopted to explain the combustion behaviors.

Mosaicing of single plane illumination microscopy images using groupwise registration and fast content-based image fusion

NASA Astrophysics Data System (ADS)

Preibisch, Stephan; Rohlfing, Torsten; Hasak, Michael P.; Tomancak, Pavel

2008-03-01

Single Plane Illumination Microscopy (SPIM; Huisken et al., Nature 305(5686):1007-1009, 2004) is an emerging microscopic technique that enables live imaging of large biological specimens in their entirety. By imaging the living biological sample from multiple angles SPIM has the potential to achieve isotropic resolution throughout even relatively large biological specimens. For every angle, however, only a relatively shallow section of the specimen is imaged with high resolution, whereas deeper regions appear increasingly blurred. In order to produce a single, uniformly high resolution image, we propose here an image mosaicing algorithm that combines state of the art groupwise image registration for alignment with content-based image fusion to prevent degrading of the fused image due to regional blurring of the input images. For the registration stage, we introduce an application-specific groupwise transformation model that incorporates per-image as well as groupwise transformation parameters. We also propose a new fusion algorithm based on Gaussian filters, which is substantially faster than fusion based on local image entropy. We demonstrate the performance of our mosaicing method on data acquired from living embryos of the fruit fly, Drosophila, using four and eight angle acquisitions.

Work Function Variations in Twisted Graphene Layers

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

Robinson, Jeremy T.; Culbertson, James; Berg, Morgann

By combining optical imaging, Raman spectroscopy, kelvin probe force microscopy (KFPM), and photoemission electron microscopy (PEEM), we show that graphene’s layer orientation, as well as layer thickness, measurably changes the surface potential (Φ). Detailed mapping of variable-thickness, rotationally-faulted graphene films allows us to correlate Φ with specific morphological features. Using KPFM and PEEM we measure ΔΦ up to 39 mV for layers with different twist angles, while ΔΦ ranges from 36–129 mV for different layer thicknesses. The surface potential between different twist angles or layer thicknesses is measured at the KPFM instrument resolution of ≤ 200 nm. The PEEM measuredmore » work function of 4.4 eV for graphene is consistent with doping levels on the order of 10 12cm -2. Here, we find that Φ scales linearly with Raman G-peak wavenumber shift (slope = 22.2 mV/cm -1) for all layers and twist angles, which is consistent with doping-dependent changes to graphene’s Fermi energy in the ‘high’ doping limit. Our results here emphasize that layer orientation is equally important as layer thickness when designing multilayer two-dimensional systems where surface potential is considered.« less

HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

PubMed

Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

2015-12-01

The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation of Microstructure and Mechanical Properties of ECAP-Processed AM Series Magnesium Alloy

NASA Astrophysics Data System (ADS)

Gopi, K. R.; Nayaka, H. Shivananda; Sahu, Sandeep

2016-09-01

Magnesium alloy Mg-Al-Mn (AM70) was processed by equal channel angular pressing (ECAP) at 275 °C for up to 4 passes in order to produce ultrafine-grained microstructure and improve its mechanical properties. ECAP-processed samples were characterized for microstructural analysis using optical microscopy, scanning electron microscopy, and transmission electron microscopy. Microstructural analysis showed that, with an increase in the number of ECAP passes, grains refined and grain size reduced from an average of 45 to 1 µm. Electron backscatter diffraction analysis showed the transition from low angle grain boundaries to high angle grain boundaries in ECAP 4 pass sample as compared to as-cast sample. The strength and hardness values an showed increasing trend for the initial 2 passes of ECAP processing and then started decreasing with further increase in the number of ECAP passes, even though the grain size continued to decrease in all the successive ECAP passes. However, the strength and hardness values still remained quite high when compared to the initial condition. This behavior was found to be correlated with texture modification in the material as a result of ECAP processing.

Probing Membrane Order and Topography in Supported Lipid Bilayers by Combined Polarized Total Internal Reflection Fluorescence-Atomic Force Microscopy

PubMed Central

Oreopoulos, John; Yip, Christopher M.

2009-01-01

Determining the local structure, dynamics, and conformational requirements for protein-protein and protein-lipid interactions in membranes is critical to understanding biological processes ranging from signaling to the translocating and membranolytic action of antimicrobial peptides. We report here the application of a combined polarized total internal reflection fluorescence microscopy-in situ atomic force microscopy platform. This platform's ability to image membrane orientational order was demonstrated on DOPC/DSPC/cholesterol model membranes containing the fluorescent membrane probe, DiI-C20 or BODIPY-PC. Spatially resolved order parameters and fluorophore tilt angles extracted from the polarized total internal reflection fluorescence microscopy images were in good agreement with the topographical details resolved by in situ atomic force microscopy, portending use of this technique for high-resolution characterization of membrane domain structures and peptide-membrane interactions. PMID:19254557

Tomographic phase microscopy and its biological applications

NASA Astrophysics Data System (ADS)

Choi, Wonshik

2012-12-01

Conventional interferometric microscopy techniques such as digital holographic microscopy and quantitative phase microscopy are often classified as 3D imaging techniques because a recorded complex field image can be numerically propagated to a different depth. In a strict sense, however, a single complex field image contains only 2D information on a specimen. The measured 2D image is only a subset of the 3D structure. For the 3D mapping of an object, multiple independent 2D images are to be taken, for example at multiple incident angles or wavelengths, and then combined by the so-called optical diffraction tomography (ODT). In this Letter, tomographic phase microscopy (TPM) is reviewed that experimentally realizes the concept of the ODT for the 3D mapping of biological cells in their native state, and some of its interesting biological and biomedical applications are introduced. [Figure not available: see fulltext.

Crew Earth Observations (CEO) taken during Expedition 8

NASA Image and Video Library

2004-02-15

ISS008-E-16328 (15 February 2004) --- A major dust storm in the Kerman Desert, just east of the city of Bam in Southeastern Iran, was featured in this image photographed by an Expedition 8 crewmember onboard the International Space Station (ISS).

A Wavefield Imaging Technique for Delamination Detection in Composite Structures

DTIC Science & Technology

2010-08-01

YANG1, M. P. DESIMIO3, S. E. OLSON3 AND E. D. SWENSON4 Joachim Schneider -Gloetzl, Gloetzl GmbH...Rheinste ten, Germany Rainer Gloetzl, RG Research, Ettling n, Germany Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal

Zap! Bam! Flop!

ERIC Educational Resources Information Center

Case, Doug

1976-01-01

Too many teachers have misguided ideas about the principles of the oral approach to teaching EFL. They are either too sure of themselves and of the theory and become complacent, or their confidence is shaken by the failure of a technique they thought to be infallible. (SCC)

Performance analysis and comparison of a minimum interconnections direct storage model with traditional neural bidirectional memories.

PubMed

Bhatti, A Aziz

2009-12-01

This study proposes an efficient and improved model of a direct storage bidirectional memory, improved bidirectional associative memory (IBAM), and emphasises the use of nanotechnology for efficient implementation of such large-scale neural network structures at a considerable lower cost reduced complexity, and less area required for implementation. This memory model directly stores the X and Y associated sets of M bipolar binary vectors in the form of (MxN(x)) and (MxN(y)) memory matrices, requires O(N) or about 30% of interconnections with weight strength ranging between +/-1, and is computationally very efficient as compared to sequential, intraconnected and other bidirectional associative memory (BAM) models of outer-product type that require O(N(2)) complex interconnections with weight strength ranging between +/-M. It is shown that it is functionally equivalent to and possesses all attributes of a BAM of outer-product type, and yet it is simple and robust in structure, very large scale integration (VLSI), optical and nanotechnology realisable, modular and expandable neural network bidirectional associative memory model in which the addition or deletion of a pair of vectors does not require changes in the strength of interconnections of the entire memory matrix. The analysis of retrieval process, signal-to-noise ratio, storage capacity and stability of the proposed model as well as of the traditional BAM has been carried out. Constraints on and characteristics of unipolar and bipolar binaries for improved storage and retrieval are discussed. The simulation results show that it has log(e) N times higher storage capacity, superior performance, faster convergence and retrieval time, when compared to traditional sequential and intraconnected bidirectional memories.

Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases

PubMed Central

Kung, Johannes W.; Löffler, Claudia; Dörner, Katerina; Heintz, Dimitri; Gallien, Sébastien; Van Dorsselaer, Alain; Friedrich, Thorsten; Boll, Matthias

2009-01-01

Aromatic compounds are widely distributed in nature and can only be biomineralized by microorganisms. In anaerobic bacteria, benzoyl-CoA (BCoA) is a central intermediate of aromatic degradation, and serves as substrate for dearomatizing BCoA reductases (BCRs). In facultative anaerobes, the mechanistically difficult reduction of BCoA to cyclohexa-1,5-dienoyl-1-carboxyl-CoA (dienoyl-CoA) is driven by a stoichiometric ATP hydrolysis, catalyzed by a soluble, three [4Fe-4S] cluster-containing BCR. In this work, an in vitro assay for BCR from the obligately anaerobic Geobacter metallireducens was established. It followed the reverse reaction, the formation of BCoA from dienoyl-CoA in the presence of various electron acceptors. The benzoate-induced activity was highly specific for dienoyl-CoA (Km = 24 ± 4 μM). The corresponding oxygen-sensitive enzyme was purified by several chromatographic steps with a 115-fold enrichment and a yield of 18%. The 185-kDa enzyme comprised 73- and 20-kDa subunits, suggesting an α2β2-composition. MS analysis revealed the subunits as products of the benzoate-induced bamBC genes. The αβ unit contained 0.9 W, 15 Fe, and 12.5 acid-labile sulfur. Results from EPR spectroscopy suggest the presence of one [3Fe-4S]0/+1 and three [4Fe-4S]+1/+2 clusters per αβ unit; oxidized BamBC exhibited an EPR signal typical for a W(V) species. The FeS clusters and the W- cofactor could only be fully reduced by dienoyl-CoA. BamBC represents the prototype of a previously undescribed class of dearomatizing BCRs that differ completely from the ATP-dependent enzymes from facultative anaerobes. PMID:19815533

Isolation of equine herpesvirus 3 (EHV-3) from equine coital exanthema of two stallions and sero-epidemiology of EHV-3 infection in Japan

PubMed Central

KIRISAWA, Rikio; TOISHI, Yuko; AKAMATSU, Ai; SOEJIMA, Kosuke; MIYASHITA, Taisuke; TSUNODA, Nobuo

2017-01-01

In the spring of 2015, two stallions reared in Farms A and B in Hokkaido in Japan showed symptoms of equine coital exanthema. Equine herpesvirus 3 (EHV-3) was isolated from penis swab samples of both stallions, and the isolates from each stallion in Farms A and B were designated as SS-1 and YS-1 strains, respectively. BamHI restriction profiles of SS-1 and Japanese reference strain Iwate-1 were indistinguishable, but the BamHI-A fragment of YS-1 was larger than those of SS-1 and Iwate-1 by 1.9 kbp because of the lack of two BamHI sites. Nucleotide sequence analyses of glycoprotein G (gG), gB, gC and VP13/14 coding regions revealed that SS-1 and YS-1 had 99.77% to 100% identities to each other. These results suggested that the origins of SS-1 and YS-1 were different. For a sero-epidemiological survey, serum neutralizing tests using SS-1 against 319 sera of horses from eight farms in Hokkaido were conducted. Six of the eight farms were EHV-3 antibody-positive, and positive rates ranged from 2.6% to 17.6%. To determine the infection time of four EHV-3 antibody-positive horses, a retrospective study was conducted. Infection time of the four horses was in the breeding season, and re-infection or reactivation of latently infected EHV-3 might have occurred in one horse. However, these four horses had never shown any clinical symptoms. The results suggested that several EHV-3 strains are distributed in Japan and that infection is maintained widely in horses without clinical symptoms. PMID:28132964

Unsupervised Segmentation of Head Tissues from Multi-modal MR Images for EEG Source Localization.

PubMed

Mahmood, Qaiser; Chodorowski, Artur; Mehnert, Andrew; Gellermann, Johanna; Persson, Mikael

2015-08-01

In this paper, we present and evaluate an automatic unsupervised segmentation method, hierarchical segmentation approach (HSA)-Bayesian-based adaptive mean shift (BAMS), for use in the construction of a patient-specific head conductivity model for electroencephalography (EEG) source localization. It is based on a HSA and BAMS for segmenting the tissues from multi-modal magnetic resonance (MR) head images. The evaluation of the proposed method was done both directly in terms of segmentation accuracy and indirectly in terms of source localization accuracy. The direct evaluation was performed relative to a commonly used reference method brain extraction tool (BET)-FMRIB's automated segmentation tool (FAST) and four variants of the HSA using both synthetic data and real data from ten subjects. The synthetic data includes multiple realizations of four different noise levels and several realizations of typical noise with a 20% bias field level. The Dice index and Hausdorff distance were used to measure the segmentation accuracy. The indirect evaluation was performed relative to the reference method BET-FAST using synthetic two-dimensional (2D) multimodal magnetic resonance (MR) data with 3% noise and synthetic EEG (generated for a prescribed source). The source localization accuracy was determined in terms of localization error and relative error of potential. The experimental results demonstrate the efficacy of HSA-BAMS, its robustness to noise and the bias field, and that it provides better segmentation accuracy than the reference method and variants of the HSA. They also show that it leads to a more accurate localization accuracy than the commonly used reference method and suggest that it has potential as a surrogate for expert manual segmentation for the EEG source localization problem.

