Breaking camouflage and detecting targets require optic flow and image structure information.

PubMed

Pan, Jing Samantha; Bingham, Ned; Chen, Chang; Bingham, Geoffrey P

2017-08-01

Use of motion to break camouflage extends back to the Cambrian [In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution (New York Basic Books, 2003)]. We investigated the ability to break camouflage and continue to see camouflaged targets after motion stops. This is crucial for the survival of hunting predators. With camouflage, visual targets and distracters cannot be distinguished using only static image structure (i.e., appearance). Motion generates another source of optical information, optic flow, which breaks camouflage and specifies target locations. Optic flow calibrates image structure with respect to spatial relations among targets and distracters, and calibrated image structure makes previously camouflaged targets perceptible in a temporally stable fashion after motion stops. We investigated this proposal using laboratory experiments and compared how many camouflaged targets were identified either with optic flow information alone or with combined optic flow and image structure information. Our results show that the combination of motion-generated optic flow and target-projected image structure information yielded efficient and stable perception of camouflaged targets.

Surface modification study of borate materials from B K-edge X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Kasrai, Masoud; Fleet, Michael E.; Muthupari, Swaminathan; Li, D.; Bancroft, G. M.

The B K-edge X-ray absorption near-edge structure (XANES) spectra of two borates with tetrahedrally-coordinated B [[4]B; natural danburite (CaB2Si2O8) and synthetic boron phosphate (BPO4)] have been recorded in total electron yield (TEY) and fluorescence yield (FY) modes to investigate the surface and bulk structure of these materials. The TEY XANES measurement shows that danburite is susceptible to surface damage involving conversion of [4]B sites to [3]B sites by reaction with moisture and/or mechanical abrasion (grinding, polishing, etc.). The bulk of the mineral is essentially unaffected. Commercial boron phosphate powder exhibits more extensive surface and bulk damage, which increases with air exposure but is recovered on heating at 650°C. In contrast to ELNES, the XANES technique is not affected by beam damage and when collected in the FY mode is capable of yielding meaningful information on the coordination and intermediate-range structure of B in borate and borosilicate materials.

[Study on Information Extraction of Clinic Expert Information from Hospital Portals].

PubMed

Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

2015-12-01

Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method.

The 10 Dimensions of Employee Involvement.

ERIC Educational Resources Information Center

Magjuka, Richard J.

1993-01-01

A survey of 923 employee involvement programs (57%) yielded 10 themes: range of problem content, team staffing, team membership status, team resources, training practices, information access, financial rewards, performance management systems, goal-setting structures, and roles of job supervisors. (JOW)

Grading options for western hemlock "pulpwood" logs from southeastern Alaska.

Treesearch

David W. Green; Kent A. McDonald; John Dramm; Kenneth Kilborn

Properties and grade yield are estimated for structural lumber produced from No. 3, No. 4, and low-end No. 2 grade western hemlock logs of the type previously used primarily for the production of pulp chips. Estimates are given for production in the Structural Framing, Machine Stress Rating, and Laminating Stock grading systems. The information shows that significant...

Geological map of parts of the state of Sao Paulo based on LANDSAT images. [Brazil

NASA Technical Reports Server (NTRS)

Dejususparada, N. (Principal Investigator); Amaral, G.; Liu, C. C.; Filho, R. A.

1979-01-01

The author has identified the following significant results. Interpretation of LANDSAT images revealed the subdivision of the Bauru formation into three distinct lithofacies. Delineation of structural features yielded new information on paleoenvironmental reconstitution and hydrogeology. Structural features and photogeological units were revealed in the precambrian basement at the eastern portion of the state.

Extraction of CT dose information from DICOM metadata: automated Matlab-based approach.

PubMed

Dave, Jaydev K; Gingold, Eric L

2013-01-01

The purpose of this study was to extract exposure parameters and dose-relevant indexes of CT examinations from information embedded in DICOM metadata. DICOM dose report files were identified and retrieved from a PACS. An automated software program was used to extract from these files information from the structured elements in the DICOM metadata relevant to exposure. Extracting information from DICOM metadata eliminated potential errors inherent in techniques based on optical character recognition, yielding 100% accuracy.

Accurate FRET Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation

PubMed Central

Lee, Nam Ki; Kapanidis, Achillefs N.; Wang, You; Michalet, Xavier; Mukhopadhyay, Jayanta; Ebright, Richard H.; Weiss, Shimon

2005-01-01

Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes. ALEX yields accurate FRET independent of instrumental factors, such as excitation intensity or detector alignment. Using DNA fragments, we showed that ALEX-based distances agree well with predictions from a cylindrical model of DNA; ALEX-based distances fit better to theory than distances obtained at the ensemble level. Distance measurements within transcription complexes agreed well with ensemble-FRET measurements, and with structural models based on ensemble-FRET and x-ray crystallography. ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature. PMID:15653725

What did Erwin mean? The physics of information from the materials genomics of aperiodic crystals and water to molecular information catalysts and life.

PubMed

Varn, D P; Crutchfield, J P

2016-03-13

Erwin Schrödinger famously and presciently ascribed the vehicle transmitting the hereditary information underlying life to an 'aperiodic crystal'. We compare and contrast this, only later discovered to be stored in the linear biomolecule DNA, with the information-bearing, layered quasi-one-dimensional materials investigated by the emerging field of chaotic crystallography. Despite differences in functionality, the same information measures capture structure and novelty in both, suggesting an intimate coherence between the information character of biotic and abiotic matter-a broadly applicable physics of information. We review layered solids and consider three examples of how information- and computation-theoretic techniques are being applied to understand their structure. In particular, (i) we review recent efforts to apply new kinds of information measures to quantify disordered crystals; (ii) we discuss the structure of ice I in information-theoretic terms; and (iii) we recount recent investigations into the structure of tris(bicyclo[2.1.1]hexeno)benzene, showing how an information-theoretic analysis yields additional insight into its structure. We then illustrate a new Second Law of Thermodynamics that describes information processing in active low-dimensional materials, reviewing Maxwell's Demon and a new class of molecular devices that act as information catalysts. Lastly, we conclude by speculating on how these ideas from informational materials science may impact biology. © 2016 The Author(s).

Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

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

Walian, P.J.

1989-11-01

One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing ofmore » these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)« less

Clinic expert information extraction based on domain model and block importance model.

PubMed

Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

2015-11-01

To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cotton growth modeling and assessment using unmanned aircraft system visual-band imagery

NASA Astrophysics Data System (ADS)

Chu, Tianxing; Chen, Ruizhi; Landivar, Juan A.; Maeda, Murilo M.; Yang, Chenghai; Starek, Michael J.

2016-07-01

This paper explores the potential of using unmanned aircraft system (UAS)-based visible-band images to assess cotton growth. By applying the structure-from-motion algorithm, the cotton plant height (ph) and canopy cover (cc) information were retrieved from the point cloud-based digital surface models (DSMs) and orthomosaic images. Both UAS-based ph and cc follow a sigmoid growth pattern as confirmed by ground-based studies. By applying an empirical model that converts the cotton ph to cc, the estimated cc shows strong correlation (R2=0.990) with the observed cc. An attempt for modeling cotton yield was carried out using the ph and cc information obtained on June 26, 2015, the date when sigmoid growth curves for both ph and cc tended to decline in slope. In a cross-validation test, the correlation between the ground-measured yield and the estimated equivalent derived from the ph and/or cc was compared. Generally, combining ph and cc, the performance of the yield estimation is most comparable against the observed yield. On the other hand, the observed yield and cc-based estimation produce the second strongest correlation, regardless of the complexity of the models.

Using directed information for influence discovery in interconnected dynamical systems

NASA Astrophysics Data System (ADS)

Rao, Arvind; Hero, Alfred O.; States, David J.; Engel, James Douglas

2008-08-01

Structure discovery in non-linear dynamical systems is an important and challenging problem that arises in various applications such as computational neuroscience, econometrics, and biological network discovery. Each of these systems have multiple interacting variables and the key problem is the inference of the underlying structure of the systems (which variables are connected to which others) based on the output observations (such as multiple time trajectories of the variables). Since such applications demand the inference of directed relationships among variables in these non-linear systems, current methods that have a linear assumption on structure or yield undirected variable dependencies are insufficient. Hence, in this work, we present a methodology for structure discovery using an information-theoretic metric called directed time information (DTI). Using both synthetic dynamical systems as well as true biological datasets (kidney development and T-cell data), we demonstrate the utility of DTI in such problems.

Rheology, tectonics, and the structure of the Venus lithosphere

NASA Technical Reports Server (NTRS)

Zuber, M. T.

1994-01-01

Given the absence of ground truth information on seismic structure, heat flow, and rock strength, or short wavelength gravity or magnetic data for Venus, information on the thermal, mechanical and compositional nature of the shallow interior must be obtained by indirect methods. Using pre-Magellan data, theoretical models constrained by the depths of impact craters and the length scales of tectonic features yielded estimates on the thickness of Venus' brittle-elastic lithosphere and the allowable range of crustal thickness and surface thermal gradient. The purpose of this study is to revisit the question of the shallow structure of Venus based on Magellan observations of the surface and recent experiments that address Venus' crustal rheology.

Prioritization of catchments based on soil erosion using remote sensing and GIS.

PubMed

Khadse, Gajanan K; Vijay, Ritesh; Labhasetwar, Pawan K

2015-06-01

Water and soil are the most essential natural resources for socioeconomic development and sustenance of life. A study of soil and water dynamics at a watershed level facilitates a scientific approach towards their conservation and management. Remote sensing and Geographic Information System are tools that help to plan and manage natural resources on watershed basis. Studies were conducted for the formulation of catchment area treatment plan based on watershed prioritization with soil erosion studies using remote sensing techniques, corroborated with Geographic Information System (GIS), secondary data and ground truth information. Estimation of runoff and sediment yield is necessary in prioritization of catchment for the design of soil conservation structures and for identifying the critical erosion-prone areas of a catchment for implementation of best management plan with limited resources. The Universal Soil Loss Equation, Sediment Yield Determination and silt yield index methods are used for runoff and soil loss estimation for prioritization of the catchments. On the basis of soil erosion classes, the watersheds were grouped into very high, high, moderate and low priorities. High-priority watersheds need immediate attention for soil and water conservation, whereas low-priority watershed having good vegetative cover and low silt yield index may not need immediate attention for such treatments.

"Chemical transformers" from nanoparticle ensembles operated with logic.

PubMed

Motornov, Mikhail; Zhou, Jian; Pita, Marcos; Gopishetty, Venkateshwarlu; Tokarev, Ihor; Katz, Evgeny; Minko, Sergiy

2008-09-01

The pH-responsive nanoparticles were coupled with information-processing enzyme-based systems to yield "smart" signal-responsive hybrid systems with built-in Boolean logic. The enzyme systems performed AND/OR logic operations, transducing biochemical input signals into reversible structural changes (signal-directed self-assembly) of the nanoparticle assemblies, thus resulting in the processing and amplification of the biochemical signals. The hybrid system mimics biological systems in effective processing of complex biochemical information, resulting in reversible changes of the self-assembled structures of the nanoparticles. The bioinspired approach to the nanostructured morphing materials could be used in future self-assembled molecular robotic systems.

Simulation Studies of Forest Structure using 3D Lidar and Radar Models

NASA Technical Reports Server (NTRS)

Sun, Guoqing; Ranson, K. Jon; Koetz, Benjamin; Liu, Dawei

2007-01-01

The use of lidars and radars to measure forest structure attributes such as height and biomass are being considered for future Earth Observation missions. Large footprint lidar makes a direct measurement of the heights of scatterers in the illuminated footprint and can yield information about the vertical profile of the canopy. Synthetic Aperture Radar (SAR) is known to sense the canopy volume, especially at longer wavelengths and is useful for estimating biomass. Interferometric SAR (InSAR) has been shown to yield forest canopy height information. For example, the height of scattering phase retrieved from InSAR data is considered to be correlated with the three height and the spatial structure of the forest stand. There is much interest in exploiting these technologies separately and together to get important information for carbon cycle and ecosystem science. More detailed information of the electromagnetic radiation interactions within forest canopies is needed. And backscattering models can be of much utility here. As part of a NASA funded project to explore data fusion, a three-dimensional (3D) coherent radar backscattering model and a 3D lidar backscatter models were used to investigate the use of large footprint lidar, SAR and InSAR for characterizing realistic forest scenes. For this paper, we use stem maps and other forest measurements to develop a realistic spatial structure of a spruce-hemlock forest canopy found in Maine, USA. The radar and lidar models used measurements of the 3D forest scene as input and simulated the coherent radar backscattering signature and 1064nm energy backscatter, respectively. The relationships of backscatter derived forest structure were compared with field measurements. In addition, we also had detailed airborne lidar (Laser Imaging Vegetation Sensor, LVIS) data available over the stem map sites that was used to study the accuracies of tree height derived from modeled SAR backscatter and the scattering phase center retrieved from the simulated InSAR data will be compared with the height indices, or other structure parameters derived from the lidar data. These results will address the possible synergies between lidar and radar in data in terms of forest structural information.

Machine learning for autonomous crystal structure identification.

PubMed

Reinhart, Wesley F; Long, Andrew W; Howard, Michael P; Ferguson, Andrew L; Panagiotopoulos, Athanassios Z

2017-07-21

We present a machine learning technique to discover and distinguish relevant ordered structures from molecular simulation snapshots or particle tracking data. Unlike other popular methods for structural identification, our technique requires no a priori description of the target structures. Instead, we use nonlinear manifold learning to infer structural relationships between particles according to the topology of their local environment. This graph-based approach yields unbiased structural information which allows us to quantify the crystalline character of particles near defects, grain boundaries, and interfaces. We demonstrate the method by classifying particles in a simulation of colloidal crystallization, and show that our method identifies structural features that are missed by standard techniques.

Highly charged ion based time of flight emission microscope

DOEpatents

Barnes, Alan V.; Schenkel, Thomas; Hamza, Alex V.; Schneider, Dieter H.; Doyle, Barney

2001-01-01

A highly charged ion based time-of-flight emission microscope has been designed, which improves the surface sensitivity of static SIMS measurements because of the higher ionization probability of highly charged ions. Slow, highly charged ions are produced in an electron beam ion trap and are directed to the sample surface. The sputtered secondary ions and electrons pass through a specially designed objective lens to a microchannel plate detector. This new instrument permits high surface sensitivity (10.sup.10 atoms/cm.sup.2), high spatial resolution (100 nm), and chemical structural information due to the high molecular ion yields. The high secondary ion yield permits coincidence counting, which can be used to enhance determination of chemical and topological structure and to correlate specific molecular species.

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.

PubMed

Cohen, Gerson H; Silverton, Enid W; Padlan, Eduardo A; Dyda, Fred; Wibbenmeyer, Jamie A; Willson, Richard C; Davies, David R

2005-05-01

The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 at 2.7 A resolution has previously been reported [Cohen et al. (1996), Acta Cryst. D52, 315-326]. With the availability of recombinant Fab, the X-ray structure of the complex has been re-evaluated at 1.7 A resolution. The refined structure has yielded a detailed picture of the Fab-lysozyme interface, showing the high complementarity of the protein surfaces as well as several water molecules within the interface that complete the good fit. The model of the full complex has improved significantly, yielding an R(work) of 19.5%. With this model, the structural results can be compared with the results of isothermal titration calorimetry. An attempt has been made to estimate the changes in bound waters that accompany complex formation and the difficulties inherent in using the crystal structures to provide the information necessary to make this calculation are discussed.

The Expansion of Dreissena and Long-term Shifts in Benthic Macroinvertebrate Community Structure in Lake Ontario, 1998-2008

EPA Science Inventory

The introduction of Dreissena to the Great lakes has profoundly impacted benthic ecosystems, resulting in the decline of native species and dramatic community restructuring. In Lake Ontario, long-term monitoring has yielded a wealth of detailed information regarding both the exp...

Genome-wide informative microsatellite database and global population structure of Fusarium virguliforme

USDA-ARS?s Scientific Manuscript database

Sudden death syndrome is one of the leading biotic stresses responsible for soybean yield loss in major soybean production areas. In North America, the disease is caused by the fungus Fusarium virguliforme, while in South America additional Fusarium species cause similar symptoms. Breeding for SDS r...

Beyond the Farmgate: Factors Related to Agricultural Performance in Two Dairy Communities.

ERIC Educational Resources Information Center

Cruise, James; Lyson, Thomas A.

1991-01-01

In two marginal dairy communities with similar physical environment, ethnic composition, and farm structure, a significant difference in productivity (milk yield per cow) was related to differences in educational attainment of farmers, proximity to an urban area, and availability of marketing outlets and agricultural information sources. Contains…

Dynamical interpretation of conditional patterns

NASA Technical Reports Server (NTRS)

Adrian, R. J.; Moser, R. D.; Moin, P.

1988-01-01

While great progress is being made in characterizing the 3-D structure of organized turbulent motions using conditional averaging analysis, there is a lack of theoretical guidance regarding the interpretation and utilization of such information. Questions concerning the significance of the structures, their contributions to various transport properties, and their dynamics cannot be answered without recourse to appropriate dynamical governing equations. One approach which addresses some of these questions uses the conditional fields as initial conditions and calculates their evolution from the Navier-Stokes equations, yielding valuable information about stability, growth, and longevity of the mean structure. To interpret statistical aspects of the structures, a different type of theory which deals with the structures in the context of their contributions to the statistics of the flow is needed. As a first step toward this end, an effort was made to integrate the structural information from the study of organized structures with a suitable statistical theory. This is done by stochastically estimating the two-point conditional averages that appear in the equation for the one-point probability density function, and relating the structures to the conditional stresses. Salient features of the estimates are identified, and the structure of the one-point estimates in channel flow is defined.

X-Ray Crystallographic Studies on Acetylcholinesterase and Related Enzymes.

DTIC Science & Technology

1999-10-01

nerve gas intoxication, as well as of insecticide poisoning. Such structures can yield direct information concerning the functional groups and steric...Glyll7His mutant (48). Recent solution of the 3D structures of conjugates of the nerve agents , sarin, soman, DFP and VX with 7cAChE (49, 50) has revealed... pesticides and chemical warfare agents is a topic of considerable environmental and toxicological importance. Hence, a substantial research effort is being

Monoterpene oxidation in an oxidative flow reactor: SOA yields and the relationship between bulk gas-phase properties and organic aerosol growth

NASA Astrophysics Data System (ADS)

Friedman, B.; Link, M.; Farmer, D.

2016-12-01

We use an oxidative flow reactor (OFR) to determine the secondary organic aerosol (SOA) yields of five monoterpenes (alpha-pinene, beta-pinene, limonene, sabinene, and terpinolene) at a range of OH exposures. These OH exposures correspond to aging timescales of a few hours to seven days. We further determine how SOA yields of beta-pinene and alpha-pinene vary as a function of seed particle type (organic vs. inorganic) and seed particle mass concentration. We hypothesize that the monoterpene structure largely accounts for the observed variance in SOA yields for the different monoterpenes. We also use high-resolution time-of-flight chemical ionization mass spectrometry to calculate the bulk gas-phase properties (O:C and H:C) of the monoterpene oxidation systems as a function of oxidant concentrations. Bulk gas-phase properties can be compared to the SOA yields to assess the capability of the precursor gas-phase species to inform the SOA yields of each monoterpene oxidation system. We find that the extent of oxygenated precursor gas-phase species corresponds to SOA yield.

Developing an automated database for monitoring ultrasound- and computed tomography-guided procedure complications and diagnostic yield.

PubMed

Itri, Jason N; Jones, Lisa P; Kim, Woojin; Boonn, William W; Kolansky, Ana S; Hilton, Susan; Zafar, Hanna M

2014-04-01

Monitoring complications and diagnostic yield for image-guided procedures is an important component of maintaining high quality patient care promoted by professional societies in radiology and accreditation organizations such as the American College of Radiology (ACR) and Joint Commission. These outcome metrics can be used as part of a comprehensive quality assurance/quality improvement program to reduce variation in clinical practice, provide opportunities to engage in practice quality improvement, and contribute to developing national benchmarks and standards. The purpose of this article is to describe the development and successful implementation of an automated web-based software application to monitor procedural outcomes for US- and CT-guided procedures in an academic radiology department. The open source tools PHP: Hypertext Preprocessor (PHP) and MySQL were used to extract relevant procedural information from the Radiology Information System (RIS), auto-populate the procedure log database, and develop a user interface that generates real-time reports of complication rates and diagnostic yield by site and by operator. Utilizing structured radiology report templates resulted in significantly improved accuracy of information auto-populated from radiology reports, as well as greater compliance with manual data entry. An automated web-based procedure log database is an effective tool to reliably track complication rates and diagnostic yield for US- and CT-guided procedures performed in a radiology department.

MRI-guided fluorescence tomography of the breast: a phantom study

NASA Astrophysics Data System (ADS)

Davis, Scott C.; Pogue, Brian W.; Dehghani, Hamid; Paulsen, Keith D.

2009-02-01

Tissue phantoms simulating the human breast were used to demonstrate the imaging capabilities of an MRI-coupled fluorescence molecular tomography (FMT) imaging system. Specifically, phantoms with low tumor-to-normal drug contrast and complex internal structure were imaged with the MR-coupled FMT system. Images of indocyanine green (ICG) fluorescence yield were recovered using a diffusion model-based approach capable of estimating the distribution of fluorescence activity in a tissue volume from tissue-boundary measurements of transmitted light. Tissue structural information, which can be determined from standard T1 and T2 MR images, was used to guide the recovery of fluorescence activity. The study revealed that this spatial guidance is critical for recovering images of fluorescence yield in tissue with low tumor-to-normal drug contrast.

Theoretical Neuroanatomy:Analyzing the Structure, Dynamics,and Function of Neuronal Networks

NASA Astrophysics Data System (ADS)

Seth, Anil K.; Edelman, Gerald M.

The mammalian brain is an extraordinary object: its networks give rise to our conscious experiences as well as to the generation of adaptive behavior for the organism within its environment. Progress in understanding the structure, dynamics and function of the brain faces many challenges. Biological neural networks change over time, their detailed structure is difficult to elucidate, and they are highly heterogeneous both in their neuronal units and synaptic connections. In facing these challenges, graph-theoretic and information-theoretic approaches have yielded a number of useful insights and promise many more.

Electronic structure of β-Ga2O3 single crystals investigated by hard X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Li, Guo-Ling; Zhang, Fabi; Cui, Yi-Tao; Oji, Hiroshi; Son, Jin-Young; Guo, Qixin

2015-07-01

By combination of hard X-ray photoelectron spectroscopy (HAXPES) and first-principles band structure calculations, the electronic states of β-Ga2O3 were investigated to deepen the understanding of bulk information for this compound. The valence band spectra of HAXPES presented the main contribution from Ga 4sp, which are well represented by photoionization cross section weighted partial density of states. The experimental data complemented with the theoretical study yield a realistic picture of the electronic structure for β-Ga2O3.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Verbal Knowledge, Working Memory, and Processing Speed as Predictors of Verbal Learning in Older Adults

ERIC Educational Resources Information Center

Rast, Philippe

2011-01-01

The present study aimed at modeling individual differences in a verbal learning task by means of a latent structured growth curve approach based on an exponential function that yielded 3 parameters: initial recall, learning rate, and asymptotic performance. Three cognitive variables--speed of information processing, verbal knowledge, working…

Nondestructive test of regenerative chambers

NASA Technical Reports Server (NTRS)

Malone, G. A.; Stauffis, R.; Wood, R.

1972-01-01

Flat panels simulating internally cooled regenerative thrust chamber walls were fabricated by electroforming, brazing and diffusion bonding to evaluate the feasibility of nondestructive evaluation techniques to detect bonds of various strength integrities. Ultrasonics, holography, and acoustic emission were investigated and found to yield useful and informative data regarding the presence of bond defects in these structures.

Modelling heterogeneity variances in multiple treatment comparison meta-analysis--are informative priors the better solution?

PubMed

Thorlund, Kristian; Thabane, Lehana; Mills, Edward J

2013-01-11

Multiple treatment comparison (MTC) meta-analyses are commonly modeled in a Bayesian framework, and weakly informative priors are typically preferred to mirror familiar data driven frequentist approaches. Random-effects MTCs have commonly modeled heterogeneity under the assumption that the between-trial variance for all involved treatment comparisons are equal (i.e., the 'common variance' assumption). This approach 'borrows strength' for heterogeneity estimation across treatment comparisons, and thus, ads valuable precision when data is sparse. The homogeneous variance assumption, however, is unrealistic and can severely bias variance estimates. Consequently 95% credible intervals may not retain nominal coverage, and treatment rank probabilities may become distorted. Relaxing the homogeneous variance assumption may be equally problematic due to reduced precision. To regain good precision, moderately informative variance priors or additional mathematical assumptions may be necessary. In this paper we describe four novel approaches to modeling heterogeneity variance - two novel model structures, and two approaches for use of moderately informative variance priors. We examine the relative performance of all approaches in two illustrative MTC data sets. We particularly compare between-study heterogeneity estimates and model fits, treatment effect estimates and 95% credible intervals, and treatment rank probabilities. In both data sets, use of moderately informative variance priors constructed from the pair wise meta-analysis data yielded the best model fit and narrower credible intervals. Imposing consistency equations on variance estimates, assuming variances to be exchangeable, or using empirically informed variance priors also yielded good model fits and narrow credible intervals. The homogeneous variance model yielded high precision at all times, but overall inadequate estimates of between-trial variances. Lastly, treatment rankings were similar among the novel approaches, but considerably different when compared with the homogenous variance approach. MTC models using a homogenous variance structure appear to perform sub-optimally when between-trial variances vary between comparisons. Using informative variance priors, assuming exchangeability or imposing consistency between heterogeneity variances can all ensure sufficiently reliable and realistic heterogeneity estimation, and thus more reliable MTC inferences. All four approaches should be viable candidates for replacing or supplementing the conventional homogeneous variance MTC model, which is currently the most widely used in practice.

Functional classification of protein structures by local structure matching in graph representation.

PubMed

Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

2018-03-31

As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Robust membrane detection based on tensor voting for electron tomography.

PubMed

Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

2014-04-01

Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

Brazilian Soybean Yields and Yield Gaps Vary with Farm Size

NASA Astrophysics Data System (ADS)

Jeffries, G. R.; Cohn, A.; Griffin, T. S.; Bragança, A.

2017-12-01

Understanding the farm size-specific characteristics of crop yields and yield gaps may help to improve yields by enabling better targeting of technical assistance and agricultural development programs. Linking remote sensing-based yield estimates with property boundaries provides a novel view of the relationship between farm size and yield structure (yield magnitude, gaps, and stability over time). A growing literature documents variations in yield gaps, but largely ignores the role of farm size as a factor shaping yield structure. Research on the inverse farm size-productivity relationship (IR) theory - that small farms are more productive than large ones all else equal - has documented that yield magnitude may vary by farm size, but has not considered other yield structure characteristics. We examined farm size - yield structure relationships for soybeans in Brazil for years 2001-2015. Using out-of-sample soybean yield predictions from a statistical model, we documented 1) gaps between the 95th percentile of attained yields and mean yields within counties and individual fields, and 2) yield stability defined as the standard deviation of time-detrended yields at given locations. We found a direct relationship between soy yields and farm size at the national level, while the strength and the sign of the relationship varied by region. Soybean yield gaps were found to be inversely related to farm size metrics, even when yields were only compared to farms of similar size. The relationship between farm size and yield stability was nonlinear, with mid-sized farms having the most stable yields. The work suggests that farm size is an important factor in understanding yield structure and that opportunities for improving soy yields in Brazil are greatest among smaller farms.

A Cultural Resources Survey of the Whitlow Ranch Dam and Reservoir Area, Eastern Pinal County, Arizona,

DTIC Science & Technology

1986-01-01

Superstition foothills. What was not expected was the high proportion of sites which show evidence of structures, and the equally high proportion which can be...to look at an attempt to hit paydirt that ultimately failed. Specifically, we can ask: what is the structure of a mining effort at this early stage...badly disturbed by looting but (as has been learned in recent years) even highly disturbed pueblo sites can be made to yield significant new information

Chlorophyll Fluorescence Analysis of Cyanobacterial Photosynthesis and Acclimation

PubMed Central

Campbell, Douglas; Hurry, Vaughan; Clarke, Adrian K.; Gustafsson, Petter; Öquist, Gunnar

1998-01-01

Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters FV/FM, FV′/FM′,qp,qN, NPQ, and φPS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial in vivo chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters can be used to estimate the electron transport rate at the acclimated growth light intensity. PMID:9729605

Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

PubMed Central

Zhang, Liangyi; Reilly, James P.

2009-01-01

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v- and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds. PMID:19113943

Bone geometry, structure and mineral distribution using Dual energy X ray Absorptiometry (DXA)

NASA Technical Reports Server (NTRS)

Whalen, Robert; Cleek, Tammy

1993-01-01

Dual energy x-ray absorptiometry (DXA) is currently the most widely used method of analyzing regional and whole body changes in bone mineral content (BMC) and areal (g/sq cm) bone mineral density (BMD). However, BMC and BMD do not provide direct measures of long bone geometry, structure, or strength nor do regional measurements detect localized changes in other regions of the same bone. The capabilities of DXA can be enhanced significantly by special processing of pixel BMC data which yields cross-sectional geometric and structural information. We have extended this method of analysis in order to develop non-uniform structural beam models of long bones.

The effect of drought and heat stress on reproductive processes in cereals.

PubMed

Barnabás, Beáta; Jäger, Katalin; Fehér, Attila

2008-01-01

As the result of intensive research and breeding efforts over the last 20 years, the yield potential and yield quality of cereals have been greatly improved. Nowadays, yield safety has gained more importance because of the forecasted climatic changes. Drought and high temperature are especially considered as key stress factors with high potential impact on crop yield. Yield safety can only be improved if future breeding attempts will be based on the valuable new knowledge acquired on the processes determining plant development and its responses to stress. Plant stress responses are very complex. Interactions between plant structure, function and the environment need to be investigated at various phases of plant development at the organismal, cellular as well as molecular levels in order to obtain a full picture. The results achieved so far in this field indicate that various plant organs, in a definite hierarchy and in interaction with each other, are involved in determining crop yield under stress. Here we attempt to summarize the currently available information on cereal reproduction under drought and heat stress and to give an outlook towards potential strategies to improve yield safety in cereals.

Instrumentation for Situational Assessment Undertaken for the Vocational Assessment for Special Needs Project.

ERIC Educational Resources Information Center

Flad, Harry R.; Canty, Jane M.

The basis for the assessment process in this project is that structured situations within curriculum areas will yield vocational information (skill and behavioral) that has a direct and indirect relationship to occupational areas in the world of work. Thus, with the assistance of school assessment teams, seven situations were identified and…

Why Is It so? The [superscript 1]H-NMR CH[subscript 2] Splitting in Substituted Propanes

ERIC Educational Resources Information Center

Lim, Kieran F.; Dereani, Marino

2010-01-01

Nuclear magnetic resonance (NMR) spectroscopy is an important tool in the structural analysis of both organic and inorganic molecules. Proton NMR spectra can yield information about the chemical or bonding environment surrounding various protons, the number of protons in those environments, and the number of neighbouring protons around each…

Informant Accuracy in Recall of Communications and Perception of One’s Place in Global Social Structure and Summary.

DTIC Science & Technology

1980-09-01

group. Perhaps- people in a more fully closed group would be more accurate. 7. The data we collected were essentially precognitive . Perhaps postcognitive...sets yield the fol- lowing results: I. Postcognitive data are (mainly) more accurate than precognitive , but not signif- icantly so. 2. With the

Development and quality of reproduction in two-age central Appalachian hardwoods - 10-year results

Treesearch

Gary W. Miller; Thomas M. Schuler

1995-01-01

Silvicultural practices that promote two-age stand structures have the potential to meet a wide range of forest resource goals. Such practices can overcome perceived disadvantages associated with clearcutting and still provide sustainable yields of desirable timber products and other woodland benefits. Forest managers need information on stand development following two...

Iso-vector form factors of the delta and nucleon in QCD sum rules

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

Ozpineci, A.

Form factors are important non-perturbative properties of hadrons. They give information about the internal structure of the hadrons. In this work, iso-vector axial-vector and iso-vector tensor form factors of the nucleon and the iso-vector axial-vector {Delta}{yields}N transition form factor calculations in QCD Sum Rules are presented.

Genetically Encoded Chemical Probes In Cells Reveal the Binding Path of Urocortin-I to CRF Class B GPCR

PubMed Central

Coin, Irene; Katritch, Vsevolod; Sun, Tingting; Xiang, Zheng; Siu, Fai Yiu; Beyermann, Michael; Stevens, Raymond C.; Wang, Lei

2014-01-01

SUMMARY Molecular determinants regulating the activation of class B G-protein coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photo-chemical and new click-chemical probes into the receptor, 44 inter-molecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation. The experimental strategy provides unique information on full-length post-translationally modified GPCRs in the native membrane of the live cell, complementing in vitro biophysical reductionist approaches. PMID:24290358

Mitigating Settlement of Structures founded on Peat

NASA Astrophysics Data System (ADS)

Wijeyesekera, D. C.; Numbikannu, L.; Ismail, T. N. H. T.; Bakar, I.

2016-07-01

Observations made of two common failures of structures founded on peat/organic soil in Johor, Malaysia is presented. Critical evaluation of current lightweight fill technology to mitigate such settlement is also discussed. Lightweight technology, such as Expanded Polystyrene (EPS), has been used in construction on soft yielding ground for decades. Regrettably, some published information of EPS failures to perform on construction sites are also cited in this paper. This paper outlines some concepts leading to the development of an alternative innovative lightweight fill is that the idealised cellular structure of the GCM permit free flow of water and complemented by the mat structure which evens out any differential settlement A further highlight of this paper is the monitoring of the field performance of this lightweight fill (GCM) as a feasible alternative to fill weight reduction on yielding ground.. Hence, a prime research objective was to compare the fill settlements observed with 1m high fill of surcharge loading on peat ground (comparison of the case of using a partial 0.6m high GCM and that of a total of 1m of conventional sand backfill).

NMR-based diffusion lattice imaging

NASA Astrophysics Data System (ADS)

Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

2016-03-01

Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

Automatic segmentation of relevant structures in DCE MR mammograms

NASA Astrophysics Data System (ADS)

Koenig, Matthias; Laue, Hendrik; Boehler, Tobias; Peitgen, Heinz-Otto

2007-03-01

The automatic segmentation of relevant structures such as skin edge, chest wall, or nipple in dynamic contrast enhanced MR imaging (DCE MRI) of the breast provides additional information for computer aided diagnosis (CAD) systems. Automatic reporting using BI-RADS criteria benefits of information about location of those structures. Lesion positions can be automatically described relatively to such reference structures for reporting purposes. Furthermore, this information can assist data reduction for computation expensive preprocessing such as registration, or for visualization of only the segments of current interest. In this paper, a novel automatic method for determining the air-breast boundary resp. skin edge, for approximation of the chest wall, and locating of the nipples is presented. The method consists of several steps which are built on top of each other. Automatic threshold computation leads to the air-breast boundary which is then analyzed to determine the location of the nipple. Finally, results of both steps are starting point for approximation of the chest wall. The proposed process was evaluated on a large data set of DCE MRI recorded by T1 sequences and yielded reasonable results in all cases.

Xylem recovery from drought-induced embolism: Where is the hydraulic point of no return?

Treesearch

Frederick C. Meinzer; Katherine A. McCulloh

2013-01-01

The hydraulic resilience of a species is determined by multiple physiological and structural traits. Understanding how these traits are integrated at the organismal level to yield adequate hydraulic fitness in a given environment would be a fertile area for future research. This type of information is essential for realistic predictions of species hydraulic limits...

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

In Vitro Self-Assembly of the Light Harvesting Pigment-Protein LH2 Revealed by Ultrafast Spectroscopy and Electron Microscopy

PubMed Central

Schubert, Axel; Stenstam, Anna; Beenken, Wichard J. D.; Herek, Jennifer L.; Cogdell, Richard; Pullerits, Tõnu; Sundström, Villy

2004-01-01

Controlled ensemble formation of protein-surfactant systems provides a fundamental concept for the realization of nanoscale devices with self-organizing capability. In this context, spectroscopic monitoring of pigment-containing proteins yields detailed structural information. Here we have studied the association behavior of the bacterial light-harvesting protein LH2 from Rhodobacter spheroides in an n,n-dimethyldodecylamine-n-oxide/water environment. Time-resolved studies of the excitation annihilation yielded information about aggregate sizes and packing of the protein complexes therein. The results are compared to transmission electron microscopy images of instantaneously frozen samples. Our data indicate the manifestation of different phases, which are discussed with respect to the thermodynamic equilibrium in ternary protein-surfactant-water systems. Accordingly, by varying the concentration the formation of different types of aggregates can be controlled. Conditions for the appearance of isolated LH2 complexes are defined. PMID:15041674

MemStar: a one-shot Escherichia coli-based approach for high-level bacterial membrane protein production.

PubMed

Lee, Chiara; Kang, Hae Joo; Hjelm, Anna; Qureshi, Abdul Aziz; Nji, Emmanuel; Choudhury, Hassanul; Beis, Konstantinos; de Gier, Jan-Willem; Drew, David

2014-10-16

Optimising membrane protein production yields in Escherichiacoli can be time- and resource-consuming. Here, we present a simple and effective Membrane protein Single shot amplification recipe: MemStar. This one-shot amplification recipe is based on the E. coli strain Lemo21(DE3), the PASM-5052 auto-induction medium and, contradictorily, an IPTG induction step. Using MemStar, production yields for most bacterial membrane proteins tested were improved to reach an average of 5 mg L(-1) per OD600 unit, which is significantly higher than yields obtained with other common production strategies. With MemStar, we have been able to obtain new structural information for several transporters, including the sodium/proton antiporter NapA. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

PubMed

Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

2006-06-06

To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.

Quantitative Analysis of Cotton Canopy Size in Field Conditions Using a Consumer-Grade RGB-D Camera.

PubMed

Jiang, Yu; Li, Changying; Paterson, Andrew H; Sun, Shangpeng; Xu, Rui; Robertson, Jon

2017-01-01

Plant canopy structure can strongly affect crop functions such as yield and stress tolerance, and canopy size is an important aspect of canopy structure. Manual assessment of canopy size is laborious and imprecise, and cannot measure multi-dimensional traits such as projected leaf area and canopy volume. Field-based high throughput phenotyping systems with imaging capabilities can rapidly acquire data about plants in field conditions, making it possible to quantify and monitor plant canopy development. The goal of this study was to develop a 3D imaging approach to quantitatively analyze cotton canopy development in field conditions. A cotton field was planted with 128 plots, including four genotypes of 32 plots each. The field was scanned by GPhenoVision (a customized field-based high throughput phenotyping system) to acquire color and depth images with GPS information in 2016 covering two growth stages: canopy development, and flowering and boll development. A data processing pipeline was developed, consisting of three steps: plot point cloud reconstruction, plant canopy segmentation, and trait extraction. Plot point clouds were reconstructed using color and depth images with GPS information. In colorized point clouds, vegetation was segmented from the background using an excess-green (ExG) color filter, and cotton canopies were further separated from weeds based on height, size, and position information. Static morphological traits were extracted on each day, including univariate traits (maximum and mean canopy height and width, projected canopy area, and concave and convex volumes) and a multivariate trait (cumulative height profile). Growth rates were calculated for univariate static traits, quantifying canopy growth and development. Linear regressions were performed between the traits and fiber yield to identify the best traits and measurement time for yield prediction. The results showed that fiber yield was correlated with static traits after the canopy development stage ( R 2 = 0.35-0.71) and growth rates in early canopy development stages ( R 2 = 0.29-0.52). Multi-dimensional traits (e.g., projected canopy area and volume) outperformed one-dimensional traits, and the multivariate trait (cumulative height profile) outperformed univariate traits. The proposed approach would be useful for identification of quantitative trait loci (QTLs) controlling canopy size in genetics/genomics studies or for fiber yield prediction in breeding programs and production environments.

User recommendation in healthcare social media by assessing user similarity in heterogeneous network.

PubMed

Jiang, Ling; Yang, Christopher C

2017-09-01

The rapid growth of online health social websites has captured a vast amount of healthcare information and made the information easy to access for health consumers. E-patients often use these social websites for informational and emotional support. However, health consumers could be easily overwhelmed by the overloaded information. Healthcare information searching can be very difficult for consumers, not to mention most of them are not skilled information searcher. In this work, we investigate the approaches for measuring user similarity in online health social websites. By recommending similar users to consumers, we can help them to seek informational and emotional support in a more efficient way. We propose to represent the healthcare social media data as a heterogeneous healthcare information network and introduce the local and global structural approaches for measuring user similarity in a heterogeneous network. We compare the proposed structural approaches with the content-based approach. Experiments were conducted on a dataset collected from a popular online health social website, and the results showed that content-based approach performed better for inactive users, while structural approaches performed better for active users. Moreover, global structural approach outperformed local structural approach for all user groups. In addition, we conducted experiments on local and global structural approaches using different weight schemas for the edges in the network. Leverage performed the best for both local and global approaches. Finally, we integrated different approaches and demonstrated that hybrid method yielded better performance than the individual approach. The results indicate that content-based methods can effectively capture the similarity of inactive users who usually have focused interests, while structural methods can achieve better performance when rich structural information is available. Local structural approach only considers direct connections between nodes in the network, while global structural approach takes the indirect connections into account. Therefore, the global similarity approach can deal with sparse networks and capture the implicit similarity between two users. Different approaches may capture different aspects of the similarity relationship between two users. When we combine different methods together, we could achieve a better performance than using each individual method. Copyright © 2017 Elsevier B.V. All rights reserved.

76 FR 55725 - Agency Information Collection Activities: Request for Comments for a New Information Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-08

... statistical surveys that yield quantitative results that can be generalized to the population of study. This... information will not be used for quantitative information collections that are designed to yield reliably... generic mechanisms that are designed to yield quantitative results. The FHWA received no comments in...

Sound propagation in a duct of periodic wall structure. [numerical analysis

NASA Technical Reports Server (NTRS)

Kurze, U.