Effective factors on menstrual health among female students in Bam city: a qualitative study

PubMed Central

Morowatisharifabad, Mohammad Ali; Vaezi, Aliakbar

2018-01-01

Background Menarche is an independent puberty event in a girl’s life, and is associated with physical growth, ability in marriage and fertility. Therefore, poor menstrual health can be a major determinant of morbidity, as well as physical, mental and social problems in this age group. Objective The aim of this study was to explore the effective factors on menstrual health among female students in Bam city. Methods The qualitative study was conducted using content analysis approach in 2017. The participants were 32 individuals consisting of 13 students, 10 mothers of the same students, 9 school associates and health educators of 5 secondary schools in Bam city, who were selected based on an objective-oriented approach. The sampling was done until data saturation. Data collection methods were semi-structured and in-depth interview. Data analysis was performed using the steps suggested by Graneheim and Landman. Results There were two categories (easy interaction and inappropriate adaptation to changes in health behavior), 13 sub-categories and 52 initial codes. The positive factors included easy access to sanitary pads, appropriate school education, easy access to health and therapeutic services and school flexibility on menstrual issues, while the negative factors included inadequate facilities for sanitary pad disposal, lack of access to informed people about menstrual issues, insufficient attention to menstrual problems, feeling ashamed, the high cost of menstrual health, self-medication with traditional medicines, inadequate self-directed education, lack of awareness and trust in health center staff, and following family and teachers in menstrual problems. Conclusion Overall, this study indicated that economic, social, cultural and educational factors affect menstrual health. Therefore, the identification of each of these factors helps planners to apply the most appropriate methods and strategies for menstrual health improvement. PMID:29629053

Parental cigarette smoking, transforming growth factor-alpha gene variant and the risk of orofacial cleft in Iranian infants

PubMed Central

Ebadifar, Asghar; Hamedi, Roya; KhorramKhorshid, Hamid Reza; Kamali, Koorosh; Moghadam, Fatemeh Aghakhani

2016-01-01

Objective(s): We investigated the influence of genetic variation of the transforming growth-factor alpha (TGFA) locus on the relationship between smoking and oral clefts. Materials and Methods: In this study 105 Iranian infants with non-syndromic cleft lip/palate and 218 controls with non-cleft birth defects were examined to test for associations among maternal exposures, genetic markers, and oral clefts. Maternal and parental smoking histories during pregnancy were obtained through questionnaire. DNA was extracted from newborn screening blood samples, and genotyping of the BamHI polymorphism in the TGFA gene was performed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods. A number of factors including gender of the newborns, type of oral cleft, consanguinity of the parents, as well as the mother’s age and education were evaluated as potential confounders and effect modifiers. Results: Maternal smoking, in the absence of paternal smoking, was associated with an increased risk for CL/P (OR = 19.2, 95% CI = [(6.2-59.5)]) and cleft palate only (OR =48.7, 95% CI = [(8-29.3)]). If both parents smoked, risks were generally greater (OR = 55.6, 95% CI = [12-20.25]). Analyses for the risk of clefting from maternal smoking, stratified by the presence or absence of the TGFA/BamH1variant, revealed that the risk of clefting among the infants with the TGFA/BamH1 variant when their mothers smoked cigarettes was much greater than the infants who had non-smoker mothers (P=0.001, OR=10.4,95% CI=[3.2,33.6]). Conclusion: The results of this study indicate that first-trimester maternal smoking and infant TGFA locus mutations are both associated with nonsyndromic cleft lip and/or palate (CL/P). PMID:27279979

Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): Implications for the evolution of the Pax gene family

PubMed Central

Miller, David J.; Hayward, David C.; Reece-Hoyes, John S.; Scholten, Ingo; Catmull, Julian; Gehring, Walter J.; Callaerts, Patrick; Larsen, Jill E.; Ball, Eldon E.

2000-01-01

Pax genes encode a family of transcription factors, many of which play key roles in animal embryonic development but whose evolutionary relationships and ancestral functions are unclear. To address these issues, we are characterizing the Pax gene complement of the coral Acropora millepora, an anthozoan cnidarian. As the simplest animals at the tissue level of organization, cnidarians occupy a key position in animal evolution, and the Anthozoa are the basal class within this diverse phylum. We have identified four Pax genes in Acropora: two (Pax-Aam and Pax-Bam) are orthologs of genes identified in other cnidarians; the others (Pax-Cam and Pax-Dam) are unique to Acropora. Pax-Aam may be orthologous with Drosophila Pox neuro, and Pax-Bam clearly belongs to the Pax-2/5/8 class. The Pax-Bam Paired domain binds specifically and preferentially to Pax-2/5/8 binding sites. The recently identified Acropora gene Pax-Dam belongs to the Pax-3/7 class. Clearly, substantial diversification of the Pax family occurred before the Cnidaria/higher Metazoa split. The fourth Acropora Pax gene, Pax-Cam, may correspond to the ancestral vertebrate Pax gene and most closely resembles Pax-6. The expression pattern of Pax-Cam, in putative neurons, is consistent with an ancestral role of the Pax family in neural differentiation and patterning. We have determined the genomic structure of each Acropora Pax gene and show that some splice sites are shared both between the coral genes and between these and Pax genes in triploblastic metazoans. Together, these data support the monophyly of the Pax family and indicate ancient origins of several introns. PMID:10781047

Three-dimensional evaluation of gettering ability for oxygen atoms at small-angle tilt boundaries in Czochralski-grown silicon crystals

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

Ohno, Yutaka, E-mail: yutakaohno@imr.tohoku.ac.jp; Inoue, Kaihei; Fujiwara, Kozo

2015-06-22

Three-dimensional distribution of oxygen atoms at small-angle tilt boundaries (SATBs) in Czochralski-grown p-type silicon ingots was investigated by atom probe tomography combined with transmission electron microscopy. Oxygen gettering along edge dislocations composing SATBs, post crystal growth, was observed. The gettering ability of SATBs would depend both on the dislocation strain and on the dislocation density. Oxygen atoms would agglomerate in the atomic sites under the tensile hydrostatic stress larger than about 2.0 GPa induced by the dislocations. It was suggested that the density of the atomic sites, depending on the tilt angle of SATBs, determined the gettering ability of SATBs.

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection.

DOT National Transportation Integrated Search

2015-12-01

Anthropogenic activities within the Silver Springs springshed over recent decades may have contributed : to elevated nutrient concentrations in stormwater runoff and groundwater, leading to the eutrophication : of Silver Springs. To remove the nutrie...

Robust state estimation for uncertain fuzzy bidirectional associative memory networks with time-varying delays

NASA Astrophysics Data System (ADS)

Vadivel, P.; Sakthivel, R.; Mathiyalagan, K.; Arunkumar, A.

2013-09-01

This paper addresses the issue of robust state estimation for a class of fuzzy bidirectional associative memory (BAM) neural networks with time-varying delays and parameter uncertainties. By constructing the Lyapunov-Krasovskii functional, which contains the triple-integral term and using the free-weighting matrix technique, a set of sufficient conditions are derived in terms of linear matrix inequalities (LMIs) to estimate the neuron states through available output measurements such that the dynamics of the estimation error system is robustly asymptotically stable. In particular, we consider a generalized activation function in which the traditional assumptions on the boundedness, monotony and differentiability of the activation functions are removed. More precisely, the design of the state estimator for such BAM neural networks can be obtained by solving some LMIs, which are dependent on the size of the time derivative of the time-varying delays. Finally, a numerical example with simulation result is given to illustrate the obtained theoretical results.

Study of structural, electrical, magnetic and optical properties of BaFe12O19 and its modified systems with Ni and Ti

NASA Astrophysics Data System (ADS)

Nayak, Debabrata; Pattanayak, Ranjit; Raut, Subhajit; Panigrahi, Simanchalo

2018-02-01

In this work, BaFe12O19 (BaM) and its modified systems (by substitution of Ni and Ti) have been synthesized by solid-state reaction method. From Rietveld refinement of X-ray diffraction pattern, it is found that volume of unit cell increased slightly in case of modified systems. SEM images provided the information about the microstructure of BaM and its modified systems. The electric, magnetic and optical properties have been carried out with the help of complex impedance spectroscopy, VSM and UV spectrum, respectively. From electrical analysis, it is perceived that Ni-substitution system has shown co-contribution of grain and grain boundary effect due to increases of grain size. The M- H loops are explored that, with substitution of Ni and Ti both M s and H c are decreased. From the variation of band gap ( E g), it is observed that E g has been significantly decreased with substitution (least for Ni-substitution).

The neuron classification problem

PubMed Central

Bota, Mihail; Swanson, Larry W.

2007-01-01

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and “Petilla Convention” guidelines, hierarchies, and relations—with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

An investigation into the socioeconomic aspects of two major earthquakes in Iran.

PubMed

Amini Hosseini, Kambod; Hosseinioon, Solmaz; Pooyan, Zhila

2013-07-01

An evaluation of the socioeconomic consequences of earthquakes is an essential part of the development of risk reduction and disaster management plans. However, these variables are not normally addressed sufficiently after strong earthquakes; researchers and relevant stakeholders focus primarily on the physical damage and casualties. The importance of the socioeconomic consequences of seismic events became clearer in Iran after the Bam earthquake on 26 December 2003, as demonstrated by the formulation and approval of various laws and ordinances. This paper reviews the country's regulatory framework in the light of the socioeconomic aspects of two major and destructive earthquakes: in Manjil-Rudbar in 1990, and in Bam in 2003. The results take the form of recommendations and practical strategies for incorporating the socioeconomic dimensions of earthquakes in disaster risk management planning. The results presented here can be applied in other countries with similar conditions to those of Iran in order to improve public preparedness and risk reduction. © 2013 The Author(s). Journal compilation © Overseas Development Institute, 2013.

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

Yin Yunpeng; Sawin, Herbert H.

The surface roughness evolutions of single crystal silicon, thermal silicon dioxide (SiO{sub 2}), and low dielectric constant film coral in argon plasma have been measured by atomic force microscopy as a function of ion bombardment energy, ion impingement angle, and etching time in an inductively coupled plasma beam chamber, in which the plasma chemistry, ion energy, ion flux, and ion incident angle can be adjusted independently. The sputtering yield (or etching rate) scales linearly with the square root of ion energy at normal impingement angle; additionally, the angular dependence of the etching yield of all films in argon plasma followedmore » the typical sputtering yield curve, with a maximum around 60 deg. -70 deg. off-normal angle. All films stayed smooth after etching at normal angle but typically became rougher at grazing angles. In particular, at grazing angles the rms roughness level of all films increased if more material was removed; additionally, the striation structure formed at grazing angles can be either parallel or transverse to the beam impingement direction, which depends on the off-normal angle. More interestingly, the sputtering caused roughness evolution at different off-normal angles can be qualitatively explained by the corresponding angular dependent etching yield curve. In addition, the roughening at grazing angles is a strong function of the type of surface; specifically, coral suffers greater roughening compared to thermal silicon dioxide.« less

Measurement of nanoscale molten polymer droplet spreading using atomic force microscopy

NASA Astrophysics Data System (ADS)

Soleymaniha, Mohammadreza; Felts, Jonathan R.

2018-03-01

We present a technique for measuring molten polymer spreading dynamics with nanometer scale spatial resolution at elevated temperatures using atomic force microscopy (AFM). The experimental setup is used to measure the spreading dynamics of polystyrene droplets with 2 μm diameters at 115-175 °C on sapphire, silicon oxide, and mica. Custom image processing algorithms determine the droplet height, radius, volume, and contact angle of each AFM image over time to calculate the droplet spreading dynamics. The contact angle evolution follows a power law with time with experimentally determined values of -0.29 ± 0.01, -0.08 ± 0.02, and -0.21 ± 0.01 for sapphire, silicon oxide, and mica, respectively. The non-zero steady state contact angles result in a slower evolution of contact angle with time consistent with theories combining molecular kinetic and hydrodynamic models. Monitoring the cantilever phase provides additional information about the local mechanics of the droplet surface. We observe local crystallinity on the molten droplet surface, where crystalline structures appear to nucleate at the contact line and migrate toward the top of the droplet. Increasing the temperature from 115 °C to 175 °C reduced surface crystallinity from 35% to 12%, consistent with increasingly energetically favorable amorphous phase as the temperature approaches the melting temperature. This platform provides a way to measure spreading dynamics of extremely small volumes of heterogeneously complex fluids not possible through other means.

Visualizing and quantifying the in vivo structure and dynamics of the Arabidopsis cortical cytoskeleton using CLSM and VAEM.

PubMed

Rosero, Amparo; Zárský, Viktor; Cvrčková, Fatima

2014-01-01

The cortical microtubules, and to some extent also the actin meshwork, play a central role in the shaping of plant cells. Transgenic plants expressing fluorescent protein markers specifically tagging the two main cytoskeletal systems are available, allowing noninvasive in vivo studies. Advanced microscopy techniques, in particular confocal laser scanning microscopy (CLSM) and variable angle epifluorescence microscopy (VAEM), can be nowadays used for imaging the cortical cytoskeleton of living cells with unprecedented spatial and temporal resolution. With the aid of suitable computing techniques, quantitative information can be extracted from microscopic images and video sequences, providing insight into both architecture and dynamics of the cortical cytoskeleton.

Even illumination in total internal reflection fluorescence microscopy using laser light.

PubMed

Fiolka, R; Belyaev, Y; Ewers, H; Stemmer, A

2008-01-01

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode. 2007 Wiley-Liss, Inc

Formation of tetragonal gas bubble superlattice in bulk molybdenum under helium ion implantation

DOE PAGES

Sun, Cheng; Sprouster, David J.; Hattar, K.; ...

2018-02-09

In this paper, we report the formation of tetragonal gas bubble superlattice in bulk molybdenum under helium ion implantation at 573 K. The transmission electron microscopy study shows that the helium bubble lattice constant measured from the in-plane d-spacing is ~4.5 nm, while it is ~3.9 nm from the out-of-plane measurement. The results of synchrotron-based small-angle x-ray scattering agree well with the transmission electron microscopy results in terms of the measurement of bubble lattice constant and bubble size. The coupling of transmission electron microscopy and synchrotron high-energy X-ray scattering provides an effective approach to study defect superlattices in irradiated materials.

Flipping interferometry and its application for quantitative phase microscopy in a micro-channel.

PubMed

Roitshtain, Darina; Turko, Nir A; Javidi, Bahram; Shaked, Natan T

2016-05-15

We present a portable, off-axis interferometric module for quantitative phase microscopy of live cells, positioned at the exit port of a coherently illuminated inverted microscope. The module creates on the digital camera an interference pattern between the image of the sample and its flipped version. The proposed simplified module is based on a retro-reflector modification in an external Michelson interferometer. The module does not contain any lenses, pinholes, or gratings and its alignment is straightforward. Still, it allows full control of the off-axis angle and does not suffer from ghost images. As experimentally demonstrated, the module is useful for quantitative phase microscopy of live cells rapidly flowing in a micro-channel.

Formation of tetragonal gas bubble superlattice in bulk molybdenum under helium ion implantation

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

Sun, Cheng; Sprouster, David J.; Hattar, K.

In this paper, we report the formation of tetragonal gas bubble superlattice in bulk molybdenum under helium ion implantation at 573 K. The transmission electron microscopy study shows that the helium bubble lattice constant measured from the in-plane d-spacing is ~4.5 nm, while it is ~3.9 nm from the out-of-plane measurement. The results of synchrotron-based small-angle x-ray scattering agree well with the transmission electron microscopy results in terms of the measurement of bubble lattice constant and bubble size. The coupling of transmission electron microscopy and synchrotron high-energy X-ray scattering provides an effective approach to study defect superlattices in irradiated materials.

Scanning Probe Microscopy for Identifying the Component Materials of a Nanostripe Structure

NASA Astrophysics Data System (ADS)

Mizuno, Akira; Ando, Yasuhisa

2010-08-01

The authors prepared a nanostripe structure in which two types of metal are arranged alternately, and successfully identified the component materials using scanning probe microscopy (SPM) to measure the lateral force distribution image. The nanostripe structure was prepared using a new method developed by the authors and joint development members. The lateral force distribution image was measured in both friction force microscopy (FFM) and lateral modulation friction force microscopy (LM-FFM) modes. In FFM mode, the effect of slope angle appeared in the lateral force distribution image; therefore, no difference in the type of material was observed. On the other hand, in LM-FFM mode, the effect of surface curvature was observed in the lateral force distribution image. A higher friction force on chromium than on gold was identified, enabling material identification.

77 FR 54927 - Comment Request for Information Collection for Unemployment Insurance (UI) Benefit Accuracy...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-06

... Collection for Unemployment Insurance (UI) Benefit Accuracy Measurement (BAM), Extension Without Revisions... Andrew Spisak, Office of Unemployment Insurance, Room S-4524, Employment and Training Administration, U.S... payments in three programs: State UI, Unemployment Compensation for Federal Employees (UCFE), and...

Container Approval for the Disposal of Radioactive Waste with Negligible Heat Generation in the German Konrad Repository - 12148

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

Voelzke, Holger; Nieslony, Gregor; Ellouz, Manel

Since the license for the Konrad repository was finally confirmed by legal decision in 2007, the Federal Institute for Radiation Protection (BfS) has been performing further planning and preparation work to prepare the repository for operation. Waste conditioning and packaging has been continued by different waste producers as the nuclear industry and federal research institutes on the basis of the official disposal requirements. The necessary prerequisites for this are approved containers as well as certified waste conditioning and packaging procedures. The Federal Institute for Materials Research and Testing (BAM) is responsible for container design testing and evaluation of quality assurancemore » measures on behalf of BfS under consideration of the Konrad disposal requirements. Besides assessing the container handling stability (stacking tests, handling loads), design testing procedures are performed that include fire tests (800 deg. C, 1 hour) and drop tests from different heights and drop orientations. This paper presents the current state of BAM design testing experiences about relevant container types (box shaped, cylindrical) made of steel sheets, ductile cast iron or concrete. It explains usual testing and evaluation methods which range from experimental testing to analytical and numerical calculations. Another focus has been laid on already existing containers and packages. The question arises as to how they can be evaluated properly especially with respect to lack of completeness of safety assessment and fabrication documentation. At present BAM works on numerous applications for container design testing for the Konrad repository. Some licensing procedures were successfully finished in the past and BfS certified several container types like steel sheet, concrete until cast iron containers which are now available for waste packaging for final disposal. However, large quantities of radioactive wastes had been placed into interim storage using containers which are not already licensed for the Konrad repository. Safety assessment of these so-called 'old' containers is a big challenge for all parties because documentation sheets about container design testing and fabrication often contain gaps or have not yet been completed. Appropriate solution strategies are currently under development and discussion. Furthermore, BAM has successfully initiated and established an information forum, called 'ERFA QM Konrad Containers', which facilitates discussions on various issues of common interest with respect to Konrad container licensing procedures as well as the interpretation of disposal requirements under consideration of operational needs. Thus, it provides additional, valuable supports for container licensing procedures. (authors)« less

Magnetic bead/capture DNA/glucose-loaded nanoliposomes for amplifying the glucometer signal in the rapid screening of hepatitis C virus RNA.

PubMed

Tu, Haijian; Lin, Kun; Lun, Yongzhi; Yu, Liuming

2018-06-01

A digital detection strategy based on a portable personal glucometer (PGM) was developed for the simple, rapid, and sensitive detection of hepatitis C virus (HCV) RNA, involving the release of glucose-loaded nanoliposomes due to coupling-site-specific cleavage by the endonuclease BamHI. The glucose-loaded nanoliposomes were synthesized using a reversed-phase evaporation method and provided an amplified signal at the PGM in the presence of HCV RNA. Initially, a 21-mer oligonucleotide complementary to HCV RNA was covalently conjugated to a magnetic bead through the amino group at the 5' end of the oligonucleotide, and then bound to a glucose-loaded liposome by typical carbodiimide coupling at its 3' end. In the presence of the target HCV RNA, the target hybridized with the oligonucleotide to form double-stranded DNA. The symmetrical duplex sequence 5'-GGATCC-3' between guanines was then catalytically cleaved by BamHI, which detached the glucose-loaded liposome from the magnetic bead. Following magnetic separation of the bead, the detached glucose-loaded liposome was lysed using Triton X-100 to release the glucose molecules within it, which were then detected as an amplified signal at the digital PGM. Under optimal conditions, the PGM signal increased with increasing HCV RNA, and displayed a strongly linear dependence on the level of HCV RNA for concentrations ranging from 10 pM to 1.0 μM. The detection limit (LOD) of the system was 1.9 pM. Good reproducibility and favorable specificity were achieved in the analysis of the target HCV RNA. Human serum samples containing HCV RNA were analyzed using this strategy, and the developed sensing platform was observed to yield satisfactory results based on a comparison with the corresponding results from a Cobas ® Amplicor HCV Test Analyzer. Graphical abstract A digital detection strategy utilizing a personal glucometer was developed for the detection of hepatitis C virus RNA. The strategy involved the use of the endonuclease BamHI along with a 21-mer oligonucleotide conjugated to both a magnetic bead and a glucose-loaded nanoliposome. Hybridization of the nucleotide with the target RNA triggered the coupling-site-specific cleavage of the duplex by BamHI, leading to the release of the glucose-loaded nanoliposome. Following separation of the magnetic bead, the free nanoliposome was dissolved, liberating the glucose molecules within it, which in turn were detected as an amplified signal by the glucometer.

Incident flux angle induced crystal texture transformation in nanostructured molybdenum films

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

Chen, L.; Lu, T.-M.; Wang, G.-C.

2012-07-15

Molybdenum films were observed to undergo a dramatic change in crystal texture orientation when the incident flux angle was varied in an oblique angle sputter deposition on amorphous substrates. Reflection high-energy electron diffraction pole figure and scanning electron microscopy were used to analyze in detail the texture orientation of the films. The normal incident deposition resulted in a fiber texture film with the minimum energy (110) crystal plane parallel to the substrate surface. A (110)[110] biaxial texture was observed for the samples grown with low incident angles of less than 45 Degree-Sign , with respect to the surface normal. Onmore » the other hand, for an oblique angle deposition of larger than 60 Degree-Sign , a (111)[112] biaxial texture was observed and appeared to be consistent with a zone T structure where the geometrically fastest growth [001] direction of a crystal plays a dominant role in defining the texture. We argue that a structural transition had occurred when the incident flux was varied from near normal incidence to a large angle.« less

Dislocation structures and electrical conduction properties of low angle tilt grain boundaries in LiNbO{sub 3}

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

Furushima, Yuho; Nakamura, Atsutomo, E-mail: nakamura@numse.nagoya-u.ac.jp; Toyoura, Kazuaki

Dislocations in crystalline materials constitute unique, atomic-scale, one-dimensional structure and have a potential to induce peculiar physical properties that are not found in the bulk. In this study, we fabricated LiNbO{sub 3} bicrystals with low angle tilt grain boundaries and investigated the relationship between the atomic structure of the boundary dislocations and their electrical conduction properties. Observations by using transmission electron microscopy revealed that dislocation structures at the (0001) low angle tilt grain boundaries depend on the tilt angle of the boundaries. Specifically, the characteristic dislocation structures with a large Burgers vector were formed in the boundary with the tiltmore » angle of 2°. It is noteworthy that only the grain boundary of 2° exhibits distinct electrical conductivity after reduction treatment, although LiNbO{sub 3} is originally insulating. This unique electrical conductivity is suggested to be due to the characteristic dislocation structures with a large Burgers vector.« less

Application of CO laser for laser balloon angioplasty

NASA Astrophysics Data System (ADS)

Miyamoto, Akira; Sakurada, Masami; Mizuno, Kyoichi; Kurita, Akira; Nakamura, Haruo; Suda, Akira; Arai, Tsunenori; Kikuchi, Makoto

1990-07-01

CO laser may be efficient for thermal fusion of intima of arterial wall without adventitial tissue damage because of high tissue absorption. To investigate the efficacy of CO laser as a laser bam for laser balloon angioplasty (LBA). CO laser was irradiated to aortic tissue through 3Oim polyethylene membrane and tissue temperature was measured by a thermistor. At 2Owatt/cm2 200joules/cm2 continuous laser exposure (CE), tissue temperature was above 100°C within a depth of 1mm and rapidly decreased to 60 °C or below between 2 and 3mm in depth. Moreover, adventitial temperature could be decreased by changing duty ratio (exposure duration/interval) of intermittent laser exposure (IE) despite of the same laser energy. Light microscopy showed high degree of medial coagulation necrosis in CE, however thermal coagulation was observed only at the surface of intima of aortic tissue in IE at duty ratio 1 / 2. These findings suggested CO laser could coagulate intimal layer with less deep thermal damage compared to Nd- YAG laser and that IE was better for superficial welding than CE at the same energy. We concluded that CO laser might be more efficient as a laser beam for LBA than Nd-YAG laser.

Synthesis, characterization, optical and antimicrobial studies of polyvinyl alcohol-silver nanocomposites

NASA Astrophysics Data System (ADS)

Mahmoud, K. H.

2015-03-01

Silver nanoparticles (Ag NPs) were synthesized by chemical reduction of silver salt (AgNO3) through sodium borohydride. The characteristic surface plasmon resonance band located at around 400 nm in the UV-Visible absorption spectrum confirmed the formation of Ag nanoparticles. Polyvinyl alcohol-silver (PVA-Ag) nanocomposite films were prepared by the casting technique. The morphology and interaction of PVA with Ag NPs were examined by transmission electron microscopy and FTIR spectroscopy. Optical studies show that PVA exhibited indirect allowed optical transition with optical energy gap of 4.8 eV, which reduced to 4.45 eV under addition of Ag NPs. Optical parameters such as refractive index, complex dielectric constant and their dispersions have been analyzed using Wemple and DiDomenco model. Color properties of the nanocomposites are discussed in the framework of CIE L∗u∗v∗ color space. The antimicrobial activity of the nanocomposite samples was tested against Gram positive bacteria (Staphylococcus aureus NCTC 7447 &Bacillus subtillis NCIB 3610), Gram negative bacteria (Escherichia coli, NTC10416 &Pseudomonas aeruginosa NCIB 9016) and fungi (Aspergillus niger Ferm - BAM C-21) using the agar diffusion technique. The antimicrobial study showed that PVA has moderate antibacterial activity against B. subtillis and the 0.04 wt% Ag NPs composite sample effect was strong against S. aureus.