1978-01-01

A boundary condition, which accounts for the coupling in the sections behind the duct boundary, is given for the sound-absorbing duct with a periodic structure of the wall lining and using regular partition walls. The soundfield in the duct is suitably described by the method of differences. For locally active walls this renders an explicit approximate solution for the propagation constant. Coupling may be accounted for by the method of differences in a clear manner. Numerical results agree with measurements and yield information which has technical applications.

Selecting practice management information systems.

PubMed

Worley, R; Ciotti, V

1997-01-01

Despite enormous advances in information systems, the process by which most medical practices select them has remained virtually unchanged for decades: the request for proposal (RFP). Unfortunately, vendors have learned ways to minimize the value of RFP checklists to where purchasers now learn little about the system functionality. The authors describe a selection methodology that replaces the RFP with scored demos, reviews of vendor user manuals and mathematically structured reference checking. In a recent selection process at a major medical center, these techniques yielded greater user buy-in and favorable contract terms as well.

Pointwise Partial Information Decomposition Using the Specificity and Ambiguity Lattices

NASA Astrophysics Data System (ADS)

Finn, Conor; Lizier, Joseph

2018-04-01

What are the distinct ways in which a set of predictor variables can provide information about a target variable? When does a variable provide unique information, when do variables share redundant information, and when do variables combine synergistically to provide complementary information? The redundancy lattice from the partial information decomposition of Williams and Beer provided a promising glimpse at the answer to these questions. However, this structure was constructed using a much criticised measure of redundant information, and despite sustained research, no completely satisfactory replacement measure has been proposed. In this paper, we take a different approach, applying the axiomatic derivation of the redundancy lattice to a single realisation from a set of discrete variables. To overcome the difficulty associated with signed pointwise mutual information, we apply this decomposition separately to the unsigned entropic components of pointwise mutual information which we refer to as the specificity and ambiguity. This yields a separate redundancy lattice for each component. Then based upon an operational interpretation of redundancy, we define measures of redundant specificity and ambiguity enabling us to evaluate the partial information atoms in each lattice. These atoms can be recombined to yield the sought-after multivariate information decomposition. We apply this framework to canonical examples from the literature and discuss the results and the various properties of the decomposition. In particular, the pointwise decomposition using specificity and ambiguity satisfies a chain rule over target variables, which provides new insights into the so-called two-bit-copy example.

Modelling heterogeneity variances in multiple treatment comparison meta-analysis – Are informative priors the better solution?

PubMed Central

2013-01-01

Background Multiple treatment comparison (MTC) meta-analyses are commonly modeled in a Bayesian framework, and weakly informative priors are typically preferred to mirror familiar data driven frequentist approaches. Random-effects MTCs have commonly modeled heterogeneity under the assumption that the between-trial variance for all involved treatment comparisons are equal (i.e., the ‘common variance’ assumption). This approach ‘borrows strength’ for heterogeneity estimation across treatment comparisons, and thus, ads valuable precision when data is sparse. The homogeneous variance assumption, however, is unrealistic and can severely bias variance estimates. Consequently 95% credible intervals may not retain nominal coverage, and treatment rank probabilities may become distorted. Relaxing the homogeneous variance assumption may be equally problematic due to reduced precision. To regain good precision, moderately informative variance priors or additional mathematical assumptions may be necessary. Methods In this paper we describe four novel approaches to modeling heterogeneity variance - two novel model structures, and two approaches for use of moderately informative variance priors. We examine the relative performance of all approaches in two illustrative MTC data sets. We particularly compare between-study heterogeneity estimates and model fits, treatment effect estimates and 95% credible intervals, and treatment rank probabilities. Results In both data sets, use of moderately informative variance priors constructed from the pair wise meta-analysis data yielded the best model fit and narrower credible intervals. Imposing consistency equations on variance estimates, assuming variances to be exchangeable, or using empirically informed variance priors also yielded good model fits and narrow credible intervals. The homogeneous variance model yielded high precision at all times, but overall inadequate estimates of between-trial variances. Lastly, treatment rankings were similar among the novel approaches, but considerably different when compared with the homogenous variance approach. Conclusions MTC models using a homogenous variance structure appear to perform sub-optimally when between-trial variances vary between comparisons. Using informative variance priors, assuming exchangeability or imposing consistency between heterogeneity variances can all ensure sufficiently reliable and realistic heterogeneity estimation, and thus more reliable MTC inferences. All four approaches should be viable candidates for replacing or supplementing the conventional homogeneous variance MTC model, which is currently the most widely used in practice. PMID:23311298

X-ray absorption spectroscopy: EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure)

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

Alp, E.E.; Mini, S.M.; Ramanathan, M.

1990-04-01

The x-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. It has also played an important role in the discovery and systematization of rare-earth elements. The discovery of synchrotron radiation in 1952, and later the availability of broadly tunable synchrotron based x-ray sources have revitalized this technique since the 1970's. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge by Sayers et. al. has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-raymore » Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. An excellent description of the principles and data analysis techniques of EXAFS is given by Teo. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, we will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and samples limitations.« less

Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Water oxidation chemistry of photosystem II.

PubMed

Brudvig, Gary W

2008-03-27

Photosystem II (PSII) uses light energy to split water into protons, electrons and O2. In this reaction, nature has solved the difficult chemical problem of efficient four-electron oxidation of water to yield O2 without significant amounts of reactive intermediate species such as superoxide, hydrogen peroxide and hydroxyl radicals. In order to use nature's solution for the design of artificial catalysts that split water, it is important to understand the mechanism of the reaction. The recently published X-ray crystal structures of cyanobacterial PSII complexes provide information on the structure of the Mn and Ca ions, the redox-active tyrosine called YZ and the surrounding amino acids that comprise the O2-evolving complex (OEC). The emerging structure of the OEC provides constraints on the different hypothesized mechanisms for O2 evolution. The water oxidation mechanism of PSII is discussed in the light of biophysical and computational studies, inorganic chemistry and X-ray crystallographic information.

Recommendations for Clinical Decision Support Deployment: Synthesis of a Roundtable of Medical Directors of Information Systems

PubMed Central

Jenders, Robert A.; Osheroff, Jerome A.; Sittig, Dean F.; Pifer, Eric A.; Teich, Jonathan M

2007-01-01

Background: Ample evidence exists that clinical decision support (CDS) can improve clinician performance. Nevertheless, additional evidence demonstrates that clinicians still do not perform adequately in many instances. This suggests an ongoing need for implementation of CDS, in turn prompting development of a roadmap for national action regarding CDS. Objective: Develop practical advice to aid CDS implementation in order to improve clinician performance. Method: Structured group interview during a roundtable discussion by medical directors of information systems (N = 30), with subsequent review by participants and synthesis. Results: Participant consensus was that CDS should be comprehensive and should involve techniques such as order sets and facilitated documentation as well as alerts; should be subject to ongoing feedback; and should flow from and be governed by an organization’s clinical goals. Conclusion: A structured roundtable discussion of clinicians experienced in health information technology can yield practical, consensus advice for implementation of CDS. PMID:18693858

Classification-free threat detection based on material-science-informed clustering

NASA Astrophysics Data System (ADS)

Yuan, Siyang; Wolter, Scott D.; Greenberg, Joel A.

2017-05-01

X-ray diffraction (XRD) is well-known for yielding composition and structural information about a material. However, in some applications (such as threat detection in aviation security), the properties of a material are more relevant to the task than is a detailed material characterization. Furthermore, the requirement that one first identify a material before determining its class may be difficult or even impossible for a sufficiently large pool of potentially present materials. We therefore seek to learn relevant composition-structure-property relationships between materials to enable material-identification-free classification. We use an expert-informed, data-driven approach operating on a library of XRD spectra from a broad array of stream of commerce materials. We investigate unsupervised learning techniques in order to learn about naturally emergent groupings, and apply supervised learning techniques to determine how well XRD features can be used to separate user-specified classes in the presence of different types and degrees of signal degradation.

Sensitive and Structure-Informative N-Glycosylation Analysis by MALDI-MS; Ionization, Fragmentation, and Derivatization

PubMed Central

Nishikaze, Takashi

2017-01-01

Mass spectrometry (MS) has become an indispensable tool for analyzing post translational modifications of proteins, including N-glycosylated molecules. Because most glycosylation sites carry a multitude of glycans, referred to as “glycoforms,” the purpose of an N-glycosylation analysis is glycoform profiling and glycosylation site mapping. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has unique characteristics that are suited for the sensitive analysis of N-glycosylated products. However, the analysis is often hampered by the inherent physico-chemical properties of N-glycans. Glycans are highly hydrophilic in nature, and therefore tend to show low ion yields in both positive- and negative-ion modes. The labile nature and complicated branched structures involving various linkage isomers make structural characterization difficult. This review focuses on MALDI-MS-based approaches for enhancing analytical performance in N-glycosylation research. In particular, the following three topics are emphasized: (1) Labeling for enhancing the ion yields of glycans and glycopeptides, (2) Negative-ion fragmentation for less ambiguous elucidation of the branched structure of N-glycans, (3) Derivatization for the stabilization and linkage isomer discrimination of sialic acid residues. PMID:28794918

Computer-based synthetic data to assess the tree delineation algorithm from airborne LiDAR survey

Treesearch

Lei Wang; Andrew G. Birt; Charles W. Lafon; David M. Cairns; Robert N. Coulson; Maria D. Tchakerian; Weimin Xi; Sorin C. Popescu; James M. Guldin

2013-01-01

Small Footprint LiDAR (Light Detection And Ranging) has been proposed as an effective tool for measuring detailed biophysical characteristics of forests over broad spatial scales. However, by itself LiDAR yields only a sample of the true 3D structure of a forest. In order to extract useful forestry relevant information, this data must be interpreted using mathematical...

In situ soft XAS study on nickel-based layered cathode material at elevated temperatures: A novel approach to study thermal stability

DOE PAGES

Yoon, Won -Sub; Yang, Xiao -Qing; Haas, Otto; ...

2014-10-29

Tracking thermally induced reactions has always been challenging for electrode materials of electrochemical battery systems. Traditionally, a variety of calorimetric techniques and in situ XRD at elevated temperatures has been used to evaluate the thermal stability of electrode materials. These techniques are capable of providing variations in heat capacity, mass and average bulk composition of materials only. Herein, we report investigation of thermal characteristics of Li 0.33Ni 0.8Co 0.15Al 0.05O 2 by using in situ soft XAS measurements in combination with XRD. Fluorescence yield and partial electron yield measurements are used simultaneously to obtain element selective surface and bulk information.more » Fluorescence yield measurements reveal no energy change of the absorption peak and thus no valence state change in the bulk. However, electron yield measurements indicate that NiO-type rock salt structure is formed at the surface at temperatures above 200°C while no evidence for a surface reaction near Co sites in investigated temperature range is found. These results clearly show that in situ soft XAS can give a unique understanding of the role of each element in the structural transformation under thermal abuse offering a useful guidance in developing new battery system with improved safety performance.« less

A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes.

PubMed

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-04-01

Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed.

A functional–structural model of rice linking quantitative genetic information with morphological development and physiological processes

PubMed Central

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-01-01

Background and Aims Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype–phenotype model, we present here a three-dimensional functional–structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. Methods The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Key Results Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. Conclusions We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed. PMID:21247905

Predicting β-Turns in Protein Using Kernel Logistic Regression

PubMed Central

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, FangXiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case. PMID:23509793

Predicting β-turns in protein using kernel logistic regression.

PubMed

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, Fangxiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case.

Measuring leader perceptions of school readiness for reforms: use of an iterative model combining classical and Rasch methods.

PubMed

Chatterji, Madhabi

2002-01-01

This study examines validity of data generated by the School Readiness for Reforms: Leader Questionnaire (SRR-LQ) using an iterative procedure that combines classical and Rasch rating scale analysis. Following content-validation and pilot-testing, principal axis factor extraction and promax rotation of factors yielded a five factor structure consistent with the content-validated subscales of the original instrument. Factors were identified based on inspection of pattern and structure coefficients. The rotated factor pattern, inter-factor correlations, convergent validity coefficients, and Cronbach's alpha reliability estimates supported the hypothesized construct properties. To further examine unidimensionality and efficacy of the rating scale structures, item-level data from each factor-defined subscale were subjected to analysis with the Rasch rating scale model. Data-to-model fit statistics and separation reliability for items and persons met acceptable criteria. Rating scale results suggested consistency of expected and observed step difficulties in rating categories, and correspondence of step calibrations with increases in the underlying variables. The combined approach yielded more comprehensive diagnostic information on the quality of the five SRR-LQ subscales; further research is continuing.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

PubMed

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Measuring and modeling diffuse scattering in protein X-ray crystallography

PubMed Central

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Wall, Michael E.

2016-01-01

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering. PMID:27035972

Measuring and modeling diffuse scattering in protein X-ray crystallography

DOE PAGES

Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; ...

2016-03-28

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

76 FR 12072 - Guidance for Agency Information Collection Activities: Proposed Collection; Comment Request...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... not statistical surveys that yield quantitative results that can be generalized to the population of... information will not be used for quantitative information collections that are designed to yield reliably... generic mechanisms that are designed to yield quantitative results. No comments were received in response...

Universal Entropy of Word Ordering Across Linguistic Families

PubMed Central

Montemurro, Marcelo A.; Zanette, Damián H.

2011-01-01

Background The language faculty is probably the most distinctive feature of our species, and endows us with a unique ability to exchange highly structured information. In written language, information is encoded by the concatenation of basic symbols under grammatical and semantic constraints. As is also the case in other natural information carriers, the resulting symbolic sequences show a delicate balance between order and disorder. That balance is determined by the interplay between the diversity of symbols and by their specific ordering in the sequences. Here we used entropy to quantify the contribution of different organizational levels to the overall statistical structure of language. Methodology/Principal Findings We computed a relative entropy measure to quantify the degree of ordering in word sequences from languages belonging to several linguistic families. While a direct estimation of the overall entropy of language yielded values that varied for the different families considered, the relative entropy quantifying word ordering presented an almost constant value for all those families. Conclusions/Significance Our results indicate that despite the differences in the structure and vocabulary of the languages analyzed, the impact of word ordering in the structure of language is a statistical linguistic universal. PMID:21603637

Direct-method SAD phasing with partial-structure iteration: towards automation.

PubMed

Wang, J W; Chen, J R; Gu, Y X; Zheng, C D; Fan, H F

2004-11-01

The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

A feast of visualization

NASA Astrophysics Data System (ADS)

2008-12-01

Strength through structure The visualization and assessment of inner human bone structures can provide better predictions of fracture risk due to osteoporosis. Using micro-computed tomography (µCT), Christoph Räth from the Max Planck Institute for Extraterrestrial Physics and colleagues based in Munich, Vienna and Salzburg have shown how complex lattice-shaped bone structures can be visualized. The structures were quantified by calculating certain "texture measures" that yield new information about the stability of the bone. A 3D visualization showing the variation with orientation of one of the texture measures for four different bone specimens (from left to right) is shown above. Such analyses may help us to improve our understanding of disease and drug-induced changes in bone structure (C Räth et al. 2008 New J. Phys. 10 125010).

X-ray free electron laser: opportunities for drug discovery.

PubMed

Cheng, Robert K Y; Abela, Rafael; Hennig, Michael

2017-11-08

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Meta-Generalis: A Novel Method for Structuring Information from Radiology Reports

PubMed Central

Barbosa, Flavio; Traina, Agma Jucci

2016-01-01

Summary Background A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists’ descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring information in radiology reports covering specifications required for the Brazilian Portuguese language, including the terminology to be used. Methods We gathered 1,701 radiological reports of magnetic resonance imaging (MRI) studies of the lumbosacral spine from three different institutions. Techniques of text mining and ontological conceptualization of lexical units extracted were used to structure information. Ten radiologists, specialists in lumbosacral MRI, evaluated the textual superstructure and terminology extracted using an electronic questionnaire. Results The established methodology consists of six steps: 1) collection of radiology reports of a specific MRI examination; 2) textual decomposition; 3) normalization of lexical units; 4) identification of textual superstructures; 5) conceptualization of candidate-terms; and 6) evaluation of superstructures and extracted terminology by experts using an electronic questionnaire. Three different textual superstructures were identified, with terminological variations in the names of their textual categories. The number of candidate-terms conceptualized was 4,183, yielding 727 concepts. There were a total of 13,963 relationships between candidate-terms and concepts and 789 relationships among concepts. Conclusions The proposed methodology allowed structuring information in a more intuitive and practical way. Indications of three textual superstructures, extraction of lexicon units and the normalization and ontologically conceptualization were achieved while maintaining references to their respective categories and free text radiology reports. PMID:27580980

Meta-generalis: A novel method for structuring information from radiology reports.

PubMed

Barbosa, Flavio; Traina, Agma Jucci; Muglia, Valdair Francisco

2016-08-24

A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists' descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring information in radiology reports covering specifications required for the Brazilian Portuguese language, including the terminology to be used. We gathered 1,701 radiological reports of magnetic resonance imaging (MRI) studies of the lumbosacral spine from three different institutions. Techniques of text mining and ontological conceptualization of lexical units extracted were used to structure information. Ten radiologists, specialists in lumbosacral MRI, evaluated the textual superstructure and terminology extracted using an electronic questionnaire. The established methodology consists of six steps: 1) collection of radiology reports of a specific MRI examination; 2) textual decomposition; 3) normalization of lexical units; 4) identification of textual superstructures; 5) conceptualization of candidate-terms; and 6) evaluation of superstructures and extracted terminology by experts using an electronic questionnaire. Three different textual superstructures were identified, with terminological variations in the names of their textual categories. The number of candidate-terms conceptualized was 4,183, yielding 727 concepts. There were a total of 13,963 relationships between candidate-terms and concepts and 789 relationships among concepts. The proposed methodology allowed structuring information in a more intuitive and practical way. Indications of three textual superstructures, extraction of lexicon units and the normalization and ontologically conceptualization were achieved while maintaining references to their respective categories and free text radiology reports.

Microscopically derived potential energy surfaces from mostly structural considerations

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

Ermamatov, M.J.; Institute of Nuclear Physics, Ulughbek, Tashkent 100214; Hess, Peter O., E-mail: hess@nucleares.unam.mx

2016-08-15

A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. Wemore » will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.« less

A Sparse Dictionary Learning-Based Adaptive Patch Inpainting Method for Thick Clouds Removal from High-Spatial Resolution Remote Sensing Imagery

PubMed Central

Yang, Xiaomei; Zhou, Chenghu; Li, Zhi

2017-01-01

Cloud cover is inevitable in optical remote sensing (RS) imagery on account of the influence of observation conditions, which limits the availability of RS data. Therefore, it is of great significance to be able to reconstruct the cloud-contaminated ground information. This paper presents a sparse dictionary learning-based image inpainting method for adaptively recovering the missing information corrupted by thick clouds patch-by-patch. A feature dictionary was learned from exemplars in the cloud-free regions, which was later utilized to infer the missing patches via sparse representation. To maintain the coherence of structures, structure sparsity was brought in to encourage first filling-in of missing patches on image structures. The optimization model of patch inpainting was formulated under the adaptive neighborhood-consistency constraint, which was solved by a modified orthogonal matching pursuit (OMP) algorithm. In light of these ideas, the thick-cloud removal scheme was designed and applied to images with simulated and true clouds. Comparisons and experiments show that our method can not only keep structures and textures consistent with the surrounding ground information, but also yield rare smoothing effect and block effect, which is more suitable for the removal of clouds from high-spatial resolution RS imagery with salient structures and abundant textured features. PMID:28914787

A Sparse Dictionary Learning-Based Adaptive Patch Inpainting Method for Thick Clouds Removal from High-Spatial Resolution Remote Sensing Imagery.

PubMed

Meng, Fan; Yang, Xiaomei; Zhou, Chenghu; Li, Zhi

2017-09-15

Cloud cover is inevitable in optical remote sensing (RS) imagery on account of the influence of observation conditions, which limits the availability of RS data. Therefore, it is of great significance to be able to reconstruct the cloud-contaminated ground information. This paper presents a sparse dictionary learning-based image inpainting method for adaptively recovering the missing information corrupted by thick clouds patch-by-patch. A feature dictionary was learned from exemplars in the cloud-free regions, which was later utilized to infer the missing patches via sparse representation. To maintain the coherence of structures, structure sparsity was brought in to encourage first filling-in of missing patches on image structures. The optimization model of patch inpainting was formulated under the adaptive neighborhood-consistency constraint, which was solved by a modified orthogonal matching pursuit (OMP) algorithm. In light of these ideas, the thick-cloud removal scheme was designed and applied to images with simulated and true clouds. Comparisons and experiments show that our method can not only keep structures and textures consistent with the surrounding ground information, but also yield rare smoothing effect and block effect, which is more suitable for the removal of clouds from high-spatial resolution RS imagery with salient structures and abundant textured features.

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

PubMed

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photosynthetic limitation as a factor influencing yield in highbush blueberries (Vaccinium corymbosum) grown in a northern European environment.

PubMed

Petridis, Antonios; van der Kaay, Jeroen; Chrysanthou, Elina; McCallum, Susan; Graham, Julie; Hancock, Robert D

2018-05-25

Published evidence indicates that nearly 60% of blueberry-producing countries experience yield instability. Yield is a complex trait determined by genetic and environmental factors. Here, using physiological and biochemical approaches, we tested the hypothesis that yield instability results from year-to-year environmental variation that limits carbon assimilation, storage and partitioning. The data indicate that fruit development depends primarily on the daily production of non-structural carbohydrates by leaves, and there is no accumulation of a starch buffer to allow continuous ripening under conditions limiting for photosynthesis. Photosynthesis was saturated at moderate light irradiance and this was mainly due to stomatal and biochemical limitations. In a dynamic light environment, photosynthesis was further limited by slow stomatal response to increasing light. Finally, labelling with 13CO2 at specific stages of fruit development revealed a relatively even distribution of newly assimilated carbon between stems, roots and fruits, suggesting that the fruit is not a strong sink. We conclude that a significant component of yield variability results from limitations in photosynthetic efficiency that are compounded by an inability to accumulate starch reserves in blueberry storage tissues in a typical northern European environment. This work informs techniques for improving agronomic management and indicates key traits required for yield stability in such environments.

Photosynthetic limitation as a factor influencing yield in highbush blueberries (Vaccinium corymbosum) grown in a northern European environment

PubMed Central

van der Kaay, Jeroen; Chrysanthou, Elina; McCallum, Susan

2018-01-01

Abstract Published evidence indicates that nearly 60% of blueberry-producing countries experience yield instability. Yield is a complex trait determined by genetic and environmental factors. Here, using physiological and biochemical approaches, we tested the hypothesis that yield instability results from year-to-year environmental variation that limits carbon assimilation, storage and partitioning. The data indicate that fruit development depends primarily on the daily production of non-structural carbohydrates by leaves, and there is no accumulation of a starch buffer to allow continuous ripening under conditions limiting for photosynthesis. Photosynthesis was saturated at moderate light irradiance and this was mainly due to stomatal and biochemical limitations. In a dynamic light environment, photosynthesis was further limited by slow stomatal response to increasing light. Finally, labelling with 13CO2 at specific stages of fruit development revealed a relatively even distribution of newly assimilated carbon between stems, roots and fruits, suggesting that the fruit is not a strong sink. We conclude that a significant component of yield variability results from limitations in photosynthetic efficiency that are compounded by an inability to accumulate starch reserves in blueberry storage tissues in a typical northern European environment. This work informs techniques for improving agronomic management and indicates key traits required for yield stability in such environments. PMID:29590429

UAS imaging for automated crop lodging detection: a case study over an experimental maize field

NASA Astrophysics Data System (ADS)

Chu, Tianxing; Starek, Michael J.; Brewer, Michael J.; Masiane, Tiisetso; Murray, Seth C.

2017-05-01

Lodging has been recognized as one of the major destructive factors for crop quality and yield, particularly in corn. A variety of contributing causes, e.g. disease and/or pest, weather conditions, excessive nitrogen, and high plant density, may lead to lodging before harvesting season. Traditional lodging detection strategies mainly rely on ground data collection, which is insufficient in efficiency and accuracy. To address this problem, this research focuses on the use of unmanned aircraft systems (UAS) for automated detection of crop lodging. The study was conducted over an experimental corn field at the Texas A and M AgriLife Research and Extension Center at Corpus Christi, Texas, during the growing season of 2016. Nadir-view images of the corn field were taken by small UAS platforms equipped with consumer grade RGB and NIR cameras on a per week basis, enabling a timely observation of the plant growth. 3D structural information of the plants was reconstructed using structure-from-motion photogrammetry. The structural information was then applied to calculate crop height, and rates of growth. A lodging index for detecting corn lodging was proposed afterwards. Ground truth data of lodging was collected on a per row basis and used for fair assessment and tuning of the detection algorithm. Results show the UAS-measured height correlates well with the ground-measured height. More importantly, the lodging index can effectively reflect severity of corn lodging and yield after harvesting.

Current work in ontario on compression wood in black spruce in relation to pulp yield and quality

Treesearch

J.L. Ladell; A.J. Carmichael; G.H.S. Thomas

1968-01-01

In 1959 and 1960, during a series of symposia on wood quality organized jointly by the Ontario Department of Lands and Forests, the Faculty of Forestry of the University of Toronto, and the Ontario Research Foundation (ORF), it became clear that there was a serious lack of information regarding the structure and variability of the wood of the commercially important...

High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites

NASA Astrophysics Data System (ADS)

Takabayashi, Sadao; Klein, William P.; Onodera, Craig; Rapp, Blake; Flores-Estrada, Juan; Lindau, Elias; Snowball, Lejmarc; Sam, Joseph T.; Padilla, Jennifer E.; Lee, Jeunghoon; Knowlton, William B.; Graugnard, Elton; Yurke, Bernard; Kuang, Wan; Hughes, William L.

2014-10-01

High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities.High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03069a

Experimental investigation of the Jahn-Teller effect in the ground and excited electronic states of the tropyl radical. Part II. Vibrational analysis of the A 2E"3-X 2E"2 electronic transition.

PubMed

Sioutis, Ilias; Stakhursky, Vadim L; Tarczay, György; Miller, Terry A

2008-02-28

Laser-induced fluorescence (LIF) and laser-excited dispersed fluorescence (LEDF) spectra of the cycloheptatrienyl (tropyl) radical C7H7 have been observed under supersonic jet-cooling conditions. Assignment of the LIF excitation spectrum yields detailed information about the A-state vibronic structure. The LEDF emission was collected by pumping different vibronic bands of the A 2E"3<--X 2E"2 electronic spectrum. Analysis of the LEDF spectra yields valuable information about the vibronic levels of the X 2E"2 state. The X- and A-state vibronic structures characterize the Jahn-Teller distortion of the respective potential energy surfaces. A thorough analysis reveals observable Jahn-Teller activity in three of the four e'3 modes for the X 2E"2 state and two of the three e'1 modes for the A 2E"3 state and provides values for their deperturbed vibrational frequencies as well as linear Jahn-Teller coupling constants. The molecular parameters characterizing the Jahn-Teller interaction in the X and A states of C7H7 are compared to theoretical results and to those previously obtained for C5H5 and C6H6+.

The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics

PubMed Central

Schneider, Sebastian; Provasi, Davide; Filizola, Marta

2015-01-01

Major advances in G Protein-Coupled Receptor (GPCR) structural biology over the past few years have yielded a significant number of high-resolution crystal structures for several different receptor subtypes. This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligands that can eventually be developed into improved therapeutics. However, these algorithms are often unable to discriminate between different, yet energetically similar, poses because of their relatively simple scoring functions. Here, we describe a metadynamics-based approach to study the dynamic process of ligand binding to/unbinding from GPCRs with a higher level of accuracy and yet satisfying efficiency. PMID:26260607

Bacterial biomarkers thermally released from dissolved organic matter

USGS Publications Warehouse

Greenwood, P.F.; Leenheer, J.A.; McIntyre, C.; Berwick, L.; Franzmann, P.D.

2006-01-01

Hopane biomarker products were detected using microscale sealed vessel (MSSV) pyrolysis gas chromatography-mass spectrometry (GC-MS) analysis of dissolved organic matter from natural aquatic systems colonised by bacterial populations. MSSV pyrolysis can reduce the polyhydroxylated alkyl side chain of bacteriohopanepolyols, yielding saturated hopane products which are more amenable to GC-MS detection than their functionalised precursors. This example demonstrates how the thermal conditions of MSSV pyrolysis can reduce the biologically-inherited structural functionality of naturally occurring organic matter such that additional structural fragments can be detected using GC methods. This approach complements traditional analytical pyrolysis methods by providing additional speciation information useful for establishing the structures and source inputs of recent or extant organic material. ?? 2006.

The superdeep well of the Kola Peninsula

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

Kozlovsky, Y.A.

1986-01-01

The structure of continental crusts is a subject of ever increasing importance in the geological sciences. Over 15 years ago, Soviet scientist began drilling a superdeep well on the Kola Peninsula near Murmansk. The well has reached a depth of 12 km and is thereby the deepest well in the world, yielding a vast amount of information on the structure of the continental crust. The geological, geophysical and technological data from the Kola well were initially published in a monographic account entitled ''Kol'skaja sverchglubokaja''. This English translation makes the results available to non-Soviet scientists as well.

Cholinesterase structure: Identification of residues and domains affecting organophosphate inhibition and catalysis. Annual report, 6 March 1995-5 March 1996

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

Taylor, P.W.

1996-04-01

In the initial year of the grant, we have made excellent progress in several arenas: (1) A crystal structure of a mouse acetylcholinesterase-fasciculin 2 complex has been solved. (2) Studies with enantiomeric organophosphates have yielded vital information on their binding orientation in the ground and transition states. (3) Studies in oxime reactivation of inhibited cholinesterase have uncovered the basis for enhanced reactivity of HI-6 compared to 2-PAM. (4) The interactions of fasciculin 2 with acetylcholinesterase have been studied by kinetic and site-specific mutagenesis methods.

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Comparison of assessment of personality disorder by patients and informants.

PubMed

Modestin, J; Puhan, A

2000-01-01

The present study evaluated the pathology of personality disorder in a group of 8 nonpatient volunteers and 32 psychiatric in- and outpatients, most of them suffering from substance abuse disorder. The patient self-reports were compared with the reports by 2 informants for each proband. All probands and informants completed the Structured Interview for DSM-III-R Axis II Personality Questionnaire. Patient self-reports and informant reports yielded the same number of diagnoses. The diagnostic agreement between the three sets of data was generally poor; however, the concordance was slightly better between both groups of informants than between patients and informants: Median kappa were 0.13 for patients versus parents, 0.14 for patients versus brothers/sisters and 0.29 for parents versus brothers/sisters. Patient and informant evaluations represent two different assessment approaches of the personality, and a complete agreement is not to be expected. Copyright 2000 S. Karger AG, Basel.

Contribution of crop model structure, parameters and climate projections to uncertainty in climate change impact assessments.

PubMed

Tao, Fulu; Rötter, Reimund P; Palosuo, Taru; Gregorio Hernández Díaz-Ambrona, Carlos; Mínguez, M Inés; Semenov, Mikhail A; Kersebaum, Kurt Christian; Nendel, Claas; Specka, Xenia; Hoffmann, Holger; Ewert, Frank; Dambreville, Anaelle; Martre, Pierre; Rodríguez, Lucía; Ruiz-Ramos, Margarita; Gaiser, Thomas; Höhn, Jukka G; Salo, Tapio; Ferrise, Roberto; Bindi, Marco; Cammarano, Davide; Schulman, Alan H

2018-03-01

Climate change impact assessments are plagued with uncertainties from many sources, such as climate projections or the inadequacies in structure and parameters of the impact model. Previous studies tried to account for the uncertainty from one or two of these. Here, we developed a triple-ensemble probabilistic assessment using seven crop models, multiple sets of model parameters and eight contrasting climate projections together to comprehensively account for uncertainties from these three important sources. We demonstrated the approach in assessing climate change impact on barley growth and yield at Jokioinen, Finland in the Boreal climatic zone and Lleida, Spain in the Mediterranean climatic zone, for the 2050s. We further quantified and compared the contribution of crop model structure, crop model parameters and climate projections to the total variance of ensemble output using Analysis of Variance (ANOVA). Based on the triple-ensemble probabilistic assessment, the median of simulated yield change was -4% and +16%, and the probability of decreasing yield was 63% and 31% in the 2050s, at Jokioinen and Lleida, respectively, relative to 1981-2010. The contribution of crop model structure to the total variance of ensemble output was larger than that from downscaled climate projections and model parameters. The relative contribution of crop model parameters and downscaled climate projections to the total variance of ensemble output varied greatly among the seven crop models and between the two sites. The contribution of downscaled climate projections was on average larger than that of crop model parameters. This information on the uncertainty from different sources can be quite useful for model users to decide where to put the most effort when preparing or choosing models or parameters for impact analyses. We concluded that the triple-ensemble probabilistic approach that accounts for the uncertainties from multiple important sources provide more comprehensive information for quantifying uncertainties in climate change impact assessments as compared to the conventional approaches that are deterministic or only account for the uncertainties from one or two of the uncertainty sources. © 2017 John Wiley & Sons Ltd.

2012 Mask Industry Survey

NASA Astrophysics Data System (ADS)

Malloy, Matt; Litt, Lloyd C.

2012-11-01

A survey supported by SEMATECH and administered by David Powell Consulting was sent to semiconductor industry leaders to gather information about the mask industry as an objective assessment of its overall condition. The survey was designed with the input of semiconductor company mask technologists and merchant mask suppliers. 2012 marks the 11th consecutive year for the mask industry survey. This year's survey and reporting structure are similar to those of the previous years with minor modifications based on feedback from past years and the need to collect additional data on key topics. Categories include general mask information, mask processing, data and write time, yield and yield loss, delivery times, and maintenance and returns. Within each category are multiple questions that result in a detailed profile of both the business and technical status of the mask industry. Results, initial observations, and key comparisons between the 2011 and 2012 survey responses are shown here, including multiple indications of a shift towards the manufacturing of higher end photomasks.

A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations

NASA Astrophysics Data System (ADS)

Larios, Edgar; Yang, Wei Y.; Schulten, K.; Gruebele, M.

2004-12-01

Computing the root-mean-square deviation (RMSD) of a partially folded protein structure from the folded state requires the two structures to be translationally and rotationally aligned. We examine the constraint matrix L that preserves orthogonality of the rotation matrix during minimization of the RMSD. L is proportional to the sensitivity of the RMSD to the rotational alignment matrix. Its trace yields an isotropic reaction coordinate, while its off-diagonal matrix elements are related to the moment of inertia derivative tensor that encodes anisotropic information about the structure. We use L to compare λ-repressor fragment 6-85 (λ 6-85) to several partially folded structures obtained from molecular dynamics simulation (MD), and find that L as a reaction coordinate indeed encodes some information about protein topology. We also apply C α RMSD, L and tryptophan sidechain mobility as criteria for native state structural fluctuations of several λ 6-85 mutants. The mutants' denaturation curves and fluorescence quenching are measured experimentally for comparison. The results are in accord with a recent proposal that structural fluctuations near the chromophore can induce increased native state fluorescence or hyperfluorescence during unfolding of proteins.

Growth and yield of shortleaf pine

Treesearch

Paul A. Murphy

1986-01-01

A survey of available growth and yield information for shortleaf pine (Pinus echinata Mill.) is given. The kinds of studies and data sources that produce this information are also evaluated, and an example of how a growth and yield model can be used to answer management questions is illustrated. Guidelines are given for using growth and yield models, and needs for...

Environmental Assessment for Aviation Foreign Internal Defense Beddown (AvFID) at Duke Field, Eglin Air Force Base, Florida

DTIC Science & Technology

2012-07-01

yielded, or may be likely to yield, information important in prehistory or history” (36 CFR § 60:4). 3.8.2 Existing Conditions The ROI for...components may lack individual distinction; or d) that have yielded, or may be likely to yield, information important in prehistory or history (Advisory

Characterisation of tissue-type metabolic content in secondary progressive multiple sclerosis: a magnetic resonance spectroscopic imaging study.

PubMed

Marshall, Ian; Thrippleton, Michael J; Bastin, Mark E; Mollison, Daisy; Dickie, David A; Chappell, Francesca M; Semple, Scott I K; Cooper, Annette; Pavitt, Sue; Giovannoni, Gavin; Wheeler-Kingshott, Claudia A M Gandini; Solanky, Bhavana S; Weir, Christopher J; Stallard, Nigel; Hawkins, Clive; Sharrack, Basil; Chataway, Jeremy; Connick, Peter; Chandran, Siddharthan

2018-05-30

Proton magnetic resonance spectroscopy yields metabolic information and has proved to be a useful addition to structural imaging in neurological diseases. We applied short-echo time Spectroscopic Imaging in a cohort of 42 patients with secondary progressive multiple sclerosis (SPMS). Linear modelling with respect to brain tissue type yielded metabolite levels that were significantly different in white matter lesions compared with normal-appearing white matter, suggestive of higher myelin turnover (higher choline), higher metabolic rate (higher creatine) and increased glial activity (higher myo-inositol) within the lesions. These findings suggest that the lesions have ongoing cellular activity that is not consistent with the usual assumption of 'chronic' lesions in SPMS, and may represent a target for repair therapies.

Intraoperative visualisation of functional structures facilitates safe frameless stereotactic biopsy in the motor eloquent regions of the brain.

PubMed

Zhang, Jia-Shu; Qu, Ling; Wang, Qun; Jin, Wei; Hou, Yuan-Zheng; Sun, Guo-Chen; Li, Fang-Ye; Yu, Xin-Guang; Xu, Ban-Nan; Chen, Xiao-Lei

2017-12-20

For stereotactic brain biopsy involving motor eloquent regions, the surgical objective is to enhance diagnostic yield and preserve neurological function. To achieve this aim, we implemented functional neuro-navigation and intraoperative magnetic resonance imaging (iMRI) into the biopsy procedure. The impact of this integrated technique on the surgical outcome and postoperative neurological function was investigated and evaluated. Thirty nine patients with lesions involving motor eloquent structures underwent frameless stereotactic biopsy assisted by functional neuro-navigation and iMRI. Intraoperative visualisation was realised by integrating anatomical and functional information into a navigation framework to improve biopsy trajectories and preserve eloquent structures. iMRI was conducted to guarantee the biopsy accuracy and detect intraoperative complications. The perioperative change of motor function and biopsy error before and after iMRI were recorded, and the role of functional information in trajectory selection and the relationship between the distance from sampling site to nearby eloquent structures and the neurological deterioration were further analyzed. Functional neuro-navigation helped modify the original trajectories and sampling sites in 35.90% (16/39) of cases to avoid the damage of eloquent structures. Even though all the lesions were high-risk of causing neurological deficits, no significant difference was found between preoperative and postoperative muscle strength. After data analysis, 3mm was supposed to be the safe distance for avoiding transient neurological deterioration. During surgery, the use of iMRI significantly reduced the biopsy errors (p = 0.042) and potentially increased the diagnostic yield from 84.62% (33/39) to 94.87% (37/39). Moreover, iMRI detected intraoperative haemorrhage in 5.13% (2/39) of patients, all of them benefited from the intraoperative strategies based on iMRI findings. Intraoperative visualisation of functional structures could be a feasible, safe and effective technique. Combined with intraoperative high-field MRI, it contributed to enhance the biopsy accuracy and lower neurological complications in stereotactic brain biopsy involving motor eloquent areas.

Psychometric properties of the 25-item Work Limitations Questionnaire in Japan: factor structure, validity, and reliability in information and communication technology company employees.

PubMed

Kono, Yuko; Matsushima, Eisuke; Uji, Masayo

2014-02-01

The 25-item Work Limitations Questionnaire (WLQ-25) measures presenteeism but has not been sufficiently validated in a Japanese population. A total of 451 employees from four information technology companies in Tokyo completed the WLQ-25 and questionnaires of other variables on two occasions, 2 weeks apart. The WLQ-25 yielded a two-factor structure: Cognitive Demand and Physical Demand. These subscales showed good internal consistency, and both were associated with adverse working conditions, greater perceived job strain, lower skill use, poorer workplace social support, and less satisfactory psychological adjustment. Intraclass correlation coefficients of the two WLQ-25 subscales between time 1 and time 2 were 0.78 and 0.55, respectively. This study suggests acceptable psychometric properties of the WLQ-25 in Japan.

Phase Averaged Measurements of the Coherent Structure of a Mach Number 0.6 Jet. M.S. Thesis

NASA Technical Reports Server (NTRS)

Emami, S.

1983-01-01

The existence of a large scale structure in a Mach number 0.6, axisymmetric jet of cold air was proven. In order to further characterize the coherent structure, phase averaged measurements of the axial mass velocity, radial velocity, and the product of the two were made. These measurements yield information about the percent of the total fluctuations contained in the coherent structure. These measured values were compared to the total fluctuation levels for each quantity and the result expressed as a percent of the total fluctuation level contained in the organized structure at a given frequency. These measurements were performed for five frequencies (St=0.16, 0.32, 0.474, 0.95, and 1.26). All of the phase averaged measurements required that the jet be artificially excited.

Differential stemflow yield from European beech saplings: the role and respective importance of individual canopy structure metrics

NASA Astrophysics Data System (ADS)

Levia, Delphis; Michalzik, Beate

2013-04-01

Stemflow yield from individual trees varies as a function of both meteorological conditions and canopy structure. The importance and differential effects of various metrics of canopy structure in relation to stemflow yield is inadequately understood and the subject of debate among forest hydrologists. It is possible to evaluate the role and respective importance of individual canopy structure metrics by holding meteorological conditions constant. Twelve isolated experimental European beech (Fagus sylvatica L.) saplings in Jena, Germany were exposed to identical meteorological conditions to examine the effects of canopy structure on stemflow production during the 2012 growing season. The canopy structure metrics being evaluated include: trunk diameter, trunk lean, tree height, projected crown area, branch inclination angle, branch count, and biomass (foliar and woody). Principal components analysis and multiple regression are utilized to determine the relative importance of different canopy structure metrics on stemflow yield. Experimental results will provide insight as to which metrics of canopy structure most strongly govern stemflow production. Ultimately, with a more thorough understanding of the unique contributions of various canopy structural metrics to stemflow yield, a useful conceptual guide of stemflow generation can be formulated on the basis of canopy structure for management purposes. Sponsor note: This research was funded by the Alexander von Humboldt Foundation.