In-situ small-angle x-ray scattering study of nanoparticles in the plasma plume induced by pulsed laser irradiation of metallic targets

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

Lavisse, L.; Jouvard, J.-M.; Girault, M.

2012-04-16

Small angle x-ray scattering was used to probe in-situ the formation of nanoparticles in the plasma plume generated by pulsed laser irradiation of a titanium metal surface under atmospheric conditions. The size and morphology of the nanoparticles were characterized as function of laser irradiance. Two families of nanoparticles were identified with sizes on the order of 10 and 70 nm, respectively. These results were confirmed by ex-situ transmission electron microscopy experiments.

Electron Source Brightness and Illumination Semi-Angle Distribution Measurement in a Transmission Electron Microscope.

PubMed

Börrnert, Felix; Renner, Julian; Kaiser, Ute

2018-05-21

The electron source brightness is an important parameter in an electron microscope. Reliable and easy brightness measurement routes are not easily found. A determination method for the illumination semi-angle distribution in transmission electron microscopy is even less well documented. Herein, we report a simple measurement route for both entities and demonstrate it on a state-of-the-art instrument. The reduced axial brightness of the FEI X-FEG with a monochromator was determined to be larger than 108 A/(m2 sr V).

Links between nanoscale and macroscale surface properties of natural root mucilage studied by atomic force microscopy and contact angle.

PubMed

Kaltenbach, Robin; Diehl, Dörte; Schaumann, Gabriele E

2018-04-15

Soil water repellency originating from organic coatings plays a crucial role for soil hydraulics and plant water uptake. Focussing on hydrophobicity in the rhizosphere induced by root-mucilage, this study aims to explore the link between macroscopic wettability and nano-microscopic surface properties. The existing knowledge of the nanostructures of organic soil compounds and its effect on wettability is limited by the lack of a method capable to assess the natural spatial heterogeneity of physical and chemical properties. In this contribution, this task is tackled by a geostatistical approach via variogram analysis of topography and adhesion force data acquired by atomic force microscopy and macroscopic sessile drop measurements on dried films of mucilage. The results are discussed following the wetting models given by Wenzel and Cassie-Baxter. Undiluted mucilage formed homogeneous films on the substrate with contact angles >90°. For diluted samples contact angles were smaller and incomplete mucilage surface coverage with hole-like structures frequently exhibited increased adhesion forces. Break-free distances of force curves indicated enhanced capillary forces due to adsorbed water films at atmospheric RH (35 ± 2%) that promote wettability. Variogram analysis enabled a description of complex surface structures exceeding the capability of comparative visual inspection. Copyright © 2018 Elsevier Inc. All rights reserved.

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Visualizing Collagen Network Within Human and Rhesus Monkey Vocal Folds Using Polarized Light Microscopy

PubMed Central

Julias, Margaret; Riede, Tobias; Cook, Douglas

2014-01-01

Objectives Collagen fiber content and orientation affect the viscoelastic properties of the vocal folds, determining oscillation characteristics during speech and other vocalization. The investigation and reconstruction of the collagen network in vocal folds remains a challenge, because the collagen network requires at least micron-scale resolution. In this study, we used polarized light microscopy to investigate the distribution and alignment of collagen fibers within the vocal folds. Methods Data were collected in sections of human and rhesus monkey (Macaca mulatta) vocal folds cut at 3 different angles and stained with picrosirius red. Results Statistically significant differences were found between different section angles, implying that more than one section angle is required to capture the network’s complexity. In the human vocal folds, the collagen fiber distribution continuously varied across the lamina propria (medial to lateral). Distinct differences in birefringence distribution were observed between the species. For the human vocal folds, high birefringence was observed near the thyroarytenoid muscle and near the epithelium. However, in the rhesus monkey vocal folds, high birefringence was observed near the epithelium, and lower birefringence was seen near the thyroarytenoid muscle. Conclusions The differences between the collagen networks in human and rhesus monkey vocal folds provide a morphological basis for differences in viscoelastic properties between species. PMID:23534129

Characterization of the shape and line-edge roughness of polymer gratings with grazing incidence small-angle X-ray scattering and atomic force microscopy

DOE PAGES

Suh, Hyo Seon; Chen, Xuanxuan; Rincon-Delgadillo, Paulina A.; ...

2016-04-22

Grazing-incidence small-angle X-ray scattering (GISAXS) is increasingly used for the metrology of substrate-supported nanoscale features and nanostructured films. In the case of line gratings, where long objects are arranged with a nanoscale periodicity perpendicular to the beam, a series of characteristic spots of high-intensity (grating truncation rods, GTRs) are recorded on a two-dimensional detector. The intensity of the GTRs is modulated by the three-dimensional shape and arrangement of the lines. Previous studies aimed to extract an average cross-sectional profile of the gratings, attributing intensity loss at GTRs to sample imperfections. Such imperfections are just as important as the average shapemore » when employing soft polymer gratings which display significant line-edge roughness. Herein are reported a series of GISAXS measurements of polymer line gratings over a range of incident angles. Both an average shape and fluctuations contributing to the intensity in between the GTRs are extracted. Lastly, the results are critically compared with atomic force microscopy (AFM) measurements, and it is found that the two methods are in good agreement if appropriate corrections for scattering from the substrate (GISAXS) and contributions from the probe shape (AFM) are accounted for.« less

Scaling behavior of the surface roughness of platinum films grown by oblique angle deposition

NASA Astrophysics Data System (ADS)

Dolatshahi-Pirouz, A.; Hovgaard, M. B.; Rechendorff, K.; Chevallier, J.; Foss, M.; Besenbacher, F.

2008-03-01

Thin platinum films with well-controlled rough surface morphologies are grown by e-gun evaporation at an oblique angle of incidence between the deposition flux and the substrate normal. Atomic force microscopy is used to determine the root-mean-square value w of the surface roughness on the respective surfaces. From the scaling behavior of w , we find that while the roughness exponent α remains nearly unchanged at about 0.90, the growth exponent β changes from 0.49±0.04 to 0.26±0.01 as the deposition angle approaches grazing incidence. The values of the growth exponent β indicate that the film growth is influenced by both surface diffusion and shadowing effects, while the observed change from 0.49 to 0.26 can be attributed to differences in the relative importance of diffusion and shadowing with the deposition angle.

Bubble evolution in Kr-irradiated UO2 during annealing

NASA Astrophysics Data System (ADS)

He, L.; Bai, X. M.; Pakarinen, J.; Jaques, B. J.; Gan, J.; Nelson, A. T.; El-Azab, A.; Allen, T. R.

2017-12-01

Transmission electron microscopy observation of Kr bubble evolution in polycrystalline UO2 annealed at high temperature was conducted in order to understand the inert gas behavior in oxide nuclear fuel. The average diameter of intragranular bubbles increased gradually from 0.8 nm in as-irradiated sample at room temperature to 2.6 nm at 1600 °C and the bubble size distribution changed from a uniform distribution to a bimodal distribution above 1300 °C. The size of intergranular bubbles increased more rapidly than intragranular ones and bubble denuded zones near grain boundaries formed in all the annealed samples. It was found that high-angle grain boundaries held bigger bubbles than low-angle grain boundaries. Complementary atomistic modeling was conducted to interpret the effects of grain boundary character on the Kr segregation. The area density of strong segregation sites in the high-angle grain boundaries is much higher than that in the low angle grain boundaries.

Wide angle near-field optical probes by reverse tube etching.

PubMed

Patanè, S; Cefalì, E; Arena, A; Gucciardi, P G; Allegrini, M

2006-04-01

We present a simple modification of the tube etching process for the fabrication of fiber probes for near-field optical microscopy. It increases the taper angle of the probe by a factor of two. The novelty is that the fiber is immersed in hydrofluoric acid and chemically etched in an upside-down geometry. The tip formation occurs inside the micrometer tube cavity formed by the polymeric jacket. By applying this approach, called reverse tube etching, to multimode fibers with 200/250 microm core/cladding diameter, we have fabricated tapered regions featuring high surface smoothness and average cone angles of approximately 30 degrees . A simple model based on the crucial role of the gravity in removing the etching products, explains the tip formation process.

Influence of Surface Properties and Impact Conditions on Adhesion of Insect Residues

NASA Technical Reports Server (NTRS)

Wohl, Christopher J.; Smith, Joseph G.; Connell, John W.; Siochi, Emilie J.; Doss, Jereme R.; Shanahan, Michelle H.; Penner, Ronald K.

2015-01-01

Insect residues can cause premature transition to turbulent flow on laminar flow airfoils. Engineered surfaces that mitigate the adhesion of insect residues provide, therefore, a route to more efficient aerodynamics and reduced fuel burn rates. Areal coverage and heights of residues depend not only on surface properties, but also on impact conditions. We report high speed photography of fruit fly impacts at different angles of inclination on a rigid aluminum surface, optical microscopy and profilometry, and contact angle goniometry to support the design of engineered surfaces. For the polyurethane and epoxy coatings studied, some of which exhibited superhydrophobicity, it was determined that impact angle and surface compositions play critical roles in the efficacy of these surfaces to reduce insect residue adhesion.

Fabrication of superhydrophobic and antibacterial surface on cotton fabric by doped silica-based sols with nanoparticles of copper

PubMed Central

2011-01-01

The study discussed the synthesis of silica sol using the sol-gel method, doped with two different amounts of Cu nanoparticles. Cotton fabric samples were impregnated by the prepared sols and then dried and cured. To block hydroxyl groups, some samples were also treated with hexadecyltrimethoxysilane. The average particle size of colloidal silica nanoparticles were measured by the particle size analyzer. The morphology, roughness, and hydrophobic properties of the surface fabricated on cotton samples were analyzed and compared via the scanning electron microscopy, the transmission electron microscopy, the scanning probe microscopy, with static water contact angle (SWC), and water shedding angle measurements. Furthermore, the antibacterial efficiency of samples was quantitatively evaluated using AATCC 100 method. The addition of 0.5% (wt/wt) Cu into silica sol caused the silica nanoparticles to agglomerate in more grape-like clusters on cotton fabrics. Such fabricated surface revealed the highest value of SWC (155° for a 10-μl droplet) due to air trapping capability of its inclined structure. However, the presence of higher amounts of Cu nanoparticles (2% wt/wt) in silica sol resulted in the most slippery smooth surface on cotton fabrics. All fabricated surfaces containing Cu nanoparticles showed the perfect antibacterial activity against both of gram-negative and gram-positive bacteria. PMID:22085594

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering.

PubMed

Baker, Matthew A B; Tuckwell, Andrew J; Berengut, Jonathan F; Bath, Jonathan; Benn, Florence; Duff, Anthony P; Whitten, Andrew E; Dunn, Katherine E; Hynson, Robert M; Turberfield, Andrew J; Lee, Lawrence K

2018-06-04

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.

Phospholipid lateral diffusion in phosphatidylcholine-sphingomyelin-cholesterol monolayers; effects of oxidatively truncated phosphatidylcholines.

PubMed

Parkkila, Petteri; Stefl, Martin; Olżyńska, Agnieszka; Hof, Martin; Kinnunen, Paavo K J

2015-01-01

Oxidative stress is involved in a number of pathological conditions and the generated oxidatively modified lipids influence membrane properties and functions, including lipid-protein interactions and cellular signaling. Brewster angle microscopy demonstrated oxidatively truncated phosphatidylcholines to promote phase separation in monolayers of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), sphingomyelin (SM) and cholesterol (Chol). More specifically, 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), was found to increase the miscibility transition pressure of the SM/Chol-phase. Lateral diffusion of lipids is influenced by a variety of membrane properties, thus making it a sensitive parameter to observe the coexistence of different lipid phases, for instance. The dependence on lipid lateral packing of the lateral diffusion of fluorophore-containing phospholipid analogs was investigated in Langmuir monolayers composed of POPC, SM, and Chol and additionally containing oxidatively truncated phosphatidylcholines, using fluorescence correlation spectroscopy (FCS). To our knowledge, these are the first FCS results on miscibility transition in ternary lipid monolayers, confirming previous results obtained using Brewster angle microscopy on such lipid monolayers. Wide-field fluorescence microscopy was additionally employed to verify the transition, i.e. the loss and reformation of SM/Chol domains. Copyright © 2014. Published by Elsevier B.V.

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection, [summary].

DOT National Transportation Integrated Search

2015-11-01

Nutrient content is a concern in Floridas aquifers and springs sources of drinking water, : recreation, and the states natural beauty. In recent years, the nitrogen content of Floridas : aquifer springs has risen. This increase in nutrie...

Visualization of the equilibrium position of colloidal particles at fluid-water interfaces by deposition of nanoparticles

NASA Astrophysics Data System (ADS)

Sabapathy, Manigandan; Kollabattula, Viswas; Basavaraj, Madivala G.; Mani, Ethayaraja

2015-08-01

We present a general yet simple method to measure the contact angle of colloidal particles at fluid-water interfaces. In this method, the particles are spread at the required fluid-water interface as a monolayer. In the water phase a chemical reaction involving reduction of a metal salt such as aurochloric acid is initiated. The metal grows as a thin film or islands of nanoparticles on the particle surface exposed to the water side of the interface. Analyzing the images of particles by high resolution scanning microscopy (HRSEM), we trace the three phase contact line up to which deposition of the metal film occurs. From geometrical relations, the three phase contact angle is then calculated. We report the measurements of the contact angle of silica and polystyrene (PS) particles at different interfaces such as air-water, decane-water and octanol-water. We have also applied this method to measure the contact angle of surfactant treated polystyrene particles at the air-water interface, and we find a non-monotonic change of the contact angle with the concentration of the surfactant. Our results are compared with the well-known gel trapping technique and we find good comparison with previous measurements.We present a general yet simple method to measure the contact angle of colloidal particles at fluid-water interfaces. In this method, the particles are spread at the required fluid-water interface as a monolayer. In the water phase a chemical reaction involving reduction of a metal salt such as aurochloric acid is initiated. The metal grows as a thin film or islands of nanoparticles on the particle surface exposed to the water side of the interface. Analyzing the images of particles by high resolution scanning microscopy (HRSEM), we trace the three phase contact line up to which deposition of the metal film occurs. From geometrical relations, the three phase contact angle is then calculated. We report the measurements of the contact angle of silica and polystyrene (PS) particles at different interfaces such as air-water, decane-water and octanol-water. We have also applied this method to measure the contact angle of surfactant treated polystyrene particles at the air-water interface, and we find a non-monotonic change of the contact angle with the concentration of the surfactant. Our results are compared with the well-known gel trapping technique and we find good comparison with previous measurements. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03369a

Solid-State Spun Fibers from 1 mm Long Carbon Nanotube Forests Synthesized by Water-Assisted Chemical Vapor Deposition

NASA Technical Reports Server (NTRS)

Zhang, Shanju; Zhu, Lingbo; Minus, Marilyn L.; Chae, han Gi; Jagannathan, Sudhakar; Wong, Ching-Ping; Kowalik, Janusz; Roberson, Luke B.; Kumar, Satish

2007-01-01

In this work, we report continuous carbon nanotube fibers dry-drawn directly from water-assisted CVD grown forests with millimeter scale length. As-drawn nanotube fibers exist as aerogel and can be transformed into more compact fibers through twisting or densification with a volatile liquid. Nanotube fibers are characterized by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), Raman microscopy and wide-angle X-ray diffraction (WAXD). Mechanical behavior and electrical conductivity of the post-treated nanotube fibers are investigated.

Structure of biodiesel based bicontinuous microemulsions for environmentally compatible decontamination: A small angle neutron scattering and freeze fracture electron microscopy study.

PubMed

Wellert, S; Karg, M; Imhof, H; Steppin, A; Altmann, H-J; Dolle, M; Richardt, A; Tiersch, B; Koetz, J; Lapp, A; Hellweg, T

2008-09-01

Most toxic industrial chemicals and chemical warfare agents are hydrophobic and can only be solubilized in organic solvents. However, most reagents employed for the degradation of these toxic compounds can only be dissolved in water. Hence, microemulsions are auspicious media for the decontamination of a variety of chemical warfare agents and pesticides. They allow for the solubilization of both the lipophilic toxics and the hydrophilic reagent. Alkyl oligoglucosides and plant derived solvents like rapeseed methyl ester enable the formulation of environmentally compatible bicontinuous microemulsions. In the present article the phase behavior of such a microemulsion is studied and the bicontinuous phase is identified. Small angle neutron scattering (SANS) and freeze fracture electron microscopy (FFEM) measurements are used to characterize the structure of the bicontinuous phase and allow for an estimation of the total internal interface. Moreover, also the influence of the co-surfactant (1-pentanol) on the structural parameters of the bicontinuous phase is studied with SANS.

One-step solvothermal deposition of ZnO nanorod arrays on a wood surface for robust superamphiphobic performance and superior ultraviolet resistance

PubMed Central

Yao, Qiufang; Wang, Chao; Fan, Bitao; Wang, Hanwei; Sun, Qingfeng; Jin, Chunde; Zhang, Hong

2016-01-01

In the present paper, uniformly large-scale wurtzite-structured ZnO nanorod arrays (ZNAs) were deposited onto a wood surface through a one-step solvothermal method. The as-prepared samples were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetry (TG), and differential thermal analysis (DTA). ZNAs with a diameter of approximately 85 nm and a length of approximately 1.5 μm were chemically bonded onto the wood surface through hydrogen bonds. The superamphiphobic performance and ultraviolet resistance were measured and evaluated by water or oil contact angles (WCA or OCA) and roll-off angles, sand abrasion tests and an artificially accelerated ageing test. The results show that the ZNA-treated wood demonstrates a robust superamphiphobic performance under mechanical impact, corrosive liquids, intermittent and transpositional temperatures, and water spray. Additionally, the as-prepared wood sample shows superior ultraviolet resistance. PMID:27775091

A simple and low temperature process for super-hydrophilic rutile TiO 2 thin films growth

NASA Astrophysics Data System (ADS)

Mane, R. S.; Joo, Oh-Shim; Min, Sun-Ki; Lokhande, C. D.; Han, Sung-Hwan

2006-11-01

We investigate an environmentally friendly aqueous solution system for rutile TiO2 violet color nanocrystalline thin films growth on ITO substrate at room temperature. Film shows considerable absorption in visible region with excitonic maxima at 434 nm. X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED), UV-vis, water surface contact angle and energy dispersive X-ray analysis (EDX) techniques in addition to actual photo-image that shows purely rutile phase of TiO2 with violet color, super-hydrophilic and densely packed nanometer-sized spherical grains of approximate diameter 3.15 ± 0.4 nm, characterize the films. Band gap energy of 4.61 eV for direct transition was obtained for the rutile TiO2 films. Film surface shows super-hydrophilic behavior, as exhibited water contact angle was 7°. Strong visible absorption (not due to chlorine) leaves future challenge to use these films in extremely thin absorber (ETA) solar cells.

Study of the interfacial reactions between a bioactive apatite-mullite glass-ceramic coating and titanium substrates using high angle annular dark field transmission electron microscopy.

PubMed

Stanton, Kenneth T; O'Flynn, Kevin P; Nakahara, Shohei; Vanhumbeeck, Jean-François; Delucca, John M; Hooghan, Bobby

2009-04-01

Glass of generic composition SiO(2) . Al(2)O(3) . P(2)O(5) . CaO . CaF(2) will crystallise predominantly to apatite and mullite upon heat-treatment. Such ceramics are bioactive, osseoconductive, and have a high resistance to fracture. As a result, they are under investigation for use as biomedical device coatings, and in particular for orthopaedic implants. Previous work has shown that the material can be successfully enamelled to titanium with an interfacial reaction zone produced during heat treatment. The present study uses high angle annular dark field transmission electron microscopy (HAADF-TEM) to conduct a detailed examination of this region. Results show evidence of complex interfacial reactions following the diffusion of titanium into an intermediate layer and the production of titanium silicides and titanium phosphides. These results confirm previously hypothesised mechanisms for the bonding of silicate bioceramics with titanium alloys.

Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy.

PubMed

Martinez, G T; Rosenauer, A; De Backer, A; Verbeeck, J; Van Aert, S

2014-02-01

High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed. © 2013 Published by Elsevier B.V. All rights reserved.

Nanotexturing of polystyrene surface in fluorocarbon plasmas: from sticky to slippery superhydrophobicity.

PubMed

Mundo, Rosa Di; Palumbo, Fabio; d'Agostino, Riccardo

2008-05-06

In this work plasma etching processes have been studied to roughen and fluorinate polystyrene surface as an easy method to achieve a superhydrophobic slippery character. Radiofrequency discharges have been fed with CF(4)/O(2) mixtures and the effect of the O(2):CF(4) ratio, the input power, and the treatment duration have been investigated in terms of wettability, with focus on sliding performances. For this purpose, surface morphological variations, evaluated by means of scanning electron microscopy and atomic force microscopy, together with the chemical assessment by X-ray photoelectron spectroscopy, have been correlated with water contact angle hysteresis and volume resolved sliding angle measurements. Results indicate that by increasing the height and decreasing the density of the structures formed by etching, within a tailored range, a transition from sticky to slippery superhydrophobicity occurs. A short treatment time (5 min) is sufficient to obtain such an effect, provided that a high power input is utilized. Optimized surfaces show a unaltered transparency to visible light according to the low roughness produced.

Microstructure and physical properties of nano-biocomposite films based on cassava starch and laponite.

PubMed

Valencia, Germán Ayala; Luciano, Carla Giovana; Lourenço, Rodrigo Vinicius; do Amaral Sobral, Paulo José

2018-02-01

The aim of this research was to study the effects of laponite concentrations on some properties of nano-biocomposite films based on cassava starch, focusing mainly the relation between the properties of the surface microstructure and roughness, water contact angle and gloss. Nano-biocomposite films were produced by casting. We analyzed gloss, color, opacity, water contact angle, crystallinity by X-ray diffraction, and microstructure by scanning electron microscopy and atomic force microscopy. Texture parameters (energy, entropy and fractal dimension) were extracted from micrographs. We observed a great impact of laponite in the morphology of nano-biocomposite films. Texture parameters correlated with surface heterogeneity and roughness. Finally, surface roughness affected the surface hydrophilicity of nano-biocomposite films. Laponite platelets were exfoliated and/or intercalated with amylose and amylopectin chains. This research reports new information on the effects of laponite concentrations on the morphological, optical and wetting properties of nano-biocomposite films aiming future industrial applications. Copyright © 2017 Elsevier B.V. All rights reserved.

One-step solvothermal deposition of ZnO nanorod arrays on a wood surface for robust superamphiphobic performance and superior ultraviolet resistance

NASA Astrophysics Data System (ADS)

Yao, Qiufang; Wang, Chao; Fan, Bitao; Wang, Hanwei; Sun, Qingfeng; Jin, Chunde; Zhang, Hong

2016-10-01

In the present paper, uniformly large-scale wurtzite-structured ZnO nanorod arrays (ZNAs) were deposited onto a wood surface through a one-step solvothermal method. The as-prepared samples were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetry (TG), and differential thermal analysis (DTA). ZNAs with a diameter of approximately 85 nm and a length of approximately 1.5 μm were chemically bonded onto the wood surface through hydrogen bonds. The superamphiphobic performance and ultraviolet resistance were measured and evaluated by water or oil contact angles (WCA or OCA) and roll-off angles, sand abrasion tests and an artificially accelerated ageing test. The results show that the ZNA-treated wood demonstrates a robust superamphiphobic performance under mechanical impact, corrosive liquids, intermittent and transpositional temperatures, and water spray. Additionally, the as-prepared wood sample shows superior ultraviolet resistance.

Preparation of the CNC/Ag/beeswax composites for enhancing antibacterial and water resistance properties of paper.

PubMed

Liu, Kai; Liang, Hunan; Nasrallah, Joseph; Chen, Lihui; Huang, Liulian; Ni, Yonghao

2016-05-20

An effective method of preparing composites containing inorganic (Ag) and organic (beeswax) particles was established in this study. Ag nanoparticles were first immobilized on the cellulose nanocrystals (CNC) during the reduction of AgNO3 in the presence of CNC, then mixed with beeswax by high speed stirring. Scanning transmission electron microscopy (STEM) images indicated that Ag and beeswax particles were uniformly dispersed and stable in the network structure formed by CNC. Upon coating on a paper surface, a layer of beeswax film was evident based on scanning electron microscopy (SEM) images. The dynamic contact angle and antibacterial activity tests indicated that the contact angle of coated paper reached 113.06° and the growth inhibition of Escherichia coli increased to 99.96%, respectively, at a coating amount of 21.53 g/m(2). When applied onto paper surface by coating, the CNC/Ag/beeswax composites can impact paper with antibacterial property and improved water resistance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enhanced light element imaging in atomic resolution scanning transmission electron microscopy.

PubMed

Findlay, S D; Kohno, Y; Cardamone, L A; Ikuhara, Y; Shibata, N

2014-01-01

We show that an imaging mode based on taking the difference between signals recorded from the bright field (forward scattering region) in atomic resolution scanning transmission electron microscopy provides an enhancement of the detectability of light elements over existing techniques. In some instances this is an enhancement of the visibility of the light element columns relative to heavy element columns. In all cases explored it is an enhancement in the signal-to-noise ratio of the image at the light column site. The image formation mechanisms are explained and the technique is compared with earlier approaches. Experimental data, supported by simulation, are presented for imaging the oxygen columns in LaAlO₃. Case studies looking at imaging hydrogen columns in YH₂ and lithium columns in Al₃Li are also explored through simulation, particularly with respect to the dependence on defocus, probe-forming aperture angle and detector collection aperture angles. © 2013 Elsevier B.V. All rights reserved.

An analysis of FtsZ assembly using small angle X-ray scattering and electron microscopy.