A Probabilistic Graphical Model to Detect Chromosomal Domains

NASA Astrophysics Data System (ADS)

Heermann, Dieter; Hofmann, Andreas; Weber, Eva

To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These experiments yield topological information, consistently showing a hierarchical subdivision of the genome into self-interacting domains across many organisms. Current methods for detecting these domains using the Hi-C contact matrix, i.e. a doubly-stochastic matrix, are mostly based on the assumption that the domains are distinct, thus non-overlapping. For overcoming this simplification and for being able to unravel a possible nested domain structure, we developed a probabilistic graphical model that makes no a priori assumptions on the domain structure. Within this approach, the Hi-C contact matrix is analyzed using an Ising like probabilistic graphical model whose coupling constant is proportional to each lattice point (entry in the contact matrix). The results show clear boundaries between identified domains and the background. These domain boundaries are dependent on the coupling constant, so that one matrix yields several clusters of different sizes, which show the self-interaction of the genome on different scales. This work was supported by a Grant from the International Human Frontier Science Program Organization (RGP0014/2014).

Intermediate- and short-range order in phosphorus-selenium glasses

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

Bytchkov, Aleksei; Hennet, Louis; Price, David L.

2011-04-01

State-of-the-art neutron and x-ray diffraction measurements have been performed to provide a definitive picture of the intermediate- and short-range structures of P{sub x}Se{sub 1-x} glasses spanning two glass regions, x 0.025-0.54 and 0.64-0.84. Liquid P{sub 4}Se{sub 3} and amorphous red P and Se were also measured. Detailed information was obtained about the development with increasing phosphorous concentration of intermediate-range order on the length scale {approx}6 A ring , based on the behavior of the first sharp diffraction peak. Attention is also paid to the feature in the structure factor at 7.5 A ring {sup -1}, identified in earlier numerical simulations,more » provides further evidence of the existence of molecular units. The real-space transforms yield a reliable statistical picture of the changing short-range order as x increases, using the information about types and concentrations of local structural units provided by previous NMR measurements to interpret the trends observed.« less

Getting connected: Both associative and semantic links structure semantic memory for newly learned persons.

PubMed

Wiese, Holger; Schweinberger, Stefan R

2015-01-01

The present study examined whether semantic memory for newly learned people is structured by visual co-occurrence, shared semantics, or both. Participants were trained with pairs of simultaneously presented (i.e., co-occurring) preexperimentally unfamiliar faces, which either did or did not share additionally provided semantic information (occupation, place of living, etc.). Semantic information could also be shared between faces that did not co-occur. A subsequent priming experiment revealed faster responses for both co-occurrence/no shared semantics and no co-occurrence/shared semantics conditions, than for an unrelated condition. Strikingly, priming was strongest in the co-occurrence/shared semantics condition, suggesting additive effects of these factors. Additional analysis of event-related brain potentials yielded priming in the N400 component only for combined effects of visual co-occurrence and shared semantics, with more positive amplitudes in this than in the unrelated condition. Overall, these findings suggest that both semantic relatedness and visual co-occurrence are important when novel information is integrated into person-related semantic memory.

Probing Cytoskeletal Structures by Coupling Optical Superresolution and AFM Techniques for a Correlative Approach

PubMed Central

Chacko, Jenu Varghese; Zanacchi, Francesca Cella; Diaspro, Alberto

2013-01-01

In this article, we describe and show the application of some of the most advanced fluorescence superresolution techniques, STED AFM and STORM AFM microscopy towards imaging of cytoskeletal structures, such as microtubule filaments. Mechanical and structural properties can play a relevant role in the investigation of cytoskeletal structures of interest, such as microtubules, that provide support to the cell structure. In fact, the mechanical properties, such as the local stiffness and the elasticity, can be investigated by AFM force spectroscopy with tens of nanometers resolution. Force curves can be analyzed in order to obtain the local elasticity (and the Young's modulus calculation by fitting the force curves from every pixel of interest), and the combination with STED/STORM microscopy integrates the measurement with high specificity and yields superresolution structural information. This hybrid modality of superresolution-AFM working is a clear example of correlative multimodal microscopy. PMID:24027190

Hydrologic effects of floodwater-retarding structures on Garza-Little Elm Reservoir, Texas

USGS Publications Warehouse

Gilbert, Clarence R.; Sauer, Stanley P.

1970-01-01

"Firm"- or "critical"-yield studies were made of the large reservoir on the basis of two sets of conditions : with floodwater-retarding structures in the drainage basin, and without such structures. Results of the firm-yield studies indicated that with full development, annual firm yield would be initially reduced by 10 percent. After 30 or more years, when the permanent pools of the floodwaterretarding reservoirs would be mostly filled with sediment, the firm yield would be almost the same with or without the upstream development.

Growth Characteristics of Organisms

NASA Astrophysics Data System (ADS)

Gatenby, Robert A.; Frieden, B. Roy

In this chapter a systems viewpoint is taken of the growth characteristics of normal and malignant tissue. We find that such growth is well analyzed by the concepts of Shannon and Fisher information. In Section 3.1 conventional mechanisms of information transmission via DNA, RNA, and proteins are identified, as well as unconventional structures such as lipids and ion gradients. Information storage, flow, and utilization are analyzed, both within cells and over a system of cells. In Section 3.2, malignant tissue growth is found to be accurately described by the use of Fisher information in particular. Cancer growth is seen to occur as a disease of information, in fact an information catastrophe due to the regression of cells to a minimally ordered state consistent with life. The analysis yields many predictions about the growth of healthy tissue and cancerous tissue, some of which are nonintuitive and have a strong bearing on cancer diagnosis and treatment.

Self-centering connections for traffic sign supporting structures.

DOT National Transportation Integrated Search

2015-03-01

Steel structures supporting traffic sign panels are designed as intended to dissipate energy by : yielding structural members during severe wind loading (ex. strong hurricanes). Yielding results : in inelastic deformations, which are permanent damage...

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

Fielding, E.J.; Barazangi, M.; Isacks, B.L.

Topography and heterogeneous crustal structure have major effects on the propagation of regional seismic phases. We are collecting topographical, geological, and geophysical datasets for Eurasia into an information system that can be accessed via Internet connections. Now available are digital topography, satellite imagery, and data on sedimentary basins and crustal structure thicknesses. New datasets for Eurasia include maps of depth to Moho beneath Europe and Scandinavia. We have created regularly spaced grids of the crustal thickness values from these maps that can be used to create profiles of crustal structure. These profiles can be compared by an analyst or anmore » automatic program with the crustal seismic phases received along the propagation path to better understand and predict the path effects on phase amplitudes, a key to estimating magnitudes and yields, and for understanding variations in travel-time delays for phases such as Pn, important for improving regional event locations. The gridded data could also be used to model propagation of crustal phases in three dimensions. Digital elevation models, Satellite imagery, Geographic information systems, Lg Propagation, Moho, Geology, Crustal structure, Topographic relief.« less

Applying the Common Sense Model to Understand Representations of Arsenic Contaminated Well Water

PubMed Central

Severtson, Dolores J.; Baumann, Linda C.; Brown, Roger L.

2015-01-01

Theory-based research is needed to understand how people respond to environmental health risk information. The common sense model of self-regulation and the mental models approach propose that information shapes individual’s personal understandings that influence their decisions and actions. We compare these frameworks and explain how the common sense model (CSM) was applied to describe and measure mental representations of arsenic contaminated well water. Educational information, key informant interviews, and environmental risk literature were used to develop survey items to measure dimensions of cognitive representations (identity, cause, timeline, consequences, control) and emotional representations. Surveys mailed to 1067 private well users with moderate and elevated arsenic levels yielded an 84% response rate (n=897). Exploratory and confirmatory factor analyses of data from the elevated arsenic group identified a factor structure that retained the CSM representational structure and was consistent across moderate and elevated arsenic groups. The CSM has utility for describing and measuring representations of environmental health risks thus supporting its application to environmental health risk communication research. PMID:18726811

76 FR 63301 - Agency Information Collection Activities: Proposed Collection; Comment Request; Generic Clearance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

... INFORMATION: Title: Comparative Effectiveness Research Inventory. Abstract: The information collection... will not be used for quantitative information collections that are designed to yield reliably... mechanisms that are designed to yield quantitative results. The Agency received no comments in response to...

Probing the structure of the stable Xe isotopes with inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Peters, Erin E.; Ross, Timothy J.; Crider, Benjamin P.; Yates, Steven W.

2018-05-01

The stable isotopes of xenon, which have attracted interest for a number of reasons, span a transitional region that evolves from γ-soft structures for the lighter mass isotopes to nearly spherical 136Xe with a closed neutron shell. The nature of this transition, which is gradual, is not well understood. To provide detailed spectroscopic information on the Xe isotopes, we have studied 130,132,134,136Xe at the University of Kentucky Accelerator Laboratory using inelastic neutron scattering and γ-ray detection. These measurements yielded γ-ray angular distributions, branching ratios, multipole mixing ratios, and level lifetimes (from the Doppler-shift attenuation method), which allowed the determination of reduced transition probabilities and provided insight into the structure of these nuclei.

Anthropic Correction of Information Estimates and Its Application to Neural Coding

PubMed Central

Gastpar, Michael C.; Gill, Patrick R.; Huth, Alexander G.; Theunissen, Frédéric E.

2015-01-01

Information theory has been used as an organizing principle in neuroscience for several decades. Estimates of the mutual information (MI) between signals acquired in neurophysiological experiments are believed to yield insights into the structure of the underlying information processing architectures. With the pervasive availability of recordings from many neurons, several information and redundancy measures have been proposed in the recent literature. A typical scenario is that only a small number of stimuli can be tested, while ample response data may be available for each of the tested stimuli. The resulting asymmetric information estimation problem is considered. It is shown that the direct plug-in information estimate has a negative bias. An anthropic correction is introduced that has a positive bias. These two complementary estimators and their combinations are natural candidates for information estimation in neuroscience. Tail and variance bounds are given for both estimates. The proposed information estimates are applied to the analysis of neural discrimination and redundancy in the avian auditory system. PMID:26900172

Anthropic Correction of Information Estimates and Its Application to Neural Coding.

PubMed

Gastpar, Michael C; Gill, Patrick R; Huth, Alexander G; Theunissen, Frédéric E

2010-02-01

Information theory has been used as an organizing principle in neuroscience for several decades. Estimates of the mutual information (MI) between signals acquired in neurophysiological experiments are believed to yield insights into the structure of the underlying information processing architectures. With the pervasive availability of recordings from many neurons, several information and redundancy measures have been proposed in the recent literature. A typical scenario is that only a small number of stimuli can be tested, while ample response data may be available for each of the tested stimuli. The resulting asymmetric information estimation problem is considered. It is shown that the direct plug-in information estimate has a negative bias. An anthropic correction is introduced that has a positive bias. These two complementary estimators and their combinations are natural candidates for information estimation in neuroscience. Tail and variance bounds are given for both estimates. The proposed information estimates are applied to the analysis of neural discrimination and redundancy in the avian auditory system.

Accounting for epistatic interactions improves the functional analysis of protein structures

PubMed Central

Wilkins, Angela D.; Venner, Eric; Marciano, David C.; Erdin, Serkan; Atri, Benu; Lua, Rhonald C.; Lichtarge, Olivier

2013-01-01

Motivation: The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure. Methods and Results: We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions. Conclusions: Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction. Contact: lichtarge@bcm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24021383

Automated global structure extraction for effective local building block processing in XCS.

PubMed

Butz, Martin V; Pelikan, Martin; Llorà, Xavier; Goldberg, David E

2006-01-01

Learning Classifier Systems (LCSs), such as the accuracy-based XCS, evolve distributed problem solutions represented by a population of rules. During evolution, features are specialized, propagated, and recombined to provide increasingly accurate subsolutions. Recently, it was shown that, as in conventional genetic algorithms (GAs), some problems require efficient processing of subsets of features to find problem solutions efficiently. In such problems, standard variation operators of genetic and evolutionary algorithms used in LCSs suffer from potential disruption of groups of interacting features, resulting in poor performance. This paper introduces efficient crossover operators to XCS by incorporating techniques derived from competent GAs: the extended compact GA (ECGA) and the Bayesian optimization algorithm (BOA). Instead of simple crossover operators such as uniform crossover or one-point crossover, ECGA or BOA-derived mechanisms are used to build a probabilistic model of the global population and to generate offspring classifiers locally using the model. Several offspring generation variations are introduced and evaluated. The results show that it is possible to achieve performance similar to runs with an informed crossover operator that is specifically designed to yield ideal problem-dependent exploration, exploiting provided problem structure information. Thus, we create the first competent LCSs, XCS/ECGA and XCS/BOA, that detect dependency structures online and propagate corresponding lower-level dependency structures effectively without any information about these structures given in advance.

Assessment of the performance of water harvesting systems in semi-arid regions

NASA Astrophysics Data System (ADS)

Lasage, Ralph

2016-04-01

Water harvesting is widely practiced and has the potential to improve water availability for domestic and agricultural use in semi-arid regions. New funds are becoming available to stimulate the implementation of water harvesting projects, for meeting the Sustainable Development Goals and to help communities to adapt to climate change. For this, it is important to understand which factors determine the success of water harvesting techniques under different conditions. For this, we review the literature, including information on the crop yield impacts of water harvesting projects in semi-arid Africa and Asia. Results show that large water harvesting structures (> 500 m3) are less expensive than small structures, when taking into account investment costs, storage capacity and lifetimes. We also find that water harvesting improves crop yields significantly, and that the relative impact of water harvesting on crop yields is largest in low rainfall years. We also see that the governance, technical knowledge and initial investment are more demanding for the larger structures than for smaller structures, which may affect their spontaneous adoption and long term sustainability when managed by local communities. To support the selection of appropriate techniques, we present a decision framework based on case specific characteristics. This framework can also be used when reporting and evaluating the performance of water harvesting techniques, which is up to now quite limited in peer reviewed literature. Based on Bouma, J., Hegde, S.E., Lasage, R., (2016). Assessing the returns to water harvesting: A meta-analysis. Agricultural Water Management 163, 100-109. Lasage, R., Verburg P.H., (2015). Evaluation of small scale water harvesting techniques for semi-arid environments. Journal of Arid Environments 118, 48-57.

76 FR 13018 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-09

... statistical surveys that yield quantitative results that can be generalized to the population of study. This... information will not be used for quantitative information collections that are designed to yield reliably... generic mechanisms that are designed to yield quantitative results. Total Burden Estimate for the...

Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

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

Raymond, Amy; Lovell, Scott; Lorimer, Don

2009-12-01

With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38{alpha}), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. colimore » and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.« less

The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media.

PubMed

Planchard, Noelya; Point, Élodie; Dahmane, Tassadite; Giusti, Fabrice; Renault, Marie; Le Bon, Christel; Durand, Grégory; Milon, Alain; Guittet, Éric; Zoonens, Manuela; Popot, Jean-Luc; Catoire, Laurent J

2014-10-01

Solution-state nuclear magnetic resonance studies of membrane proteins are facilitated by the increased stability that trapping with amphipols confers to most of them as compared to detergent solutions. They have yielded information on the state of folding of the proteins, their areas of contact with the polymer, their dynamics, water accessibility, and the structure of protein-bound ligands. They benefit from the diversification of amphipol chemical structures and the availability of deuterated amphipols. The advantages and constraints of working with amphipols are discussed and compared to those associated with other non-conventional environments, such as bicelles and nanodiscs.

[Development of medical supplies management system].

PubMed

Zhong, Jianping; Shen, Beijun; Zhu, Huili

2012-11-01

This paper adopts advanced information technology to manage medical supplies, in order to improve the medical supplies management level and reduce material cost. It develops a Medical Supplies Management System with B/S and C/S mixed structure, optimizing material management process, building large equipment performance evaluation model, providing interface solution with HIS, and realizing real-time information briefing of high value material's consumption. The medical materials are managed during its full life-cycle. The material consumption of the clinical departments is monitored real-timely. Through the closed-loop management with pre-event budget, mid-event control and after-event analysis, it realizes the final purpose of management yielding benefit.

Prosocial coping and substance use during pregnancy.

PubMed

Blechman, E A; Lowell, E S; Garrett, J

1999-01-01

In structured interviews of pregnant inner-city residents, 38 substance users reported more current liking of drugs and polysubstance use, disengagement coping, depressive symptoms, negative affect, and antisocial behavior than did 45 nonusers. During videotaped interviews, trained observers coded less warmth and less prosocial information exchange (e.g., self-disclosure, question asking) among users. Factor analysis of measures of coping and its concomitants yielded a three-factor (prosocial, antisocial, asocial) solution, with asocial and antisocial coping predominating among substance users. These results suggest that coping has emotional, social, and cognitive elements. This study is the first to demonstrate an association between a substance-using lifestyle and limited prosocial information exchange.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

On the non-uniqueness of sediment yield

NASA Astrophysics Data System (ADS)

Kim, J.; Ivanov, V. Y.; Katopodes, N.

2012-12-01

Estimation of sediment yield at the catchment scale plays an important role for optimal design of hydraulic structures, such as bridges, culverts, reservoirs, and detention basins, as well as making informed decisions in environmental management. Many experimental studies focused on obtaining flow and sediment data in search of unique relationships between runoff (specifically, volume and peak) and sediment characteristics. These relationships were employed to predict sediment yield from flow information. However, despite the same flow volume, the actual sediment yield produced by river basins can vary significantly depending on several conditions: (i) the catchment size, (ii) land use, topography, and soil type, (iii) climatic variations or characteristics , and (iv) initial conditions of soil moisture and soil surface . Additionally, shield formation by relatively larger particles can be one of the possible controllers of erosion and net sediment transport. Smaller particles have low settling velocities and tend to move far from their original position of detachment. Conversely, larger particles can settle quickly near their original locations. Eventually, such particles can form a shield on soil bed and protect underlying soil from rainfall detachment and runoff entrainment. The shield formation and temporal development can be influenced by rainfall intensity, frequency, and volume. Rainfall influences the generation of runoff leading to different conditions of flow depth and velocity that can perturb intact soil into a loose condition. In this study, we numerically investigate the effects of precipitation patterns on the generation of sediment yield. In particular, we address reasons of non-uniqueness of basin sediment yield for the same runoff volume as well as causes of unsteady phenomena in erosion processes under steady state flow conditions. For numerical simulations, the two-dimensional Hairsine-Rose model coupled with a fully distributed hydrology and hydraulics model (tRIBS-OFM: Triangulated irregular network - based Real time Integrated Basin Simulator-Overland Flow Model) is used.

Normal yield tables for red alder.

Treesearch

Norman P. Worthington; Floyd A. Johnson; George R. Staebler; William J. Lloyd

1960-01-01

Increasing interest in the management of red alder (Alnus rubra) has created a need for reliable yield information. Existing yield tables for red alder have been very useful as interim sources of information, but they are generally inadequate for current and prospective management needs. The advisory committee for the Station's Olympia...

77 FR 75498 - Request for Comments on a New Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-20

... statistical surveys that yield quantitative results that can be generalized to the population of study. DATES... surveys that yield quantitative results that can be generalized to the population of study. This feedback... qualitative information will not be used for quantitative information collections that are designed to yield...

Clinical exome sequencing reports: current informatics practice and future opportunities.

PubMed

Swaminathan, Rajeswari; Huang, Yungui; Astbury, Caroline; Fitzgerald-Butt, Sara; Miller, Katherine; Cole, Justin; Bartlett, Christopher; Lin, Simon

2017-11-01

The increased adoption of clinical whole exome sequencing (WES) has improved the diagnostic yield for patients with complex genetic conditions. However, the informatics practice for handling information contained in whole exome reports is still in its infancy, as evidenced by the lack of a common vocabulary within clinical sequencing reports generated across genetic laboratories. Genetic testing results are mostly transmitted using portable document format, which can make secondary analysis and data extraction challenging. This paper reviews a sample of clinical exome reports generated by Clinical Laboratory Improvement Amendments-certified genetic testing laboratories at tertiary-care facilities to assess and identify common data elements. Like structured radiology reports, which enable faster information retrieval and reuse, structuring genetic information within clinical WES reports would help facilitate integration of genetic information into electronic health records and enable retrospective research on the clinical utility of WES. We identify elements listed as mandatory according to practice guidelines but are currently missing from some of the clinical reports, which might help to organize the data when stored within structured databases. We also highlight elements, such as patient consent, that, although they do not appear within any of the current reports, may help in interpreting some of the information within the reports. Integrating genetic and clinical information would assist the adoption of personalized medicine for improved patient care and outcomes. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

In Situ X-Ray Studies of Crystallization Kinetics and Ordering in Functional Organic and Hybrid Materials

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

Yang, Bin; Keum, Jong K.; Geohegan, David B.

In-Situ and time-resolved X-ray scattering and diffraction is dedicated to yielding the change of structural information as the materials are processed or grown in a controlled environment. In this chapter, we introduce the use of in situ and time-resolved X-ray techniques to understand molecular packing, crystal orientation, and phase transformation during the synthesis and processing of functional organic semiconductors, organic nanowires, and hybrid perovskite materials.

Two-photon Microscopy and Polarimetry for Assessment of Myocardial Tissue Organization

NASA Astrophysics Data System (ADS)

Archambault-Wallenburg, Marika

Optical methods can provide useful tissue characterization tools. For this project, two-photon microscopy and polarized light examinations (polarimetry) were used to assess the organizational state of myocardium in healthy, infarcted, and stem-cell regenerated states. Two-photon microscopy visualizes collagen through second-harmonic generation and myocytes through two-photon excitation autofluorescence, providing information on the composition and structure/organization of the tissue. Polarimetry measurements yield a value of linear retardance that can serve as an indicator of tissue anisotropy, and with a dual-projection method, information about the anisotropy axis orientation can also be extracted. Two-photon microscopy results reveal that stem-cell treated tissue retains more myocytes and structure than infarcted myocardium, while polarimetry findings suggest that the injury caused by temporary ligation of a coronary artery is less severe and more diffuse that than caused by a permanent ligation. Both these methods show potential for tissue characterization.

Model selection for multi-component frailty models.

PubMed

Ha, Il Do; Lee, Youngjo; MacKenzie, Gilbert

2007-11-20

Various frailty models have been developed and are now widely used for analysing multivariate survival data. It is therefore important to develop an information criterion for model selection. However, in frailty models there are several alternative ways of forming a criterion and the particular criterion chosen may not be uniformly best. In this paper, we study an Akaike information criterion (AIC) on selecting a frailty structure from a set of (possibly) non-nested frailty models. We propose two new AIC criteria, based on a conditional likelihood and an extended restricted likelihood (ERL) given by Lee and Nelder (J. R. Statist. Soc. B 1996; 58:619-678). We compare their performance using well-known practical examples and demonstrate that the two criteria may yield rather different results. A simulation study shows that the AIC based on the ERL is recommended, when attention is focussed on selecting the frailty structure rather than the fixed effects.

Applications of condensed matter understanding to medical tissues and disease progression: Elemental analysis and structural integrity of tissue scaffolds

NASA Astrophysics Data System (ADS)

Bradley, D. A.; Farquharson, M. J.; Gundogdu, O.; Al-Ebraheem, Alia; Che Ismail, Elna; Kaabar, W.; Bunk, O.; Pfeiffer, F.; Falkenberg, G.; Bailey, M.

2010-02-01

The investigations reported herein link tissue structure and elemental presence with issues of environmental health and disease, exemplified by uptake and storage of potentially toxic elements in the body, the osteoarthritic condition and malignancy in the breast and other soft tissues. Focus is placed on application of state-of-the-art ionizing radiation techniques, including, micro-synchrotron X-ray fluorescence (μ-SXRF) and particle-induced X-ray emission/Rutherford backscattering mapping (μ-PIXE/RBS), coherent small-angle X-ray scattering (cSAXS) and X-ray phase-contrast imaging, providing information on elemental make-up, the large-scale organisation of collagen and anatomical features of moderate and low atomic number media. For the particular situations under investigation, use of such facilities is allowing information to be obtained at an unprecedented level of detail, yielding new understanding of the affected tissues and the progression of disease.

Polymer-encapsulated metal nanoparticles: optical, structural, micro-analytical and hydrogenation studies of a composite material.

PubMed

Scalzullo, Stefania; Mondal, Kartick; Witcomb, Mike; Deshmukh, Amit; Scurrell, Mike; Mallick, Kaushik

2008-02-20

A single-step synthesis route is described for the preparation of a metal-polymer composite in which palladium acetate and meta-amino benzoic acid were used as the precursors for palladium nanoparticles and poly(meta-amino benzoic acid) (PABA). The palladium nanoparticles were found to be uniformly dispersed and highly stabilized throughout the macromolecule matrix. The resultant composite material was characterized by means of different techniques, such as IR and Raman spectroscopy, which provided information regarding the chemical structure of the polymer, whereas electron microscopy images yielded information regarding the morphology of the composite material and the distribution of the metal particles in the composite material. The composite material was used as a catalyst for the ethylene hydrogenation reaction and showed catalytic activity at higher temperatures. TEM studies confirmed the changed environment of the nanoparticles at these temperatures.

Application guide for AFINCH (Analysis of Flows in Networks of Channels) described by NHDPlus

USGS Publications Warehouse

Holtschlag, David J.

2009-01-01

AFINCH (Analysis of Flows in Networks of CHannels) is a computer application that can be used to generate a time series of monthly flows at stream segments (flowlines) and water yields for catchments defined in the National Hydrography Dataset Plus (NHDPlus) value-added attribute system. AFINCH provides a basis for integrating monthly flow data from streamgages, water-use data, monthly climatic data, and land-cover characteristics to estimate natural monthly water yields from catchments by user-defined regression equations. Images of monthly water yields for active streamgages are generated in AFINCH and provide a basis for detecting anomalies in water yields, which may be associated with undocumented flow diversions or augmentations. Water yields are multiplied by the drainage areas of the corresponding catchments to estimate monthly flows. Flows from catchments are accumulated downstream through the streamflow network described by the stream segments. For stream segments where streamgages are active, ratios of measured to accumulated flows are computed. These ratios are applied to upstream water yields to proportionally adjust estimated flows to match measured flows. Flow is conserved through the NHDPlus network. A time series of monthly flows can be generated for stream segments that average about 1-mile long, or monthly water yields from catchments that average about 1 square mile. Estimated monthly flows can be displayed within AFINCH, examined for nonstationarity, and tested for monotonic trends. Monthly flows also can be used to estimate flow-duration characteristics at stream segments. AFINCH generates output files of monthly flows and water yields that are compatible with ArcMap, a geographical information system analysis and display environment. Chloropleth maps of monthly water yield and flow can be generated and analyzed within ArcMap by joining NHDPlus data structures with AFINCH output. Matlab code for the AFINCH application is presented.

Finite element predictions of active buckling control of stiffened panels

NASA Astrophysics Data System (ADS)

Thompson, Danniella M.; Griffin, O. H., Jr.

1993-04-01

Materials systems and structures that can respond 'intelligently' to their environment are currently being proposed and investigated. A series of finite element analyses was performed to investigate the potential for active buckling control of two different stiffened panels by embedded shape memory alloy (SMA) rods. Changes in the predicted buckling load increased with the magnitude of the actuation level for a given structural concept. Increasing the number of actuators for a given concept yielded greater predicted increases in buckling load. Considerable control authority was generated with a small number of actuators, with greater authority demonstrated for those structural concepts where the activated SMA rods could develop greater forces and moments on the structure. Relatively simple and inexpensive analyses were performed with standard finite elements to determine such information, indicating the viability of these types of models for design purposes.

Results from CoMStOC - The Coronal Magnetic Structures Observing Campaign

NASA Technical Reports Server (NTRS)

Schmelz, J. T.; Holman, G. D.

1991-01-01

The Coronal Magnetic Structures Observing Campaign (CoMStOC) was designed to measure the magnetic field strength and determine its structure in the solar corona. Simultaneous soft X-ray and microwave observations were taken by the Solar Maximum Mission's X-ray Polychromator (XRP) and the Very Large Array (VLA) on four days in the campaign period (Nov 25 to Dec 21, 1987). XRP maps in soft X-ray resonance lines formed at different coronal temperatures provide accurate temperature and emission measure diagnostics. VLA maps at several frequencies in the 20 cm and 6 cm bands yield information on microwave structure, spectrum and polarization. The combined data set separates contributions from the two dominant microwave emission mechanisms, thermal bremsstrahlung and gyroresonance. Where gyroresonance dominates, the coronal magnetic field strength has been determined with the aid of theoretical modeling.

Results from CoMStOC - The Coronal Magnetic Structures Observing Campaign

NASA Astrophysics Data System (ADS)

Schmelz, J. T.; Holman, G. D.

The Coronal Magnetic Structures Observing Campaign (CoMStOC) was designed to measure the magnetic field strength and determine its structure in the solar corona. Simultaneous soft X-ray and microwave observations were taken by the Solar Maximum Mission's X-ray Polychromator (XRP) and the Very Large Array (VLA) on four days in the campaign period (Nov 25 to Dec 21, 1987). XRP maps in soft X-ray resonance lines formed at different coronal temperatures provide accurate temperature and emission measure diagnostics. VLA maps at several frequencies in the 20 cm and 6 cm bands yield information on microwave structure, spectrum and polarization. The combined data set separates contributions from the two dominant microwave emission mechanisms, thermal bremsstrahlung and gyroresonance. Where gyroresonance dominates, the coronal magnetic field strength has been determined with the aid of theoretical modeling.

Information flow in layered networks of non-monotonic units

NASA Astrophysics Data System (ADS)

Schittler Neves, Fabio; Martim Schubert, Benno; Erichsen, Rubem, Jr.

2015-07-01

Layered neural networks are feedforward structures that yield robust parallel and distributed pattern recognition. Even though much attention has been paid to pattern retrieval properties in such systems, many aspects of their dynamics are not yet well characterized or understood. In this work we study, at different temperatures, the memory activity and information flows through layered networks in which the elements are the simplest binary odd non-monotonic function. Our results show that, considering a standard Hebbian learning approach, the network information content has its maximum always at the monotonic limit, even though the maximum memory capacity can be found at non-monotonic values for small enough temperatures. Furthermore, we show that such systems exhibit rich macroscopic dynamics, including not only fixed point solutions of its iterative map, but also cyclic and chaotic attractors that also carry information.

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

PubMed

Shamim, Mohammad Tabrez Anwar; Anwaruddin, Mohammad; Nagarajaram, H A

2007-12-15

Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.

Structural Studies on Dy to 119 GPa and Applications to Lanthanide Systematics

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

Patterson, J; Akella, J

2005-05-31

The Rare Earth elements (REE) are known to undergo crystallographic as well as electronic structure changes with applied pressure. On increasing pressure, the trivalent lanthanides follow the sequence hcp {yields} Sm-type {yields} dhcp {yields} fcc {yields} dfcc. In this report we present room-temperature high-pressure x-ray diffraction data for Dy as well as our observations on the post-dfcc phases and concomitant volume changes in the heavy REE.

Is structural stigma's effect on the mortality of sexual minorities robust? A failure to replicate the results of a published study.

PubMed

Regnerus, Mark

2017-09-01

The study of stigma's influence on health has surged in recent years. Hatzenbuehler et al.'s (2014) study of structural stigma's effect on mortality revealed an average of 12 years' shorter life expectancy for sexual minorities who resided in communities thought to exhibit high levels of anti-gay prejudice, using data from the 1988-2002 administrations of the US General Social Survey linked to mortality outcome data in the 2008 National Death Index. In the original study, the key predictor variable (structural stigma) led to results suggesting the profound negative influence of structural stigma on the mortality of sexual minorities. Attempts to replicate the study, in order to explore alternative hypotheses, repeatedly failed to generate the original study's key finding on structural stigma. Efforts to discern the source of the disparity in results revealed complications in the multiple imputation process for missing values of the components of structural stigma. This prompted efforts at replication using 10 different imputation approaches. Efforts to replicate Hatzenbuehler et al.'s (2014) key finding on structural stigma's notable influence on the premature mortality of sexual minorities, including a more refined imputation strategy than described in the original study, failed. No data imputation approach yielded parameters that supported the original study's conclusions. Alternative hypotheses, which originally motivated the present study, revealed little new information. Ten different approaches to multiple imputation of missing data yielded none in which the effect of structural stigma on the mortality of sexual minorities was statistically significant. Minimally, the original study's structural stigma variable (and hence its key result) is so sensitive to subjective measurement decisions as to be rendered unreliable. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

The Rest of the Story: A Qualitative Study of Complementing Standardized Assessment Data with Informal Interviews with Older Patients and Families.

PubMed

Lafortune, Claire; Elliott, Jacobi; Egan, Mary Y; Stolee, Paul

2017-04-01

While standardized health assessments capture valuable information on patients' demographic and diagnostic characteristics, health conditions, and physical and mental functioning, they may not capture information of most relevance to individual patients and their families. Given that patients and their informal caregivers are the experts on that patient's unique context, it is important to ensure they are able to convey all relevant personal information to formal healthcare providers so that high-quality, patient-centered care may be delivered. This study aims to identify information that older patients and families consider important but that might not be included in standardized assessments. Transcripts were analyzed from 29 interviews relating to eight patients with hip fractures from three sites (large urban, smaller urban, rural) in two provinces in Canada. These interviews were conducted as part of a larger ethnographic study. Each transcript was analyzed by two researchers using content analysis. Results were reviewed in two focus group interviews with older adults and family caregivers. Identified themes were compared with items from two standardized assessments used in healthcare settings. Three broad themes emerged from the qualitative analysis that were not covered in the standardized assessments: informal caregiver and family considerations, insider healthcare knowledge, and patients' healthcare attitudes and experiences. The importance of these themes was confirmed through focus group interviews. Focus group participants also emphasized the importance of conducting assessments in a patient-centered way and the importance of open-ended questions. A less structured interview approach may yield information that would otherwise be missed in standardized assessments. Combining both sources could yield better-informed healthcare planning and quality-improvement efforts.

Metal-assisted SIMS and cluster ion bombardment for ion yield enhancement

NASA Astrophysics Data System (ADS)

Heile, A.; Lipinsky, D.; Wehbe, N.; Delcorte, A.; Bertrand, P.; Felten, A.; Houssiau, L.; Pireaux, J.-J.; De Mondt, R.; Van Vaeck, L.; Arlinghaus, H. F.

2008-12-01

In addition to structural information, a detailed knowledge of the local chemical environment proves to be of ever greater importance, for example for the development of new types of materials as well as for specific modifications of surfaces and interfaces in multiple fields of materials science or various biomedical and chemical applications. But the ongoing miniaturization and therefore reduction of the amount of material available for analysis constitute a challenge to the detection limits of analytical methods. In the case of time-of-flight secondary ion mass spectrometry (TOF-SIMS), several methods of secondary ion yield enhancement have been proposed. This paper focuses on the investigation of the effects of two of these methods, metal-assisted SIMS and polyatomic primary ion bombardment. For this purpose, thicker layers of polystyrene (PS), both pristine and metallized with different amounts of gold, were analyzed using monoatomic (Ar +, Ga +, Xe +, Bi +) and polyatomic (SF 5+, Bi 3+, C 60+) primary ions. It was found that polyatomic ions generally induce a significant increase of the secondary ion yield. On the other hand, with gold deposition, a yield enhancement can only be detected for monoatomic ion bombardment.

MALDI-MS/MS with Traveling Wave Ion Mobility for the Structural Analysis of N-Linked Glycans

NASA Astrophysics Data System (ADS)

Harvey, David J.; Scarff, Charlotte A.; Crispin, Max; Scanlan, Christopher N.; Bonomelli, Camille; Scrivens, James H.

2012-11-01

The preference for singly charged ion formation by MALDI makes it a better choice than electrospray ionization for profiling mixtures of N-glycans. For structural analysis, fragmentation of negative ions often yields more informative spectra than fragmentation of positive ones but such ions are more difficult to produce from neutral glycans under MALDI conditions. This work investigates conditions for the formation of both positive and negative ions by MALDI from N-linked glycans released from glycoproteins and their subsequent MS/MS and ion mobility behaviour. 2,4,6-Trihydroxyacetophenone (THAP) doped with ammonium nitrate was found to give optimal ion yields in negative ion mode. Ammonium chloride or phosphate also yielded prominent adducts but anionic carbohydrates such as sulfated N-glycans tended to ionize preferentially. Carbohydrates adducted with all three adducts (phosphate, chloride, and nitrate) produced good negative ion CID spectra but those adducted with iodide and sulfate did not yield fragment ions although they gave stronger signals. Fragmentation paralleled that seen following electrospray ionization providing superior spectra than could be obtained by PSD on MALDI-TOF instruments or with ion traps. In addition, ion mobility drift times of the adducted glycans and the ability of this technique to separate isomers also mirrored those obtained following ESI sample introduction. Ion mobility also allowed profiles to be obtained from samples whose MALDI spectra showed no evidence of such ions allowing the technique to be used in conditions where sample amounts were limiting. The method was applied to N-glycans released from the recombinant human immunodeficiency virus glycoprotein, gp120.

High-pressure studies with x-rays using diamond anvil cells

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

Shen, Guoyin; Mao, Ho Kwang

2016-11-22

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. Thesemore » HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.« less

High-pressure studies with x-rays using diamond anvil cells

NASA Astrophysics Data System (ADS)

Shen, Guoyin; Mao, Ho Kwang

2017-01-01

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials’ properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.

From Paris to Iowa and Back: Global Temperature Targets, Agricultural Impacts, and Producer Response

NASA Astrophysics Data System (ADS)

Anderson, C.; Hayhoe, K.; Terando, A. J.

2016-12-01

Traditionally, assessments such as those produced by IPCC and USGCRP have been structured to provide a one-way flow of information from scientists to national and international policy makers. Because the Paris Agreement will ultimately require corresponding domestic policies, the traditional one-way information flow could be inadequate, since it lacks both direct participation and informed feedback from many of the important entities that influence domestic policy. We have engaged Iowa row crop producers in identifying impacts and feasibility of adaptation under global warming of 1.0 and 2.0OC. Our engagement seeks to create within climate impacts assessment a decision-maker feedback loop. We have engaged an expert panel by using yield data modeling as a first step to communicate vividly the potential yield impacts of global average temperature targets. This engagement included validation with historical global average temperature before presenting yield impact under global mean surface temperature increase of 1.0 and 2.0OC. The expert panel requested further analysis of targets at 0.25 and 0.50OC increase and of possible impacts should they pursue adaptation by increasing maize plant population density and soil moisture storage. Several clear messages have emerged that can be voiced by Iowa agribusiness leaders to national and international decision-makers. While Iowa soybean agriculture may remain robust for the foreseeable future, the Paris Agreement is insufficient to protect Iowa maize production from substantial changes in productivity and volatility. These effects could be largely (though not entirely) mitigated by moving from the current +2OC to the "high ambition" +1.5OC target. The projected spring rainfall increase of 10% under +1OC would increase the cost of spring planting. The data model predicts a 5-day reduction in average number of fieldwork days, which requires the addition of one half-time person or larger planting equipment. The current annual rate of increase in maize plant density will maintain historical yield increase through +1OC but by +2OC is substantially reduced and results in unprecedented yield volatility. By increasing soil moisture during July, Iowa maize production can reduce markedly the impacts of +2OC.

Crop monitoring & yield forecasting system based on Synthetic Aperture Radar (SAR) and process-based crop growth model: Development and validation in South and South East Asian Countries

NASA Astrophysics Data System (ADS)

Setiyono, T. D.

2014-12-01

Accurate and timely information on rice crop growth and yield helps governments and other stakeholders adapting their economic policies and enables relief organizations to better anticipate and coordinate relief efforts in the wake of a natural catastrophe. Such delivery of rice growth and yield information is made possible by regular earth observation using space-born Synthetic Aperture Radar (SAR) technology combined with crop modeling approach to estimate yield. Radar-based remote sensing is capable of observing rice vegetation growth irrespective of cloud coverage, an important feature given that in incidences of flooding the sky is often cloud-covered. The system allows rapid damage assessment over the area of interest. Rice yield monitoring is based on a crop growth simulation and SAR-derived key information, particularly start of season and leaf growth rate. Results from pilot study sites in South and South East Asian countries suggest that incorporation of SAR data into crop model improves yield estimation for actual yields. Remote-sensing data assimilation into crop model effectively capture responses of rice crops to environmental conditions over large spatial coverage, which otherwise is practically impossible to achieve. Such improvement of actual yield estimates offers practical application such as in a crop insurance program. Process-based crop simulation model is used in the system to ensure climate information is adequately captured and to enable mid-season yield forecast.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Information Management of a Structured Admissions Interview Process in a Medical College with an Apple II System

PubMed Central

O'Reilly, Robert; Fedorko, Steve; Nicholson, Nigel

1983-01-01

This paper describes a structured interview process for medical school admissions supported by an Apple II computer system which provides feedback to interviewers and the College admissions committee. Presented are the rationale for the system, the preliminary results of analysis of some of the interview data, and a brief description of the computer program and output. The present data show that the structured interview yields very high interrater reliability coefficients, is acceptable to the medical school faculty, and results in quantitative data useful in the admission process. The system continues in development at this time, a second year of data will be shortly available, and further refinements are being made to the computer program to enhance its utilization and exportability.

Metallic Properties of the Si(111) - 5 × 2 - Au Surface from Infrared Plasmon Polaritons and Ab Initio Theory.

PubMed

Hötzel, Fabian; Seino, Kaori; Huck, Christian; Skibbe, Olaf; Bechstedt, Friedhelm; Pucci, Annemarie

2015-06-10

The metal-atom chains on the Si(111) - 5 × 2 - Au surface represent an exceedingly interesting system for the understanding of one-dimensional electrical interconnects. While other metal-atom chain structures on silicon suffer from metal-to-insulator transitions, Si(111) - 5 × 2 - Au stays metallic at least down to 20 K as we have proven by the anisotropic absorption from localized plasmon polaritons in the infrared. A quantitative analysis of the infrared plasmonic signal done here for the first time yields valuable band structure information in agreement with the theoretically derived data. The experimental and theoretical results are consistently explained in the framework of the atomic geometry, electronic structure, and IR spectra of the recent Kwon-Kang model.