PubMed

Kuchibhatla, Anuradha; Abdul Rasheed, A S; Narayanan, Janaky; Bellare, Jayesh; Panda, Dulal

2009-04-09

Small angle X-ray scattering (SAXS) was used for the first time to study the self-assembly of the bacterial cell division protein, FtsZ, with three different additives: calcium chloride, monosodium glutamate and DEAE-dextran hydrochloride in solution. The SAXS data were analyzed assuming a model form factor and also by a model-independent analysis using the pair distance distribution function. Transmission electron microscopy (TEM) was used for direct observation of the FtsZ filaments. By sectioning and negative staining with glow discharged grids, very high bundling as well as low bundling polymers were observed under different assembly conditions. FtsZ polymers formed different structures in the presence of different additives and these additives were found to increase the bundling of FtsZ protofilaments by different mechanisms. The combined use of SAXS and TEM provided us a significant insight of the assembly of FtsZ and microstructures of the assembled FtsZ polymers.

Superhydrophobic NiTi shape memory alloy surfaces fabricated by anodization and surface mechanical attrition treatment

NASA Astrophysics Data System (ADS)

Ou, Shih-Fu; Wang, Kuang-Kuo; Hsu, Yen-Chi

2017-12-01

This paper describes the fabrication of superhydrophobic NiTi shape memory alloy (SMA) surfaces using an environmentally friendly method based on an economical anodizing process. Perfluorooctyltriethoxysilane was used to reduce the surface energy of the anodized surfaces. The wettability, morphology, composition, and microstructure of the surfaces were investigated by scanning electron microscopy, transmission electron microscopy, and x-ray photoelectron spectroscopy. The surface of the treated NiTi SMA exhibited superhydrophobicity, with a water contact angle of 150.6° and sliding angle of 8°. The anodic film on the NiTi SMA comprised of TiO2 and NiO, as well as traces of TiCl3. In addition, before the NiTi SMA was anodized, it underwent a surface mechanical attrition treatment to grain-refine its surface. This method efficiently enhanced the growth rate of the anodic oxide film, and improved the hydrophobic uniformity of the anodized NiTi-SMA-surface.

Relationship of Optical Anomalies, Zoning, and Microtopography in Vesuvianite from Jeffrey Mine, Asbestos, Quebec

NASA Astrophysics Data System (ADS)

Smith, Varina Campbell

The role of growth steps in inducing disequilibrium is investigated in crystals of vesuvianite from the Jeffrey mine, Asbestos, Quebec, using optical microscopy, atomic force microscopy, electron microprobe analysis, and single-crystal X-ray diffraction. The selective uptake of elements Fe and Al by asymmetric growth-steps on three crystallographic forms, {100}, {110}, and {121}, is documented. The prisms {100} and {110} show hillocks that display kinetically controlled oscillatory zoning along growth steps parallel to <010> and <11¯1>, but not on vicinal faces defined by [001] steps. Sector-specific zoning of extinction angles and 2V angles indicate different degrees of optical dissymmetrization in crystals spanning a range of growth habits. Unit-cell parameters and the presence of violating reflections confirm sectoral deviations from P4/nnc symmetry in the prismatic sectors. The partial loss of three glide planes follows the pattern expected from order of the cations Al and Fe induced by tangential selectivity at the edge of non-equivalent steps during layer-by-layer growth.

Hierarchical super-structure identified by polarized light microscopy, electron microscopy and nanoindentation: Implications for the limits of biological control over the growth mode of abalone sea shells

PubMed Central

2012-01-01

Background Mollusc shells are commonly investigated using high-resolution imaging techniques based on cryo-fixation. Less detailed information is available regarding the light-optical properties. Sea shells of Haliotis pulcherina were embedded for polishing in defined orientations in order to investigate the interface between prismatic calcite and nacreous aragonite by standard materialographic methods. A polished thin section of the interface was prepared with a defined thickness of 60 μm for quantitative birefringence analysis using polarized light and LC-PolScope microscopy. Scanning electron microscopy images were obtained for comparison. In order to study structural-mechanical relationships, nanoindentation experiments were performed. Results Incident light microscopy revealed a super-structure in semi-transparent regions of the polished cross-section under a defined angle. This super-structure is not visible in transmitted birefringence analysis due to the blurred polarization of small nacre platelets and numerous organic interfaces. The relative orientation and homogeneity of calcite prisms was directly identified, some of them with their optical axes exactly normal to the imaging plane. Co-oriented "prism colonies" were identified by polarized light analyses. The nacreous super-structure was also visualized by secondary electron imaging under defined angles. The domains of the super-structure were interpreted to consist of crystallographically aligned platelet stacks. Nanoindentation experiments showed that mechanical properties changed with the same periodicity as the domain size. Conclusions In this study, we have demonstrated that insights into the growth mechanisms of nacre can be obtained by conventional light-optical methods. For example, we observed super-structures formed by co-oriented nacre platelets as previously identified using X-ray Photo-electron Emission Microscopy (X-PEEM) [Gilbert et al., Journal of the American Chemical Society 2008, 130:17519–17527]. Polarized optical microscopy revealed unprecedented super-structures in the calcitic shell part. This bears, in principle, the potential for in vivo studies, which might be useful for investigating the growth modes of nacre and other shell types. PMID:22967319

An ultrahigh pressure homogenization technique for easily exfoliating few-layer phosphorene from bulk black phosphorus

NASA Astrophysics Data System (ADS)

Guan, Qing-Qing; Zhou, Hua-Jing; Ning, Ping; Lian, Pei-Chao; Wang, Bo; He, Liang; Chai, Xin-Sheng

2018-05-01

We have developed an easy and efficient method for exfoliating few-layer sheets of black phosphorus (BP) in N-methyl-2-pyrrolidone, using ultra-high pressure homogenization (UPH). The BP was first exfoliated into sheets that were a few atomic layers thick, using a homogenizer for only 30 min. Next, a double centrifugation procedure was used to separate the material into few-layer nanosheets that were examined by X-ray diffraction, atomic force microscopy (AFM), transmission electron microscopy (TEM), high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), and energy-dispersive X-ray (EDX) spectroscopy. The results show that the products are specimens of phosphorene that are only a few-layer thick.

Direct observation of anti-phase boundaries in heteroepitaxy of GaSb thin films grown on Si(001) by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Woo, S. Y.; Hosseini Vajargah, S.; Ghanad-Tavakoli, S.; Kleiman, R. N.; Botton, G. A.

2012-10-01

Unambiguous identification of anti-phase boundaries (APBs) in heteroepitaxial films of GaSb grown on Si has been so far elusive. In this work, we present conventional transmission electron microscopy (TEM) diffraction contrast imaging using superlattice reflections, in conjunction with convergent beam electron diffraction analysis, to determine a change in polarity across APBs in order to confirm the presence of anti-phase disorder. In-depth analysis of anti-phase disorder is further supported with atomic resolution high-angle annular dark-field scanning transmission electron microscopy. The nature of APBs in GaSb is further elucidated by a comparison to previous results for GaAs epilayers grown on Si.

Numerical tilting compensation in microscopy based on wavefront sensing using transport of intensity equation method

NASA Astrophysics Data System (ADS)

Hu, Junbao; Meng, Xin; Wei, Qi; Kong, Yan; Jiang, Zhilong; Xue, Liang; Liu, Fei; Liu, Cheng; Wang, Shouyu

2018-03-01

Wide-field microscopy is commonly used for sample observations in biological research and medical diagnosis. However, the tilting error induced by the oblique location of the image recorder or the sample, as well as the inclination of the optical path often deteriorates the imaging quality. In order to eliminate the tilting in microscopy, a numerical tilting compensation technique based on wavefront sensing using transport of intensity equation method is proposed in this paper. Both the provided numerical simulations and practical experiments prove that the proposed technique not only accurately determines the tilting angle with simple setup and procedures, but also compensates the tilting error for imaging quality improvement even in the large tilting cases. Considering its simple systems and operations, as well as image quality improvement capability, it is believed the proposed method can be applied for tilting compensation in the optical microscopy.

Direct observation for atomically flat and ordered vertical {111} side-surfaces on three-dimensionally figured Si(110) substrate using scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Yang, Haoyu; Hattori, Azusa N.; Ohata, Akinori; Takemoto, Shohei; Hattori, Ken; Daimon, Hiroshi; Tanaka, Hidekazu

2017-11-01

A three-dimensional Si{111} vertical side-surface structure on a Si(110) wafer was fabricated by reactive ion etching (RIE) followed by wet-etching and flash-annealing treatments. The side-surface was studied with scanning tunneling microscopy (STM) in atomic scale for the first time, in addition to atomic force microscopy (AFM), scanning electron microscopy (SEM), and low-energy electron diffraction (LEED). AFM and SEM showed flat and smooth vertical side-surfaces without scallops, and STM proved the realization of an atomically-flat 7 × 7-reconstructed structure, under optimized RIE and wet-etching conditions. STM also showed that a step-bunching occurred on the produced {111} side-surface corresponding to a reversely taped side-surface with a tilt angle of a few degrees, but did not show disordered structures. Characteristic LEED patterns from both side- and top-reconstructed surfaces were also demonstrated.

Cell adhesion on nanotextured slippery superhydrophobic substrates.

PubMed

Di Mundo, Rosa; Nardulli, Marina; Milella, Antonella; Favia, Pietro; d'Agostino, Riccardo; Gristina, Roberto

2011-04-19

In this work, the response of Saos2 cells to polymeric surfaces with different roughness/density of nanometric dots produced by a tailored plasma-etching process has been studied. Topographical features have been evaluated by atomic force microscopy, while wetting behavior, in terms of water-surface adhesion energy, has been evaluated by measurements of drop sliding angle. Saos2 cytocompatibility has been investigated by scanning electron microscopy, fluorescent microscopy, and optical microscopy. The similarity in outer chemical composition has allowed isolation of the impact of the topographical features on cellular behavior. The results indicate that Saos2 cells respond differently to surfaces with different nanoscale topographical features, clearly showing a certain inhibition in cell adhesion when the nanoscale is particularly small. This effect appears to be attenuated in surfaces with relatively bigger nanofeatures, though these express a more pronounced slippery/dry wetting character. © 2011 American Chemical Society

Gaps analysis for CD metrology beyond the 22nm node

NASA Astrophysics Data System (ADS)

Bunday, Benjamin; Germer, Thomas A.; Vartanian, Victor; Cordes, Aaron; Cepler, Aron; Settens, Charles

2013-04-01

This paper will examine the future for critical dimension (CD) metrology. First, we will present the extensive list of applications for which CD metrology solutions are needed, showing commonalities and differences among the various applications. We will then report on the expected technical limits of the metrology solutions currently being investigated by SEMATECH and others in the industry to address the metrology challenges of future nodes, including conventional CD scanning electron microscopy (CD-SEM) and optical critical dimension (OCD) metrology and new potential solutions such as He-ion microscopy (HeIM, sometimes elsewhere referred to as HIM), CD atomic force microscopy (CD-AFM), CD small-angle x-ray scattering (CD-SAXS), high-voltage scanning electron microscopy (HV-SEM), and other types. A technical gap analysis matrix will then be demonstrated, showing the current state of understanding of the future of the CD metrology space.

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

Lazauskas, A., E-mail: Algirdas.LAZAUSKAS@stud.ktu.lt; Guobienė, A., E-mail: Asta.GUOBIENE@ktu.lt; Prosyčevas, I., E-mail: IGORPROS@mail.ru

This work investigates water droplet behavior on superhydrophobic (water contact angle value of 162 ± 1°) SiO{sub 2} nanocomposite films subjected to repetitive icing/deicing treatments, changes in SiO{sub 2} nanocomposite film surface morphology and their non-wetting characteristics. During the experiment, water droplets on SiO{sub 2} nanocomposite film surface are subjected to a series of icing and deicing cycles in a humid (∼ 70% relative humidity) atmosphere and the resulting morphological changes are monitored and characterized using atomic force microscopy (AFM) and contact angle measurements. Our data show that the formation of the frozen or thawed water droplet, with no furthermore » shape change, on superhydrophobic SiO{sub 2} nanocomposite film, is obtained faster within each cycle as the number of the icing/deicing cycles increases. After 10 icing and deicing cycles, the superhydrophobic SiO{sub 2} nanocomposite film had a water contact angle value of 146 ± 2° which is effectively non-superhydrophobic. AFM analysis showed that the superhydrophobic SiO{sub 2} nanocomposite film surface area under the water droplet undergoes gradual mechanical damage during the repetitive icing/deicing cycles. We propose a possible mechanism of the morphological changes to the film surface that take place during the consecutive icing/deicing experiments. - Highlights: • Superhydrophobic film is subjected to repetitive icing/deicing treatments. • Water droplet shape transition is recorded and characterized thereafter. • Atomic force microscopy and contact angle measurements are performed. • The surface undergoes gradual mechanical damage during repetitive icing/deicing. • Mechanism for the observed surface morphological changes is suggested.« less

Preparation of MTMS based transparent superhydrophobic silica films by sol-gel method.

PubMed

Venkateswara Rao, A; Latthe, Sanjay S; Nadargi, Digambar Y; Hirashima, H; Ganesan, V

2009-04-15

Superhydrophobic surfaces with water contact angle higher than 150 degrees generated a lot of interest both in academia and in industry because of the self-cleaning properties. Optically transparent superhydrophobic silica films were synthesized at room temperature (27 degrees C) using sol-gel process by a simple dip coating technique. The molar ratio of MTMS:MeOH:H(2)O (5 M NH(4)OH) was kept constant at 1:10.56:4.16, respectively. Emphasis is given to the effect of the surface modifying agents on the hydrophobic behavior of the films. Methyl groups were introduced in the silica film by post-synthesis grafting from two solutions using trimethylchlorosilane (TMCS) and hexamethyldisilazane (HMDZ) silylating agents in hexane solvent, individually. The percentage of silylating agents and silylation period was varied from 2.5 to 7.5% and 1 to 3 h, respectively. The TMCS modified films exhibited a very high water contact angle (166+/-2 degrees) in comparison to the HMDZ (138+/-2 degrees) modified films, indicating the water repellent behavior of the surface. When the TMCS and HMDZ modified films were heated at temperatures higher than 350 degrees C and 335 degrees C, respectively, the films became superhydrophilic; the contact angle for water on the films was smaller than 5 degrees. Further, the humidity study was carried out at a relative humidity of 85% at 30 degrees C temperature over 30 days. The films have been characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FT-IR), % optical transmission, humidity tests and contact angle (CA) measurements.

Direct Measurement of the Wettability of Minerals Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Deng, Y.; Xu, L.; Lu, H.; Wang, H.; Shi, Y.

2016-12-01

The wettability of reservoir rock plays an essential role in affecting the states of fluids (water, oil, etc) in pores which are constructed with various minerals. The contact angle method, which is based on the optical microscope photographs of millimeter-sized droplets on a smooth mineral surface, is one of the most widely employed methods to evaluate the wettability of a rock. However, the real reservoir rocks are composed of several kinds of minerals and thus nonhomogeneous, which leads to different wettability at different location of the rock. The mineral grains are usually micrometer-sized so that the traditional optical contact angle method cannot obtain the wettability of different minerals in the rock. Here we used a tapping-mode atomic force microscopy (TM-AFM, MFP-3D-BIO, Asylum Research) to measure the contact angles of micrometer-sized water droplets on different minerals in a tight sand rock which is mainly composed of quartz, albite, potash feldspar and anorthite. The water droplets varied from submicron to several tens micron in diameter. With the optimization of tool and operation parameters, the AFM tip was well controlled so that the nanoscale morphology of the contact configuration between water film and the mineral surface can be obtained at high resolution without disturbing the liquid surface. The AFM results showed that the contact angles of water on quartz and albite were 30-40 ° and 37-45 °, respectively. The AFM method provides a new measure for the wettability evaluation of reservoir rocks, and it is with potential to be applied to oil and gas hydrate studies.

Morphogenesis of nanostructures in glancing angle deposition of metal thin film coatings

NASA Astrophysics Data System (ADS)

Brown, Timothy James

Atomic vapors condensed onto solid surfaces form a remarkable category of condensed matter materials, the so-called thin films, with a myriad of compositions, morphological structures, and properties. The dynamic process of atomic condensation exhibits self-assembled pattern formation, producing morphologies with atomic-scale three- dimensional structures of seemingly limitless variety. This study attempts to shed new light on the dynamical growth processes of thin film deposition by analyzing in detail a previously unreported specific distinct emergent structure, a crystalline triangular-shaped spike that grows within copper and silver thin films. I explored the deposition parameters that lead to the growth of these unique structures, referred to as "nanospikes", fabricating approximately 55 thin films and used scanning electron microscopy and x-ray diffraction analysis. The variation of parameters include: vapor incidence angle, film thickness, substrate temperature, deposition rate, deposition material, substrate, and source-to-substrate distance. Microscopy analysis reveals that the silver and copper films deposited at glancing vapor incidence angles, 80 degrees and greater, have a high degree of branching interconnectivity between adjacent inclined nanorods. Diffraction analysis reveals that the vapor incidence angle influences the sub-populations of crystallites in the films, producing two different [110] crystal texture orientations. I hypothesize that the growth of nanospikes from nanorods is initiated by the stochastic arrival of vapor atoms and photons emitted from the deposition source at small diameter nanorods, and then driven by localized heating from vapor condensation and photon absorption. Restricted heat flow due to nanoscale thermal conduction maintains an elevated local temperature at the nanorod, enhancing adatom diffusion and enabling fast epitaxial crystal growth, leading to the formation and growth of nanospikes. Electron microscopy and x-ray diffraction analysis, and comparisons to related scientific literature, support this hypothesis. I also designed a highly modular ultrahigh vacuum deposition chamber, capable of concurrently mounting several different pieces of deposition equipment, that allows for a high degree of control of the growth dynamics of deposited thin films. I used the newly designed chamber to fabricate tailor-made nanostructured tantalum films for use in ultracapacitors, for the Cabot Corporation.

CIDR

Science.gov Websites

Sequencing Information Investigators have a wealth of study design options available to them using next (whole exome and custom only). SNVs and indels called and annotated Data quality evaluated using a robust contamination is estimated using VerifyBamID. The QC report is used in-house to monitor QC metrics real-time and

Recycling rate of bile acids in the enterohepatic recirculation as a major determinant of whole body 75SeHCAT retention.

PubMed

Peters, A Michael; Walters, Julian R F

2013-10-01

Measurement of the whole body retention of orally administered (75)SeHCAT is used to investigate patients with unexplained diarrhoea. Retention values of <15 % at 7 days post-administration are taken to indicate bile acid malabsorption (BAM). Whilst idiopathic BAM is frequently diagnosed with (75)SeHCAT, functional and morphological studies of the terminal ileum rarely show any abnormality, so the disorder may be more appropriately termed bile acid diarrhoea (BAD). In addition to malabsorption, excess bile acid may reach the colon, where the events leading to diarrhoea take place, as a result firstly of increased bile acid synthesis and secondly of an increased recycling rate of bile acids. Increased recycling has been largely ignored as a cause of BAD, but, as shown in this study, can readily result in excess bile acids reaching the colon even when ileal absorption efficiency is normal (i.e. 95-97 %). There needs to be a re-evaluation of the causes of BAD in patients without a history of previous intestinal resection or evidence of ileal pathology, such as Crohn's disease.

Synthesis and photoluminescence properties of a cyan-emitting phosphor Ca3(PO4)2:Eu2+ for white light-emitting diodes

NASA Astrophysics Data System (ADS)

Zhou, Wenli; Han, Jin; Zhang, Xuejie; Qiu, Zhongxian; Xie, Qingji; Liang, Hongbin; Lian, Shixun; Wang, Jing

2015-01-01

In this paper, a cyan-emitting phosphor Ca3(PO4)2:Eu2+ (TCP:Eu2+) was synthesized and evaluated as a candidate for white light emitting diodes (WLEDs). This phosphor shows strong and broad absorption in 250-450 nm region, but the emission spectrum is prominent at around 480 nm. The emission intensity of the TCP:Eu2+ was found to be 60% and 82% of that of the commercial BaMgAl10O17:Eu2+ (BAM) under excitation at 340 nm and 370 nm, respectively. Upon excitation at 370 nm, the absolute internal and external quantum efficiencies of the Ca3(PO4)2:1.5%Eu2+ are 60% and 42%, respectively. Moreover, a white LED lamp was fabricated by coating TCP:Eu2+ with a blue-emitting BAM and a red-emitting CaAlSiN3:Eu2+ on a near-ultraviolet (375 nm) LED chip, driven by a 350 mA forward bias current, and it produces an intense white light with a color rendering index of 75.

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

PubMed

Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

2012-09-15

To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

Mechanisms of Molecular Mimicry of Plant CLE Peptide Ligands by the Parasitic Nematode Globodera rostochiensis1[C][W

PubMed Central

Guo, Yongfeng; Ni, Jun; Denver, Robert; Wang, Xiaohong; Clark, Steven E.

2011-01-01

Nematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry. PMID:21750229

Pathobiologic Roles of Epstein–Barr Virus-Encoded MicroRNAs in Human Lymphomas

PubMed Central

Navari, Mohsen; Etebari, Maryam; Ibrahimi, Mostafa; Leoncini, Lorenzo

2018-01-01

Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas. PMID:29649101

Mechanisms of molecular mimicry of plant CLE peptide ligands by the parasitic nematode Globodera rostochiensis.

PubMed

Guo, Yongfeng; Ni, Jun; Denver, Robert; Wang, Xiaohong; Clark, Steven E

2011-09-01

Nematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry.

Flower-like Rh/Cu superhydrophobic coating via electrodeposition and its self-cleaning property

NASA Astrophysics Data System (ADS)

Zhao, N.; Lu, S. X.; Xu, W. G.; Cheng, X. L.

2017-01-01

Rh/Cu superhydrophobic coatings with textured flower-like dual micro-nano structures were fabricated on copper substrates via electrodesposition of Rh followed by annealing treatment. The scanning electron microscopy and X-ray diffraction pattern were conducted to analyse the morphology and chemical composition of the coating surfaces, respectively. The water drops exhibited a water contact angle of 168±1° and a sliding angle of 0±1° on the coating surfaces which were obtained by etching in concentrated hydrochloric acid and nitric acid, electrodeposited at -1.0 V for 30 min and annealing in an oven at 180°C for 60 min. The prepared superhydrophobic coatings showed excellent water repellence and self-cleaning property due to its extremely high water contact angle.

Laser Surface Preparation and Bonding of Aerospace Structural Composites

NASA Technical Reports Server (NTRS)

Belcher, Marcus A.; Wohl, Christopher J.; Connell, John W.

2009-01-01

A Nd:YAG laser was used to etch patterns conducive to adhesive bonding onto CFRP surfaces. These were compared to typical pre-bonding surface treatments including grit blasting, manual abrasion, and peel ply. Laser treated composites were then subjected to optical microscopy, contact angle measurements, and post-bonding mechanical testing.

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

Wang, Yang; Liu, Xiao Wei; Zhang, Hai Feng, E-mail: wy3121685@163.com

In this work, we present a method of fabricating super-hydrophobic surface on aluminum alloy substrate. The etching of aluminum surfaces has been performed using Beck's dislocation etchant for different time to create micrometer-sized irregular steps. An optimised etching time of 50 s is found to be essential before polytetrafluoroethylene (PTFE) coating, to obtain a highest water contact angle of 165±2° with a lowest contact angle hysteresis as low as 5±2°. The presence of patterned microstructure as revealed by scanning electron microscopy (SEM) together with the low surface energy ultrathin RF-sputtered PTFE films renders the aluminum alloy surfaces highly super-hydrophobic.

Thiolated poly(ɛ-caprolactone) macroligand with vacant coordination sites on gold substrate: Synthesis and surface characterization

NASA Astrophysics Data System (ADS)

Farah, Abdiaziz A.; Zheng, Susan H.; Morin, Sylvie; Bensebaa, Farid; Pietro, William J.

2007-04-01

Surface-confined telechelic poly(ɛ-caprolactone) macroligand with two distinct functional groups per polymeric chain has been synthesized and characterized. The molecular microstructure of the macroligand with regard to the properties of the end-capped functionalities and with those on surface substrate has been studied by solution and surface analytical methods (i.e., X-ray photoelectron spectroscopy (XPS), grazing angle reflectance-Fourier transform IR spectroscopy (GA-FTIR), water contact angle measurements, and atomic force microscopy (AFM)) to elucidate the structure and properties of such multifunctional polymer on gold (1 1 1) substrate.

Local texture and strongly linked conduction in spray-pyrolyzed TlBa2Ca2Cu3O(8+x) deposits

NASA Astrophysics Data System (ADS)

Kroeger, D. M.; Goyal, A.; Specht, E. D.; Wang, Z. L.; Tkaczyk, J. E.; Sutliff, J. A.; Deluca, J. A.

Local texture in polycrystalline TlBa2Ca2 Cu3O(8+x) deposits has been determined from transmission electron microscopy, electron backscatter diffraction patterns and x-ray diffraction. The small-grained deposits had excellent c-axis alignment and contained colonies of grains with similar but not identical a-axis orientations. Most grain boundaries within a colony have small misorientation angles and should not be weak links. It is proposed that long range conduction utilizes a percolative network of small angle grain boundaries at colony intersections.

Patterns and conformations in molecularly thin films

NASA Astrophysics Data System (ADS)

Basnet, Prem B.

Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn increasing attention because of the richness in phases that they exhibit. Due to the unique coupling between dipole properties and the packing constraints placed by the bent shape, these molecules are emerging as strong candidates in electromechanical devices. However, most applications require that the molecules be aligned, which has proved difficult. Our group has tested such molecules both as Langmuir layers and, when transferred to a solid, as alignment layers with some limited success. However, these molecules do not behave well with the surfaces and the domains at the air/water interface tend to form ill-controlled multilayer structures since attraction with the surfaces is relatively weak. New bent-core molecules obtained from Prof. Dr. C. Tsehiemke from Department of Chemistry Institute of Organic Chemistry, Martin-Luther-University, Germany, have a hydrophilic group at one end. We expect this molecule to behave better on the surface because of the stronger attraction of the hydrophilic group towards the surface than for the bent-core molecules without the hydrophilic group. Polydimethylsiloxane (PDMS) is a polymer which finds many applications in modifying surface properties. It is used in manufacturing lubricants, protective coatings, hair conditioner and glass-coating. However its properties are not well understood. This polymer has been proposed to follow either helical or caterpillar conformations on a surface. The orientational order of CH3 side groups can test for these conformations (they would be predominantly up/down for the caterpillar conformation, but rotating through the entire 360 degree for the helical one). Thus previous work on the Langmuir polymer films at the air/water interface were complemented by deuterium NMR studies to probe their conformations at a surface. These experiments were performed using humid porous solids, in order to provide sufficient surface area for the technique. Previous tests in this group at room temperature were suggestive but inconclusive because of the rapid averaging motion of the molecules. Here, we attempt to freeze the molecules on the surface.