An Interdisciplinary Approach to Predictive Modeling of Structural Adhesive Bonding. Factors Affecting the Durability of Titanium/Epoxy Bonds.

DTIC Science & Technology

1987-10-01

durability test at 800 C, 95% r.h. 71 SEM photomicrograph at 1600 x of E-8385 film spun coat . from a 2 wt% solution onto a ferrotype plate. .I 72 Theoretical ...TiO2 to the high energy side. While Auger line shapes theoretically yield oxidation state information, stoichiometry conclusions from experi- 0 mental...the justification for the methods chosen in this work. ,*p-* ., Fadley et al. [37] present a detailed theoretical discussion on quantitative XPS

Informed Materials Discovery: Designing New Engineering Polymer Systems Using High Throughput Modeling Techniques

DTIC Science & Technology

2016-10-27

and molecu- lar physical structure into the prediction of the macroscopic constitutive properties and behaviour of the polymers. GIM uses a mean field...Cβ and Cg are related to the loss of DOFs over beta and glass transitions, where R is the molar gas constant and C is defined by: (2) C = NR (6.7T θ1...The compression yield behaviour of polymethyl methacrylate over a wide range of temperatures and strain-rates, Journal of Materials Science 8 (7

Optimization of processing parameters of UAV integral structural components based on yield response

NASA Astrophysics Data System (ADS)

Chen, Yunsheng

2018-05-01

In order to improve the overall strength of unmanned aerial vehicle (UAV), it is necessary to optimize the processing parameters of UAV structural components, which is affected by initial residual stress in the process of UAV structural components processing. Because machining errors are easy to occur, an optimization model for machining parameters of UAV integral structural components based on yield response is proposed. The finite element method is used to simulate the machining parameters of UAV integral structural components. The prediction model of workpiece surface machining error is established, and the influence of the path of walking knife on residual stress of UAV integral structure is studied, according to the stress of UAV integral component. The yield response of the time-varying stiffness is analyzed, and the yield response and the stress evolution mechanism of the UAV integral structure are analyzed. The simulation results show that this method is used to optimize the machining parameters of UAV integral structural components and improve the precision of UAV milling processing. The machining error is reduced, and the deformation prediction and error compensation of UAV integral structural parts are realized, thus improving the quality of machining.

Isotopic Ratio, Isotonic Ratio, Isobaric Ratio and Shannon Information Uncertainty

NASA Astrophysics Data System (ADS)

Ma, Chun-Wang; Wei, Hui-Ling

2014-11-01

The isoscaling and the isobaric yield ratio difference (IBD) probes, both of which are constructed by yield ratio of fragment, provide cancelation of parameters. The information entropy theory is introduced to explain the physical meaning of the isoscaling and IBD probes. The similarity between the isoscaling and IBD results is found, i.e., the information uncertainty determined by the IBD method equals to β - α determined by the isoscaling (α (β) is the parameter fitted from the isotopic (isotonic) yield ratio).

Electro Optical Properties of Copolymer Blends: Lasing, Electroluminescence and Photophysics

DTIC Science & Technology

2006-04-15

conjugated main chain structures with high photoluminescent and electroluminescent quantum yields. The structures incorporated fluorene containing moieties...The systems studied focused on novel conjugated main chain structures with high photoluminescent and electroluminescent quantum yields. The structures...the quantum efficient fluorine group. The properties of segmented copolymers that incorporate fluorenes were compared to the homo-PPV type systems

Modulus and yield stress of drawn LDPE

NASA Astrophysics Data System (ADS)

Thavarungkul, Nandh

Modulus and yield stress were investigated in drawn low density polyethylene (LDPE) film. Uniaxially drawn polymeric films usually show high values of modulus and yield stress, however, studies have normally only been conducted to identify the structural features that determine modulus. In this study small-angle x-ray scattering (SAXS), thermal shrinkage, birefringence, differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA) were used to examine, directly and indirectly, the structural features that determine both modulus and yield stress, which are often closely related in undrawn materials. Shish-kebab structures are proposed to account for the mechanical properties in drawn LDPE. The validity of this molecular/morphological model was tested using relationships between static mechanical data and structural and physical parameters. In addition, dynamic mechanical results are also in line with static data in supporting the model. In the machine direction (MD), "shish" and taut tie molecules (TTM) anchored in the crystalline phase account for E; whereas crystal lamellae with contributions from "shish" and TTM determine yield stress. In the transverse direction (TD), the crystalline phase plays an important roll in both modulus and yield stress. Modulus is determined by crystal lamellae functioning as platelet reinforcing elements in the amorphous matrix with an additional contributions from TTM and yield stress is determined by the crystal lamellae's resistance to deformation.

Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA.

PubMed

Ikeya, Teppei; Terauchi, Tsutomu; Güntert, Peter; Kainosho, Masatsune

2006-07-01

Recently we have developed the stereo-array isotope labeling (SAIL) technique to overcome the conventional molecular size limitation in NMR protein structure determination by employing complete stereo- and regiospecific patterns of stable isotopes. SAIL sharpens signals and simplifies spectra without the loss of requisite structural information, thus making large classes of proteins newly accessible to detailed solution structure determination. The automated structure calculation program CYANA can efficiently analyze SAIL-NOESY spectra and calculate structures without manual analysis. Nevertheless, the original SAIL method might not be capable of determining the structures of proteins larger than 50 kDa or membrane proteins, for which the spectra are characterized by many broadened and overlapped peaks. Here we have carried out simulations of new SAIL patterns optimized for minimal relaxation and overlap, to evaluate the combined use of SAIL and CYANA for solving the structures of larger proteins and membrane proteins. The modified approach reduces the number of peaks to nearly half of that observed with uniform labeling, while still yielding well-defined structures and is expected to enable NMR structure determinations of these challenging systems.

76 FR 43353 - Agency Information Collection Activities: Proposed Collection; Comment Request; Generic Clearance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-20

... and opinions, but are not statistical surveys that yield quantitative results that can be generalized... generic clearance for qualitative information will not be used for quantitative information collections... for submission for other generic mechanisms that are designed to yield quantitative results. The...

Characteristics of water-well yields in part of the blue ridge geologic Province in Loudoun County, Virginia

USGS Publications Warehouse

Sutphin, D.M.; Drew, L.J.; Schuenemeyer, J.H.; Burton, W.C.

2001-01-01

Loudoun County, Virginia, which is located about 50 km to the west of Washington, DC, was the site of intensive suburban development during the 1980s and 1990s. In the western half of the county, the source of water for domestic use has been from wells drilled into the fractured crystalline bedrock of the Blue Ridge Geologic Province. A comprehensive digital database that contains information on initial yield, location, depth, elevation, and other data for 3651 wells drilled in this 825.5-km2 area was combined with a digital geologic map to form the basis for a study of geologic and temporal controls on water-well yields. Statistical modeling procedures were used to determine that mean yields for the wells were significantly different as a function of structural setting, genetic rock type, and geologic map unit. The Bonferroni procedure then was used to determine which paired comparisons contributed to these significant differences. The data were divided into 15 temporal drilling increments to determine if the time-dependent trends that exist for the Loudoun County data are similar to those discovered in a previous study of water-well yields in the Pinardville 7.5-min quadrangle, New Hampshire. In both regions, trends, which include increasing proportions of very low yield wells and increasing well depths through time, and the counterintuitive result of increasing mean well yields through time, were similar. In addition, a yield-to-depth curve similar to that discovered in the Pinardville quadrangle was recognized in this study. Thus, the temporal model with a feed-forward-loop mechanism to explain the temporal trends in well characteristics proposed for the New Hampshire study appears to apply to western Loudoun County. ?? 2001 International Association for Mathematical Geology.

Characterization and classification of vegetation canopy structure and distribution within the Great Smoky Mountains National Park using LiDAR

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

Kumar, Jitendra; HargroveJr., William Walter; Norman, Steven P

Vegetation canopy structure is a critically important habit characteristic for many threatened and endangered birds and other animal species, and it is key information needed by forest and wildlife managers for monitoring and managing forest resources, conservation planning and fostering biodiversity. Advances in Light Detection and Ranging (LiDAR) technologies have enabled remote sensing-based studies of vegetation canopies by capturing three-dimensional structures, yielding information not available in two-dimensional images of the landscape pro- vided by traditional multi-spectral remote sensing platforms. However, the large volume data sets produced by airborne LiDAR instruments pose a significant computational challenge, requiring algorithms to identify andmore » analyze patterns of interest buried within LiDAR point clouds in a computationally efficient manner, utilizing state-of-art computing infrastructure. We developed and applied a computationally efficient approach to analyze a large volume of LiDAR data and to characterize and map the vegetation canopy structures for 139,859 hectares (540 sq. miles) in the Great Smoky Mountains National Park. This study helps improve our understanding of the distribution of vegetation and animal habitats in this extremely diverse ecosystem.« less

Limits on reliable information flows through stochastic populations.

PubMed

Boczkowski, Lucas; Natale, Emanuele; Feinerman, Ofer; Korman, Amos

2018-06-06

Biological systems can share and collectively process information to yield emergent effects, despite inherent noise in communication. While man-made systems often employ intricate structural solutions to overcome noise, the structure of many biological systems is more amorphous. It is not well understood how communication noise may affect the computational repertoire of such groups. To approach this question we consider the basic collective task of rumor spreading, in which information from few knowledgeable sources must reliably flow into the rest of the population. We study the effect of communication noise on the ability of groups that lack stable structures to efficiently solve this task. We present an impossibility result which strongly restricts reliable rumor spreading in such groups. Namely, we prove that, in the presence of even moderate levels of noise that affect all facets of the communication, no scheme can significantly outperform the trivial one in which agents have to wait until directly interacting with the sources-a process which requires linear time in the population size. Our results imply that in order to achieve efficient rumor spread a system must exhibit either some degree of structural stability or, alternatively, some facet of the communication which is immune to noise. We then corroborate this claim by providing new analyses of experimental data regarding recruitment in Cataglyphis niger desert ants. Finally, in light of our theoretical results, we discuss strategies to overcome noise in other biological systems.

High Resolution Imaging of the Sun with CORONAS-1

NASA Technical Reports Server (NTRS)

Karovska, Margarita

1998-01-01

We applied several image restoration and enhancement techniques, to CORONAS-I images. We carried out the characterization of the Point Spread Function (PSF) using the unique capability of the Blind Iterative Deconvolution (BID) technique, which recovers the real PSF at a given location and time of observation, when limited a priori information is available on its characteristics. We also applied image enhancement technique to extract the small scale structure imbeded in bright large scale structures on the disk and on the limb. The results demonstrate the capability of the image post-processing to substantially increase the yield from the space observations by improving the resolution and reducing noise in the images.

“Playing around” with Field-Effect Sensors on the Basis of EIS Structures, LAPS and ISFETs

PubMed Central

Schöning, Michael J.

2005-01-01

Microfabricated semiconductor devices are becoming increasingly relevant, also for the detection of biological and chemical quantities. Especially, the “marriage” of biomolecules and silicon technology often yields successful new sensor concepts. The fabrication techniques of such silicon-based chemical sensors and biosensors, respectively, will have a distinct impact in different fields of application such as medicine, food technology, environment, chemistry and biotechnology as well as information processing. Moreover, scientists and engineers are interested in the analytical benefits of miniaturised and microfabricated sensor devices. This paper gives a survey on different types of semiconductor-based field-effect structures that have been recently developed in our laboratory.

The roles of tertiary amine structure, background organic matter and chloramine species on NDMA formation.

PubMed

Selbes, Meric; Kim, Daekyun; Ates, Nuray; Karanfil, Tanju

2013-02-01

N-nitrosodimethylamine (NDMA), a probable human carcinogen, is a disinfection by-product that has been detected in chloraminated and chlorinated drinking waters and wastewaters. Formation mechanisms and precursors of NDMA are still not well understood. The main objectives of this study were to systematically investigate (i) the effect of tertiary amine structure, (ii) the effect of background natural organic matter (NOM), and (iii) the roles of mono vs. dichloramine species on the NDMA formation. Dimethylamine (DMA) and 20 different tertiary aliphatic and aromatic amines were carefully examined based on their functional groups attached to the basic DMA structure. The wide range (0.02-83.9%) of observed NDMA yields indicated the importance of the structure of tertiary amines, and both stability and electron distribution of the leaving group of tertiary amines on NDMA formation. DMA associated with branched alkyl groups or benzyl like structures having only one carbon between the ring and DMA structure consistently gave higher NDMA yields. Compounds with electron withdrawing groups (EWG) reacted preferentially with monochloramine, whereas compounds with electron donating group (EDG) showed tendency to react with dichloramine to form NDMA. When the selected amines were present in NOM solutions, NDMA formation increased for compounds with EWG while decreased for compounds with EDG. This impact was attributed to the competitions between NOM and amines for chloramine species. The results provided additional information to the commonly accepted mechanism for NDMA formation including chloramine species reacting with tertiary amines and the role of the leaving group on overall NDMA conversion. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape.

PubMed

Fossat, Martin J; Dao, Thuy P; Jenkins, Kelly; Dellarole, Mariano; Yang, Yinshan; McCallum, Scott A; Garcia, Angel E; Barrick, Doug; Roumestand, Christian; Royer, Catherine A

2016-12-06

A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic. Here we present a highly detailed structural and energetic map of the entire folding landscape of the leucine-rich repeat protein, pp32 (Anp32), obtained by combining pressure-dependent site-specific 1 H- 15 N HSQC data with coarse-grained molecular dynamics simulations. The results obtained using this equilibrium approach demonstrate that the main barrier to folding of pp32 is quite broad and lies near the unfolded state, with structure apparent only in the C-terminal region. Significant deviation from two-state unfolding under pressure reveals an intermediate on the folded side of the main barrier in which the N-terminal region is disordered. A nonlinear temperature dependence of the population of this intermediate suggests a large heat capacity change associated with its formation. The combination of pressure, which favors the population of folding intermediates relative to chemical denaturants; NMR, which allows their observation; and constrained structure-based simulations yield unparalleled insight into protein folding mechanisms. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The NUMEN project @ LNS: Status and perspectives

NASA Astrophysics Data System (ADS)

Cappuzzello, F.; Agodi, C.; Acosta, L.; Auerbach, N.; Bellone, J.; Bijker, R.; Bonanno, D.; Bongiovanni, D.; Borello-Lewin, T.; Boztosun, I.; Branchina, V.; Bussa, M. P.; Calabrese, S.; Calabretta, L.; Calanna, A.; Carbone, D.; Cavallaro, M.; Calvo, D.; Lomelí, E. R. Chávez; Coban, A.; Colonna, M.; D'Agostino, G.; Degeronimo, G.; Delaunay, F.; Deshmukh, N.; de Faria, P. N.; Ferraresi, C.; Ferreira, J. L.; Fisichella, M.; Foti, A.; Finocchiaro, P.; Gallo, G.; Garcia, U.; Giraudo, G.; Greco, V.; Hacisalihoglu, A.; Kotila, J.; Iazzi, F.; Introzzi, R.; Lanzalone, G.; Lavagno, A.; Via, F. La; Lay, J. A.; Lenske, H.; Linares, R.; Litrico, G.; Longhitano, F.; Presti, D. Lo; Lubian, J.; Medina, N.; Mendes, D. R.; Muoio, A.; Oliveira, J. R. B.; Pakou, A.; Pandola, L.; Petrascu, H.; Pinna, F.; Reito, S.; Rifuggiato, D.; Rodrigues, M. R. D.; Russo, A. D.; Russo, G.; Santagati, G.; Santopinto, E.; Sgouros, O.; Solakcı, S. O.; Souliotis, G.; Soukeras, V.; Spatafora, A.; Torresi, D.; Tudisco, S.; Vsevolodovna, R. I. M.; Wheadon, R. J.; Yildirin, A.; Zagatto, V.

2017-10-01

The NUMEN project aims at accessing experimentally driven information on Nuclear Matrix Elements (NME) involved in the half-life of the neutrinoless double beta decay (0νββ), by high-accuracy measurements of the cross sections of Heavy Ion (HI) induced Double Charge Exchange (DCE) reactions. Particular attention is given to the (18O,18Ne) and (20Ne,20O) reactions as tools for β+β+ and β-β-decays, respectively. First evidence about the possibility to get quantitative information about NME from experiments is found for both kind of reactions. In the experiments, performed at INFN - Laboratory Nazionali del Sud (LNS) in Catania, the beams are accelerated by the Superconducting Cyclotron (CS) and the reaction products are detected the MAGNEX magnetic spectrometer. The measured cross sections are challengingly low, limiting the present exploration to few selected isotopes of interest in the context of typically low-yield experimental runs. A major upgrade of the LNS facility is foreseen in order to increase the experimental yield of at least two orders of magnitude, thus making feasible a systematic study of all the cases of interest. Frontiers technologies are going to be developed, to this purpose, for the accelerator and the detection systems. In parallel, advanced theoretical models will be developed in order to extract the nuclear structure information from the measured cross sections.

Automated structure determination of proteins with the SAIL-FLYA NMR method.

PubMed

Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

2007-01-01

The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto.

PubMed

Barge, Laura M; Cardoso, Silvana S S; Cartwright, Julyan H E; Doloboff, Ivria J; Flores, Erika; Macías-Sánchez, Elena; Sainz-Díaz, C Ignacio; Sobrón, Pablo

2016-11-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments.

Self-assembling iron oxyhydroxide/oxide tubular structures: laboratory-grown and field examples from Rio Tinto

PubMed Central

Barge, Laura M.; Doloboff, Ivria J.; Flores, Erika; Sobrón, Pablo

2016-01-01

Rio Tinto in southern Spain has become of increasing astrobiological significance, in particular for its similarity to environments on early Mars. We present evidence of tubular structures from sampled terraces in the stream bed at the source of the river, as well as ancient, now dry, terraces. This is the first reported finding of tubular structures in this particular environment. We propose that some of these structures could be formed through self-assembly via an abiotic mechanism involving templated precipitation around a fluid jet, a similar mechanism to that commonly found in so-called chemical gardens. Laboratory experiments simulating the formation of self-assembling iron oxyhydroxide tubes via chemical garden/chemobrionic processes form similar structures. Fluid-mechanical scaling analysis demonstrates that the proposed mechanism is plausible. Although the formation of tube structures is not itself a biosignature, the iron mineral oxidation gradients across the tube walls in laboratory and field examples may yield information about energy gradients and potentially habitable environments. PMID:27956875

Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

PubMed

Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

2016-07-26

Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.

Diagnosis of an intense atmospheric river impacting the pacific northwest: Storm summary and offshore vertical structure observed with COSMIC satellite retrievals

USGS Publications Warehouse

Neiman, P.J.; Ralph, F.M.; Wick, G.A.; Kuo, Y.-H.; Wee, T.-K.; Ma, Z.; Taylor, G.H.; Dettinger, M.D.

2008-01-01

This study uses the new satellite-based Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) mission to retrieve tropospheric profiles of temperature and moisture over the data-sparse eastern Pacific Ocean. The COSMIC retrievals, which employ a global positioning system radio occultation technique combined with "first-guess" information from numerical weather prediction model analyses, are evaluated through the diagnosis of an intense atmospheric river (AR; i.e., a narrow plume of strong water vapor flux) that devastated the Pacific Northwest with flooding rains in early November 2006. A detailed analysis of this AR is presented first using conventional datasets and highlights the fact that ARs are critical contributors to West Coast extreme precipitation and flooding events. Then, the COSMIC evaluation is provided. Offshore composite COSMIC soundings north of, within, and south of this AR exhibited vertical structures that are meteorologically consistent with satellite imagery and global reanalysis fields of this case and with earlier composite dropsonde results from other landfalling ARs. Also, a curtain of 12 offshore COSMIC soundings through the AR yielded cross-sectional thermodynamic and moisture structures that were similarly consistent, including details comparable to earlier aircraft-based dropsonde analyses. The results show that the new COSMIC retrievals, which are global (currently yielding ???2000 soundings per day), provide high-resolution vertical-profile information beyond that found in the numerical model first-guess fields and can help monitor key lower-tropospheric mesoscale phenomena in data-sparse regions. Hence, COSMIC will likely support a wide array of applications, from physical process studies to data assimilation, numerical weather prediction, and climate research. ?? 2008 American Meteorological Society.

The underlying pathway structure of biochemical reaction networks

PubMed Central

Schilling, Christophe H.; Palsson, Bernhard O.

1998-01-01

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function. PMID:9539712

Multivariate Non-Symmetric Stochastic Models for Spatial Dependence Models

NASA Astrophysics Data System (ADS)

Haslauer, C. P.; Bárdossy, A.

2017-12-01

A copula based multivariate framework allows more flexibility to describe different kind of dependences than what is possible using models relying on the confining assumption of symmetric Gaussian models: different quantiles can be modelled with a different degree of dependence; it will be demonstrated how this can be expected given process understanding. maximum likelihood based multivariate quantitative parameter estimation yields stable and reliable results; not only improved results in cross-validation based measures of uncertainty are obtained but also a more realistic spatial structure of uncertainty compared to second order models of dependence; as much information as is available is included in the parameter estimation: incorporation of censored measurements (e.g., below detection limit, or ones that are above the sensitive range of the measurement device) yield to more realistic spatial models; the proportion of true zeros can be jointly estimated with and distinguished from censored measurements which allow estimates about the age of a contaminant in the system; secondary information (categorical and on the rational scale) has been used to improve the estimation of the primary variable; These copula based multivariate statistical techniques are demonstrated based on hydraulic conductivity observations at the Borden (Canada) site, the MADE site (USA), and a large regional groundwater quality data-set in south-west Germany. Fields of spatially distributed K were simulated with identical marginal simulation, identical second order spatial moments, yet substantially differing solute transport characteristics when numerical tracer tests were performed. A statistical methodology is shown that allows the delineation of a boundary layer separating homogenous parts of a spatial data-set. The effects of this boundary layer (macro structure) and the spatial dependence of K (micro structure) on solute transport behaviour is shown.

Establishment of a Photon Data Section of the BNL National Nuclear Data Center: A preliminary proposal

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

Hanson, A.L.; Pearlstein, S.

1992-05-01

It is proposed to establish a Photon Data Section (PDS) of the BNL National Nuclear Data Center (NNDC). This would be a total program encompassing both photon-atom and photon-nucleus interactions. By utilizing the existing NNDC data base management expertise and on-line access capabilities, the implementation of photon interaction data activities within the existing NNDC nuclear structure and nuclear-reaction activities can reestablish a viable photon interaction data program at minimum cost. By taking advantage of the on-line capabilities, the x-ray users' community will have access to a dynamic, state-of-the-art data base of interaction information. The proposed information base would include datamore » that presently are scattered throughout the literature usually in tabulated form. It is expected that the data bases would include at least the most precise data available in photoelectric cross sections, atomic form factors and incoherent scattering functions, anomalous scattering factors, oscillator strengths and oscillator densities, fluorescence yields, Auger electron yields, etc. It could also include information not presently available in tabulations or in existing data bases such as EXAFS (extended x-ray absorption fine structure) reference spectra, chemical bonding induced shifts in the photoelectric absorption edge, matrix corrections, x-ray Raman, and x-ray resonant Raman cross sections. The data base will also include the best estimates of the accuracy of the interaction data as it exists in the data base. It is proposed that the PDS would support computer programs written for calculating scattering cross sections for given solid angles, sample geometries, and polarization of incident x-rays, for calculating Compton profiles, and for analyzing data as in EXAFS and x-ray fluorescence.« less

Establishment of a Photon Data Section of the BNL National Nuclear Data Center: A preliminary proposal

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

Hanson, A.L.; Pearlstein, S.

1992-05-01

It is proposed to establish a Photon Data Section (PDS) of the BNL National Nuclear Data Center (NNDC). This would be a total program encompassing both photon-atom and photon-nucleus interactions. By utilizing the existing NNDC data base management expertise and on-line access capabilities, the implementation of photon interaction data activities within the existing NNDC nuclear structure and nuclear-reaction activities can reestablish a viable photon interaction data program at minimum cost. By taking advantage of the on-line capabilities, the x-ray users` community will have access to a dynamic, state-of-the-art data base of interaction information. The proposed information base would include datamore » that presently are scattered throughout the literature usually in tabulated form. It is expected that the data bases would include at least the most precise data available in photoelectric cross sections, atomic form factors and incoherent scattering functions, anomalous scattering factors, oscillator strengths and oscillator densities, fluorescence yields, Auger electron yields, etc. It could also include information not presently available in tabulations or in existing data bases such as EXAFS (extended x-ray absorption fine structure) reference spectra, chemical bonding induced shifts in the photoelectric absorption edge, matrix corrections, x-ray Raman, and x-ray resonant Raman cross sections. The data base will also include the best estimates of the accuracy of the interaction data as it exists in the data base. It is proposed that the PDS would support computer programs written for calculating scattering cross sections for given solid angles, sample geometries, and polarization of incident x-rays, for calculating Compton profiles, and for analyzing data as in EXAFS and x-ray fluorescence.« less

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis.

PubMed

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence.

Yield of bedrock wells in the Nashoba terrane, central and eastern Massachusetts

USGS Publications Warehouse

DeSimone, Leslie A.; Barbaro, Jeffrey R.

2012-01-01

The yield of bedrock wells in the fractured-bedrock aquifers of the Nashoba terrane and surrounding area, central and eastern Massachusetts, was investigated with analyses of existing data. Reported well yield was compiled for 7,287 wells from Massachusetts Department of Environmental Protection and U.S. Geological Survey databases. Yield of these wells ranged from 0.04 to 625 gallons per minute. In a comparison with data from 103 supply wells, yield and specific capacity from aquifer tests were well correlated, indicating that reported well yield was a reasonable measure of aquifer characteristics in the study area. Statistically significant relations were determined between well yield and a number of cultural and hydrogeologic factors. Cultural variables included intended water use, well depth, year of construction, and method of yield measurement. Bedrock geology, topography, surficial geology, and proximity to surface waters were statistically significant hydrogeologic factors. Yield of wells was higher in areas of granites, mafic intrusive rocks, and amphibolites than in areas of schists and gneisses or pelitic rocks; higher in valleys and low-slope areas than on hills, ridges, or high slopes; higher in areas overlain by stratified glacial deposits than in areas overlain by till; and higher in close proximity to streams, ponds, and wetlands than at greater distances from these surface-water features. Proximity to mapped faults and to lineaments from aerial photographs also were related to well yield by some measures in three quadrangles in the study area. Although the statistical significance of these relations was high, their predictive power was low, and these relations explained little of the variability in the well-yield data. Similar results were determined from a multivariate regression analysis. Multivariate regression models for the Nashoba terrane and for a three-quadrangle subarea included, as significant variables, many of the cultural and hydrogeologic factors that were individually related to well yield, in ways that are consistent with conceptual understanding of their effects, but the models explained only 21 percent (regional model for the entire terrane) and 30 percent (quadrangle model) of the overall variance in yield. Moreover, most of the explained variance was due to well characteristics rather than hydrogeologic factors. Hydrogeologic factors such as topography and geology are likely important. However, the overall high variability in the well-yield data, which results from the high variability in aquifer hydraulic properties as well as from limitations of the dataset, would make it difficult to use hydrogeologic factors to predict well yield in the study area. Geostatistical analysis (variograms), on the other hand, indicated that, although highly variable, the well-yield data are spatially correlated. The spatial continuity appears greater in the northeast-southwest direction and less in the southeast-northwest direction, directions that are parallel and perpendicular, respectively, to the regional geologic structural trends. Geostatistical analysis (kriging), used to estimate yield values throughout the study area, identified regional-scale areas of higher and lower yield that may be related to regional structural features—in particular, to a northeast-southwest trending regional fault zone within the Nashoba terrane. It also would be difficult to use kriging to predict yield at specific locations, however, because of the spatial variability in yield, particularly at small scales. The regional-scale analyses in this study, both with hydrogeologic variables and geostatistics, provide a context for understanding the variability in well yield, rather a basis for precise predictions, and site-specific information would be needed to understand local conditions.

Visualization of Topology through Simulation

NASA Astrophysics Data System (ADS)

Mulderig, Andrew; Beaucage, Gregory; Vogtt, Karsten; Jiang, Hanqiu

Complex structures can be decomposed into their minimal topological description coupled with complications of tortuosity. We have found that a stick figure representation can account for the topological content of any structure and coupling with scaling measures of tortuosity we can reconstruct an object. This deconstruction is native to static small-angle scattering measurements where we can obtain quantitative measures of the tortuous structure and the minimal topological structure. For example, a crumpled sheet of paper is composed of a minimal sheet structure and parameters reflecting the extent of crumpling. This quantification yields information that can be used to calculate the hydrodynamic radius, radius of gyration, structural conductive pathway, modulus, and other properties of complex structures. The approach is general and has been applied to a wide range of nanostructures from crumpled graphene to branched polymers and unfolded proteins and RNA. In this poster we will demonstrate how simple structural simulations can be used to reconstruct from these parameters a 3d representation of the complex structure through a heuristic approach. Several examples will be given from nano-fractal aggregates.

An optimal transportation approach for nuclear structure-based pathology.

PubMed

Wang, Wei; Ozolek, John A; Slepčev, Dejan; Lee, Ann B; Chen, Cheng; Rohde, Gustavo K

2011-03-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g., normal versus cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers.

An optimal transportation approach for nuclear structure-based pathology

PubMed Central

Wang, Wei; Ozolek, John A.; Slepčev, Dejan; Lee, Ann B.; Chen, Cheng; Rohde, Gustavo K.

2012-01-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g. normal vs. cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers. PMID:20977984

The intellectual core of enterprise information systems: a co-citation analysis

NASA Astrophysics Data System (ADS)

Shiau, Wen-Lung

2016-10-01

Enterprise information systems (EISs) have evolved in the past 20 years, attracting the attention of international practitioners and scholars. Although literature reviews and analyses have been conducted to examine the multiple dimensions of EISs, no co-citation analysis has been conducted to examine the knowledge structures involved in EIS studies; thus, the current study fills this research gap. This study investigated the intellectual structures of EISs. All data source documents (1083 articles and 24,090 citations) were obtained from the Institute for Scientific Information Web of Knowledge database. A co-citation analysis was used to analyse EIS data. By using factor analysis, we identified eight critical factors: (a) factors affecting the implementation and success of information systems (ISs); (b) the successful implementation of enterprise resource planning (ERP); (c) IS evaluation and success, (d) system science studies; (e) factors influencing ERP success; (f) case research and theoretical models; (g) user acceptance of information technology; and (h) IS frameworks. Multidimensional scaling and cluster analysis were used to visually map the resultant EIS knowledge. It is difficult to implement an EIS in an enterprise and each organisation exhibits specific considerations. The current findings indicate that managers must focus on ameliorating inferior project performance levels, enabling a transition from 'vicious' to 'virtuous' projects. Successful EIS implementation yields substantial organisational advantages.

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

Venkadesh, S.; Mandal, P.K.; Gautham, N., E-mail: n_gautham@hotmail.com

Highlights: {yields} This is the first crystal structure of a four-way junction with sticky ends. {yields} Four junction structures bind to each other and form a rhombic cavity. {yields} Each rhombus binds to others to form 'infinite' 2D tiles. {yields} This is an example of bottom-up fabrication of a DNA nano-lattice. -- Abstract: We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind tomore » each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5 A. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.« less

Structure of S-shaped growth in innovation diffusion

NASA Astrophysics Data System (ADS)

Shimogawa, Shinsuke; Shinno, Miyuki; Saito, Hiroshi

2012-05-01

A basic question on innovation diffusion is why the growth curve of the adopter population in a large society is often S shaped. From macroscopic, microscopic, and mesoscopic viewpoints, the growth of the adopter population is observed as the growth curve, individual adoptions, and differences among individual adoptions, respectively. The S shape can be explained if an empirical model of the growth curve can be deduced from models of microscopic and mesoscopic structures. However, even the structure of growth curve has not been revealed yet because long-term extrapolations by proposed models of S-shaped curves are unstable and it has been very difficult to predict the long-term growth and final adopter population. This paper studies the S-shaped growth from the viewpoint of social regularities. Simple methods to analyze power laws enable us to extract the structure of the growth curve directly from the growth data of recent basic telecommunication services. This empirical model of growth curve is singular at the inflection point and a logarithmic function of time after this point, which explains the unstable extrapolations obtained using previously proposed models and the difficulty in predicting the final adopter population. Because the empirical S curve can be expressed in terms of two power laws of the regularity found in social performances of individuals, we propose the hypothesis that the S shape represents the heterogeneity of the adopter population, and the heterogeneity parameter is distributed under the regularity in social performances of individuals. This hypothesis is so powerful as to yield models of microscopic and mesoscopic structures. In the microscopic model, each potential adopter adopts the innovation when the information accumulated by the learning about the innovation exceeds a threshold. The accumulation rate of information is heterogeneous among the adopter population, whereas the threshold is a constant, which is the opposite of previously proposed models. In the mesoscopic model, flows of innovation information incoming to individuals are organized as dimorphic and partially clustered. These microscopic and mesoscopic models yield the empirical model of the S curve and explain the S shape as representing the regularities of information flows generated through a social self-organization. To demonstrate the validity and importance of the hypothesis, the models of three level structures are applied to reveal the mechanism determining and differentiating diffusion speeds. The empirical model of S curves implies that the coefficient of variation of the flow rates determines the diffusion speed for later adopters. Based on this property, a model describing the inside of information flow clusters can be given, which provides a formula interconnecting the diffusion speed, cluster populations, and a network topological parameter of the flow clusters. For two recent basic telecommunication services in Japan, the formula represents the variety of speeds in different areas and enables us to explain speed gaps between urban and rural areas and between the two services. Furthermore, the formula provides a method to estimate the final adopter population.

Estimation by simulation of the efficiency of the French marker-assisted selection program in dairy cattle (Open Access publication)

PubMed Central

Guillaume, François; Fritz, Sébastien; Boichard, Didier; Druet, Tom

2008-01-01

The efficiency of the French marker-assisted selection (MAS) was estimated by a simulation study. The data files of two different time periods were used: April 2004 and 2006. The simulation method used the structure of the existing French MAS: same pedigree, same marker genotypes and same animals with records. The program simulated breeding values and new records based on this existing structure and knowledge on the QTL used in MAS (variance and frequency). Reliabilities of genetic values of young animals (less than one year old) obtained with and without marker information were compared to assess the efficiency of MAS for evaluation of milk, fat and protein yields and fat and protein contents. Mean gains of reliability ranged from 0.015 to 0.094 and from 0.038 to 0.114 in 2004 and 2006, respectively. The larger number of animals genotyped and the use of a new set of genetic markers can explain the improvement of MAS reliability from 2004 to 2006. This improvement was also observed by analysis of information content for young candidates. The gain of MAS reliability with respect to classical selection was larger for sons of sires with genotyped progeny daughters with records. Finally, it was shown that when superiority of MAS over classical selection was estimated with daughter yield deviations obtained after progeny test instead of true breeding values, the gain was underestimated. PMID:18096117

An Abraded Surface of Doxorubicin-Loaded Surfactant-Containing Drug Delivery Systems Effectively Reduces the Survival of Carcinoma Cells.

PubMed

Schmidt, Christian; Yokaichiya, Fabiano; Doğangüzel, Nurdan; Dias Franco, Margareth K K; Cavalcanti, Leide P; Brown, Mark A; Alkschbirs, Melissa I; de Araujo, Daniele R; Kumpugdee-Vollrath, Mont; Storsberg, Joachim

2016-09-15

An effective antitumor remedy is yet to be developed. All previous approaches for a targeted delivery of anticancer medicine have relied on trial and error. The goal of this study was to use structural insights gained from the study of delivery systems and malignant cells to provide for a systematic approach to the development of next-generation drugs. We used doxorubicin (Dox) liposomal formulations. We assayed for cytotoxicity via the electrical current exclusion method. Dialysis of the samples yielded information about their drug release profiles. Information about the surface of the delivery systems was obtained through synchrotron small-angle X-ray scattering (SAXS) measurements. SAXS measurements revealed that Dox-loading yielded an abraded surface of our Dox liposomal formulation containing soybean oil, which also correlated with an effective reduction of the survival of carcinoma cells. Furthermore, a dialysis assay revealed that a higher burst of Dox was released from soybean oil-containing preparations within the first five hours. We conclude from our results that an abraded surface of Dox-loaded drug delivery system increases their efficacy. The apparent match between surface geometry of drug delivery systems and target cells is suggested as a steppingstone for refined development of drug delivery systems. This is the first study to provide a systematic approach to developing next-generation drug carrier systems using structural insights to guide the development of next-generation drug delivery systems with increased efficacy and reduced side effects.

A global experimental dataset for assessing grain legume production

PubMed Central

Cernay, Charles; Pelzer, Elise; Makowski, David

2016-01-01

Grain legume crops are a significant component of the human diet and animal feed and have an important role in the environment, but the global diversity of agricultural legume species is currently underexploited. Experimental assessments of grain legume performances are required, to identify potential species with high yields. Here, we introduce a dataset including results of field experiments published in 173 articles. The selected experiments were carried out over five continents on 39 grain legume species. The dataset includes measurements of grain yield, aerial biomass, crop nitrogen content, residual soil nitrogen content and water use. When available, yields for cereals and oilseeds grown after grain legumes in the crop sequence are also included. The dataset is arranged into a relational database with nine structured tables and 198 standardized attributes. Tillage, fertilization, pest and irrigation management are systematically recorded for each of the 8,581 crop*field site*growing season*treatment combinations. The dataset is freely reusable and easy to update. We anticipate that it will provide valuable information for assessing grain legume production worldwide. PMID:27676125

Uncertainty in simulating wheat yields under climate change

NASA Astrophysics Data System (ADS)

Asseng, S.; Ewert, F.; Rosenzweig, C.; Jones, J. W.; Hatfield, J. L.; Ruane, A. C.; Boote, K. J.; Thorburn, P. J.; Rötter, R. P.; Cammarano, D.; Brisson, N.; Basso, B.; Martre, P.; Aggarwal, P. K.; Angulo, C.; Bertuzzi, P.; Biernath, C.; Challinor, A. J.; Doltra, J.; Gayler, S.; Goldberg, R.; Grant, R.; Heng, L.; Hooker, J.; Hunt, L. A.; Ingwersen, J.; Izaurralde, R. C.; Kersebaum, K. C.; Müller, C.; Naresh Kumar, S.; Nendel, C.; O'Leary, G.; Olesen, J. E.; Osborne, T. M.; Palosuo, T.; Priesack, E.; Ripoche, D.; Semenov, M. A.; Shcherbak, I.; Steduto, P.; Stöckle, C.; Stratonovitch, P.; Streck, T.; Supit, I.; Tao, F.; Travasso, M.; Waha, K.; Wallach, D.; White, J. W.; Williams, J. R.; Wolf, J.

2013-09-01

Projections of climate change impacts on crop yields are inherently uncertain. Uncertainty is often quantified when projecting future greenhouse gas emissions and their influence on climate. However, multi-model uncertainty analysis of crop responses to climate change is rare because systematic and objective comparisons among process-based crop simulation models are difficult. Here we present the largest standardized model intercomparison for climate change impacts so far. We found that individual crop models are able to simulate measured wheat grain yields accurately under a range of environments, particularly if the input information is sufficient. However, simulated climate change impacts vary across models owing to differences in model structures and parameter values. A greater proportion of the uncertainty in climate change impact projections was due to variations among crop models than to variations among downscaled general circulation models. Uncertainties in simulated impacts increased with CO2 concentrations and associated warming. These impact uncertainties can be reduced by improving temperature and CO2 relationships in models and better quantified through use of multi-model ensembles. Less uncertainty in describing how climate change may affect agricultural productivity will aid adaptation strategy development andpolicymaking.

One-pot and ultrafast synthesis of nitrogen and phosphorus co-doped carbon dots possessing bright dual wavelength fluorescence emission

NASA Astrophysics Data System (ADS)

Sun, Xiangcheng; Brückner, Christian; Lei, Yu

2015-10-01

Very brief microwave heating of aniline, ethylene diamine, and phosphoric acid in water at ambient pressure generated nitrogen and phosphorus co-doped carbon dots (N,P-CDs) that exhibit bright dual blue (centred at 450 nm; 51% quantum yield) and green (centred at 510 nm, 38% quantum yield) fluorescence emission bands. The N,P-CDs were characterized using TEM, XRD, XPS, IR, UV-vis, and fluorescence spectroscopy, demonstrating their partially crystalline carbon, partially amorphous structures, and the incorporation of O, N, and P into the carbogenic scaffold. The N,P-CDs demonstrated excitation-dependent and nearly pH-independent emission properties. The unique dual emission properties lay the foundation for the use of N,P-CDs in ratiometric sensing applications.Very brief microwave heating of aniline, ethylene diamine, and phosphoric acid in water at ambient pressure generated nitrogen and phosphorus co-doped carbon dots (N,P-CDs) that exhibit bright dual blue (centred at 450 nm; 51% quantum yield) and green (centred at 510 nm, 38% quantum yield) fluorescence emission bands. The N,P-CDs were characterized using TEM, XRD, XPS, IR, UV-vis, and fluorescence spectroscopy, demonstrating their partially crystalline carbon, partially amorphous structures, and the incorporation of O, N, and P into the carbogenic scaffold. The N,P-CDs demonstrated excitation-dependent and nearly pH-independent emission properties. The unique dual emission properties lay the foundation for the use of N,P-CDs in ratiometric sensing applications. Electronic supplementary information (ESI) available: Detailed experimental section, XRD, FTIR, explosive sensing and the applications results. See DOI: 10.1039/c5nr05549k

Channel morphology and bed-load yield in fluvial, formerly-glaciated headwater streams of the Columbia Mountains, Canada

NASA Astrophysics Data System (ADS)

Green, K. C.; Brardinoni, F.; Alila, Y.

2013-04-01

This study examines channel-reach morphology and bedload yield dynamics in relation to landscape structure and snowmelt hydrology in headwater streams of the Columbia Mountains, Canada. Data collection relies on field surveys and geographic information systems analysis in conjunction with a nested monitoring network of water discharge and bedload transfer. The landscape is characterized by subdued, formerly-glaciated upland topography in which the geomorphic significance of landslides and debris flows is negligible and fluvial processes prevail. While the spatial organization of channel morphology is chiefly controlled by glacially imposed local slope in conjunction with wood abundance and availability of glacigenic deposits, downstream patterns of the coarse grain-size fraction, bankfull width, bankfull depth, and stream power are all insensitive to systematic changes of local slope along the typically stepped long profiles. This is an indication that these alluvial systems have adjusted to the contemporary snowmelt-driven water and sediment transport regimes, and as such are able to compensate for the glacially-imposed boundary conditions. Bedload specific yield increases with drainage area suggesting that fluvial re-mobilization of glacial and paraglacial deposits dominate the sedimentary dynamics of basins as small as 2 km2. Stepwise multiple regression analysis shows that annual rates of sediment transfer are mainly controlled by the number of peak events over threshold discharge. During such events, repeated destabilization of channel bed armoring and re-mobilization of sediment temporarily stored behind LWD structures can generate bedload transport across the entire snowmelt season. In particular, channel morphology controls the variability of bedload response to hydrologic forcing. In the present case studies, we show that the observed spatial variability in annual bedload yield appears to be modulated by inter-basin differences in morphometric characteristics, among which slope aspect plays a critical part.

A probabilistic model framework for evaluating year-to-year variation in crop productivity

NASA Astrophysics Data System (ADS)

Yokozawa, M.; Iizumi, T.; Tao, F.

2008-12-01

Most models describing the relation between crop productivity and weather condition have so far been focused on mean changes of crop yield. For keeping stable food supply against abnormal weather as well as climate change, evaluating the year-to-year variations in crop productivity rather than the mean changes is more essential. We here propose a new framework of probabilistic model based on Bayesian inference and Monte Carlo simulation. As an example, we firstly introduce a model on paddy rice production in Japan. It is called PRYSBI (Process- based Regional rice Yield Simulator with Bayesian Inference; Iizumi et al., 2008). The model structure is the same as that of SIMRIW, which was developed and used widely in Japan. The model includes three sub- models describing phenological development, biomass accumulation and maturing of rice crop. These processes are formulated to include response nature of rice plant to weather condition. This model inherently was developed to predict rice growth and yield at plot paddy scale. We applied it to evaluate the large scale rice production with keeping the same model structure. Alternatively, we assumed the parameters as stochastic variables. In order to let the model catch up actual yield at larger scale, model parameters were determined based on agricultural statistical data of each prefecture of Japan together with weather data averaged over the region. The posterior probability distribution functions (PDFs) of parameters included in the model were obtained using Bayesian inference. The MCMC (Markov Chain Monte Carlo) algorithm was conducted to numerically solve the Bayesian theorem. For evaluating the year-to-year changes in rice growth/yield under this framework, we firstly iterate simulations with set of parameter values sampled from the estimated posterior PDF of each parameter and then take the ensemble mean weighted with the posterior PDFs. We will also present another example for maize productivity in China. The framework proposed here provides us information on uncertainties, possibilities and limitations on future improvements in crop model as well.

Effects of phenylpropanolamine (PPA) on in vitro human erythrocyte membranes and molecular models

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

Suwalsky, Mario, E-mail: msuwalsk@udec.cl; Zambrano, Pablo; Mennickent, Sigrid

Research highlights: {yields} PPA is a common ingredient in cough-cold medication and appetite suppressants. {yields} Reports on its effects on human erythrocytes are very scarce. {yields} We found that PPA induced in vitro morphological changes to human erythrocytes. {yields} PPA interacted with isolated unsealed human erythrocyte membranes. {yields} PPA interacted with class of lipid present in the erythrocyte membrane outer monolayer. -- Abstract: Norephedrine, also called phenylpropanolamine (PPA), is a synthetic form of the ephedrine alkaloid. After reports of the occurrence of intracranial hemorrhage and other adverse effects, including several deaths, PPA is no longer sold in USA and Canada.more » Despite the extensive information about PPA toxicity, reports on its effects on cell membranes are scarce. With the aim to better understand the molecular mechanisms of the interaction of PPA with cell membranes, ranges of concentrations were incubated with intact human erythrocytes, isolated unsealed human erythrocyte membranes (IUM), and molecular models of cell membranes. The latter consisted in bilayers built-up of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), phospholipid classes present in the outer and inner monolayers of most plasmatic cell membranes, respectively. The capacity of PPA to perturb the bilayer structures of DMPC and DMPE was assessed by X-ray diffraction, DMPC large unilamellar vesicles (LUV) and IUM were studied by fluorescence spectroscopy, and intact human erythrocytes were observed by scanning electron microscopy (SEM). This study presents evidence that PPA affects human red cell membranes as follows: (a) in SEM studies on human erythrocytes it was observed that 0.5 mM PPA induced shape changes; (b) in IUM PPA induced a sharp decrease in the fluorescence anisotropy in the lipid bilayer acyl chains in a concentration range lower than 100 {mu}M; (c) X-ray diffraction studies showed that PPA in the 0.1-0.5 mM range induced increasing structural perturbation to DMPC, but no effects on DMPE multibilayers were detected.« less

A method for the on-site determination of prestressing forces using long-gauge fiber optic strain sensors

NASA Astrophysics Data System (ADS)

Abdel-Jaber, H.; Glisic, B.

2014-07-01

Structural health monitoring (SHM) consists of the continuous or periodic measurement of structural parameters and their analysis with the aim of deducing information about the performance and health condition of a structure. The significant increase in the construction of prestressed concrete bridges motivated this research on an SHM method for the on-site determination of the distribution of prestressing forces along prestressed concrete beam structures. The estimation of the distribution of forces is important as it can give information regarding the overall performance and structural integrity of the bridge. An inadequate transfer of the designed prestressing forces to the concrete cross-section can lead to a reduced capacity of the bridge and consequently malfunction or failure at lower loads than predicted by design. This paper researches a universal method for the determination of the distribution of prestressing forces along concrete beam structures at the time of transfer of the prestressing force (e.g., at the time of prestressing or post-tensioning). The method is based on the use of long-gauge fiber optic sensors, and the sensor network is similar (practically identical) to the one used for damage identification. The method encompasses the determination of prestressing forces at both healthy and cracked cross-sections, and for the latter it can yield information about the condition of the cracks. The method is validated on-site by comparison to design forces through the application to two structures: (1) a deck-stiffened arch and (2) a curved continuous girder. The uncertainty in the determination of prestressing forces was calculated and the comparison with the design forces has shown very good agreement in most of the structures’ cross-sections, but also helped identify some unusual behaviors. The method and its validation are presented in this paper.

Embodied memory allows accurate and stable perception of hidden objects despite orientation change.

PubMed

Pan, Jing Samantha; Bingham, Ned; Bingham, Geoffrey P

2017-07-01

Rotating a scene in a frontoparallel plane (rolling) yields a change in orientation of constituent images. When using only information provided by static images to perceive a scene after orientation change, identification performance typically decreases (Rock & Heimer, 1957). However, rolling generates optic flow information that relates the discrete, static images (before and after the change) and forms an embodied memory that aids recognition. The embodied memory hypothesis predicts that upon detecting a continuous spatial transformation of image structure, or in other words, seeing the continuous rolling process and objects undergoing rolling observers should accurately perceive objects during and after motion. Thus, in this case, orientation change should not affect performance. We tested this hypothesis in three experiments and found that (a) using combined optic flow and image structure, participants identified locations of previously perceived but currently occluded targets with great accuracy and stability (Experiment 1); (b) using combined optic flow and image structure information, participants identified hidden targets equally well with or without 30° orientation changes (Experiment 2); and (c) when the rolling was unseen, identification of hidden targets after orientation change became worse (Experiment 3). Furthermore, when rolling was unseen, although target identification was better when participants were told about the orientation change than when they were not told, performance was still worse than when there was no orientation change. Therefore, combined optic flow and image structure information, not mere knowledge about the rolling, enables accurate and stable perception despite orientation change. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Architectural Survey of Pershing Elementary School, Fort Leonard Wood, Missouri

DTIC Science & Technology

2013-08-01

information important in prehistory or history. 16 NPS 1991. 17 Excerpted from...school has yielded, or was likely to yield, any information important in prehistory or history. Final Determination for Building 6501 It is the

Static High Pressure Structural studies on Dy to 119 GPa

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

Patterson, J R; Saw, C K; Akella, J

2003-11-12

Structural phase transitions in the rare-earth metal Dysprosium have been studied in a Diamond Anvil Cell (DAC) to 119 GPa by x-ray diffraction. Four transformations following the sequence hcp {yields} Sm-type {yields} dhcp {yields} hR24 (hexagonal) {yields} bcm (monoclinic) are observed at 6, 15, 43, and 73 GPa respectively. The hexagonal to monoclinic transformation is accompanied by a 6% reduction in volume, which is attributed to delocalization of the 4f electrons, similar to that seen in Ce, Pr, and Gd.

A Computational Approach From Gene to Structure Analysis of the Human ABCA4 Transporter Involved in Genetic Retinal Diseases.

PubMed

Trezza, Alfonso; Bernini, Andrea; Langella, Andrea; Ascher, David B; Pires, Douglas E V; Sodi, Andrea; Passerini, Ilaria; Pelo, Elisabetta; Rizzo, Stanislao; Niccolai, Neri; Spiga, Ottavia

2017-10-01

The aim of this article is to report the investigation of the structural features of ABCA4, a protein associated with a genetic retinal disease. A new database collecting knowledge of ABCA4 structure may facilitate predictions about the possible functional consequences of gene mutations observed in clinical practice. In order to correlate structural and functional effects of the observed mutations, the structure of mouse P-glycoprotein was used as a template for homology modeling. The obtained structural information and genetic data are the basis of our relational database (ABCA4Database). Sequence variability among all ABCA4-deposited entries was calculated and reported as Shannon entropy score at the residue level. The three-dimensional model of ABCA4 structure was used to locate the spatial distribution of the observed variable regions. Our predictions from structural in silico tools were able to accurately link the functional effects of mutations to phenotype. The development of the ABCA4Database gathers all the available genetic and structural information, yielding a global view of the molecular basis of some retinal diseases. ABCA4 modeled structure provides a molecular basis on which to analyze protein sequence mutations related to genetic retinal disease in order to predict the risk of retinal disease across all possible ABCA4 mutations. Additionally, our ABCA4 predicted structure is a good starting point for the creation of a new data analysis model, appropriate for precision medicine, in order to develop a deeper knowledge network of the disease and to improve the management of patients.

Designing and benchmarking the MULTICOM protein structure prediction system

PubMed Central

2013-01-01

Background Predicting protein structure from sequence is one of the most significant and challenging problems in bioinformatics. Numerous bioinformatics techniques and tools have been developed to tackle almost every aspect of protein structure prediction ranging from structural feature prediction, template identification and query-template alignment to structure sampling, model quality assessment, and model refinement. How to synergistically select, integrate and improve the strengths of the complementary techniques at each prediction stage and build a high-performance system is becoming a critical issue for constructing a successful, competitive protein structure predictor. Results Over the past several years, we have constructed a standalone protein structure prediction system MULTICOM that combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model generation, model assessment, and model refinement. The system was blindly tested during the ninth Critical Assessment of Techniques for Protein Structure Prediction (CASP9) in 2010 and yielded very good performance. In addition to studying the overall performance on the CASP9 benchmark, we thoroughly investigated the performance and contributions of each component at each stage of prediction. Conclusions Our comprehensive and comparative study not only provides useful and practical insights about how to select, improve, and integrate complementary methods to build a cutting-edge protein structure prediction system but also identifies a few new sources of information that may help improve the design of a protein structure prediction system. Several components used in the MULTICOM system are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:23442819

A hybrid system identification methodology for wireless structural health monitoring systems based on dynamic substructuring

NASA Astrophysics Data System (ADS)

Dragos, Kosmas; Smarsly, Kay

2016-04-01

System identification has been employed in numerous structural health monitoring (SHM) applications. Traditional system identification methods usually rely on centralized processing of structural response data to extract information on structural parameters. However, in wireless SHM systems the centralized processing of structural response data introduces a significant communication bottleneck. Exploiting the merits of decentralization and on-board processing power of wireless SHM systems, many system identification methods have been successfully implemented in wireless sensor networks. While several system identification approaches for wireless SHM systems have been proposed, little attention has been paid to obtaining information on the physical parameters (e.g. stiffness, damping) of the monitored structure. This paper presents a hybrid system identification methodology suitable for wireless sensor networks based on the principles of component mode synthesis (dynamic substructuring). A numerical model of the monitored structure is embedded into the wireless sensor nodes in a distributed manner, i.e. the entire model is segmented into sub-models, each embedded into one sensor node corresponding to the substructure the sensor node is assigned to. The parameters of each sub-model are estimated by extracting local mode shapes and by applying the equations of the Craig-Bampton method on dynamic substructuring. The proposed methodology is validated in a laboratory test conducted on a four-story frame structure to demonstrate the ability of the methodology to yield accurate estimates of stiffness parameters. Finally, the test results are discussed and an outlook on future research directions is provided.

The extraction and integration framework: a two-process account of statistical learning.

PubMed

Thiessen, Erik D; Kronstein, Alexandra T; Hufnagle, Daniel G

2013-07-01

The term statistical learning in infancy research originally referred to sensitivity to transitional probabilities. Subsequent research has demonstrated that statistical learning contributes to infant development in a wide array of domains. The range of statistical learning phenomena necessitates a broader view of the processes underlying statistical learning. Learners are sensitive to a much wider range of statistical information than the conditional relations indexed by transitional probabilities, including distributional and cue-based statistics. We propose a novel framework that unifies learning about all of these kinds of statistical structure. From our perspective, learning about conditional relations outputs discrete representations (such as words). Integration across these discrete representations yields sensitivity to cues and distributional information. To achieve sensitivity to all of these kinds of statistical structure, our framework combines processes that extract segments of the input with processes that compare across these extracted items. In this framework, the items extracted from the input serve as exemplars in long-term memory. The similarity structure of those exemplars in long-term memory leads to the discovery of cues and categorical structure, which guides subsequent extraction. The extraction and integration framework provides a way to explain sensitivity to both conditional statistical structure (such as transitional probabilities) and distributional statistical structure (such as item frequency and variability), and also a framework for thinking about how these different aspects of statistical learning influence each other. 2013 APA, all rights reserved

Likelihood analysis of spatial capture-recapture models for stratified or class structured populations

USGS Publications Warehouse

Royle, J. Andrew; Sutherland, Christopher S.; Fuller, Angela K.; Sun, Catherine C.

2015-01-01

We develop a likelihood analysis framework for fitting spatial capture-recapture (SCR) models to data collected on class structured or stratified populations. Our interest is motivated by the necessity of accommodating the problem of missing observations of individual class membership. This is particularly problematic in SCR data arising from DNA analysis of scat, hair or other material, which frequently yields individual identity but fails to identify the sex. Moreover, this can represent a large fraction of the data and, given the typically small sample sizes of many capture-recapture studies based on DNA information, utilization of the data with missing sex information is necessary. We develop the class structured likelihood for the case of missing covariate values, and then we address the scaling of the likelihood so that models with and without class structured parameters can be formally compared regardless of missing values. We apply our class structured model to black bear data collected in New York in which sex could be determined for only 62 of 169 uniquely identified individuals. The models containing sex-specificity of both the intercept of the SCR encounter probability model and the distance coefficient, and including a behavioral response are strongly favored by log-likelihood. Estimated population sex ratio is strongly influenced by sex structure in model parameters illustrating the importance of rigorous modeling of sex differences in capture-recapture models.

Using iMCFA to Perform the CFA, Multilevel CFA, and Maximum Model for Analyzing Complex Survey Data.

PubMed

Wu, Jiun-Yu; Lee, Yuan-Hsuan; Lin, John J H

2018-01-01

To construct CFA, MCFA, and maximum MCFA with LISREL v.8 and below, we provide iMCFA (integrated Multilevel Confirmatory Analysis) to examine the potential multilevel factorial structure in the complex survey data. Modeling multilevel structure for complex survey data is complicated because building a multilevel model is not an infallible statistical strategy unless the hypothesized model is close to the real data structure. Methodologists have suggested using different modeling techniques to investigate potential multilevel structure of survey data. Using iMCFA, researchers can visually set the between- and within-level factorial structure to fit MCFA, CFA and/or MAX MCFA models for complex survey data. iMCFA can then yield between- and within-level variance-covariance matrices, calculate intraclass correlations, perform the analyses and generate the outputs for respective models. The summary of the analytical outputs from LISREL is gathered and tabulated for further model comparison and interpretation. iMCFA also provides LISREL syntax of different models for researchers' future use. An empirical and a simulated multilevel dataset with complex and simple structures in the within or between level was used to illustrate the usability and the effectiveness of the iMCFA procedure on analyzing complex survey data. The analytic results of iMCFA using Muthen's limited information estimator were compared with those of Mplus using Full Information Maximum Likelihood regarding the effectiveness of different estimation methods.

The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

PubMed Central

Briones, Carlos; Stich, Michael; Manrubia, Susanna C.

2009-01-01

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. PMID:19318464

Local structure of In0.5Ga0.5As from joint high-resolution and differential pair distribution function analysis

NASA Astrophysics Data System (ADS)

Petkov, V.; Jeong, I.-K.; Mohiuddin-Jacobs, F.; Proffen, Th.; Billinge, S. J. L.; Dmowski, W.

2000-07-01

High resolution total and indium differential atomic pair distribution functions (PDFs) for In0.5Ga0.5As alloys have been obtained by high energy and anomalous x-ray diffraction experiments, respectively. The first peak in the total PDF is resolved as a doublet due to the presence of two distinct bond lengths, In-As and Ga-As. The In differential PDF, which involves only atomic pairs containing In, yields chemical specific information and helps ease the structure data interpretation. Both PDFs have been fit with structure models and the way in that the underlying cubic zinc-blende lattice of In0.5Ga0.5As semiconductor alloy distorts locally to accommodate the distinct In-As and Ga-As bond lengths present has been quantified.

Laboratory Investigation of the Growth and Crystal Structure of Nitric Acid Hydrates by Transmission Electron Microscopy (TEM)

NASA Technical Reports Server (NTRS)

Blake, David F.; Chang, Sherwood (Technical Monitor)

1994-01-01

A great deal of recent laboratory work has focussed on the characterization of the nitric acid hydrates, thought to be present in type I Polar Stratospheric Clouds (PSCs). Phase relationships and vapor pressure measurements (1-3) and infrared characterizations (4-5) have been made. However, the observed properties of crystalline solids (composition, melting point, vapor pressure, surface reactivity, thermodynamic stability, extent of solid solution with other components, etc.) are controlled by their crystal structure. The only means of unequivocal structural identification for crystalline solids is diffraction (using electrons, X-rays, neutrons, etc.). Other observed properties of crystalline solids, such as their infrared spectra, their vapor pressure as a function of temperature, etc. yield only indirect information about what phases are present, their relative proportions, or whether they are crystalline or amorphous.

Enhanced intersystem crossing in core-twisted aromatics† †Electronic supplementary information (ESI) available: Includes details of the synthesis, structural information for all of the compounds (NMR, elemental analysis and mass spectra) and experimental details for the photophysical studies. CCDC 1402604 and 1402605. For ESI and crystallographic data in CIF or other electronic formats see DOI: 10.1039/c6sc05126j Click here for additional data file. Click here for additional data file.

PubMed Central

Nagarajan, Kalaivanan; Mallia, Ajith R.; Muraleedharan, Keerthi

2017-01-01

We describe the design, bottom-up synthesis and X-ray single crystal structure of systematically twisted aromatics 1c and 2d for efficient intersystem crossing. Steric congestion at the cove region creates a nonplanar geometry that induces a significant yield of triplet excited states in the electron-poor core-twisted aromatics 1c and 2d. A systematic increase in the number of twisted regions in 1c and 2d results in a concomitant enhancement in the rate and yield of intersystem crossing, monitored using femtosecond and nanosecond transient absorption spectroscopy. Time-resolved absorption spectroscopic measurements display enhanced triplet quantum yields (Φ T = 10 ± 1% for 1c and Φ T = 30 ± 2% for 2d) in the twisted aromatics when compared to a negligible Φ T (<1%) in the planar analog 3c. Twist-induced spin–orbit coupling via activated out-of-plane C–H/C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C vibrations can facilitate the formation of triplet excited states in twisted aromatics 1c and 2d, in contrast to the negligible intersystem crossing in the planar analog 3c. The ease of synthesis, high solubility, access to triplet excited states and strong electron affinity make such imide functionalized core-twisted aromatics desirable materials for organic electronics such as solar cells. PMID:28694952

Insights into Fanconi Anaemia from the structure of human FANCE

PubMed Central

Nookala, Ravi K.; Hussain, Shobbir; Pellegrini, Luca

2007-01-01

Fanconi Anaemia (FA) is a cancer predisposition disorder characterized by spontaneous chromosome breakage and high cellular sensitivity to genotoxic agents. In response to DNA damage, a multi-subunit assembly of FA proteins, the FA core complex, monoubiquitinates the downstream FANCD2 protein. The FANCE protein plays an essential role in the FA process of DNA repair as the FANCD2-binding component of the FA core complex. Here we report a crystallographic and biological study of human FANCE. The first structure of a FA protein reveals the presence of a repeated helical motif that provides a template for the structural rationalization of other proteins defective in Fanconi Anaemia. The portion of FANCE defined by our crystallographic analysis is sufficient for interaction with FANCD2, yielding structural information into the mode of FANCD2 recruitment to the FA core complex. Disease-associated mutations disrupt the FANCE–FANCD2 interaction, providing structural insight into the molecular mechanisms of FA pathogenesis. PMID:17308347

Spatial planning using probabilistic flood maps

NASA Astrophysics Data System (ADS)

Alfonso, Leonardo; Mukolwe, Micah; Di Baldassarre, Giuliano

2015-04-01

Probabilistic flood maps account for uncertainty in flood inundation modelling and convey a degree of certainty in the outputs. Major sources of uncertainty include input data, topographic data, model structure, observation data and parametric uncertainty. Decision makers prefer less ambiguous information from modellers; this implies that uncertainty is suppressed to yield binary flood maps. Though, suppressing information may potentially lead to either surprise or misleading decisions. Inclusion of uncertain information in the decision making process is therefore desirable and transparent. To this end, we utilise the Prospect theory and information from a probabilistic flood map to evaluate potential decisions. Consequences related to the decisions were evaluated using flood risk analysis. Prospect theory explains how choices are made given options for which probabilities of occurrence are known and accounts for decision makers' characteristics such as loss aversion and risk seeking. Our results show that decision making is pronounced when there are high gains and loss, implying higher payoffs and penalties, therefore a higher gamble. Thus the methodology may be appropriately considered when making decisions based on uncertain information.

Methods for Remote Determination of CO2 Emissions

DTIC Science & Technology

2011-01-01

support monitoring of compliance with international agreements. • It is difficult to predict when direct measurements of CO2 will yield useful emission...level of reasonable prior information, which is combined with the direct measurements to yield an emissions estimate. This prior information might...infrastructure of a country could yield a “proxy” estimate of CO2 emissions by assuming emission factors for various supply and demand sectors a

Regional crop yield forecasting: a probabilistic approach

NASA Astrophysics Data System (ADS)

de Wit, A.; van Diepen, K.; Boogaard, H.

2009-04-01

Information on the outlook on yield and production of crops over large regions is essential for government services dealing with import and export of food crops, for agencies with a role in food relief, for international organizations with a mandate in monitoring the world food production and trade, and for commodity traders. Process-based mechanistic crop models are an important tool for providing such information, because they can integrate the effect of crop management, weather and soil on crop growth. When properly integrated in a yield forecasting system, the aggregated model output can be used to predict crop yield and production at regional, national and continental scales. Nevertheless, given the scales at which these models operate, the results are subject to large uncertainties due to poorly known weather conditions and crop management. Current yield forecasting systems are generally deterministic in nature and provide no information about the uncertainty bounds on their output. To improve on this situation we present an ensemble-based approach where uncertainty bounds can be derived from the dispersion of results in the ensemble. The probabilistic information provided by this ensemble-based system can be used to quantify uncertainties (risk) on regional crop yield forecasts and can therefore be an important support to quantitative risk analysis in a decision making process.

Status of growth and yield information for northern forest types

Treesearch

Dale S. Solomon

1977-01-01

Existing regional growth-and-yield information for most of the northern forest types is summarized by species. Present research is concentrated on growth-simulation models, constructed by either aggregating available information or through individual tree growth studies. A uniformity of more refined measurements is needed so that future growth models can be tried for...

Novel cookie-with-chocolate carbon dots displaying extremely acidophilic high luminescence

NASA Astrophysics Data System (ADS)

Lu, Siyu; Zhao, Xiaohuan; Zhu, Shoujun; Song, Yubin; Yang, Bai

2014-10-01

A fluorescent carbon dot with a cookie-with-chocolate film structure (about 5 × 5 μm2) showed a high fluorescence quantum yield (61.12%) at low pH. It was hydrothermally synthesized from l-serine and l-tryptophan. The formation mechanism of the film with carbon dots (CDs) was investigated. The film structure was formed by hydrogen bonding and π-π stacking interactions between aromatic rings. The strong blue fluorescence of the CDs increased under strong acidic conditions owing to the changes in the N-groups. These cookie-like CDs are attractive for their potential use as effective fluorescent probes for the sensitive detection of aqueous H+ and Fe3+.A fluorescent carbon dot with a cookie-with-chocolate film structure (about 5 × 5 μm2) showed a high fluorescence quantum yield (61.12%) at low pH. It was hydrothermally synthesized from l-serine and l-tryptophan. The formation mechanism of the film with carbon dots (CDs) was investigated. The film structure was formed by hydrogen bonding and π-π stacking interactions between aromatic rings. The strong blue fluorescence of the CDs increased under strong acidic conditions owing to the changes in the N-groups. These cookie-like CDs are attractive for their potential use as effective fluorescent probes for the sensitive detection of aqueous H+ and Fe3+. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03965c

Predicting Great Lakes fish yields: tools and constraints

USGS Publications Warehouse

Lewis, C.A.; Schupp, D.H.; Taylor, W.W.; Collins, J.J.; Hatch, Richard W.

1987-01-01

Prediction of yield is a critical component of fisheries management. The development of sound yield prediction methodology and the application of the results of yield prediction are central to the evolution of strategies to achieve stated goals for Great Lakes fisheries and to the measurement of progress toward those goals. Despite general availability of species yield models, yield prediction for many Great Lakes fisheries has been poor due to the instability of the fish communities and the inadequacy of available data. A host of biological, institutional, and societal factors constrain both the development of sound predictions and their application to management. Improved predictive capability requires increased stability of Great Lakes fisheries through rehabilitation of well-integrated communities, improvement of data collection, data standardization and information-sharing mechanisms, and further development of the methodology for yield prediction. Most important is the creation of a better-informed public that will in turn establish the political will to do what is required.

Spectrally-Based Assessment of Crop Seasonal Performance and Yield

NASA Astrophysics Data System (ADS)

Kancheva, Rumiana; Borisova, Denitsa; Georgiev, Georgy

The rapid advances of space technologies concern almost all scientific areas from aeronautics to medicine, and a wide range of application fields from communications to crop yield predictions. Agricultural monitoring is among the priorities of remote sensing observations for getting timely information on crop development. Monitoring agricultural fields during the growing season plays an important role in crop health assessment and stress detection provided that reliable data is obtained. Successfully spreading is the implementation of hyperspectral data to precision farming associated with plant growth and phenology monitoring, physiological state assessment, and yield prediction. In this paper, we investigated various spectral-biophysical relationships derived from in-situ reflectance measurements. The performance of spectral data for the assessment of agricultural crops condition and yield prediction was examined. The approach comprisesd development of regression models between plant spectral and state-indicative variables such as biomass, vegetation cover fraction, leaf area index, etc., and development of yield forecasting models from single-date (growth stage) and multitemporal (seasonal) reflectance data. Verification of spectral predictions was performed through comparison with estimations from biophysical relationships between crop growth variables. The study was carried out for spring barley and winter wheat. Visible and near-infrared reflectance data was acquired through the whole growing season accompanied by detailed datasets on plant phenology and canopy structural and biochemical attributes. Empirical relationships were derived relating crop agronomic variables and yield to various spectral predictors. The study findings were tested using airborne remote sensing inputs. A good correspondence was found between predicted and actual (ground-truth) estimates

Development of a European Ensemble System for Seasonal Prediction: Application to crop yield

NASA Astrophysics Data System (ADS)

Terres, J. M.; Cantelaube, P.

2003-04-01

Western European agriculture is highly intensive and the weather is the main source of uncertainty for crop yield assessment and for crop management. In the current system, at the time when a crop yield forecast is issued, the weather conditions leading up to harvest time are unknown and are therefore a major source of uncertainty. The use of seasonal weather forecast would bring additional information for the remaining crop season and has valuable benefit for improving the management of agricultural markets and environmentally sustainable farm practices. An innovative method for supplying seasonal forecast information to crop simulation models has been developed in the frame of the EU funded research project DEMETER. It consists in running a crop model on each individual member of the seasonal hindcasts to derive a probability distribution of crop yield. Preliminary results of cumulative probability function of wheat yield provides information on both the yield anomaly and the reliability of the forecast. Based on the spread of the probability distribution, the end-user can directly quantify the benefits and risks of taking weather-sensitive decisions.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

An instructive model of entropy

NASA Astrophysics Data System (ADS)

Zimmerman, Seth

2010-09-01

This article first notes the misinterpretation of a common thought experiment, and the misleading comment that 'systems tend to flow from less probable to more probable macrostates'. It analyses the experiment, generalizes it and introduces a new tool of investigation, the simplectic structure. A time-symmetric model is built upon this structure, yielding several non-intuitive results. The approach is combinatorial rather than statistical, and assumes that entropy is equivalent to 'missing information'. The intention of this article is not only to present interesting results, but also, by deliberately starting with a simple example and developing it through proof and computer simulation, to clarify the often confusing subject of entropy. The article should be particularly stimulating to students and instructors of discrete mathematics or undergraduate physics.

Soft X-ray spectroscopy of transition metal compounds: a theoretical perspective

NASA Astrophysics Data System (ADS)

Bokarev, S. I.; Hilal, R.; Aziz, S. G.; Kühn, O.

2017-01-01

To date, X-ray spectroscopy has become a routine tool that can reveal highly local and element-specific information on the electronic structure of atoms in complex environments. Here, we report on the development of an efficient and versatile theoretical methodology for the treatment of soft X-ray spectra of transition metal compounds based on the multi-configurational self-consistent field electronic structure theory. A special focus is put on the L-edge photon-in/photon-out and photon-in/electron-out processes, i.e. X-ray absorption, resonant inelastic scattering, partial fluorescence yield, and photoelectron spectroscopy, all treated on the same theoretical footing. The investigated systems range from small prototypical coordination compounds and catalysts to aggregates of biomolecules.

Comprehensive and accurate tracking of carbon origin of LC-tandem mass spectrometry collisional fragments for 13C-MFA.

PubMed

Kappelmann, Jannick; Klein, Bianca; Geilenkirchen, Petra; Noack, Stephan

2017-03-01

In recent years the benefit of measuring positionally resolved 13 C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of 13 C-Metabolic Flux Analysis ( 13 C-MFA) has become evident. However, the usage of positional labeling information for 13 C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known. The present contribution addresses the latter challenge by deducing the maximal positional labeling information contained in LC-ESI-MS/MS spectra of product anions of central metabolism as well as product cations of amino acids. For this purpose, we draw on accurate mass spectrometry, selectively labeled standards, and published fragmentation pathways to structurally annotate all dominant mass peaks of a large collection of metabolites, some of which with a complete fragmentation pathway. Compiling all available information, we arrive at the most detailed map of carbon atom fate of LC-ESI-MS/MS collisional fragments yet, comprising 170 intense and structurally annotated product ions with unique carbon origin from 76 precursor ions of 72 metabolites. Our 13 C-data proof that heuristic fragmentation rules often fail to yield correct fragment structures and we expose common pitfalls in the structural annotation of product ions. We show that the positionally resolved 13 C-label information contained in the product ions that we structurally annotated allows to infer the entire isotopomer distribution of several central metabolism intermediates, which is experimentally demonstrated for malate using quadrupole-time-of-flight MS technology. Finally, the inclusion of the label information from a subset of these fragments improves flux precision in a Corynebacterium glutamicum model of the central carbon metabolism.

Examining live cell cultures during apoptosis by digital holographic phase imaging and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Khmaladze, Alexander

2017-11-01

Cellular apoptosis is a unique, organized series of events, leading to programmed cell death. In this work, we present a combined digital holography/Raman spectroscopy technique to study live cell cultures during apoptosis. Digital holographic microscopy measurements of live cell cultures yield information about cell shape and volume, changes to which are indicative of alterations in cell cycle and initiation of cell death mechanisms. Raman spectroscopic measurements provide complementary information about cells, such as protein, lipid and nucleic acid content, and the spectral signatures associated with structural changes in molecules. Our work indicates that the chemical changes in proteins, which were detected by Raman measurements, preceded morphological changes, which were seen with digital holographic microscopy.

Representation of high frequency Space Shuttle data by ARMA algorithms and random response spectra

NASA Technical Reports Server (NTRS)

Spanos, P. D.; Mushung, L. J.

1990-01-01

High frequency Space Shuttle lift-off data are treated by autoregressive (AR) and autoregressive-moving-average (ARMA) digital algorithms. These algorithms provide useful information on the spectral densities of the data. Further, they yield spectral models which lend themselves to incorporation to the concept of the random response spectrum. This concept yields a reasonably smooth power spectrum for the design of structural and mechanical systems when the available data bank is limited. Due to the non-stationarity of the lift-off event, the pertinent data are split into three slices. Each of the slices is associated with a rather distinguishable phase of the lift-off event, where stationarity can be expected. The presented results are rather preliminary in nature; it is aimed to call attention to the availability of the discussed digital algorithms and to the need to augment the Space Shuttle data bank as more flights are completed.

Fission yield covariances for JEFF: A Bayesian Monte Carlo method

NASA Astrophysics Data System (ADS)

Leray, Olivier; Rochman, Dimitri; Fleming, Michael; Sublet, Jean-Christophe; Koning, Arjan; Vasiliev, Alexander; Ferroukhi, Hakim

2017-09-01

The JEFF library does not contain fission yield covariances, but simply best estimates and uncertainties. This situation is not unique as all libraries are facing this deficiency, firstly due to the lack of a defined format. An alternative approach is to provide a set of random fission yields, themselves reflecting covariance information. In this work, these random files are obtained combining the information from the JEFF library (fission yields and uncertainties) and the theoretical knowledge from the GEF code. Examples of this method are presented for the main actinides together with their impacts on simple burn-up and decay heat calculations.

The role of off-line mass spectrometry in nuclear fission.

PubMed

De Laeter, J R

1996-01-01

The role of mass spectrometry in nuclear fission has been invaluable since 1940, when A. O. C. Nier separated microgram quantities of (235) U from (238) U, using a gas source mass spectrometer. This experiment enabled the fissionable nature of (235) U to be established. During the Manhattan Project, the mass spectrometer was used to measure the isotope abundances of uranium after processing in various separation systems, in monitoring the composition of the gaseous products in the Oak Ridge Diffusion Plant, and as a helium leak detector. Following the construction of the first reactor at the University of Chicago, it was necessary to unravel the nuclear systematics of the various fission products produced in the fission process. Off-line mass spectrometry was able to identify stable and long-lived isotopes produced in fission, but more importantly, was used in numerous studies of the distribution of mass of the cumulative fission yields. Improvements in sensitivity enabled off-line mass spectrometric studies to identify fine structure in the mass-yield curve and, hence, demonstrate the importance of shell structure in nuclear fission. Solid-source mass spectrometry was also able to measure the cumulative fission yields in the valley of symmetry in the mass-yield curve, and enabled spontaneous fission yields to be quantified. Apart from the accurate measurement of abundances, the stable isotope mass spectrometric technique has been invaluable in establishing absolute cumulative fission yields for many isotopes making up the mass-yield distribution curve for a variety of fissile nuclides. Extensive mass spectrometric studies of noble gases in primitive meteorites revealed the presence of fission products from the now extinct nuclide (244) Pu, and have eliminated the possibility of fission products from a super-heavy nuclide contributing to isotopic anomalies in meteoritic material. Numerous mass spectrometric studies of the isotopic and elemental abundances of samples from the Oklo Natural Reactor have enabled the nuclear parameters of the various reactor zones to be calculated, and the mobility/retentivity of a number of elements to be established in the reactor zones and the surrounding rocks. These isotopic studies have given valuable information on the geochemical behavior of natural geological repositories for radioactive waste containment. © 1997 John Wiley & Sons, Inc. Copyright © 1997 John Wiley & Sons, Inc.

Mechanics of Carbon Nanotubes and their Polymer Composites

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Cho, K. J.; Srivastava, Deepak; Tang, Harry (Technical Monitor)

2002-01-01

Contents include the folloving: carbon nanotube (CNT): structures, application of carbon nanotubes, simulation method, Elastic properties of carbon nanotubes, yield strain of CNT, yielding under tensile stress, yielding: strain-rate and temperature dependence, yield strain under tension, yielding at realistic conditions, nano fibers, polymer CNT composite, force field, density dependency on temperature, diffusion coefficients, young modulus, and conclusions.

Variation of inulin content, inulin yield and water use efficiency for inulin yield in Jerusalem artichoke genotypes under different water regimes

USDA-ARS?s Scientific Manuscript database

The information on genotypic variation for inulin content, inulin yield and water use efficiency of inulin yield (WUEi) in response to drought is limited. This study was to investigate the genetic variability in inulin content, inulin yield and WUEi of Jerusalem artichoke (Helianthus tuberosus L.) ...

Structural alphabets derived from attractors in conformational space

PubMed Central

2010-01-01

Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. PMID:20170534

Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

Information Theory to Probe Intrapartum Fetal Heart Rate Dynamics

NASA Astrophysics Data System (ADS)

Granero-Belinchon, Carlos; Roux, Stéphane; Abry, Patrice; Doret, Muriel; Garnier, Nicolas

2017-11-01

Intrapartum fetal heart rate (FHR) monitoring constitutes a reference tool in clinical practice to assess the baby health status and to detect fetal acidosis. It is usually analyzed by visual inspection grounded on FIGO criteria. Characterization of Intrapartum fetal heart rate temporal dynamics remains a challenging task and continuously receives academic research efforts. Complexity measures, often implemented with tools referred to as \\emph{Approximate Entropy} (ApEn) or \\emph{Sample Entropy} (SampEn), have regularly been reported as significant features for intrapartum FHR analysis. We explore how Information Theory, and especially {\\em auto mutual information} (AMI), is connected to ApEn and SampEn and can be used to probe FHR dynamics. Applied to a large (1404 subjects) and documented database of FHR data, collected in a French academic hospital, it is shown that i) auto mutual information outperforms ApEn and SampEn for acidosis detection in the first stage of labor and continues to yield the best performance in the second stage; ii) Shannon entropy increases as labor progresses, and is always much larger in the second stage;iii) babies suffering from fetal acidosis additionally show more structured temporal dynamics than healthy ones and that this progressive structuration can be used for early acidosis detection.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

PubMed

Meyer, Irmtraud M

2017-05-01

RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive. Copyright © 2017. Published by Elsevier Inc.

Comparison of the Light-Harvesting Networks of Plant and Cyanobacterial Photosystem I

PubMed Central

Şener, Melih K.; Jolley, Craig; Ben-Shem, Adam; Fromme, Petra; Nelson, Nathan; Croce, Roberta; Schulten, Klaus

2005-01-01

With the availability of structural models for photosystem I (PSI) in cyanobacteria and plants it is possible to compare the excitation transfer networks in this ubiquitous photosystem from two domains of life separated by over one billion years of divergent evolution, thus providing an insight into the physical constraints that shape the networks' evolution. Structure-based modeling methods are used to examine the excitation transfer kinetics of the plant PSI-LHCI supercomplex. For this purpose an effective Hamiltonian is constructed that combines an existing cyanobacterial model for structurally conserved chlorophylls with spectral information for chlorophylls in the Lhca subunits. The plant PSI excitation migration network thus characterized is compared to its cyanobacterial counterpart investigated earlier. In agreement with observations, an average excitation transfer lifetime of ∼49 ps is computed for the plant PSI-LHCI supercomplex with a corresponding quantum yield of 95%. The sensitivity of the results to chlorophyll site energy assignments is discussed. Lhca subunits are efficiently coupled to the PSI core via gap chlorophylls. In contrast to the chlorophylls in the vicinity of the reaction center, previously shown to optimize the quantum yield of the excitation transfer process, the orientational ordering of peripheral chlorophylls does not show such optimality. The finding suggests that after close packing of chlorophylls was achieved, constraints other than efficiency of the overall excitation transfer process precluded further evolution of pigment ordering. PMID:15994896

Molecular Basis for Cyclooxygenase Inhibition by the Non-steroidal Anti-inflammatory Drug Naproxen

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

Duggan, Kelsey C.; Walters, Matthew J.; Musee, Joel

Naproxen ((S)-6-methoxy-{alpha}-methyl-2-naphthaleneacetic acid) is a powerful non-selective non-steroidal anti-inflammatory drug that is extensively used as a prescription and over-the-counter medication. Naproxen exhibits gastrointestinal toxicity, but its cardiovascular toxicity may be reduced compared with other drugs in its class. Despite the fact that naproxen has been marketed for many years, the molecular basis of its interaction with cyclooxygenase (COX) enzymes is unknown. We performed a detailed study of naproxen-COX-2 interactions using site-directed mutagenesis, structure-activity analysis, and x-ray crystallography. The results indicate that each of the pendant groups of the naphthyl scaffold are essential for COX inhibition, and only minimal substitutions aremore » tolerated. Mutation of Trp-387 to Phe significantly reduced inhibition by naproxen, a result that appears unique to this inhibitor. Substitution of S or CH2 for the O atom of the p-methoxy group yielded analogs that were not affected by the W387F substitution and that exhibited increased COX-2 selectivity relative to naproxen. Crystallization and x-ray analysis yielded structures of COX-2 complexed to naproxen and its methylthio analog at 1.7 and 2.3 {angstrom} resolution, respectively. The combination of mutagenesis, structure analysis, and x-ray crystallography provided comprehensive information on the unique interactions responsible for naproxen binding to COX-2.« less

Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

PubMed Central

Patil, Gunvant; Do, Tuyen; Vuong, Tri D.; Valliyodan, Babu; Lee, Jeong-Dong; Chaudhary, Juhi; Shannon, J. Grover; Nguyen, Henry T.