Wetting of nanophases: Nanobubbles, nanodroplets and micropancakes on hydrophobic surfaces.

PubMed

An, Hongjie; Liu, Guangming; Craig, Vincent S J

2015-08-01

The observation by Atomic Force Microscopy of a range of nanophases on hydrophobic surfaces poses some challenging questions, not only related to the stability of these objects but also regarding their wetting properties. Spherical capped nanobubbles are observed to exhibit contact angles that far exceed the macroscopic contact angle measured for the same materials, whereas nanodroplets exhibit contact angles that are much the same as the macroscopic contact angle. Micropancakes are reported to consist of gas, in which case their wetting properties are mysterious. They should only be stable when the van der Waals forces act to thicken the film whereas for a gas, the van der Waals forces will always act to thin the film. Here we examine the available evidence and contribute some additional experiments in order to review our understanding of the wetting properties of these nanophases. We demonstrate that if in fact micropancakes consist of a contaminant their wetting properties can be explained, though the very high contact angles of nanobubbles remain unexplained. Copyright © 2014 Elsevier B.V. All rights reserved.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

PubMed

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Mineralogical Controls over Carbon Storage and Residence Times in Grassland Soils

NASA Astrophysics Data System (ADS)

Dwivedi, D.; Riley, W. J.; Torn, M. S.; Spycher, N.

2014-12-01

Globally, soil organic matter (SOM) contains approximately three times more carbon than the atmosphere and terrestrial vegetation contain combined. However, it is not well understood why some SOM persists for a long time while other SOM decomposes quickly. For future climate predictions, representing soil organic matter (SOM) dynamics accurately in Earth system models is essential. Soil minerals stabilize organic carbon in soil; however, there are gaps in our understanding of how soil mineralogy controls the quantity and turnover of long-residence-time organic carbon. To investigate the impact of soil mineralogy on SOM dynamics, we used a new model (Biotic and Abiotic Model of SOM—BAMS1 [Riley et al., 2014]) integrated with a three-dimensional, multiphase reactive transport solver (TOUGHREACT). The model represents bacterial and fungal activity, archetypal polymer and monomer carbon substrate groups, aqueous chemistry, gaseous diffusion, aqueous advection and diffusion, and adsorption and desorption processes. BAMS1 can predict bulk SOM and radiocarbon signatures without resorting to an arbitrary depth-dependent decline in SOM turnover rates. Results show a reasonable match between observed and simulated depth-resolved SOM and Δ14C in grassland ecosystems (soils formed on terraces south of Eureka, California, and the Central Chernozem Region of Russia) and were consistent with expectations of depth-resolved profiles of lignin content and fungi:aerobic bacteria ratios. Results also suggest that clay-mineral surface area and soil sorption coefficients constitute dominant controls over organic carbon stocks and residence times, respectively. Bibliography: Riley, W.J., F.M. Maggi, M. Kleber, M.S. Torn, J.Y. Tang, D. Dwivedi, and N. Guerry (2014), Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics, Geoscientific Model Development, vol. 7, 1335-2014, doi:10.5194/gmd-7-1335-2014.

Unique variations of Epstein-Barr virus-encoded BARF1 gene in nasopharyngeal carcinoma biopsies.

PubMed

Wang, Yun; Wang, Xiao-Feng; Sun, Zhi-Fu; Luo, Bing

2012-06-01

The Epstein-Barr virus (EBV) BamHI-A rightward frame 1 (BARF1) gene is frequently expressed in EBV-associated epithelial malignancies and involves in oncogenicity and immunomodulation. To characterize the variations of BARF1 gene in different populations, the sequences of BARF1 gene in Northern Chinese nasopharyngeal carcinoma (NPC), EBV-associated gastric carcinoma (EBVaGC) and healthy donors were analyzed. The correlation of BARF1 variation with polymorphisms of BamHI F fragment (type F and f variants) and EBV-coded viral interleukin-10 (vIL-10) gene (B95-8 and SPM patterns) was also explored. Two major subtypes of BARF1 gene, designated as B95-8 and V29A, were identified. B95-8 subtype had identical amino acid sequence to B95-8 and was the dominant subtype among the EBV isolates from Northern China. V29A subtype, with one consistent amino acid change at residue 29 (V→A) and several nucleotide changes, showed higher frequency in NPC cases (25.3%, 20/79) than in EBVaGC cases (0/45) or healthy donors (4.3%, 2/46) (NPC vs. EBVaGC: P=0.0001; NPC vs. healthy donor: P=0.004). A preferential linkage between BamHI F and BARF1/vIL-10 polymorphisms was found. Type f isolates was specially correlated with the V29A/SPM genotype in NPC isolates and type f/V29A/SPM was preferentially found in NPC. BARF1/c-fms homology domain, transforming domain and cytotoxic T lymphocyte (CTL) epitopes of BARF1 were highly conserved in most isolates, suggesting the important role of BARF1 in virus infection and the potential usefulness in EBV-targeting immunotherapy of EBV-associated tumors. The relatively higher prevalence of type f/V29A/SPM strains in NPC may also suggest the association between these variations in multiple viral genes and NPC. Copyright © 2012 Elsevier B.V. All rights reserved.

Genetic and isotope ratio mass spectrometric evidence for the occurrence of starch degradation and cycling in illuminated Arabidopsis leaves

PubMed Central

Baslam, Marouane; Baroja-Fernández, Edurne; Ricarte-Bermejo, Adriana; Sánchez-López, Ángela María; Aranjuelo, Iker; Bahaji, Abdellatif; Muñoz, Francisco José; Almagro, Goizeder; Pujol, Pablo; Galarza, Regina; Teixidor, Pilar; Pozueta-Romero, Javier

2017-01-01

Although there is a great wealth of data supporting the occurrence of simultaneous synthesis and breakdown of storage carbohydrate in many organisms, previous 13CO2 pulse-chase based studies indicated that starch degradation does not operate in illuminated Arabidopsis leaves. Here we show that leaves of gwd, sex4, bam4, bam1/bam3 and amy3/isa3/lda starch breakdown mutants accumulate higher levels of starch than wild type (WT) leaves when cultured under continuous light (CL) conditions. We also show that leaves of CL grown dpe1 plants impaired in the plastidic disproportionating enzyme accumulate higher levels of maltotriose than WT leaves, the overall data providing evidence for the occurrence of extensive starch degradation in illuminated leaves. Moreover, we show that leaves of CL grown mex1/pglct plants impaired in the chloroplastic maltose and glucose transporters display a severe dwarf phenotype and accumulate high levels of maltose, strongly indicating that the MEX1 and pGlcT transporters are involved in the export of starch breakdown products to the cytosol to support growth during illumination. To investigate whether starch breakdown products can be recycled back to starch during illumination through a mechanism involving ADP-glucose pyrophosphorylase (AGP) we conducted kinetic analyses of the stable isotope carbon composition (δ13C) in starch of leaves of 13CO2 pulsed-chased WT and AGP lacking aps1 plants. Notably, the rate of increase of δ13C in starch of aps1 leaves during the pulse was exceedingly higher than that of WT leaves. Furthermore, δ13C decline in starch of aps1 leaves during the chase was much faster than that of WT leaves, which provides strong evidence for the occurrence of AGP-mediated cycling of starch breakdown products in illuminated Arabidopsis leaves. PMID:28152100

The Epstein-Barr virus (EBV) nuclear antigen 1 BamHI F promoter is activated on entry of EBV-transformed B cells into the lytic cycle.

PubMed Central

Lear, A L; Rowe, M; Kurilla, M G; Lee, S; Henderson, S; Kieff, E; Rickinson, A B

1992-01-01

In Epstein-Barr virus (EBV)-positive Burkitt's lymphoma cell lines exhibiting the latency I form of infection (i.e., EBV nuclear antigen 1 [EBNA1] positive in the absence of other latent proteins), the EBNA1 mRNA has a unique BamHI Q/U/K splice structure and is expressed from a novel promoter, Fp, located near the BamHI FQ boundary. This contrasts with the situation in EBV-transformed lymphoblastoid cell lines (LCLs) exhibiting the latency III form of infection (i.e., positive for all latent proteins), in which transcription from the upstream Cp or Wp promoters is the principal source of EBNA mRNAs. We carried out cDNA amplifications with oligonucleotide primer-probe combinations to determine whether Fp is ever active in an LCL environment. The results clearly showed that some LCLs express a Q/U/K-spliced EBNA1 mRNA in addition to the expected Cp/Wp-initiated transcripts; this seemed inconsistent with the concept of Cp/Wp and Fp as mutually exclusive promoters. Here we show that Fp is indeed silent in latency III cells but is activated at an early stage following the switch from latency III into the virus lytic cycle. Four pieces of evidence support this conclusion: (i) examples of coincident Cp/Wp and Fp usage in LCLs are restricted to those lines in which a small subpopulation of cells have spontaneously entered the lytic cycle; (ii) transcripts initiating from Fp can readily be demonstrated in spontaneously productive lines by S1 nuclease protection; (iii) the presence of Fp-initiated transcripts is not affected by acyclovir blockade of the late lytic cycle; and (iv) infection of latently infected LCLs with a recombinant vaccinia virus encoding the EBV immediate-early protein BZLF1, a transcriptional transactivator which normally initiates the lytic cycle, results in the appearance of the diagnostic Q/U/K-spliced transcripts. Images PMID:1331531

Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.

PubMed

Culka, Martin; Huwiler, Simona G; Boll, Matthias; Ullmann, G Matthias

2017-10-18

Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strictly anaerobic bacterium Geobacter metallireducens uses the class II benzoyl-CoA reductase complex for this reaction. The catalytic BamB subunit of this complex harbors an active site tungsten-bis-pyranopterin cofactor with the metal being coordinated by five protein/cofactor-derived sulfur atoms and a sixth, so far unknown, ligand. Although BamB has been biochemically and structurally characterized, its mechanism still remains elusive. Here we use continuum electrostatic and QM/MM calculations to model benzoyl-CoA reduction by BamB. We aim to elucidate the identity of the sixth ligand of the active-site tungsten ion together with the interplay of the electron and proton transfer events during the aromatic ring reduction. On the basis of our calculations, we propose that benzoyl-CoA reduction is initiated by a hydrogen atom transfer from a W(IV) species with an aqua ligand, yielding W(V)-[OH - ] and a substrate radical intermediate. In the next step, a proton-assisted second electron transfer takes place with a conserved active-site histidine serving as the second proton donor. Interestingly, our calculations suggest that the electron for the second reduction step is taken from the pyranopterin cofactors rather than from the tungsten ion. The resulting cationic radical, which is distributed over both pyranopterins, is stabilized by conserved anionic amino acid residues. The stepwise mechanism of the reduction shows similarities to the Birch reduction known from organic chemistry. However, the strict coupling of protons and electrons allows the reaction to proceed under milder conditions.

Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences.

PubMed Central

Sockett, R E; Donohue, T J; Varga, A R; Kaplan, S

1989-01-01

A reaction center H- strain (RCH-) of Rhodobacter sphaeroides, PUHA1, was made by in vitro deletion of an XhoI restriction endonuclease fragment from the puhA gene coupled with insertion of a kanamycin resistance gene cartridge. The resulting construct was delivered to R. sphaeroides wild-type 2.4.1, with the defective puhA gene replacing the wild-type copy by recombination, followed by selection for kanamycin resistance. When grown under conditions known to induce intracytoplasmic membrane development, PUHA1 synthesized a pigmented intracytoplasmic membrane. Spectral analysis of this membrane showed that it was deficient in B875 spectral complexes as well as functional reaction centers and that the level of B800-850 spectral complexes was greater than in the wild type. The RCH- strain was photosythetically incompetent, but photosynthetic growth was restored by complementation with a 1.45-kilobase (kb) BamHI restriction endonuclease fragment containing the puhA gene carried in trans on plasmid pRK404. B875 spectral complexes were not restored by complementation with the 1.45-kb BamHI restriction endonuclease fragment containing the puhA gene but were restored along with photosynthetic competence by complementation with DNA from a cosmid carrying the puhA gene, as well as a flanking DNA sequence. Interestingly, B875 spectral complexes, but not photosynthetic competence, were restored to PUHA1 by introduction in trans of a 13-kb BamHI restriction endonuclease fragment carrying genes encoding the puf operon region of the DNA. The effect of the puhA deletion was further investigated by an examination of the levels of specific mRNA species derived from the puf and puc operons, as well as by determinations of the relative abundances of polypeptides associated with various spectral complexes by immunological methods. The roles of puhA and other genetic components in photosynthetic gene expression and membrane assembly are discussed. Images PMID:2644200