2016-01-01

Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars. PMID:26781337

Integrating remote sensing, geographic information system and modeling for estimating crop yield

NASA Astrophysics Data System (ADS)

Salazar, Luis Alonso

This thesis explores various aspects of the use of remote sensing, geographic information system and digital signal processing technologies for broad-scale estimation of crop yield in Kansas. Recent dry and drought years in the Great Plains have emphasized the need for new sources of timely, objective and quantitative information on crop conditions. Crop growth monitoring and yield estimation can provide important information for government agencies, commodity traders and producers in planning harvest, storage, transportation and marketing activities. The sooner this information is available the lower the economic risk translating into greater efficiency and increased return on investments. Weather data is normally used when crop yield is forecasted. Such information, to provide adequate detail for effective predictions, is typically feasible only on small research sites due to expensive and time-consuming collections. In order for crop assessment systems to be economical, more efficient methods for data collection and analysis are necessary. The purpose of this research is to use satellite data which provides 50 times more spatial information about the environment than the weather station network in a short amount of time at a relatively low cost. Specifically, we are going to use Advanced Very High Resolution Radiometer (AVHRR) based vegetation health (VH) indices as proxies for characterization of weather conditions.

Transforming information from silicon testing and design characterization into numerical data sets for yield learning

NASA Astrophysics Data System (ADS)

Yang, Thomas; Shen, Yang; Zhang, Yifan; Sweis, Jason; Lai, Ya-Chieh

2017-03-01

Silicon testing results are regularly collected for a particular lot of wafers to study yield loss from test result diagnostics. Product engineers will analyze the diagnostic results and perform a number of physical failure analyses to detect systematic defects which cause yield loss for these sets of wafers in order to feedback the information to process engineers for process improvements. Most of time, the systematic defects that are detected are major issues or just one of the causes for the overall yield loss. This paper will present a working flow for using design analysis techniques combined with diagnostic methods to systematically transform silicon testing information into physical layout information. A new set of the testing results are received from a new lot of wafers for the same product. We can then correlate all the diagnostic results from different periods of time to check which blocks or nets have been highlighted or stop occurring on the failure reports in order to monitor process changes which impact the yield. The design characteristic analysis flow is also implemented to find 1) the block connections on a design that have failed electrical test or 2) frequently used cells that been highlighted multiple times.

Improved design of tunnel supports. volume 2: aspects of yielding in ground-structure interaction

DOT National Transportation Integrated Search

1980-06-30

Volume 2 focuses on a particularly complex and often misunderstood aspect of ground-structure interaction, which is ground yielding and loosening, and reports new findings in this area. The findings are based on previous research, on the knowledge ga...

Clustering network layers with the strata multilayer stochastic block model.

PubMed

Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J

2016-01-01

Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the "strata multilayer stochastic block model" (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called "strata", which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project.

Global industrial impact coefficient based on random walk process and inter-country input-output table

NASA Astrophysics Data System (ADS)

Xing, Lizhi; Dong, Xianlei; Guan, Jun

2017-04-01

Input-output table is very comprehensive and detailed in describing the national economic system with lots of economic relationships, which contains supply and demand information among industrial sectors. The complex network, a theory and method for measuring the structure of complex system, can describe the structural characteristics of the internal structure of the research object by measuring the structural indicators of the social and economic system, revealing the complex relationship between the inner hierarchy and the external economic function. This paper builds up GIVCN-WIOT models based on World Input-Output Database in order to depict the topological structure of Global Value Chain (GVC), and assumes the competitive advantage of nations is equal to the overall performance of its domestic sectors' impact on the GVC. Under the perspective of econophysics, Global Industrial Impact Coefficient (GIIC) is proposed to measure the national competitiveness in gaining information superiority and intermediate interests. Analysis of GIVCN-WIOT models yields several insights including the following: (1) sectors with higher Random Walk Centrality contribute more to transmitting value streams within the global economic system; (2) Half-Value Ratio can be used to measure robustness of open-economy macroeconomics in the process of globalization; (3) the positive correlation between GIIC and GDP indicates that one country's global industrial impact could reveal its international competitive advantage.

Clustering network layers with the strata multilayer stochastic block model

PubMed Central

Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J.

2016-01-01

Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the “strata multilayer stochastic block model” (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called “strata”, which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project. PMID:28435844

Radiation use efficiency, biomass production, and grain yield in two maize hybrids differing in drought tolerance

USDA-ARS?s Scientific Manuscript database

Drought tolerant (DT) maize (Zea mays L.) hybrids have potential to increase yield under drought conditions. However, little information is known about the physiological determinations of yield in DT hybrids. Our objective was to assess radiation use efficiency (RUE), biomass production, and yield ...

Estimating oak growth and yield

Treesearch

Martin E. Dale; Donald E. Hilt

1989-01-01

Yields from upland oak stands vary widely from stand to stand due to differences in age, site quality, species composition, and stand structure. Cutting history and other past disturbances such as grazing or fire also affect yields.

The use of XAFS to determine the nature of interaction of iron and molybdenum metal salts within PS-b-P2VP micelles.

PubMed

Riskin, Alexander; Beale, Andrew M; Boyen, Hans-Gerhard; Vantomme, André; Hardy, An; Van Bael, Marlies K

2013-02-07

The poly(styrene)-block-poly(2-vinylpyridine) (PS-b-P2VP) micelle route is a well established method for the preparation of bimetallic nanoparticles used for the catalysis of carbon nanotubes and other applications like ultrahigh density storage devices, yet to date no information is available concerning the internal structure of the P2VP-metal salt complex. For the first time, XAFS measurements were performed on micelles loaded with either iron(III) chloride or molybdenum(V) chloride and a combination of both. Analysis of the data revealed that iron is tetrahedrally coordinated within the core, whereas molybdenum is octahedrally coordinated in the pure loaded micelles and trigonally coordinated in the mixed micelles. For the bimetallic samples, analysis of the Fe and Mo K-edge data revealed the existence of an interaction between iron and molybdenum. This approach to obtain detailed structural information during the preparation of these catalyst samples will allow for a deeper understanding of the effects of structure on the function of catalysts used for CNT growth i.e. to explain differences in yield as well as potentially providing a deeper understanding of the CNT growth mechanism itself.

Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures.

PubMed

Ehrlich, Matthias; Schüffny, René

2013-01-01

One of the major outcomes of neuroscientific research are models of Neural Network Structures (NNSs). Descriptions of these models usually consist of a non-standardized mixture of text, figures, and other means of visual information communication in print media. However, as neuroscience is an interdisciplinary domain by nature, a standardized way of consistently representing models of NNSs is required. While generic descriptions of such models in textual form have recently been developed, a formalized way of schematically expressing them does not exist to date. Hence, in this paper we present Neural Schematics as a concept inspired by similar approaches from other disciplines for a generic two dimensional representation of said structures. After introducing NNSs in general, a set of current visualizations of models of NNSs is reviewed and analyzed for what information they convey and how their elements are rendered. This analysis then allows for the definition of general items and symbols to consistently represent these models as Neural Schematics on a two dimensional plane. We will illustrate the possibilities an agreed upon standard can yield on sampled diagrams transformed into Neural Schematics and an example application for the design and modeling of large-scale NNSs.

Active learning for semi-supervised clustering based on locally linear propagation reconstruction.

PubMed

Chang, Chin-Chun; Lin, Po-Yi

2015-03-01

The success of semi-supervised clustering relies on the effectiveness of side information. To get effective side information, a new active learner learning pairwise constraints known as must-link and cannot-link constraints is proposed in this paper. Three novel techniques are developed for learning effective pairwise constraints. The first technique is used to identify samples less important to cluster structures. This technique makes use of a kernel version of locally linear embedding for manifold learning. Samples neither important to locally linear propagation reconstructions of other samples nor on flat patches in the learned manifold are regarded as unimportant samples. The second is a novel criterion for query selection. This criterion considers not only the importance of a sample to expanding the space coverage of the learned samples but also the expected number of queries needed to learn the sample. To facilitate semi-supervised clustering, the third technique yields inferred must-links for passing information about flat patches in the learned manifold to semi-supervised clustering algorithms. Experimental results have shown that the learned pairwise constraints can capture the underlying cluster structures and proven the feasibility of the proposed approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structure sensitivity in the nonscalable regime explored via catalysed ethylene hydrogenation on supported platinum nanoclusters

DOE PAGES

Crampton, Andrew S.; Rötzer, Marian D.; Ridge, Claron J.; ...

2016-01-28

The sensitivity, or insensitivity, of catalysed reactions to catalyst structure is a commonly employed fundamental concept. Here we report on the nature of nano-catalysed ethylene hydrogenation, investigated through experiments on size-selected Pt n (n=8-15) clusters soft-landed on magnesia and first-principles simulations, yielding benchmark information about the validity of structure sensitivity/insensitivity at the bottom of the catalyst size range. Both ethylene-hydrogenation-to-ethane and the parallel hydrogenation–dehydrogenation ethylidyne-producing route are considered, uncovering that at the <1 nm size-scale the reaction exhibits characteristics consistent with structure sensitivity, in contrast to structure insensitivity found for larger particles. The onset of catalysed hydrogenation occurs for Ptmore » n (n≥10) clusters at T>150 K, with maximum room temperature reactivity observed for Pt 13. Structure insensitivity, inherent for specific cluster sizes, is induced in the more active Pt 13 by a temperature increase up to 400 K leading to ethylidyne formation. As a result, control of sub-nanometre particle size may be used for tuning catalysed hydrogenation activity and selectivity.« less

Structure sensitivity in the nonscalable regime explored via catalysed ethylene hydrogenation on supported platinum nanoclusters

PubMed Central

Crampton, Andrew S.; Rötzer, Marian D.; Ridge, Claron J.; Schweinberger, Florian F.; Heiz, Ueli; Yoon, Bokwon; Landman, Uzi

2016-01-01

The sensitivity, or insensitivity, of catalysed reactions to catalyst structure is a commonly employed fundamental concept. Here we report on the nature of nano-catalysed ethylene hydrogenation, investigated through experiments on size-selected Ptn (n=8–15) clusters soft-landed on magnesia and first-principles simulations, yielding benchmark information about the validity of structure sensitivity/insensitivity at the bottom of the catalyst size range. Both ethylene-hydrogenation-to-ethane and the parallel hydrogenation–dehydrogenation ethylidyne-producing route are considered, uncovering that at the <1 nm size-scale the reaction exhibits characteristics consistent with structure sensitivity, in contrast to structure insensitivity found for larger particles. The onset of catalysed hydrogenation occurs for Ptn (n≥10) clusters at T>150 K, with maximum room temperature reactivity observed for Pt13. Structure insensitivity, inherent for specific cluster sizes, is induced in the more active Pt13 by a temperature increase up to 400 K leading to ethylidyne formation. Control of sub-nanometre particle size may be used for tuning catalysed hydrogenation activity and selectivity. PMID:26817713

Structure sensitivity in the nonscalable regime explored via catalysed ethylene hydrogenation on supported platinum nanoclusters

NASA Astrophysics Data System (ADS)

Crampton, Andrew S.; Rötzer, Marian D.; Ridge, Claron J.; Schweinberger, Florian F.; Heiz, Ueli; Yoon, Bokwon; Landman, Uzi

2016-01-01

The sensitivity, or insensitivity, of catalysed reactions to catalyst structure is a commonly employed fundamental concept. Here we report on the nature of nano-catalysed ethylene hydrogenation, investigated through experiments on size-selected Ptn (n=8-15) clusters soft-landed on magnesia and first-principles simulations, yielding benchmark information about the validity of structure sensitivity/insensitivity at the bottom of the catalyst size range. Both ethylene-hydrogenation-to-ethane and the parallel hydrogenation-dehydrogenation ethylidyne-producing route are considered, uncovering that at the <1 nm size-scale the reaction exhibits characteristics consistent with structure sensitivity, in contrast to structure insensitivity found for larger particles. The onset of catalysed hydrogenation occurs for Ptn (n>=10) clusters at T>150 K, with maximum room temperature reactivity observed for Pt13. Structure insensitivity, inherent for specific cluster sizes, is induced in the more active Pt13 by a temperature increase up to 400 K leading to ethylidyne formation. Control of sub-nanometre particle size may be used for tuning catalysed hydrogenation activity and selectivity.

Generalized pixel profiling and comparative segmentation with application to arteriovenous malformation segmentation.

PubMed

Babin, D; Pižurica, A; Bellens, R; De Bock, J; Shang, Y; Goossens, B; Vansteenkiste, E; Philips, W

2012-07-01

Extraction of structural and geometric information from 3-D images of blood vessels is a well known and widely addressed segmentation problem. The segmentation of cerebral blood vessels is of great importance in diagnostic and clinical applications, with a special application in diagnostics and surgery on arteriovenous malformations (AVM). However, the techniques addressing the problem of the AVM inner structure segmentation are rare. In this work we present a novel method of pixel profiling with the application to segmentation of the 3-D angiography AVM images. Our algorithm stands out in situations with low resolution images and high variability of pixel intensity. Another advantage of our method is that the parameters are set automatically, which yields little manual user intervention. The results on phantoms and real data demonstrate its effectiveness and potentials for fine delineation of AVM structure. Copyright © 2012 Elsevier B.V. All rights reserved.

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

Chromophore Structure of Photochromic Fluorescent Protein Dronpa: Acid-Base Equilibrium of Two Cis Configurations.

PubMed

Higashino, Asuka; Mizuno, Misao; Mizutani, Yasuhisa

2016-04-07

Dronpa is a novel photochromic fluorescent protein that exhibits fast response to light. The present article is the first report of the resonance and preresonance Raman spectra of Dronpa. We used the intensity and frequency of Raman bands to determine the structure of the Dronpa chromophore in two thermally stable photochromic states. The acid-base equilibrium in one photochromic state was observed by spectroscopic pH titration. The Raman spectra revealed that the chromophore in this state shows a protonation/deprotonation transition with a pKa of 5.2 ± 0.3 and maintains the cis configuration. The observed resonance Raman bands showed that the other photochromic state of the chromophore is in a trans configuration. The results demonstrate that Raman bands selectively enhanced for the chromophore yield valuable information on the molecular structure of the chromophore in photochromic fluorescent proteins after careful elimination of the fluorescence background.

Negative input for grammatical errors: effects after a lag of 12 weeks.

PubMed

Saxton, Matthew; Backley, Phillip; Gallaway, Clare

2005-08-01

Effects of negative input for 13 categories of grammatical error were assessed in a longitudinal study of naturalistic adult-child discourse. Two-hour samples of conversational interaction were obtained at two points in time, separated by a lag of 12 weeks, for 12 children (mean age 2;0 at the start). The data were interpreted within the framework offered by Saxton's (1997, 2000) contrast theory of negative input. Corrective input was associated with subsequent improvements in the grammaticality of child speech for three of the target structures. No effects were found for two forms of positive input: non-contingent models, where the adult produces target structures in non-error-contingent contexts; and contingent models, where grammatical forms follow grammatical child usages. The findings lend support to the view that, in some cases at least, the structure of adult-child discourse yields information on the bounds of grammaticality for the language-learning child.

Applications of Electronic Health Information in Public Health: Uses, Opportunities & Barriers

PubMed Central

Tomines, Alan; Readhead, Heather; Readhead, Adam; Teutsch, Steven

2013-01-01

Electronic health information systems can reshape the practice of public health including public health surveillance, disease and injury investigation and control, decision making, quality assurance, and policy development. While these opportunities are potentially transformative, and the federal program for the Meaningful Use (MU) of electronic health records (EHRs) has included important public health components, significant barriers remain. Unlike incentives in the clinical care system, scant funding is available to public health departments to develop the necessary information infrastructure and workforce capacity to capitalize on EHRs, personal health records, or Big Data. Current EHR systems are primarily built to serve clinical systems and practice rather than being structured for public health use. In addition, there are policy issues concerning how broadly the data can be used by public health officials. As these issues are resolved and workable solutions emerge, they should yield a more efficient and effective public health system. PMID:25848571

A deep learning framework for modeling structural features of RNA-binding protein targets

PubMed Central

Zhang, Sai; Zhou, Jingtian; Hu, Hailin; Gong, Haipeng; Chen, Ligong; Cheng, Chao; Zeng, Jianyang

2016-01-01

RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time. Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp. PMID:26467480

77 FR 74191 - Information Collection; Proposed Collection; Comment Request; General Services Administration...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-13

... insights on perceptions and opinions, but are not statistical surveys that yield quantitative results that.... This type of generic clearance for qualitative information will not be used for quantitative... for submission for other generic mechanisms that are designed to yield quantitative results. The...

Reactive Molecular Dynamics Simulations on the Disintegration of PVDF, FP-POSS, and Their Composite during Atomic Oxygen Impact.

PubMed

Zeng, Fanlin; Peng, Chao; Liu, Yizhi; Qu, Jianmin

2015-07-30

Poly(vinylidene fluoride) (PVDF) is a kind of important piezoelectric polymer used in spacecraft industry. But the atomic oxygen (AO) is the most abundant element in the low Earth orbit (LEO) environment. AO collision degradation is an important issue in the application of PVDF on spacecrafts. To investigate the erosion behaviors of PVDF during AO impacts and how to improve the stability of PVDF against AO impacts, the temperature evolution, mass loss, and erosion yields of neat PVDF, neat polyhedral oligomeric silsesquioxanes compound (3,3,3-trifluoropropyl)8Si8O12 (FP-POSS) and the PVDF/FP-POSS composite under AO impacts, as well as some key disintegrated structures and separated chemical compositions, were researched using the molecular dynamics (MD) simulations and the reactive ReaxFF force field. The simulation erosion yield result of PVDF is very close to the experiment results, which shows our simulations are reliable. The results of the temperature evolution, mass loss, and erosion yield of three materials show that the antierosion performance of PVDF is not outstanding. However, incorporating FP-POSS into PVDF matrix enhances the stability of PVDF against AO impact greatly and reduces the temperature rise, mass loss, and the erosion yield of PVDF rapidly. A detailed analysis on the flight chemical compositions and key snapshots of the structures reveals that the erosion process on PVDF and PVDF/FP-POSS is continuous and should be derived from the same PVDF matrix in two materials. In contrast, the erosion process on FP-POSS is stepped. The erosion will not take place until the number of AO reaches a specific value. There is a barrier for the erosion of high-energy AO because of the stable cagelike Si-O frame in FP-POSS molecules. This should be chiefly responsible for the high stability of FP-POSS and the reinforcement mechanism of FP-POSS on PVDF against AO impacts. This work is helpful for people to understand the erosion details of PVDF and POSS and provides valuable information to design effective protective structure for PVDF against AO impacts in LEO environment.

Phenotyping Drought Tolerance and Yield Potential of Warm-Season Legumes Through Field- and Airborne-Based Hyperspectral VSWIR Sensing

NASA Astrophysics Data System (ADS)

Drewry, D.; Berny-Mier y Teran, J. C.; Dutta, D.; Gepts, P.

2017-12-01

Hyperspectral sensing in the visible through shortwave infrared (VSWIR) portion of the spectrum has been demonstrated to provide significant information on the structural and functional properties of vegetation, resulting in powerful techniques to discern species differences, characterize crop nutrient or water stress, and quantify the density of foliage in agricultural fields. Modern machine-learning techniques allow for the entire set of spectral bands, on the order of hundreds with modern field and airborne spectrometers, to be used to develop models that can simultaneously retrieve a variety of foliar chemical compounds and hydrological and structural states. The application of these techniques, in the context of leaf-level measurements of VSWIR reflectance, or more complicated remote airborne surveys, has the potential to revolutionize high-throughput methods to phenotype germplasm that optimizes yield, resource-use efficiencies, or alternate objectives related to disease resistance or biomass accumulation, for example. Here we focus on breeding trials for a set of warm-season legumes, conducted in both greenhouse and field settings, and spanning a set of diverse genotypes providing a range of adaptation to drought and yield potential in the context of the semi-arid climate cultivation. At the leaf-level, a large set of spectral reflectance measurements spanning 400-2500 nanometers were made for plants across various growth stages in field experiments that induced severe drought, along with sampling for relevant trait values. Here we will discuss the development and performance of algorithms for a range of leaf traits related to gas exchange, leaf structure, hydrological status, nutrient contents and stable isotope discrimination, along with their relationships to drought resistance and yield. We likewise discuss the effectiveness of quantifying relevant foliar and canopy traits through airborne imaging spectroscopy from small unmanned vehicles (sUAVs), and future directions that augment VSWIR spectral coverage to include the thermal infrared portion of the spectrum, including our recent efforts to accurately retrieve vegetation surface temperature and estimate consumptive water use in agricultural systems throughout the diurnal cycle.

X-rays in the Cryo-EM Era: Structural Biology’s Dynamic Future

PubMed Central

Shoemaker, Susannah C.; Ando, Nozomi

2018-01-01

Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa), while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kDa in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions on the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology. PMID:29227642

Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

NASA Technical Reports Server (NTRS)

Monk, Joshua D.; Lawson, John W.

2016-01-01

Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

Wheat yield dynamics: a structural econometric analysis.

PubMed

Sahin, Afsin; Akdi, Yilmaz; Arslan, Fahrettin

2007-10-15

In this study we initially have tried to explore the wheat situation in Turkey, which has a small-open economy and in the member countries of European Union (EU). We have observed that increasing the wheat yield is fundamental to obtain comparative advantage among countries by depressing domestic prices. Also the changing structure of supporting schemes in Turkey makes it necessary to increase its wheat yield level. For this purpose, we have used available data to determine the dynamics of wheat yield by Ordinary Least Square Regression methods. In order to find out whether there is a linear relationship among these series we have checked each series whether they are integrated at the same order or not. Consequently, we have pointed out that fertilizer usage and precipitation level are substantial inputs for producing high wheat yield. Furthermore, in respect for our model, fertilizer usage affects wheat yield more than precipitation level.

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

PubMed

Poitevin, Frédéric; Orland, Henri; Doniach, Sebastian; Koehl, Patrice; Delarue, Marc

2011-07-01

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).

Long term records provide insights on the relative influence of climate and forest community structure on water yield in the southern Appalachians

Treesearch

Peter Caldwell; Chelcy Ford Miniat; Steven Brantley; Katherine Elliott; Stephanie Laseter; Wayne Swank

2016-01-01

In forested watersheds, changes in climate and forest structure or age can affect water yield; yet few long-term observational records from such watersheds exist that allow an assessment of these impacts over time. In this study, we used long-term (~80 yrs) observational records of climate and water yield in six reference watersheds at the Coweeta Hydrologic Laboratory...

Computer optimization of cutting yield from multiple ripped boards

Treesearch

A.R. Stern; K.A. McDonald

1978-01-01

RIPYLD is a computer program that optimizes the cutting yield from multiple-ripped boards. Decisions are based on automatically collected defect information, cutting bill requirements, and sawing variables. The yield of clear cuttings from a board is calculated for every possible permutation of specified rip widths and both the maximum and minimum percent yield...

Nitrogen, phosphorus, and potassium effects on biomass yield and flavonoid content of American Skullcap (Scutellaria Lateriflora)

USDA-ARS?s Scientific Manuscript database

Information on optimum dosage of nitrogen (N), phosphorus (P) and potassium (K) fertilizer for high dry matter yield and flavonoid yield of American Skullcap is lacking. Greenhouse experiments were conducted to determine the effects of N, P and K fertilizer on biomass yield and flavonoid content of...

An energy balance approach for mapping crop waterstress and yield impacts over the Czech Republic

USDA-ARS?s Scientific Manuscript database

There is a growing demand for timely, spatially distributed information regarding crop condition and water use to inform agricultural decision making and yield forecasting efforts. Remote sensing of land-surface temperature has proven valuable for mapping evapotranspiration (ET) and crop stress from...

76 FR 12140 - Agency Information Collection Activities: Proposed Collection; Comment Request; Generic Clearance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... provides useful insights on perceptions and opinions, but are not statistical surveys that yield quantitative results that can be generalized to the population of study. This feedback will provide insights... used for quantitative information collections that are designed to yield reliably actionable results...

Final Environmental Assessment of Military Service Station Privatization at Five AETC Installations

DTIC Science & Technology

2013-10-01

distinction (Criterion C); or • Have yielded, or may likely yield, information important in prehistory or history (Criterion D). Resources less than 50...important information in history or prehistory ; thus, it does not meet the requirement of Criterion D. Building 2109 is recommended not eligible for

Colonoscopy yields fewer polyps as the day progresses despite using social influence theory to reverse the trend.

PubMed

Kaneshiro, Marc; Ho, Andrew; Chan, Michael; Cohen, Hartley; Spiegel, Brennan M R

2010-12-01

We previously reported that fewer polyps are detected by colonoscopy as the day progresses, a phenomenon that could be modified with "social influence theory" by using auditing and feedback. To measure the impact of a social influence informational poster on the relationship between time of day and colonoscopy yield. Controlled before-and-after study comparing the polyp yield and time of day relationship in a historical cohort versus a 3-month intervention period. University-based Veterans Affairs medical center. Patients undergoing outpatient screening, surveillance, or diagnostic colonoscopies. Placement of informational posters in endoscopy rooms within view of operators and nurses. The poster depicted a bar graph of the previously documented hour-by-hour decreases in polyp yield coupled with prominent text: "What Time Is It Now?" Polyp yield, including secondary end point limited to adenoma detection. We performed regression to measure the effect of start time on polyp yield. There were 477 and 301 patients in the control and intervention periods, respectively. There was a negative relationship between start time and polyp yield, including adenoma detection, for both periods (P = .001). Start time remained negatively predictive of polyp and adenoma yield after adjusting for poster exposure and confounders (P = .01). Nonrandomized study design. An informational poster did not alter the relationship between colonoscopy start time and polyp yield. This strengthens the previous finding that start time may affect polyp yield and suggests that passive use of social influence theory is inadequate to modify this effect. Shortening endoscopy shifts and active auditing with feedback may be necessary. Copyright © 2010 American Society for Gastrointestinal Endoscopy. Published by Mosby, Inc. All rights reserved.

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

PubMed Central

Burns, Lynne E; Frasier, Timothy R; Broders, Hugh G

2014-01-01

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global FST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation. PMID:25505539

Uncertainty in Simulating Wheat Yields Under Climate Change

NASA Technical Reports Server (NTRS)

Asseng, S.; Ewert, F.; Rosenzweig, Cynthia; Jones, J. W.; Hatfield, J. W.; Ruane, A. C.; Boote, K. J.; Thornburn, P. J.; Rotter, R. P.; Cammarano, D.;

A compendium of forest growth and yield simulators for the Pacific coast states

Treesearch

Martin W. Ritchie

1999-01-01

This manuscript provides information needed for the user to access current information about forest growth and yield simulators. Ultimately, the best source of information for any simulator is the user’s guide and the sage advice of those who built the simulator. In some instances, these people are easy to find and are willing to provide all the support for the program...

Fractionation and physicochemical characterization of lignin from waste jute bags: Effect of process parameters on yield and thermal degradation.

PubMed

Ahuja, Dheeraj; Kaushik, Anupama; Chauhan, Ghanshyam S

2017-04-01

In this work lignin was extracted from waste jute bags using soda cooking method and effect of varying alkali concentration and pH on yield, purity, structure and thermal degradation of lignin were studied. The Lignin yield, chemical composition and purity were assessed using TAPPI method and UV-vis spectroscopy. Yield and purity of lignin ranged from 27 to 58% and 50-94%, respectively for all the samples and was maximum for 8% alkali concentration and at pH 2 giving higher thermal stability. Chemical structure, thermal stability and elementary analysis of lignin were studied using FTIR, H NMR, thermo gravimetric analysis (TGA) and Elemental analyzer. FTIR and H NMR results showed that core structure of lignin starts breaking beyond 10% alkali concentration. S/G ratio shows the dominance of Syringyl unit over guaiacyl unit. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural analysis of a reflux pool-boiler solar receiver

NASA Astrophysics Data System (ADS)

Hoffman, E. L.; Stone, C. M.

1991-06-01

Coupled thermal-structural finite element calculations of a reflux pool-boiler solar receiver were performed to characterize the operating stresses and to address issues affecting the service life of the receiver. Analyses performed using shell elements provided information for receiver material selection and design optimization. Calculations based on linear elastic fracture mechanics principles were performed using continuum elements to assess the vulnerability of a seam-weld to fatigue crack growth. All calculations were performed using ABAQUS, a general purpose finite element code, and elements specifically formulated for coupled thermal-structural analysis. Two materials were evaluated: 316L SS and Haynes 230 alloys. The receiver response was simulated for a combination of structural and thermal loads that represent the startup and operating conditions of the receiver. For both materials, maximum stresses in the receiver developed shortly after startup due to uneven temperature distribution across the receiver surface. The largest effective stress was near yield in the 316L SS receiver and below 39 percent of yield in the Haynes 230 receiver. The calculations demonstrated that stress reductions of over 25 percent could be obtained by reducing the aft dome thickness to one closer to the absorber. The fatigue calculations demonstrated that the stress distribution near the seam-weld notch depends primarily on the structural load created by internal pressurization of the receiver rather than the thermal, indicating that the thermal loads can be neglected when assessing the stress intensity near the seam-weld notch. The stress intensity factor, computed using the J-integral method and crack opening-displacement field equations, was significantly below the fatigue threshold for most steels. The calculations indicated that the weld notch was always loaded in compression, a condition which is not conducive to fatigue crack growth.

Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation

DOE PAGES

Orfield, Noah J.; McBride, James R.; Wang, Feng; ...

2016-02-05

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging,more » rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.« less

Utility of aeromagnetic studies for mapping of potentially active faults in two forearc basins: Puget Sound, Washington, and Cook Inlet, Alaska

USGS Publications Warehouse

Saltus, R.W.; Blakely, R.J.; Haeussler, Peter J.; Wells, R.E.

2005-01-01

High-resolution aeromagnetic surveys over forearc basins can detect faults and folds in weakly magnetized sediments, thus providing geologic constraints on tectonic evolution and improved understanding of seismic hazards in convergent-margin settings. Puget Sound, Washington, and Cook Inlet, Alaska, provide two case histories. In each lowland region, shallow-source magnetic anomalies are related to active folds and/or faults. Mapping these structures is critical for understanding seismic hazards that face the urban regions of Seattle, Washington, and Anchorage, Alaska. Similarities in aeromagnetic anomaly patterns and magnetic stratigraphy between the two regions suggest that we can expect the aeromagnetic method to yield useful structural information that may contribute to earth-hazard and energy resource investigations in other forearc basins.

VLBI observations of the 0957 + 561 gravitational lens system

NASA Technical Reports Server (NTRS)

Gorenstein, M. V.; Falco, E. E.; Shapiro, I. I.; Bartel, N.; Bonometti, R. J.; Cohen, N. L.; Rogers, A. E. E.; Marcaide, J. M.; Clark, T. A.

1988-01-01

A series of VLBI observations of the gravitational lens system 0957 + 561 at a wavelength of 13 cm has yielded the positions of the A and B images, the relative magnification of their largest discernible radio structures, and the time variability of their smallest discernible radio structures. These observations have also allowed upper limits to be placed on the flux density of an expected third image. The positions and relative magnification of the A and B images provide new information with which to constrain models of the lens that forms the images. The detection of variations in the flux densities of the cores of A and B suggests that observations at shorter wavelengths may reveal superluminal motion, which may in turn provide a means to measure the relative time delay.

Frequency response of electrochemical cells

NASA Technical Reports Server (NTRS)

Thomas, Daniel L.

1989-01-01

Impedance concepts can be applied to the analysis of battery electrodes, yielding information about the structure of the electrode and the processes occurring in the electrode. Structural parameters such as the specific area (surface area per gram of electrode) can be estimated. Electrode variables such as surface overpotential, ohmic losses, and diffusion limitations may be studied. Nickel and cadmium electrodes were studied by measuring the ac impedance as a function of frequency, and the specific areas that were determined were well within the range of specific areas determined from BET measurements. Impedance spectra were measured for the nickel and cadmium electrodes, and for a 20 A-hr NiCd battery as functions of the state of charge. More work is needed to determine the feasibility of using frequency response as a nondestructive testing technique for batteries.

Molecular structure of P2X receptors.

PubMed

Egan, Terrance M; Cox, Jane A; Voigt, Mark M

2004-01-01

P2X receptors are ligand-gated ion channels that transduce many of the physiological effects of extracellular ATP. There has been a dramatic increase in awareness of these receptors over the past 5 or so years, in great part due to their molecular cloning and characterization. The availability of cDNA clones for the various subunits has led to rapid progress in identifying their tissue-specific expression, resulting in new ideas concerning the functional roles these receptors might play in physiological and pathophysiological processes. In addition, molecular approaches have yielded much information regarding the structure and function of the receptor proteins themselves. In this review we seek to review recent findings concerning the molecular determinants of receptor-channel function, with particular focus on ligand binding and gating, ion selectivity, and subunit assembly.

A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment

PubMed Central

Mobli, Mehdi; Stern, Alan S.; Bermel, Wolfgang; King, Glenn F.; Hoch, Jeffrey C.

2010-01-01

One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives. PMID:20299257

Neptune's small dark spot (D2)

NASA Technical Reports Server (NTRS)

1999-01-01

This bulls-eye view of Neptune's small dark spot (D2) was obtained by Voyager 2's narrow-angle camera. Banding surrounding the feature indicates unseen strong winds, while structures within the bright spot suggest both active upwelling of clouds and rotation about the center. A rotation rate has not yet been measured, but the V-shaped structure near the right edge of the bright area indicates that the spot rotates clockwise. Unlike the Great Red Spot on Jupiter, which rotates counterclockwise, if the D2 spot on Neptune rotates clockwise, the material will be descending in the dark oval region. The fact that infrared data will yield temperature information about the region above the clouds makes this observation especially valuable. The Voyager Mission is conducted by JPL for NASA's Office of Space Science and Applications.

Nanoscale cluster dynamics in the martensitic phase of Ni-Mn-Sn shape-memory alloys

NASA Astrophysics Data System (ADS)

Hoch, Michael; Yuan, Shaojie; Kuhns, Phillip; Reyes, Arneil; Brooks, James; Phelan, Daniel; Srivastava, Vijay; James, Richard; Leighton, Chris

2015-03-01

The martensitic phases of Ni-Mn-Sn magnetic shape memory alloys exhibit interesting low temperature magnetic properties, including intrinsic superparamagnetism and exchange bias effects, which have previously been rationalized in terms of spin clusters. We show here that spin-echo NMR, involving 55Mn hyperfine fields, permits ferromagnetic and antiferromagnetic nanoregions to be directly identified in these materials and yields estimates of their size distributions. Nuclear relaxation rate measurements, made as a function of temperature, provide information on both the dynamics and on the electronic structure of the nanoregions. The relaxation rates are analyzed using a combination of Redfield and Korringa mechanisms, the Korringa procedure providing information on the density of states at the Fermi level. Results will be presented for a number of these alloys. DMR-1309463.

Tubular structured hierarchical mesoporous titania material derived from natural cellulosic substances and application as photocatalyst for degradation of methylene blue

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

Huang, Haiqing; Liu, Xiaoyan; Huang, Jianguo, E-mail: jghuang@zju.edu.cn

Graphical abstract: Bio-inspired, tubular structured hierarchical mesoporous titania material with high photocatalytic activity under UV light was fabricated employing natural cellulosic substance (cotton) as hard template and cetyltrimethylammonium bromide (CTAB) surfactant as soft template using a one-pot sol-gel method. Highlights: {yields} Tubular structured mesoporous titania material was fabricated by sol-gel method. {yields} The titania material faithfully recorded the hierarchical structure of the template substrate (cotton). {yields} The titania material exhibited high photocatalytic activity in decomposition of methylene blue. -- Abstract: Bio-inspired, tubular structured hierarchical mesoporous titania material was designed and fabricated employing natural cellulosic substance (cotton) as hard template andmore » cetyltrimethylammonium bromide (CTAB) surfactant as soft template by one-pot sol-gel method. The tubular structured hierarchical mesoporous titania material processes large specific surface area (40.23 m{sup 2}/g) and shows high photocatalytic activity in the photodegradation of methylene blue under UV light irradiation.« less

Structure and reactivity studies of CoHNO{sup +} in the gas phase

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

Chen, H.; Jacobson, D.B.; Freiser, B.S.

1999-12-16

The structure and energetics of three CoHNO{sup +} isomers [HCo(NO){sup +} (1), Co(HNO){sup +} (2), Co(NOH){sup +} (3)] were probed by using density functional theory (DFT). Theory predicts that 2 is the most stable structure with 1 and 3 14.1 and 15.4 kcal/mol less stable. The transition states for 2 {yields} 1 and 2 {yields} 3 conversions were not located. DFT calculations predict D{degree}(CoH{sup +}-NO) = 34.6 kcal/mol and D{degree}(Co{sup +}-HNO) = 45.5 kcal/mol. The gas-phase ion chemistry of CoHNO{sup +} was also studied by using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. CID and SORI-CID of CoHNO{sup +}more » yield competitive formation of Co{sup +}, CoH{sup +}, and CoNO{sup +}. These results suggest that the barrier for 2 {yields} 1 conversion is less than 45.5 kcal/mol. Reactions with simple molecules were dominated by NO and HNO displacements. Potential energy surface diagrams are presented to explain these displacement reactions. Surprisingly, CoHNO{sup +} reacts with methane by dehydrogenation to yield CoCH{sub 3}NO{sup +}. Studies suggest CH{sub 3}CoNO{sup +} rather than Co(CH{sub 3}NO){sup +}as the structure for this ion.« less

Soil and Land Resources Information System (SLISYS-Tarim) for Sustainable Management of River Oases along the Tarim River, China

NASA Astrophysics Data System (ADS)

Othmanli, Hussein; Zhao, Chengyi; Stahr, Karl

2017-04-01

The Tarim River Basin is the largest continental basin in China. The region has extremely continental desert climate characterized by little rainfall <50 mm/a and high potential evaporation >3000 mm/a. The climate change is affecting severely the basin causing soil salinization, water shortage, and regression in crop production. Therefore, a Soil and Land Resources Information System (SLISYS-Tarim) for the regional simulation of crop yield production in the basin was developed. The SLISYS-Tarim consists of a database and an agro-ecological simulation model EPIC (Environmental Policy Integrated Climate). The database comprises relational tables including information about soils, terrain conditions, land use, and climate. The soil data implicate information of 50 soil profiles which were dug, analyzed, described and classified in order to characterize the soils in the region. DEM data were integrated with geological maps to build a digital terrain structure. Remote sensing data of Landsat images were applied for soil mapping, and for land use and land cover classification. An additional database for climate data, land management and crop information were linked to the system, too. Construction of the SLISYS-Tarim database was accomplished by integrating and overlaying the recommended thematic maps within environment of the geographic information system (GIS) to meet the data standard of the global and national SOTER digital database. This database forms appropriate input- and output data for the crop modelling with the EPIC model at various scales in the Tarim Basin. The EPIC model was run for simulating cotton production under a constructed scenario characterizing the current management practices, soil properties and climate conditions. For the EPIC model calibration, some parameters were adjusted so that the modeled cotton yield fits to the measured yield on the filed scale. The validation of the modeling results was achieved in a later step based on remote sensing data. The simulated cotton yield varied according to field management, soil type and salinity level, where soil salinity was the main limiting factor. Furthermore, the calibrated and validated EPIC model was run under several scenarios of climate conditions and land management practices to estimate the effect of climate change on cotton production and sustainability of agriculture systems in the basin. The application of SLISYS-Tarim showed that this database can be a suitable framework for storage and retrieval of soil and terrain data at various scales. The simulation with the EPIC model can assess the impact of climate change and management strategies. Therefore, SLISYS-Tarim can be a good tool for regional planning and serve the decision support system on regional and national scale.

3D FSE Cube and VIPR-aTR 3.0 Tesla magnetic resonance imaging predicts canine cranial cruciate ligament structural properties.

PubMed

Racette, Molly; Al saleh, Habib; Waller, Kenneth R; Bleedorn, Jason A; McCabe, Ronald P; Vanderby, Ray; Markel, Mark D; Brounts, Sabrina H; Block, Walter F; Muir, Peter

2016-03-01

Estimation of cranial cruciate ligament (CrCL) structural properties in client-owned dogs with incipient cruciate rupture would be advantageous. The objective of this study was to determine whether magnetic resonance imaging (MRI) measurement of normal CrCL volume in an ex-vivo canine model predicts structural properties. Stifles from eight dogs underwent 3.0 Tesla 3D MRI. CrCL volume and normalized median grayscale values were determined using 3D Fast Spin Echo (FSE) Cube and Vastly under-sampled Isotropic PRojection (VIPR)-alternative repetition time (aTR) sequences. Stifles were then mechanically tested. After joint laxity testing, CrCL structural properties were determined, including displacement at yield, yield load, load to failure, and stiffness. Yield load and load to failure (R(2)=0.56, P <0.01) were correlated with CrCL volume determined by VIPR-aTR. Yield load was also correlated with CrCL volume determined by 3D FSE Cube (R(2)=0.32, P <0.05). Structural properties were not related to median grayscale values. Joint laxity and CrCL stiffness were not related to MRI parameters, but displacement at yield load was related to CrCL volume for both sequences during testing (R(2)>0.57, P <0.005). In conclusion, 3D MRI offers a predictive method for estimating canine CrCL structural properties. 3D MRI may be useful for monitoring CrCL properties in clinical trials. Copyright © 2016 Elsevier Ltd. All rights reserved.

Compression of freestanding gold nanostructures: from stochastic yield to predictable flow

NASA Astrophysics Data System (ADS)

Mook, W. M.; Niederberger, C.; Bechelany, M.; Philippe, L.; Michler, J.

2010-02-01

Characterizing the mechanical response of isolated nanostructures is vitally important to fields such as microelectromechanical systems (MEMS) where the behaviour of nanoscale contacts can in large part determine system reliability and lifetime. To address this challenge directly, single crystal gold nanodots are compressed inside a high resolution scanning electron microscope (SEM) using a nanoindenter equipped with a flat punch tip. These structures load elastically, and then yield in a stochastic manner, at loads ranging from 16 to 110 µN, which is up to five times higher than the load necessary for flow after yield. Yielding is immediately followed by displacement bursts equivalent to 1-50% of the initial height, depending on the yield point. During the largest displacement bursts, strain energy within the structure is released while new surface area is created in the form of localized slip bands, which are evident in both the SEM movies and still-images. A first order estimate of the apparent energy release rate, in terms of fracture mechanics concepts, for bursts representing 5-50% of the structure's initial height is on the order of 10-100 J m-2, which is approximately two orders of magnitude lower than bulk values. Once this initial strain burst during yielding has occurred, the structures flow in a ductile way. The implications of this behaviour, which is analogous to a brittle to ductile transition, are discussed with respect to mechanical reliability at the micro- and nanoscales.

Aqueous synthesis of highly luminescent AgInS2-ZnS quantum dots and their biological applications

NASA Astrophysics Data System (ADS)

Regulacio, Michelle D.; Win, Khin Yin; Lo, Seong Loong; Zhang, Shuang-Yuan; Zhang, Xinhai; Wang, Shu; Han, Ming-Yong; Zheng, Yuangang

2013-02-01

Highly emissive and air-stable AgInS2-ZnS quantum dots (ZAIS QDs) with quantum yields of up to 20% have been successfully synthesized directly in aqueous media in the presence of polyacrylic acid (PAA) and mercaptoacetic acid (MAA) as stabilizing and reactivity-controlling agents. The as-prepared water-dispersible ZAIS QDs are around 3 nm in size, possess the tetragonal chalcopyrite crystal structure, and exhibit long fluorescence lifetimes (>100 ns). In addition, these ZAIS QDs are found to exhibit excellent optical and colloidal stability in physiologically relevant pH values as well as very low cytotoxicity, which render them particularly suitable for biological applications. Their potential use in biological labelling of baculoviral vectors is demonstrated.Highly emissive and air-stable AgInS2-ZnS quantum dots (ZAIS QDs) with quantum yields of up to 20% have been successfully synthesized directly in aqueous media in the presence of polyacrylic acid (PAA) and mercaptoacetic acid (MAA) as stabilizing and reactivity-controlling agents. The as-prepared water-dispersible ZAIS QDs are around 3 nm in size, possess the tetragonal chalcopyrite crystal structure, and exhibit long fluorescence lifetimes (>100 ns). In addition, these ZAIS QDs are found to exhibit excellent optical and colloidal stability in physiologically relevant pH values as well as very low cytotoxicity, which render them particularly suitable for biological applications. Their potential use in biological labelling of baculoviral vectors is demonstrated. Electronic supplementary information (ESI) available: Quantum yields, EDX spectrum and photoluminescence decay curves. See DOI: 10.1039/c3nr34159c

NEANDC specialists meeting on yields and decay data of fission product nuclides

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

Chrien, R.E.; Burrows, T.W.

Separate abstracts were prepared for the 29 papers presented. Workshop reports on decay heat, fission yields, beta- and gamma-ray spectroscopy, and delayed neutrons are included. An appendix contains a survey of the most recent compilations and evaluations containing fission product yield, fission product decay data, and delayed neutron yield information. (WHK)

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.

PubMed

Huang, Wei; Ravikumar, Krishnakumar M; Parisien, Marc; Yang, Sichun

2016-12-01

Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.2Å and 4.2Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT-using either rigid-body or MD-based flexible docking-is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes. Copyright © 2016 Elsevier Inc. All rights reserved.

High char yield epoxy curing agents

NASA Technical Reports Server (NTRS)

Delvigs, P.; Serafini, T. T.; Vanucci, R. D.

1981-01-01

Class of imide-amine curing agents preserves structural integrity, prevents fiber release, and is fully compatible with conventional epoxy resins; agents do not detract from composite properties while greatly reducing char yield. Materials utilizing curing are used in aerospace, automotive, and other structural components where deterioration must be minimized and fiber release avoided in event of fire.

X-ray K-edge absorption spectra of Fe minerals and model compounds: II. EXAFS

NASA Astrophysics Data System (ADS)

Waychunas, Glenn A.; Brown, Gordon E.; Apted, Michael J.

1986-01-01

K-edge extended X-ray absorption fine structure (EXAFS) spectra of Fe in varying environments in a suite of well-characterized silicate and oxide minerals were collected using synchrotron radiation and analyzed using single scattering approximation theory to yield nearest neighbor Fe-O distances and coordination numbers. The partial inverse character of synthetic hercynite spinal was verified in this way. Comparison of the results from all samples with structural data from X-ray diffraction crystal structure refinements indicates that EXAFS-derived first neighbor distances are generally accurate to ±0.02 Å using only theoretically generated phase information, and may be improved over this if similar model compounds are used to determine EXAFS phase functions. Coordination numbers are accurate to ±20 percent and can be similarly improved using model compound EXAFS amplitude information. However, in particular cases the EXAFS-derived distances may be shortened, and the coordination number reduced, by the effects of static and thermal disorder or by partial overlap of the longer Fe-O first neighbor distances with second neighbor distances in the EXAFS structure function. In the former case the total information available in the EXAFS is limited by the disorder, while in the latter case more accurate results can in principle be obtained by multiple neighbor EXAFS analysis. The EXAFS and XANES spectra of Fe in Nain, Labrador osumulite and Lakeview, Oregon plagioclase are also analyzed as an example of the application of X-ray absorption spectroscopy to metal ion site occupation determination in minerals.

An evaluation of information-theoretic methods for detecting structural microbial biosignatures.

PubMed

Wagstaff, Kiri L; Corsetti, Frank A

2010-05-01

The first observations of extraterrestrial environments will most likely be in the form of digital images. Given an image of a rock that contains layered structures, is it possible to determine whether the layers were created by life (biogenic)? While conclusive judgments about biogenicity are unlikely to be made solely on the basis of image features, an initial assessment of the importance of a given sample can inform decisions about follow-up searches for other types of possible biosignatures (e.g., isotopic or chemical analysis). In this study, we evaluated several quantitative measures that capture the degree of complexity in visible structures, in terms of compressibility (to detect order) and the entropy (spread) of their intensity distributions. Computing complexity inside a sliding analysis window yields a map of each of these features that indicates how they vary spatially across the sample. We conducted experiments on both biogenic and abiogenic terrestrial stromatolites and on laminated structures found on Mars. The degree to which each feature separated biogenic from abiogenic samples (separability) was assessed quantitatively. None of the techniques provided a consistent, statistically significant distinction between all biogenic and abiogenic samples. However, the PNG compression ratio provided the strongest distinction (2.80 in standard deviation units) and could inform future techniques. Increasing the analysis window size or the magnification level, or both, improved the separability of the samples. Finally, data from all four Mars samples plotted well outside the biogenic field suggested by the PNG analyses, although we caution against a direct comparison of terrestrial stromatolites and martian non-stromatolites.

Photo-CIDNP NMR spectroscopy of amino acids and proteins.

PubMed

Kuhn, Lars T

2013-01-01

Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.

Noninvasive characterization of the fission yeast cell cycle by monitoring dry mass with digital holographic microscopy.

PubMed

Rappaz, Benjamin; Cano, Elena; Colomb, Tristan; Kühn, Jonas; Depeursinge, Christian; Simanis, Viesturs; Magistretti, Pierre J; Marquet, Pierre

2009-01-01

Digital holography microscopy (DHM) is an optical technique which provides phase images yielding quantitative information about cell structure and cellular dynamics. Furthermore, the quantitative phase images allow the derivation of other parameters, including dry mass production, density, and spatial distribution. We have applied DHM to study the dry mass production rate and the dry mass surface density in wild-type and mutant fission yeast cells. Our study demonstrates the applicability of DHM as a tool for label-free quantitative analysis of the cell cycle and opens the possibility for its use in high-throughput screening.

Quantum-state reconstruction by maximizing likelihood and entropy.

PubMed

Teo, Yong Siah; Zhu, Huangjun; Englert, Berthold-Georg; Řeháček, Jaroslav; Hradil, Zdeněk

2011-07-08

Quantum-state reconstruction on a finite number of copies of a quantum system with informationally incomplete measurements, as a rule, does not yield a unique result. We derive a reconstruction scheme where both the likelihood and the von Neumann entropy functionals are maximized in order to systematically select the most-likely estimator with the largest entropy, that is, the least-bias estimator, consistent with a given set of measurement data. This is equivalent to the joint consideration of our partial knowledge and ignorance about the ensemble to reconstruct its identity. An interesting structure of such estimators will also be explored.

Synthesis of Large Quantities of Single-Walled Aluminogermanante Nanotube

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

Levard,C.; Rose, J.; Mision, A.

2008-01-01

A simple aqueous synthesis yielded about 100 times more structurally well-organized single-walled aluminogermanate nanotubes than previously reported 'standard' procedures. The structure analyses using XRD, IRTF, TEM, and XAS were greatly facilitated by the high concentrations available, and they ascertained the imogolite-like structure of the nanotubes. Simplicity and yield of the synthesis protocol are likely to favor commercial applications of theses materials as well as simplified syntheses of other nanophases.

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

PubMed Central

Clifton, Matthew C.; Dranow, David M.; Leed, Alison; Fulroth, Ben; Fairman, James W.; Abendroth, Jan; Atkins, Kateri A.; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z. J.; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B.; Golub, Todd R.; Hubbard, Brian K.; Serrano-Wu, Michael H.

2015-01-01

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors. PMID:25909780

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

PubMed Central

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Covariance Matrix Evaluations for Independent Mass Fission Yields

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

Terranova, N., E-mail: nicholas.terranova@unibo.it; Serot, O.; Archier, P.

2015-01-15

Recent needs for more accurate fission product yields include covariance information to allow improved uncertainty estimations of the parameters used by design codes. The aim of this work is to investigate the possibility to generate more reliable and complete uncertainty information on independent mass fission yields. Mass yields covariances are estimated through a convolution between the multi-Gaussian empirical model based on Brosa's fission modes, which describe the pre-neutron mass yields, and the average prompt neutron multiplicity curve. The covariance generation task has been approached using the Bayesian generalized least squared method through the CONRAD code. Preliminary results on mass yieldsmore » variance-covariance matrix will be presented and discussed from physical grounds in the case of {sup 235}U(n{sub th}, f) and {sup 239}Pu(n{sub th}, f) reactions.« less

Influence of management and environment on Australian wheat: information for sustainable intensification and closing yield gaps

NASA Astrophysics Data System (ADS)

Bryan, B. A.; King, D.; Zhao, G.

2014-04-01

In the future, agriculture will need to produce more, from less land, more sustainably. But currently, in many places, actual crop yields are below those attainable. We quantified the ability for agricultural management to increase wheat yields across 179 Mha of potentially arable land in Australia. Using the Agricultural Production Systems Simulator (APSIM), we simulated the impact on wheat yield of 225 fertilization and residue management scenarios at a high spatial, temporal, and agronomic resolution from 1900 to 2010. The influence of management and environmental variables on wheat yield was then assessed using Spearman’s non-parametric correlation test with bootstrapping. While residue management showed little correlation, fertilization strongly increased wheat yield up to around 100 kg N ha-1 yr-1. However, this effect was highly dependent on the key environment variables of rainfall, temperature, and soil water holding capacity. The influence of fertilization on yield was stronger in cooler, wetter climates, and in soils with greater water holding capacity. We conclude that the effectiveness of management intensification to increase wheat yield is highly dependent upon local climate and soil conditions. We provide context-specific information on the yield benefits of fertilization to support adaptive agronomic decision-making and contribute to the closure of yield gaps. We also suggest that future assessments consider the economic and environmental sustainability of management intensification for closing yield gaps.

Computing wheat nitrogen requirements from grain yield and protein maps

USDA-ARS?s Scientific Manuscript database

Optical protein sensors and mass-flow yield monitors provide the opportunity to continuously measure grain quality and quantity during harvesting. This chapter illustrates how yield monitor and grain protein measurements may provide useful postharvest information for evaluating water or nitrogen (N)...

Computing wheat nitrogen requirements from grain yield and protein maps

USDA-ARS?s Scientific Manuscript database

Optical protein sensors and mass-flow yield monitors provide the opportunity to continuously measure grain quality and quantity during harvesting. This chapter illustrates how yield monitor and grain protein measurements may provide useful post-harvest information for evaluating water or nitrogen (...

Hyperspectral imagery for mapping crop yield for precision agriculture

USDA-ARS?s Scientific Manuscript database

Crop yield is perhaps the most important piece of information for crop management in precision agriculture. It integrates the effects of various spatial variables such as soil properties, topographic attributes, tillage, plant population, fertilization, irrigation, and pest infestations. A yield map...

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

Operation of the yield estimation subsystem

NASA Technical Reports Server (NTRS)

Mccrary, D. G.; Rogers, J. L.; Hill, J. D. (Principal Investigator)

1979-01-01

The organization and products of the yield estimation subsystem (YES) are described with particular emphasis on meteorological data acquisition, yield estimation, crop calendars, weekly weather summaries, and project reports. During the three phases of LACIE, YES demonstrated that it is possible to use the flow of global meteorological data and provide valuable information regarding global wheat production. It was able to establish a capability to collect, in a timely manner, detailed weather data from all regions of the world, and to evaluate and convert that data into information appropriate to the project's needs.

The Cosmic Microwave Background Radiation - A Unique Window on the Early Universe

NASA Technical Reports Server (NTRS)

Hinshaw, Gary F.

2009-01-01

The cosmic microwave background radiation is the remnant heat from the Big Bang. It provides us with a unique probe of conditions in the early universe, long before any organized structures had yet formed. The anisotropy in the radiation's brightness yields important clues about primordial structure and additionally provides a wealth of information about the physics of the early universe. Within the framework of inflationary dark matter models, observations of the anisotropy on sub-degree angular scales reveals the signatures of acoustic oscillations of the photon-baryon fluid at a redshift of approx. 1100. Data from the first five years of operation of the Wilkinson Microwave Anisotropy Probe (WMAP) satellite provide detailed full-sky maps of the cosmic microwave background temperature and polarization anisotropy. Together, the data provide a wealth of cosmological information, including the age of the universe, the epoch when the first stars formed, and the overall composition of baryonic matter, dark matter, and dark energy. The results also provide constraints on the period of inflationary expansion in the very first moments of time.

Automatic segmentation of colon glands using object-graphs.

PubMed

Gunduz-Demir, Cigdem; Kandemir, Melih; Tosun, Akif Burak; Sokmensuer, Cenk

2010-02-01

Gland segmentation is an important step to automate the analysis of biopsies that contain glandular structures. However, this remains a challenging problem as the variation in staining, fixation, and sectioning procedures lead to a considerable amount of artifacts and variances in tissue sections, which may result in huge variances in gland appearances. In this work, we report a new approach for gland segmentation. This approach decomposes the tissue image into a set of primitive objects and segments glands making use of the organizational properties of these objects, which are quantified with the definition of object-graphs. As opposed to the previous literature, the proposed approach employs the object-based information for the gland segmentation problem, instead of using the pixel-based information alone. Working with the images of colon tissues, our experiments demonstrate that the proposed object-graph approach yields high segmentation accuracies for the training and test sets and significantly improves the segmentation performance of its pixel-based counterparts. The experiments also show that the object-based structure of the proposed approach provides more tolerance to artifacts and variances in tissues.

Spectral behavior of hydrated sulfate salts: implications for Europa mission spectrometer design

NASA Technical Reports Server (NTRS)

Dalton, James Bradley 3rd

2003-01-01

Remote sensing of the surface of Europa with near-infrared instruments has suggested the presence of hydrated materials, including sulfate salts. Attention has been focused on these salts for the information they might yield regarding the evolution of a putative interior ocean, and the evaluation of its astrobiological potential. These materials exhibit distinct infrared absorption features due to bound water. The interactions of this water with the host molecules lead to fine structure that can be used to discriminate among these materials on the basis of their spectral behavior. This fine structure is even more pronounced at the low temperatures prevalent on icy satellites. Examination of hydrated sulfate salt spectra measured under cryogenic temperature conditions provides realistic constraints for future remote-sensing missions to Europa. In particular, it suggests that a spectrometer system capable of 2-5 nm spectral resolution or better, with a spatial resolution approaching 100 m, would be able to differentiate among proposed hydrated surface materials, if present, and constrain their distributions across the surface. Such information would provide valuable insights into the evolutionary history of Europa.

Robust Measurement via A Fused Latent and Graphical Item Response Theory Model.

PubMed

Chen, Yunxiao; Li, Xiaoou; Liu, Jingchen; Ying, Zhiliang

2018-03-12

Item response theory (IRT) plays an important role in psychological and educational measurement. Unlike the classical testing theory, IRT models aggregate the item level information, yielding more accurate measurements. Most IRT models assume local independence, an assumption not likely to be satisfied in practice, especially when the number of items is large. Results in the literature and simulation studies in this paper reveal that misspecifying the local independence assumption may result in inaccurate measurements and differential item functioning. To provide more robust measurements, we propose an integrated approach by adding a graphical component to a multidimensional IRT model that can offset the effect of unknown local dependence. The new model contains a confirmatory latent variable component, which measures the targeted latent traits, and a graphical component, which captures the local dependence. An efficient proximal algorithm is proposed for the parameter estimation and structure learning of the local dependence. This approach can substantially improve the measurement, given no prior information on the local dependence structure. The model can be applied to measure both a unidimensional latent trait and multidimensional latent traits.

Using complex networks for text classification: Discriminating informative and imaginative documents

NASA Astrophysics Data System (ADS)

de Arruda, Henrique F.; Costa, Luciano da F.; Amancio, Diego R.

2016-01-01

Statistical methods have been widely employed in recent years to grasp many language properties. The application of such techniques have allowed an improvement of several linguistic applications, such as machine translation and document classification. In the latter, many approaches have emphasised the semantical content of texts, as is the case of bag-of-word language models. These approaches have certainly yielded reasonable performance. However, some potential features such as the structural organization of texts have been used only in a few studies. In this context, we probe how features derived from textual structure analysis can be effectively employed in a classification task. More specifically, we performed a supervised classification aiming at discriminating informative from imaginative documents. Using a networked model that describes the local topological/dynamical properties of function words, we achieved an accuracy rate of up to 95%, which is much higher than similar networked approaches. A systematic analysis of feature relevance revealed that symmetry and accessibility measurements are among the most prominent network measurements. Our results suggest that these measurements could be used in related language applications, as they play a complementary role in characterising texts.

Nucleation and particle coagulation experiments in microgravity

NASA Technical Reports Server (NTRS)

Nuth, J.

1987-01-01

Measurements of the conditions under which carbon, aluminum oxide, and silicon carbide smokes condense and of the morphology and crystal structure of the resulting grains are essential if the nature of the materials ejected into the interstellar medium and the nature of the grains which eventually became part of the proto solar nebular are to be understood. Little information is currently available on the vapor-solid phase transitions of refractory metals and solids. What little experimental data do exist are, however, not in agreement with currently accepted models of the nucleation process for more volatile materials. The major obstacle to performing such experiments in earth-based laboratories is the susceptibility of these systems to convection. Evaporation of refractory materials into a low-pressure environment with a carefully controlled temperature gradient will produce refractory smokes when the critical supersaturation of the system is exceeded. Measurement of the point at which nucleation occurs, via light scattering or extinction, can not only yield nucleation data but also, information on the chemical composition and crystal structure of the condensate. Experimental requirements are presented.

Stellar occultation spikes as probes of atmospheric structure and composition. [for Jupiter

NASA Technical Reports Server (NTRS)

Elliot, J. L.; Veverka, J.

1976-01-01

The characteristics of spikes observed in occultation light curves of Beta Scorpii by Jupiter are discussed in terms of the gravity-gradient model. The occultation of Beta Sco by Jupiter on May 13, 1971, is reviewed, and the gravity-gradient model is defined as an isothermal atmosphere of constant composition in which the refractivity is a function only of the radial coordinate from the center of refraction, which is assumed to lie parallel to the local gravity gradient. The derivation of the occultation light curve in terms of the atmosphere, the angular diameter of the occulted star, and the occultation geometry is outlined. It is shown that analysis of the light-curve spikes can yield the He/H2 concentration ratio in a well-mixed atmosphere, information on fine-scale atmospheric structure, high-resolution images of the occulted star, and information on ray crossing. Observational limits are placed on the magnitude of horizontal refractivity gradients, and it is concluded that the spikes are the result of local atmospheric density variations: atmospheric layers, density waves, or turbulence.

Spectral behavior of hydrated sulfate salts: implications for Europa mission spectrometer design.

PubMed

Dalton, James Bradley

2003-01-01

Remote sensing of the surface of Europa with near-infrared instruments has suggested the presence of hydrated materials, including sulfate salts. Attention has been focused on these salts for the information they might yield regarding the evolution of a putative interior ocean, and the evaluation of its astrobiological potential. These materials exhibit distinct infrared absorption features due to bound water. The interactions of this water with the host molecules lead to fine structure that can be used to discriminate among these materials on the basis of their spectral behavior. This fine structure is even more pronounced at the low temperatures prevalent on icy satellites. Examination of hydrated sulfate salt spectra measured under cryogenic temperature conditions provides realistic constraints for future remote-sensing missions to Europa. In particular, it suggests that a spectrometer system capable of 2-5 nm spectral resolution or better, with a spatial resolution approaching 100 m, would be able to differentiate among proposed hydrated surface materials, if present, and constrain their distributions across the surface. Such information would provide valuable insights into the evolutionary history of Europa.

Lunar Seismology: the Internal Structure of the Moon. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Goins, N. R.

1978-01-01

The direct P and S wave arrival times are the primary data set that can be measured on the seismograms of natural lunar seismic events. Polarization filtering techniques allow the enhancement of secondary body wave arrivals and record curves to identify the secondary phases and deduce structural information. Finally, shear wave amplitude vs. distance curves yield information on the location and magnitude of seismic velocity gradients in the interior. The results of these analyses show that the moon appears to have a two-layer crust at all four seismic stations: a 20 km upper crust that seems to be constant at all sites and a lower crust that is 40 km thick at stations 12 and 14 (mare), 55 + or - 10 km at station 16 (highland), and tentatively either 40 km or 70 km at station 15. The lower mantle extends from 480 km to at least 1100 km depth which is the maximum depth of penetration of all but a few seismic waves used as data. No definitive evidence for or against a lunar core exists.

Stand-level growth and yield component models for red oak-sweetgum forests on Mid-South minor stream bottoms

Treesearch

Emily B. Schultz; J. Clint Iles; Thomas G. Matney; Andrew W. Ezell; James S. Meadows; Theodor D. Leininger; al. et.

2010-01-01

Greater emphasis is being placed on Southern bottomland hardwood management, but relatively few growth and yield prediction systems exist that are based on sufficient measurements. We present the aggregate stand-level expected yield and structural component equations for a red oak (Quercus section Lobatae)-sweetgum (Liquidambar styraciflua L.) growth and yield model....

Mind the Roots: Phenotyping Below-Ground Crop Diversity and Its Influence on Final Yield

NASA Astrophysics Data System (ADS)

Nieters, C.; Guadagno, C. R.; Lemli, S.; Hosseini, A.; Ewers, B. E.

2017-12-01

Changes in global climate patterns and water regimes are having profound impacts on worldwide crop production. An ever-growing population paired with increasing temperatures and unpredictable periods of severe drought call for accurate modeling of future crop yield. Although novel approaches are being developed in high-throughput, above-ground image phenotyping, the below-ground plant system is still poorly phenotyped. Collection of plant root morphology and hydraulics are needed to inform mathematical models to reliably estimate yields of crops grown in sub-optimal conditions. We used Brassica rapa to inform our model as it is a globally cultivated crop with several functionally diverse cultivars. Specifically, we use 7 different accessions from oilseed (R500 and Yellow Sarson), leafy type (Pac choi and Chinese cabbage), a vegetable turnip, and two Wisconsin Fast Plants (Imb211 and Fast Plant self-compatible), which have shorter life cycles and potentially large differences in allocation to roots. Bi-weekly, we harvested above and below-ground biomass to compare the varieties in terms of carbon allocation throughout their life cycle. Using WinRhizo software, we analyzed root system length and surface area to compare and contrast root morphology among cultivars. Our results confirm that root structural characteristics are crucial to explain plant water use and carbon allocation. The root:shoot ratio reveals a significant (p < 0.01) difference among crop accession. To validate the procedure across different varieties and life stages we also compared surface area results from the image-based technology to dry biomass finding a strong linear relationship (R2= 0.85). To assess the influence of a diverse above-ground morphology on the root system we also measured above-ground anatomical and physiological traits such as gas exchange, chlorophyll content, and chlorophyll a fluorescence. A thorough analysis of the root system will clarify carbon dynamics and hydraulics at the whole-plant level, improving final yield predictions.

Information theory analysis of Australian humpback whale song.

PubMed

Miksis-Olds, Jennifer L; Buck, John R; Noad, Michael J; Cato, Douglas H; Stokes, M Dale

2008-10-01

Songs produced by migrating whales were recorded off the coast of Queensland, Australia, over six consecutive weeks in 2003. Forty-eight independent song sessions were analyzed using information theory techniques. The average length of the songs estimated by correlation analysis was approximately 100 units, with song sessions lasting from 300 to over 3100 units. Song entropy, a measure of structural constraints, was estimated using three different methodologies: (1) the independently identically distributed model, (2) a first-order Markov model, and (3) the nonparametric sliding window match length (SWML) method, as described by Suzuki et al. [(2006). "Information entropy of humpback whale song," J. Acoust. Soc. Am. 119, 1849-1866]. The analysis finds that the song sequences of migrating Australian whales are consistent with the hierarchical structure proposed by Payne and McVay [(1971). "Songs of humpback whales," Science 173, 587-597], and recently supported mathematically by Suzuki et al. (2006) for singers on the Hawaiian breeding grounds. Both the SWML entropy estimates and the song lengths for the Australian singers in 2003 were lower than that reported by Suzuki et al. (2006) for Hawaiian whales in 1976-1978; however, song redundancy did not differ between these two populations separated spatially and temporally. The average total information in the sequence of units in Australian song was approximately 35 bits/song. Aberrant songs (8%) yielded entropies similar to the typical songs.

Greater taxol yield of fungus Pestalotiopsis hainanensis from dermatitic scurf of the giant panda (Ailuropoda melanoleuca).

PubMed

Gu, Yu; Wang, Yanlin; Ma, Xiaoping; Wang, Chengdong; Yue, Guizhou; Zhang, Yuetian; Zhang, Yunyan; Li, Shanshan; Ling, Shanshan; Liu, Xiaomin; Wen, Xintian; Cao, Sanjie; Huang, Xiaobo; Deng, Junliang; Zuo, Zhicai; Yu, Shumin; Shen, Liuhong; Wu, Rui

2015-01-01

While taxol yields of fungi from non-animal sources are still low, whether Pestalotiopsis hainanensis isolated from the scurf of a dermatitic giant panda, Ailuropoda melanoleuca, provides a greater taxol yield remains unknown. The objective of the study was to determine the corresponding taxol yield. The structure of the taxol produced by the fungus was evaluated by thin layer chromatography (TLC), ultraviolet (UV) spectroscopy, high-performance liquid chromatography (HPLC), (1)H and (13)C nuclear magnetic resonance spectroscopy ((1)H-NMR and (13)C-NMR), and time-of-flight mass spectrometry (TOF-MS), with standard taxol as a control. The results demonstrated that the P. hainanensis fungus produced taxol, which had the same structure as the standard taxol and yield of 1,466.87 μg/L. This fungal taxol yield from the dermatitic giant panda was significantly greater than those of fungus from non-animal sources. The taxol-producing fungus may be a potential candidate for the production of taxol on an industrial scale.

Classical and Bayesian Seismic Yield Estimation: The 1998 Indian and Pakistani Tests

NASA Astrophysics Data System (ADS)

Shumway, R. H.

2001-10-01

- The nuclear tests in May, 1998, in India and Pakistan have stimulated a renewed interest in yield estimation, based on limited data from uncalibrated test sites. We study here the problem of estimating yields using classical and Bayesian methods developed by Shumway (1992), utilizing calibration data from the Semipalatinsk test site and measured magnitudes for the 1998 Indian and Pakistani tests given by Murphy (1998). Calibration is done using multivariate classical or Bayesian linear regression, depending on the availability of measured magnitude-yield data and prior information. Confidence intervals for the classical approach are derived applying an extension of Fieller's method suggested by Brown (1982). In the case where prior information is available, the posterior predictive magnitude densities are inverted to give posterior intervals for yield. Intervals obtained using the joint distribution of magnitudes are comparable to the single-magnitude estimates produced by Murphy (1998) and reinforce the conclusion that the announced yields of the Indian and Pakistani tests were too high.

Classical and Bayesian Seismic Yield Estimation: The 1998 Indian and Pakistani Tests

NASA Astrophysics Data System (ADS)

Shumway, R. H.

The nuclear tests in May, 1998, in India and Pakistan have stimulated a renewed interest in yield estimation, based on limited data from uncalibrated test sites. We study here the problem of estimating yields using classical and Bayesian methods developed by Shumway (1992), utilizing calibration data from the Semipalatinsk test site and measured magnitudes for the 1998 Indian and Pakistani tests given by Murphy (1998). Calibration is done using multivariate classical or Bayesian linear regression, depending on the availability of measured magnitude-yield data and prior information. Confidence intervals for the classical approach are derived applying an extension of Fieller's method suggested by Brown (1982). In the case where prior information is available, the posterior predictive magnitude densities are inverted to give posterior intervals for yield. Intervals obtained using the joint distribution of magnitudes are comparable to the single-magnitude estimates produced by Murphy (1998) and reinforce the conclusion that the announced yields of the Indian and Pakistani tests were too high.

Improvement in Saccharification Yield of Mixed Rumen Enzymes by Identification of Recalcitrant Cell Wall Constituents Using Enzyme Fingerprinting.

PubMed

Badhan, Ajay; Wang, Yu-Xi; Gruninger, Robert; Patton, Donald; Powlowski, Justin; Tsang, Adrian; McAllister, Tim A

2015-01-01

Identification of recalcitrant factors that limit digestion of forages and the development of enzymatic approaches that improve hydrolysis could play a key role in improving the efficiency of meat and milk production in ruminants. Enzyme fingerprinting of barley silage fed to heifers and total tract indigestible fibre residue (TIFR) collected from feces was used to identify cell wall components resistant to total tract digestion. Enzyme fingerprinting results identified acetyl xylan esterases as key to the enhanced ruminal digestion. FTIR analysis also suggested cross-link cell wall polymers as principal components of indigested fiber residues in feces. Based on structural information from enzymatic fingerprinting and FTIR, enzyme pretreatment to enhance glucose yield from barley straw and alfalfa hay upon exposure to mixed rumen-enzymes was developed. Prehydrolysis effects of recombinant fungal fibrolytic hydrolases were analyzed using microassay in combination with statistical experimental design. Recombinant hemicellulases and auxiliary enzymes initiated degradation of plant structural polysaccharides upon application and improved the in vitro saccharification of alfalfa and barley straw by mixed rumen enzymes. The validation results showed that microassay in combination with statistical experimental design can be successfully used to predict effective enzyme pretreatments that can enhance plant cell wall digestion by mixed rumen enzymes.

Tracking multiple particles in fluorescence time-lapse microscopy images via probabilistic data association.

PubMed

Godinez, William J; Rohr, Karl

2015-02-01

Tracking subcellular structures as well as viral structures displayed as 'particles' in fluorescence microscopy images yields quantitative information on the underlying dynamical processes. We have developed an approach for tracking multiple fluorescent particles based on probabilistic data association. The approach combines a localization scheme that uses a bottom-up strategy based on the spot-enhancing filter as well as a top-down strategy based on an ellipsoidal sampling scheme that uses the Gaussian probability distributions computed by a Kalman filter. The localization scheme yields multiple measurements that are incorporated into the Kalman filter via a combined innovation, where the association probabilities are interpreted as weights calculated using an image likelihood. To track objects in close proximity, we compute the support of each image position relative to the neighboring objects of a tracked object and use this support to recalculate the weights. To cope with multiple motion models, we integrated the interacting multiple model algorithm. The approach has been successfully applied to synthetic 2-D and 3-D images as well as to real 2-D and 3-D microscopy images, and the performance has been quantified. In addition, the approach was successfully applied to the 2-D and 3-D image data of the recent Particle Tracking Challenge at the IEEE International Symposium on Biomedical Imaging (ISBI) 2012.

Ultrasonic imaging of material flaws exploiting multipath information

NASA Astrophysics Data System (ADS)

Shen, Xizhong; Zhang, Yimin D.; Demirli, Ramazan; Amin, Moeness G.

2011-05-01

In this paper, we consider ultrasonic imaging for the visualization of flaws in a material. Ultrasonic imaging is a powerful nondestructive testing (NDT) tool which assesses material conditions via the detection, localization, and classification of flaws inside a structure. Multipath exploitations provide extended virtual array apertures and, in turn, enhance imaging capability beyond the limitation of traditional multisensor approaches. We utilize reflections of ultrasonic signals which occur when encountering different media and interior discontinuities. The waveforms observed at the physical as well as virtual sensors yield additional measurements corresponding to different aspect angles. Exploitation of multipath information addresses unique issues observed in ultrasonic imaging. (1) Utilization of physical and virtual sensors significantly extends the array aperture for image enhancement. (2) Multipath signals extend the angle of view of the narrow beamwidth of the ultrasound transducers, allowing improved visibility and array design flexibility. (3) Ultrasonic signals experience difficulty in penetrating a flaw, thus the aspect angle of the observation is limited unless access to other sides is available. The significant extension of the aperture makes it possible to yield flaw observation from multiple aspect angles. We show that data fusion of physical and virtual sensor data significantly improves the detection and localization performance. The effectiveness of the proposed multipath exploitation approach is demonstrated through experimental studies.

Identifying and designing chemicals with minimal acute aquatic toxicity.

PubMed

Kostal, Jakub; Voutchkova-Kostal, Adelina; Anastas, Paul T; Zimmerman, Julie Beth

2015-05-19

Industrial ecology has revolutionized our understanding of material stocks and flows in our economy and society. For this important discipline to have even deeper impact, we must understand the inherent nature of these materials in terms of human health and the environment. This paper focuses on methods to design synthetic chemicals to reduce their intrinsic ability to cause adverse consequence to the biosphere. Advances in the fields of computational chemistry and molecular toxicology in recent decades allow the development of predictive models that inform the design of molecules with reduced potential to be toxic to humans or the environment. The approach presented herein builds on the important work in quantitative structure-activity relationships by linking toxicological and chemical mechanistic insights to the identification of critical physical-chemical properties needed to be modified. This in silico approach yields design guidelines using boundary values for physiochemical properties. Acute aquatic toxicity serves as a model endpoint in this study. Defining value ranges for properties related to bioavailability and reactivity eliminates 99% of the chemicals in the highest concern for acute aquatic toxicity category. This approach and its future implementations are expected to yield very powerful tools for life cycle assessment practitioners and molecular designers that allow rapid assessment of multiple environmental and human health endpoints and inform modifications to minimize hazard.

Evaluation in undergraduate medical education: Conceptualizing and validating a novel questionnaire for assessing the quality of bedside teaching.

PubMed

Dreiling, Katharina; Montano, Diego; Poinstingl, Herbert; Müller, Tjark; Schiekirka-Schwake, Sarah; Anders, Sven; von Steinbüchel, Nicole; Raupach, Tobias

2017-08-01

Evaluation is an integral part of curriculum development in medical education. Given the peculiarities of bedside teaching, specific evaluation tools for this instructional format are needed. Development of these tools should be informed by appropriate frameworks. The purpose of this study was to develop a specific evaluation tool for bedside teaching based on the Stanford Faculty Development Program's clinical teaching framework. Based on a literature review yielding 47 evaluation items, an 18-item questionnaire was compiled and subsequently completed by undergraduate medical students at two German universities. Reliability and validity were assessed in an exploratory full information item factor analysis (study one) and a confirmatory factor analysis as well as a measurement invariance analysis (study two). The exploratory analysis involving 824 students revealed a three-factor structure. Reliability estimates of the subscales were satisfactory (α = 0.71-0.84). The model yielded satisfactory fit indices in the confirmatory factor analysis involving 1043 students. The new questionnaire is short and yet based on a widely-used framework for clinical teaching. The analyses presented here indicate good reliability and validity of the instrument. Future research needs to investigate whether feedback generated from this tool helps to improve teaching quality and student learning outcome.

ANALYSIS OF CLINICAL AND DERMOSCOPIC FEATURES FOR BASAL CELL CARCINOMA NEURAL NETWORK CLASSIFICATION

PubMed Central

Cheng, Beibei; Stanley, R. Joe; Stoecker, William V; Stricklin, Sherea M.; Hinton, Kristen A.; Nguyen, Thanh K.; Rader, Ryan K.; Rabinovitz, Harold S.; Oliviero, Margaret; Moss, Randy H.

2012-01-01

Background Basal cell carcinoma (BCC) is the most commonly diagnosed cancer in the United States. In this research, we examine four different feature categories used for diagnostic decisions, including patient personal profile (patient age, gender, etc.), general exam (lesion size and location), common dermoscopic (blue-gray ovoids, leaf-structure dirt trails, etc.), and specific dermoscopic lesion (white/pink areas, semitranslucency, etc.). Specific dermoscopic features are more restricted versions of the common dermoscopic features. Methods Combinations of the four feature categories are analyzed over a data set of 700 lesions, with 350 BCCs and 350 benign lesions, for lesion discrimination using neural network-based techniques, including Evolving Artificial Neural Networks and Evolving Artificial Neural Network Ensembles. Results Experiment results based on ten-fold cross validation for training and testing the different neural network-based techniques yielded an area under the receiver operating characteristic curve as high as 0.981 when all features were combined. The common dermoscopic lesion features generally yielded higher discrimination results than other individual feature categories. Conclusions Experimental results show that combining clinical and image information provides enhanced lesion discrimination capability over either information source separately. This research highlights the potential of data fusion as a model for the diagnostic process. PMID:22724561

A review of the global relationship among freshwater fish, autotrophic activity, and regional climate

USGS Publications Warehouse

Deines, Andrew M.; Bunnell, David B.; Rogers, Mark W.; Beard, T. Douglas; Taylor, William W.

2015-01-01

The relationship between autotrophic activity and freshwater fish populations is an important consideration for ecologists describing trophic structure in aquatic communities, fisheries managers tasked with increasing sustainable fisheries development, and fish farmers seeking to maximize production. Previous studies of the empirical relationships of autotrophic activity and freshwater fish yield have found positive relationships but were limited by small sample sizes, small geographic scopes, and the inability to compare patterns among many types of measurement techniques. Individual studies and reviews have also lacked consistent consideration of regional climate factors which may inform relationships between fisheries and autotrophic activity. We compiled data from over 700 freshwater systems worldwide and used meta-analysis and linear models to develop a comprehensive global synthesis between multiple metrics of autotrophic activity, fisheries, and climate indicators. Our results demonstrate that multiple metrics of fish (i.e., catch per unit effort, yield, and production) increase with autotrophic activity across a variety of fisheries. At the global scale additional variation in this positive relationship can be ascribed to regional climate differences (i.e., temperature and precipitation) across systems. Our results provide a method and proof-of-concept for assessing inland fisheries production at the global scale, where current estimates are highly uncertain, and may therefore inform the continued sustainable use of global inland fishery resources.

InfoDROUGHT: Technical reliability assessment using crop yield data at the Spanish-national level

NASA Astrophysics Data System (ADS)

Contreras, Sergio; Garcia-León, David; Hunink, Johannes E.

2017-04-01

Drought monitoring (DM) is a key component of risk-centered drought preparedness plans and drought policies. InfoDROUGHT (www.infosequia.es) is a a site- and user-tailored and fully-integrated DM system which combines functionalities for: a) the operational satellite-based weekly-1km tracking of severity and spatial extent of drought impacts, b) the interactive and faster query and delivery of drought information through a web-mapping service. InfoDROUGHT has a flexible and modular structure. The calibration (threshold definitions) and validation of the system is performed by combining expert knowledge and auxiliary impact assessments and datasets. Different technical solutions (basic or advanced versions) or deployment options (open-standard or restricted-authenticated) can be purchased by end-users and customers according to their needs. In this analysis, the technical reliability of InfoDROUGHT and its performance for detecting drought impacts on agriculture has been evaluated in the 2003-2014 period by exploring and quantifying the relationships among the drought severity indices reported by InfoDROUGHT and the annual yield anomalies observed for different rainfed crops (maize, wheat, barley) at Spain. We hypothesize a positive relationship between the crop anomalies and the drought severity level detected by InfoDROUGHT. Annual yield anomalies were computed at the province administrative level as the difference between the annual yield reported by the Spanish Annual Survey of Crop Acreages and Yields (ESYRCE database) and the mean annual yield estimated during the study period. Yield anomalies were finally compared against drought greenness-based and thermal-based drought indices (VCI and TCI, respectively) to check the coherence of the outputs and the hypothesis stated. InfoDROUGHT has been partly funded by the Spanish Ministry of Economy and Competiveness through a Torres-Quevedo grant, and by the H2020-EU project "Bridging the Gap for Innovations in Disaster Resilience" (www.brigaid.eu).

An Information-Theoretic-Cluster Visualization for Self-Organizing Maps.

PubMed

Brito da Silva, Leonardo Enzo; Wunsch, Donald C

2018-06-01

Improved data visualization will be a significant tool to enhance cluster analysis. In this paper, an information-theoretic-based method for cluster visualization using self-organizing maps (SOMs) is presented. The information-theoretic visualization (IT-vis) has the same structure as the unified distance matrix, but instead of depicting Euclidean distances between adjacent neurons, it displays the similarity between the distributions associated with adjacent neurons. Each SOM neuron has an associated subset of the data set whose cardinality controls the granularity of the IT-vis and with which the first- and second-order statistics are computed and used to estimate their probability density functions. These are used to calculate the similarity measure, based on Renyi's quadratic cross entropy and cross information potential (CIP). The introduced visualizations combine the low computational cost and kernel estimation properties of the representative CIP and the data structure representation of a single-linkage-based grouping algorithm to generate an enhanced SOM-based visualization. The visual quality of the IT-vis is assessed by comparing it with other visualization methods for several real-world and synthetic benchmark data sets. Thus, this paper also contains a significant literature survey. The experiments demonstrate the IT-vis cluster revealing capabilities, in which cluster boundaries are sharply captured. Additionally, the information-theoretic visualizations are used to perform clustering of the SOM. Compared with other methods, IT-vis of large SOMs yielded the best results in this paper, for which the quality of the final partitions was evaluated using external validity indices.

Is there a domain-general cognitive structuring system? Evidence from structural priming across music, math, action descriptions, and language.

PubMed

Van de Cavey, Joris; Hartsuiker, Robert J

2016-01-01

Cognitive processing in many domains (e.g., sentence comprehension, music listening, and math solving) requires sequential information to be organized into an integrational structure. There appears to be some overlap in integrational processing across domains, as shown by cross-domain interference effects when for example linguistic and musical stimuli are jointly presented (Koelsch, Gunter, Wittfoth, & Sammler, 2005; Slevc, Rosenberg, & Patel, 2009). These findings support theories of overlapping resources for integrational processing across domains (cfr. SSIRH Patel, 2003; SWM, Kljajevic, 2010). However, there are some limitations to the studies mentioned above, such as the frequent use of unnaturalistic integrational difficulties. In recent years, the idea has risen that evidence for domain-generality in structural processing might also be yielded though priming paradigms (cfr. Scheepers, 2003). The rationale behind this is that integrational processing across domains regularly requires the processing of dependencies across short or long distances in the sequence, involving respectively less or more syntactic working memory resources (cfr. SWM, Kljajevic, 2010), and such processing decisions might persist over time. However, whereas recent studies have shown suggestive priming of integrational structure between language and arithmetics (though often dependent on arithmetic performance, cfr. Scheepers et al., 2011; Scheepers & Sturt, 2014), it remains to be investigated to what extent we can also find evidence for priming in other domains, such as music and action (cfr. SWM, Kljajevic, 2010). Experiment 1a showed structural priming from the processing of musical sequences onto the position in the sentence structure (early or late) to which a relative clause was attached in subsequent sentence completion. Importantly, Experiment 1b showed that a similar structural manipulation based on non-hierarchically ordered color sequences did not yield any priming effect, suggesting that the priming effect is not based on linear order, but integrational dependency. Finally, Experiment 2 presented primes in four domains (relative clause sentences, music, mathematics, and structured descriptions of actions), and consistently showed priming within and across domains. These findings provide clear evidence for domain-general structural processing mechanisms. Copyright © 2015 Elsevier B.V. All rights reserved.

A standardized data structure for describing and exchanging data from remeasured growth and yield plots

Treesearch

Michael D. Sweet; John C. Byrne

1990-01-01

Proposes standard data definitions and format to facilitate the sharing of growth and yield permanent plot data for the development, testing, and improvement of tree or stand growth models. The data structure presented provides standards for documenting sampling design, plot location and summary descriptors, measurement dates, treatments, site attributes, and...

A Quantitative Method to Identify Lithology Beneath Cover

NASA Astrophysics Data System (ADS)

Gettings, M. E.

2008-12-01

Geophysical terranes (map areas of similar potential field data response) can be used in the estimation of geological map units beneath cover (bedrock, alluvium, or tectonic block). Potential field data over nearby bedrock terranes defines "candidate terranes". Geophysical anomaly dimensions, shapes, amplitudes, trends/structural grain, and fractal measures yield a vector of measures characterizing the terrane. To compare candidate terranes fields with those for covered areas, the effect of depth of cover must be taken into account. Gravity anomaly data yields depth estimates by which the aeromagnetic data of candidate terranes are then upward continued. Comparison of characteristics of the upward continued fields from the candidate terranes to those of covered areas rank the candidates. Because of signal loss in upward continuation and overlap of physical properties, the vectors of measures for the candidate terranes are usually not unique. Possibility theory offers a relatively objective and robust method that can be used to rank terrane types that includes uncertainty. The strategy is to prepare membership functions for each measure of each candidate terrane and the covered area, based on observed values and degree of knowledge, and then form the fuzzy-logical combination of these to estimate the possibility and its uncertainty for each candidate terrane. Membership functions include uncertainty by the degree of membership for various possibility values. With no other information, uncertainty is based on information content from survey specifications and geologic features dimensions. Geologic data can also be included, such as structural trends, proximity, and tectonic history. Little knowledge implies wide membership functions; perfect knowledge, a delta function. This and the combination rules in fuzzy logic yield a robust estimation method. An uncertain membership function of a characteristic contributes much less to the possibility than a precise one. The final result for each covered area is a ranked possibility function for each candidate terrane as the underlying bedrock of the covered area that honors the aeromagnetic field and the geologic constraints that have been included. An example of the application of this method is presented for an area in south central Arizona.

How model and input uncertainty impact maize yield simulations in West Africa

NASA Astrophysics Data System (ADS)

Waha, Katharina; Huth, Neil; Carberry, Peter; Wang, Enli

2015-02-01

Crop models are common tools for simulating crop yields and crop production in studies on food security and global change. Various uncertainties however exist, not only in the model design and model parameters, but also and maybe even more important in soil, climate and management input data. We analyze the performance of the point-scale crop model APSIM and the global scale crop model LPJmL with different climate and soil conditions under different agricultural management in the low-input maize-growing areas of Burkina Faso, West Africa. We test the models’ response to different levels of input information from little to detailed information on soil, climate (1961-2000) and agricultural management and compare the models’ ability to represent the observed spatial (between locations) and temporal variability (between years) in crop yields. We found that the resolution of different soil, climate and management information influences the simulated crop yields in both models. However, the difference between models is larger than between input data and larger between simulations with different climate and management information than between simulations with different soil information. The observed spatial variability can be represented well from both models even with little information on soils and management but APSIM simulates a higher variation between single locations than LPJmL. The agreement of simulated and observed temporal variability is lower due to non-climatic factors e.g. investment in agricultural research and development between 1987 and 1991 in Burkina Faso which resulted in a doubling of maize yields. The findings of our study highlight the importance of scale and model choice and show that the most detailed input data does not necessarily improve model performance.

From lows to highs: using low-resolution models to phase X-ray data

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

Stuart, David I.; Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot; Abrescia, Nicola G. A., E-mail: nabrescia@cicbiogune.es

2013-11-01

An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here,more » the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.« less

Quantum process tomography of excitonic dimers from two-dimensional electronic spectroscopy. I. General theory and application to homodimers.

PubMed

Yuen-Zhou, Joel; Aspuru-Guzik, Alán

2011-04-07

Is it possible to infer the time evolving quantum state of a multichromophoric system from a sequence of two-dimensional electronic spectra (2D-ES) as a function of waiting time? Here we provide a positive answer for a tractable model system: a coupled dimer. After exhaustively enumerating the Liouville pathways associated to each peak in the 2D-ES, we argue that by judiciously combining the information from a series of experiments varying the polarization and frequency components of the pulses, detailed information at the amplitude level about the input and output quantum states at the waiting time can be obtained. This possibility yields a quantum process tomography (QPT) of the single-exciton manifold, which completely characterizes the open quantum system dynamics through the reconstruction of the process matrix. In this manuscript, we present the general theory as well as specific and numerical results for a homodimer, for which we prove that signals stemming from coherence to population transfer and vice versa vanish upon isotropic averaging, therefore, only allowing for a partial QPT in such case. However, this fact simplifies the spectra, and it follows that only two polarization controlled experiments (and no pulse-shaping requirements) suffice to yield the elements of the process matrix, which survive under isotropic averaging. Redundancies in the 2D-ES amplitudes allow for the angle between the two site transition dipole moments to be self-consistently obtained, hence simultaneously yielding structural and dynamical information of the dimer. Model calculations are presented, as well as an error analysis in terms of the angle between the dipoles and peak amplitude extraction. In the second article accompanying this study, we numerically exemplify the theory for heterodimers and carry out a detailed error analysis for such case. This investigation reveals an exciting quantum information processing (QIP) approach to spectroscopic experiments of excitonic systems, and hence, bridges an important gap between theoretical studies on excitation energy transfer from the QIP standpoint and experimental methods to study such systems in the chemical physics community.

Atomistic basis for the plastic yield criterion of metallic glass.

PubMed

Schuh, Christopher A; Lund, Alan C

2003-07-01

Because of their disordered atomic structure, amorphous metals (termed metallic glasses) have fundamentally different deformation mechanisms compared with polycrystalline metals. These different mechanisms give metallic glasses high strength, but the extent to which they affect other macroscopic deformation properties is uncertain. For example, the nature of the plastic-yield criterion is a point of contention, with some studies reporting yield behaviour roughly in line with that of polycrystalline metals, and others indicating strong fundamental differences. In particular, it is unclear whether pressure- or normal stress-dependence needs to be included in the plastic-yield criterion of metallic glasses, and how such a dependence could arise from their disordered structure. In this work we provide an atomic-level explanation for pressure-dependent yield in amorphous metals, based on an elementary unit of deformation. This simple model compares favourably with new atomistic simulations of metallic glasses, as well as existing experimental data.

Prediction of the Dynamic Yield Strength of Metals Using Two Structural-Temporal Parameters

NASA Astrophysics Data System (ADS)

Selyutina, N. S.; Petrov, Yu. V.

2018-02-01

The behavior of the yield strength of steel and a number of aluminum alloys is investigated in a wide range of strain rates, based on the incubation time criterion of yield and the empirical models of Johnson-Cook and Cowper-Symonds. In this paper, expressions for the parameters of the empirical models are derived through the characteristics of the incubation time criterion; a satisfactory agreement of these data and experimental results is obtained. The parameters of the empirical models can depend on some strain rate. The independence of the characteristics of the incubation time criterion of yield from the loading history and their connection with the structural and temporal features of the plastic deformation process give advantage of the approach based on the concept of incubation time with respect to empirical models and an effective and convenient equation for determining the yield strength in a wider range of strain rates.

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

Doppler Fourier Domain Optical Coherence Tomography for Label-Free Tissue Angiography

NASA Astrophysics Data System (ADS)

Leitgeb, Rainer A.; Szkulmowski, Maciej; Blatter, Cedric; Wojtkowski, Maciej

Information about tissue perfusion and the vascular structure is certainly most important for assessment of tissue state or personal health and the diagnosis of any pathological conditions. It is therefore of key medical interest to have tools available for both quantitative blood flow assessment as well as qualitative vascular imaging. The strength of optical techniques is the unprecedented level of detail even for small capillary structures or microaneurysms and the possibility to combine different techniques for additional tissue spectroscopy giving insight into tissue metabolism. There is an immediate diagnostic and pharmacological demand for high-resolution, label-free, tissue angiography and flow assessment that in addition allow for precise depth gating of flow information. The most promising candidate is Doppler optical coherence tomography (DOCT) being noncontact, label free, and without employing hazardous radiation. DOCT provides fully quantitative volumetric information about blood flow together with the vascular and structural anatomy. Besides flow quantification, analysis of OCT signal fluctuations allows to contrast moving scatterers in tissue such as red blood cells from static tissue. This allows for non-invasive optical angiography and yields high resolution even for smallest capillaries. Because of the huge potential of DOCT and lable-free optical angiography for diagnosis, the last years saw a rapid increase of publications in this field with many different approaches. The present chapter gives an overview over existing Doppler OCT approaches and angiography techniques. It furthermore discusses limitations and noise issues, and gives examples for angiography in the eye and the skin.

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

PubMed

Ye, Xiaoduan; O'Neil, Patrick K; Foster, Adrienne N; Gajda, Michal J; Kosinski, Jan; Kurowski, Michal A; Bujnicki, Janusz M; Friedman, Alan M; Bailey-Kellogg, Chris

2004-12-01

Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross-linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade-offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue-specific chemical cross-linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross-linkers and introduced mutations. We also describe an experiment plan for the bacteriophage lambda Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross-linking experiments.

Computer Simulations to Study Diffraction Effects of Stacking Faults in Beta-SiC: II. Experimental Verification. 2; Experimental Verification

NASA Technical Reports Server (NTRS)

Pujar, Vijay V.; Cawley, James D.; Levine, S. (Technical Monitor)

2000-01-01

Earlier results from computer simulation studies suggest a correlation between the spatial distribution of stacking errors in the Beta-SiC structure and features observed in X-ray diffraction patterns of the material. Reported here are experimental results obtained from two types of nominally Beta-SiC specimens, which yield distinct XRD data. These samples were analyzed using high resolution transmission electron microscopy (HRTEM) and the stacking error distribution was directly determined. The HRTEM results compare well to those deduced by matching the XRD data with simulated spectra, confirming the hypothesis that the XRD data is indicative not only of the presence and density of stacking errors, but also that it can yield information regarding their distribution. In addition, the stacking error population in both specimens is related to their synthesis conditions and it appears that it is similar to the relation developed by others to explain the formation of the corresponding polytypes.

An easy-to-prepare mini-scaffold for DNA origami

NASA Astrophysics Data System (ADS)

Brown, S.; Majikes, J.; Martínez, A.; Girón, T. M.; Fennell, H.; Samano, E. C.; Labean, T. H.

2015-10-01

The DNA origami strategy for assembling designed supramolecular complexes requires ssDNA as a scaffold strand. A system is described that was designed approximately one third the length of the M13 bacteriophage genome for ease of ssDNA production. Folding of the 2404-base ssDNA scaffold into a variety of origami shapes with high assembly yields is demonstrated.The DNA origami strategy for assembling designed supramolecular complexes requires ssDNA as a scaffold strand. A system is described that was designed approximately one third the length of the M13 bacteriophage genome for ease of ssDNA production. Folding of the 2404-base ssDNA scaffold into a variety of origami shapes with high assembly yields is demonstrated. Electronic supplementary information (ESI) available: Flow chart of the production process, base sequences of the scaffold strand, and synthetic staple strands, as well as caDNAnao files for all three mini-M13 origami structures. See DOI: 10.1039/c5nr04921k

Life-History Traits and Population Structure of Pederson Cleaner Shrimps Ancylomenes pedersoni.

PubMed

Gilpin, Jessica A; Chadwick, Nanette E

2017-12-01

Cleaner organisms perform key functional roles in reducing rates of parasitism in marine communities. Pederson cleaner shrimps Ancylomenes pedersoni are major cleaners of reef fishes in the tropical western Atlantic and form obligate symbioses with host sea anemones. Information about their life-history traits would contribute to understanding how symbiosis impacts life-history evolution in crustaceans, but little is known about patterns of growth and reproduction in this anemone shrimp. We quantified growth, sexual reproduction, senescence, and mortality in individuals of A. pedersoni under laboratory conditions and their abundance and population size structure on coral reefs in St. Thomas, U.S. Virgin Islands. Von Bertalanffy growth curves were fitted to the data to determine age-size relationships, and the Beverton-Holt model was used to estimate mortality rates and size at maximum yield. Individuals grew rapidly when young, then slowed their growth after reaching sexual maturity at ~6 months. Individuals were gonochoric, with males attaining significantly smaller body sizes and shorter life spans than did females. Prior to death at <2 years, members of both genders exhibited senescence during which they ceased reproducing, shrank (females only), and decreased their activity levels over ~1-4 weeks. Field populations were abundant and composed mostly of juveniles during both years examined. Populations appeared to be stable but highly dynamic in terms of individuals, reaching maximum yield at 4 months of age. We conclude that obligate symbiosis with large sea anemones and cleaner mutualism with reef fishes both contribute to explaining aspects of the life history of Pederson shrimps, especially their apparent mating system of pure-search polygynandry. This life-history information also provides a scientific basis for sustainable fishery management and aquaculture of this key coral reef organism.

Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

PubMed Central

Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

2009-01-01

15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

Enhancing the enzymatic hydrolysis of corn stover by an integrated wet-milling and alkali pretreatment.

PubMed

He, Xun; Miao, Yelian; Jiang, Xuejian; Xu, Zidong; Ouyang, Pingkai

2010-04-01

An integrated wet-milling and alkali pretreatment was applied to corn stover prior to enzymatic hydrolysis. The effects of NaOH concentration in the pretreatment on crystalline structure, chemical composition, and reducing-sugar yield of corn stover were investigated, and the mechanism of increasing reducing-sugar yield by the pretreatment was discussed. The experimental results showed that the crystalline structure of corn stover was disrupted, and lignin was removed, while cellulose and hemicellulose were retained in corn stover by the pretreatment with 1% NaOH in 1 h. The reducing-sugar yield from the pretreated corn stovers increased from 20.2% to 46.7% when the NaOH concentration increased from 0% to 1%. The 1% NaOH pretreated corn stover had a holocellulose conversion of 55.1%. The increase in reducing-sugar yield was related to the crystalline structure disruption and delignification of corn stover. It was clarified that the pretreatment significantly enhanced the conversion of cellulose and hemicellulose in the corn stover to sugars.

Slow pyrolysis polygeneration of bamboo (Phyllostachys pubescens): Product yield prediction and biochar formation mechanism.

PubMed

Wang, Huihui; Wang, Xin; Cui, Yanshan; Xue, Zhongcai; Ba, Yuxin

2018-05-11

Slow pyrolysis of bamboo was conducted at 400-600 °C and pyrolysis products were characterized with FTIR, BET, XRD, SEM, EDS and GC to establish a pyrolysis product yield prediction model and biochar formation mechanism. Pyrolysis biochar yield was predicted based on content of cellulose, hemicellulose and lignin in biomass with their carbonization index of 0.20, 0.35 and 0.45. The formation mechanism of porous structure in pyrolysis biochar was established based on its physicochemical property evolution and emission characteristics of pyrolysis gas. The main components (cellulose, hemicellulose and lignin) had different pyrolysis or chemical reaction pathways to biochar. Lignin had higher aromatic structure, which resulted higher biochar yield. It was the main biochar precursor during biomass pyrolysis. Cellulose was likely to improve porous structure of pyrolysis biochar due to its high mass loss percentage. Higher pyrolysis temperatures (600 °C) promoted inter- and intra-molecular condensation reactions and aromaticity in biochar. Copyright © 2018 Elsevier Ltd. All rights reserved.

Supportability of a High-Yield-Stress Slurry in a New Stereolithography-Based Ceramic Fabrication Process

NASA Astrophysics Data System (ADS)

He, Li; Song, Xuan

2018-03-01

In recent years, ceramic fabrication using stereolithography (SLA) has gained in popularity because of its high accuracy and density that can be achieved in the final part of production. One of the key challenges in ceramic SLA is that support structures are required for building overhanging features, whereas removing these support structures without damaging the components is difficult. In this research, a suspension-enclosing projection-stereolithography process is developed to overcome this challenge. This process uses a high-yield-stress ceramic slurry as the feedstock material and exploits the elastic force of the material to support overhanging features without the need for building additional support structures. Ceramic slurries with different solid loadings are studied to identify the rheological properties most suitable for supporting overhanging features. An analytical model of a double doctor-blade module is established to obtain uniform and thin recoating layers from a high-yield-stress slurry. Several test cases highlight the feasibility of using a high-yield-stress slurry to support overhanging features in SLA.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Survey of patient-oriented total hip replacement information on the World Wide Web.

PubMed

Mabrey, J D

2000-12-01

The author conducted an informal survey of materials relating to diseases of the hip and total hip replacement as they appeared on the World Wide Web. The results varied depending on the key words used: hip and replacement yielded 1,818 matches; total hip replacement yielded 1,740 matches; hip replacement yielded 4,565 sites; and hip surgery yielded 1,073 sites. The number of sites for total hip replacement was observed to increase with time, having found an additional 30 sites from an identical search performed only 6 weeks earlier. The nature and quality of these sites varied from well-organized and informative, to personal testaments, to obvious commercial endeavors. Overall, this survey found an abundance of material regarding the hip and hip replacements on the World Wide Web, but orthopaedic societies need to take a more active role in constructing, maintaining, and monitoring these sites to best serve the needs of their patients and their members.

Dimension-independent likelihood-informed MCMC

DOE PAGES

Cui, Tiangang; Law, Kody J. H.; Marzouk, Youssef M.

2015-10-08

Many Bayesian inference problems require exploring the posterior distribution of highdimensional parameters that represent the discretization of an underlying function. Our work introduces a family of Markov chain Monte Carlo (MCMC) samplers that can adapt to the particular structure of a posterior distribution over functions. There are two distinct lines of research that intersect in the methods we develop here. First, we introduce a general class of operator-weighted proposal distributions that are well defined on function space, such that the performance of the resulting MCMC samplers is independent of the discretization of the function. Second, by exploiting local Hessian informationmore » and any associated lowdimensional structure in the change from prior to posterior distributions, we develop an inhomogeneous discretization scheme for the Langevin stochastic differential equation that yields operator-weighted proposals adapted to the non-Gaussian structure of the posterior. The resulting dimension-independent and likelihood-informed (DILI) MCMC samplers may be useful for a large class of high-dimensional problems where the target probability measure has a density with respect to a Gaussian reference measure. Finally, we use two nonlinear inverse problems in order to demonstrate the efficiency of these DILI samplers: an elliptic PDE coefficient inverse problem and path reconstruction in a conditioned diffusion.« less

Wholeness and primary and secondary food structure effects on in vitro digestion patterns determine nutritionally distinct carbohydrate fractions in cereal foods.

PubMed

Mishra, Suman; Monro, John

2012-12-01

Starchy foods of differing structure, including bakery products, breakfast cereals, pastas, and pulses were digested in vitro. Bakery products and processed breakfast cereals with little resilient structure yielded large amounts of rapidly available carbohydrate (RAC), less slowly digested starch (SDS) and little inaccessible digestible starch (IDS) (70:22:8%). Partially processed grains, such as rolled oats contained an increased proportion of SDS (55:38:7%). Pastas, being dense starch structures digested more gradually to completion by superficial erosion, yielding approximately equal proportions of RAC and SDS but little IDS (43:52:4%). Pulses, which retained their cellular morphology, digested more linearly yielding a lower proportion of RAC, a larger proportion of SDS and more IDS (9:69:22%). Preservation of native "primary" structure, and use of processing to create "secondary" structure, are both means by which wholeness, in the sense of intactness, can be used to influence carbohydrate digestion to make foods of lower glycaemic impact. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structural investigation of porcine stomach mucin by X-ray fiber diffraction and homology modeling

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

Veluraja, K., E-mail: veluraja@msuniv.ac.in; Vennila, K.N.; Umamakeshvari, K.

Research highlights: {yields} Techniques to get oriented mucin fibre. {yields} X-ray fibre diffraction pattern for mucin. {yields} Molecular modeling of mucin based on X-ray fibre diffraction pattern. -- Abstract: The basic understanding of the three dimensional structure of mucin is essential to understand its physiological function. Technology has been developed to achieve orientated porcine stomach mucin molecules. X-ray fiber diffraction of partially orientated porcine stomach mucin molecules show d-spacing signals at 2.99, 4.06, 4.22, 4.7, 5.37 and 6.5 A. The high intense d-spacing signal at 4.22 A is attributed to the antiparallel {beta}-sheet structure identified in the fraction of themore » homology modeled mucin molecule (amino acid residues 800-980) using Nidogen-Laminin complex structure as a template. The X-ray fiber diffraction signal at 6.5 A reveals partial organization of oligosaccharides in porcine stomach mucin. This partial structure of mucin will be helpful in establishing a three dimensional structure for the whole mucin molecule.« less

(I Can't Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research.

PubMed

van Rijnsoever, Frank J

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: "random chance," which is based on probability sampling, "minimal information," which yields at least one new code per sampling step, and "maximum information," which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario.

In situ pre-growth calibration using reflectance as a control strategy for MOCVD fabrication of device structures

NASA Astrophysics Data System (ADS)

Breiland, William G.; Hou, Hong Q.; Chui, Herman C.; Hammons, Burrel E.

1997-04-01

In situ normal incidence reflectance, combined with a virtual interface model, is being used routinely on a commercial metal organic chemical vapor deposition reactor to measure growth rates of compound semiconductor films. The technique serves as a pre-growth calibration tool analogous to the use of reflection high-energy electron diffraction in molecular beam epitaxy as well as a real-time monitor throughout the run. An application of the method to the growth of a vertical cavity surface emitting laser (VCSEL) device structure is presented. All necessary calibration information can be obtained using a single run lasting less than 1 h. Working VCSEL devices are obtained on the first try after calibration. Repeated runs have yielded ±0.3% reproducibility of the Fabry-Perot cavity wavelength over the course of more than 100 runs.

Chemical Behavior of Sulfur in Minerals and Silicate Glasses Studied Using Inner Shell Spectroscopy

NASA Astrophysics Data System (ADS)

Alonso Mori, R.; Paris, E.; Glatzel, P.; Giuli, G.; Scaillet, B.

2008-12-01

Understanding the chemical behaviour of sulfur is of fundamental importance in explaining different geological mechanisms ranging from volcano-climatic interactions to the genesis of ore deposits. Understanding how sulphur behaves is also of great economic importance in industrial activities including glass-forming processes and the treatment of vitreous waste material from refuse incineration. The chemical behaviour of sulfur in minerals and glasses has been widely studied via X-ray absorption near edge structure (XANES) spectroscopy, which probes the unoccupied density of states and thus provides information on the oxidation state and local structure of the species under study. However, the XANES spectral shape is influenced by various effects, namely the local symmetry, the ligand type, even up to high coordination spheres, and the valence electron occupation, making it difficult to systematically analyze the different spectral contributions. We use X-ray emission spectroscopy (XES) as a complementary technique to avoid some of the inherent difficulties of XANES analysis, and to extract additional information on the electronic structure. The Kb lines, close to the K-edge, directly yield the p-density of occupied valence states, giving valuable information on the local coordination. We have compared XANES and Kb XES experimental data on sulfur- bearing minerals with ab initio quantum-chemical calculations based on density functional theory (DFT), in order to visualize the molecular orbitals and to extract information about the chemical bonding in these compounds. The S Ka emission lines, which arise from 2p to 1s transitions, are expected to be mostly free from chemical bond effects except for small energy shifts that reflect the valence orbital electron population via screening effects. S Ka shifts can be readily used to determine the speciation of sulfur in silicate glasses. The electronic configuration of the sulfur atoms is obtained by calculating the effective charge around the sulfur atom based on the Mulliken population analysis generated by DFT calculations, and then successfully correlated with the observed experimental shifts. In order to check these results using a theoretical framework other than DFT, we also performed calculations using a multiple scattering approach (FEFF8.4). X-ray absorption and emission spectroscopy has been applied to three series of peralkaline rhyolitic obsidians each with different alkali/alumina ratios ((Na2O + K2O)/Al2O3). The occurrence of sulfur was accurately determined by using the energy shift of the S Ka emission lines to make a quantitative analysis. We observe that we can follow the evolution of sulfur as a function of controlled formation conditions with respect to pressure, temperature or oxygen fugacity, and determine whether it is present as sulfate or sulfide. XANES and Kb emission lines also yield detailed information on the local chemistry and structure, and thus help us to understand the geochemical role of S in these systems.

Computer synthesis of high resolution electron micrographs

NASA Technical Reports Server (NTRS)

Nathan, R.

1976-01-01

Specimen damage, spherical aberration, low contrast and noisy sensors combine to prevent direct atomic viewing in a conventional electron microscope. The paper describes two methods for obtaining ultra-high resolution in biological specimens under the electron microscope. The first method assumes the physical limits of the electron objective lens and uses a series of dark field images of biological crystals to obtain direct information on the phases of the Fourier diffraction maxima; this information is used in an appropriate computer to synthesize a large aperture lens for a 1-A resolution. The second method assumes there is sufficient amplitude scatter from images recorded in focus which can be utilized with a sensitive densitometer and computer contrast stretching to yield fine structure image details. Cancer virus characterization is discussed as an illustrative example. Numerous photographs supplement the text.

Incorporating conditional random fields and active learning to improve sentiment identification.

PubMed

Zhang, Kunpeng; Xie, Yusheng; Yang, Yi; Sun, Aaron; Liu, Hengchang; Choudhary, Alok

2014-10-01

Many machine learning, statistical, and computational linguistic methods have been developed to identify sentiment of sentences in documents, yielding promising results. However, most of state-of-the-art methods focus on individual sentences and ignore the impact of context on the meaning of a sentence. In this paper, we propose a method based on conditional random fields to incorporate sentence structure and context information in addition to syntactic information for improving sentiment identification. We also investigate how human interaction affects the accuracy of sentiment labeling using limited training data. We propose and evaluate two different active learning strategies for labeling sentiment data. Our experiments with the proposed approach demonstrate a 5%-15% improvement in accuracy on Amazon customer reviews compared to existing supervised learning and rule-based methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

In the right place at the right time: visualizing and understanding mRNA localization

PubMed Central

Buxbaum, Adina R.; Haimovich, Gal

2015-01-01

The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization. PMID:25549890

Analysis And Assistant Planning System Ofregional Agricultural Economic Inform

NASA Astrophysics Data System (ADS)

Han, Jie; Zhang, Junfeng

For the common problems existed in regional development and planning, we try to design a decision support system for assisting regional agricultural development and alignment as a decision-making tool for local government and decision maker. The analysis methods of forecast, comparative advantage, liner programming and statistical analysis are adopted. According to comparative advantage theory, the regional advantage can be determined by calculating and comparing yield advantage index (YAI), Scale advantage index (SAI), Complicated advantage index (CAI). Combining with GIS, agricultural data are presented as a form of graph such as area, bar and pie to uncover the principle and trend for decision-making which can't be found in data table. This system provides assistant decisions for agricultural structure adjustment, agro-forestry development and planning, and can be integrated to information technologies such as RS, AI and so on.

Residual stress measurements in carbon steel

NASA Technical Reports Server (NTRS)

Heyman, J. S.; Min, N.

1986-01-01

External dc magnetic field-induced changes in natural velocity of Rayleigh surface waves were measured in steel specimens under various stress conditions. The low field slopes of curves representing the fractional changes of natural velocity were proved to provide correct stress information in steels with different metallurgical properties. The slopes of curves under uniaxial compression, exceeding about one third of the yield stress, fell below zero in all the specimens when magnetized along the stress axis. The slopes under tension varied among different steels but remained positive in any circumstances. The stress effect was observed for both applied and residual stress. A physical interpretation of these results is given based on the stress-induced domain structure changes and the delta epsilon effect. Most importantly, it is found that the influence of detailed metallurgical properties cause only secondary effects on the obtained stress information.

An Introduction to Structural Reliability Theory

DTIC Science & Technology

1989-01-01

Test Samples psi COV Distribution Remarks Yield stress 66 (XX 0.09 assumed lognormal mill test I containment vesel SA537 GrB Yield stress 󈧗 6W8...straightened shape Tension :32 57.909 0.089 cold straightened shape Tension 9 84.039 0.1124 annealed , alloy steel Tension 9 124,9 0.1796 . quenched...alloys, annealed and quenched, and drawn samples Tension 22 29.50 X 103 0.0072 .. structural steel Compression 22 29.49 X 103 0.0146 ... structural

Temporal Correlations and Neural Spike Train Entropy

NASA Astrophysics Data System (ADS)

Schultz, Simon R.; Panzeri, Stefano

2001-06-01

Sampling considerations limit the experimental conditions under which information theoretic analyses of neurophysiological data yield reliable results. We develop a procedure for computing the full temporal entropy and information of ensembles of neural spike trains, which performs reliably for limited samples of data. This approach also yields insight to the role of correlations between spikes in temporal coding mechanisms. The method, when applied to recordings from complex cells of the monkey primary visual cortex, results in lower rms error information estimates in comparison to a ``brute force'' approach.

Pre-K Benefits: The Facts on Fade-Out

ERIC Educational Resources Information Center

Southern Regional Education Board (SREB), 2015

2015-01-01

As policymakers adopt policies for pre-K programs, they want to know that the programs are effective. Do the gains last? This brief report presents information that pre-k yields short-term academic gains; pre-k yields long-term academic gains; and pre-k yields substantial nonacademic benefits.

Loblolly Pine Growth and Yield Prediction for Managed West Gulf Plantations

Treesearch

V. Clark Baldwin; D.P. Feduccia

1987-01-01

Complete description, including tables, graphs, computer output, of a growth and yield prediction system providing volume and weight yields in stand and stock table format. An example of system use is given along with information about the computer program, COMPUTE P-LOB, that operates the system.

Responses of inulin content and inulin yield of Jerusalem artichoke genotypes to seasonal environments

USDA-ARS?s Scientific Manuscript database

Seasonal variation (e.g. temperature and photoperiod) between growing seasons might affect inulin content and inulin yield of Jerusalem artichoke. However, there is limited information on genotypic response to seasons for inulin content and inulin yield. The objective of this study was to investig...

Ecological forestry in an uneven-aged, late-successional forest: Simulated effects of contrasting treatments on structure and yield

Treesearch

Jacob J. Hanson; Craig G. Lorimer; Corey R. Halpin; Brian J. Palik

2012-01-01

Ecological forestry practices are designed to retain species and structural features important for maintaining ecosystem function but which may be deficient in conventionally managed stands. We used the spatially-explicit, individual tree model CANOPY to assess tradeoffs in enhanced ecological attributes vs. reductions in timber yield for a wide variety of treatments...

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

NASA Astrophysics Data System (ADS)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Nuclear Forensics and Radiochemistry: Fission

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

Rundberg, Robert S.

Radiochemistry has been used to study fission since it’ discovery. Radiochemical methods are used to determine cumulative mass yields. These measurements have led to the two-mode fission hypothesis to model the neutron energy dependence of fission product yields. Fission product yields can be used for the nuclear forensics of nuclear explosions. The mass yield curve depends on both the fuel and the neutron spectrum of a device. Recent studies have shown that the nuclear structure of the compound nucleus can affect the mass yield distribution.

Development of Field Information Monitoring System Based on the Internet of Things

NASA Astrophysics Data System (ADS)

Cai, Ken; Liang, Xiaoying; Wang, Keqiang

With the rapid development and wide application of electronics, communication and embedded system technologies, the global agriculture is changing from traditional agriculture that is to improve the production relying on the increase of labor, agricultural inputs to the new stage of modern agriculture with low yields, high efficiency, real-time and accuracy. On the other hand the research and development of the Internet of Things, which is an information network to connect objects, with the full capacity to perceive objects, and having the capabilities of reliable transmission and intelligence processing for information, allows us to obtain real-time information of anything. The application of the Internet of Things in field information online monitoring is an effective solution for present wired sensor monitoring system, which has much more disadvantages, such as high cost, the problems of laying lines and so on. In this paper, a novel field information monitoring system based on the Internet of Things is proposed. It can satisfy the requirements of multi-point measurement, mobility, convenience in the field information monitoring process. The whole structure of system is given and the key designs of system design are described in the hardware and software aspect. The studies have expanded current field information measurement methods and strengthen the application of the Internet of Things.

Ultrasound criteria and guided fine-needle aspiration diagnostic yields in small animal peritoneal, mesenteric and omental disease.

PubMed

Feeney, Daniel A; Ober, Christopher P; Snyder, Laura A; Hill, Sara A; Jessen, Carl R

2013-01-01

Peritoneal, mesenteric, and omental diseases are important causes of morbidity and mortality in humans and animals, although information in the veterinary literature is limited. The purposes of this retrospective study were to determine whether objectively applied ultrasound interpretive criteria are statistically useful in differentiating among cytologically defined normal, inflammatory, and neoplastic peritoneal conditions in dogs and cats. A second goal was to determine the cytologically interpretable yield on ultrasound-guided, fine-needle sampling of peritoneal, mesenteric, or omental structures. Sonographic criteria agreed upon by the authors were retrospectively and independently applied by two radiologists to the available ultrasound images without knowledge of the cytologic diagnosis and statistically compared to the ultrasound-guided, fine-needle aspiration cytologic interpretations. A total of 72 dogs and 49 cats with abdominal peritoneal, mesenteric, or omental (peritoneal) surface or effusive disease and 17 dogs and 3 cats with no cytologic evidence of inflammation or neoplasia were included. The optimized, ultrasound criteria-based statistical model created independently for each radiologist yielded an equation-based diagnostic category placement accuracy of 63.2-69.9% across the two involved radiologists. Regional organ-associated masses or nodules as well as aggregated bowel and peritoneal thickening were more associated with peritoneal neoplasia whereas localized, severely complex fluid collections were more associated with inflammatory peritoneal disease. The cytologically interpretable yield for ultrasound-guided fine-needle sampling was 72.3% with no difference between species, making this a worthwhile clinical procedure. © 2013 Veterinary Radiology & Ultrasound.

Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization.

PubMed

Zenk, John; Tuntivate, Chanon; Schulman, Rebecca

2016-03-16

We investigate the kinetics and thermodynamics of DNA origami dimerization using flat rectangle origami components and different architectures of Watson-Crick complementary single-stranded DNA ("sticky end") linking strategies. We systematically vary the number of linkers, the length of the sticky ends on the linker, and linker architecture and measure the corresponding yields as well as forward and reverse reaction rate constants through fluorescence quenching assays. Yields were further verified using atomic force microscopy. We calculate values of H° and ΔS° for various interface designs and find nonlinear van't Hoff behavior, best described by two linear equations, suggesting distinct regimes of dimerization between those with and those without well-formed interfaces. We find that self-assembly reactions can be tuned by manipulating the interface architecture without suffering a loss in yield, even when yield is high, ∼75-80%. We show that the second-order forward reaction rate constant (k(on)) depends on both linker architecture and number of linkers used, with typical values on the order of 10(5)-10(6) (M·s)(-1), values that are similar to those of bimolecular association of small, complementary DNA strands. The k(on) values are generally non-Arrhenius, tending to increase with decreasing temperature. Finally, we use kinetic and thermodynamic information about the optimal linking architecture to extend the system to an infinite, two-component repeating lattice system and show that we can form micron-sized lattices, with well-formed structures up to 8 μm(2).

Influence of hydration and annealing on structure, PSL yield and spatial resolution of pressed powder imaging plates of the X-ray storage phosphor CsBr:Eu2+

NASA Astrophysics Data System (ADS)

Kersting, E.; von Seggern, H.

2017-08-01

A new production route for europium doped cesium bromide (CsBr:Eu2+) imaging plates has been developed, synthesizing CsBr:Eu2+ powder from a precipitation reaction of aqueous CsBr solution with ethanol. This new route allows the control of features like homogeneous grain size and grain shape of the obtained powder. After drying and subsequent compacting the powder, disk-like samples were fabricated, and their resulting photostimulated luminescence (PSL) properties like yield and spatial resolution were determined. It will be shown that hydration of such disks causes the CsBr:Eu2+ powder to recrystallize starting from the humidity exposed surfaces to the sample interior up to a completely polycrystalline sample resulting in a decreasing PSL yield and an increasing resolution. Subsequent annealing leads to grain refinement combined with a large PSL yield increment and a minor effect on the spatial resolution. By first annealing the "as made" disk, one observes a strong increment of the PSL yield and almost no effect on the spatial resolution. During subsequent hydration, the recrystallization is hindered by minor structural changes of the grains. The related PSL yield drops slightly with increasing hydration time, and the spatial resolution drops considerably. The obtained PSL properties with respect to structure will be discussed with a simple model.

Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif

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

Maruyama, Yukie; Ochiai, Akihito; Mikami, Bunzo

Research highlights: {yields} Bacterial alginate-binding Algp7 is similar to component EfeO of Fe{sup 2+} transporter. {yields} We determined the crystal structure of Algp7 with a metal-binding motif. {yields} Algp7 consists of two helical bundles formed through duplication of a single bundle. {yields} A deep cleft involved in alginate binding locates around the metal-binding site. {yields} Algp7 may function as a Fe{sup 2+}-chelated alginate-binding protein. -- Abstract: A gram-negative Sphingomonas sp. A1 directly incorporates alginate polysaccharide into the cytoplasm via the cell-surface pit and ABC transporter. A cell-surface alginate-binding protein, Algp7, functions as a concentrator of the polysaccharide in the pit.more » Based on the primary structure and genetic organization in the bacterial genome, Algp7 was found to be homologous to an M75 peptidase motif-containing EfeO, a component of a ferrous ion transporter. Despite the presence of an M75 peptidase motif with high similarity, the Algp7 protein purified from recombinant Escherichia coli cells was inert on insulin B chain and N-benzoyl-Phe-Val-Arg-p-nitroanilide, both of which are substrates for a typical M75 peptidase, imelysin, from Pseudomonas aeruginosa. The X-ray crystallographic structure of Algp7 was determined at 2.10 A resolution by single-wavelength anomalous diffraction. Although a metal-binding motif, HxxE, conserved in zinc ion-dependent M75 peptidases is also found in Algp7, the crystal structure of Algp7 contains no metal even at the motif. The protein consists of two structurally similar up-and-down helical bundles as the basic scaffold. A deep cleft between the bundles is sufficiently large to accommodate macromolecules such as alginate polysaccharide. This is the first structural report on a bacterial cell-surface alginate-binding protein with an M75 peptidase motif.« less

Correlation of Factor IXa Subsite Modulations with Effects on Substrate Discrimination

PubMed Central

Neuenschwander, Pierre F.; Deadmond, Kimberly J.; Zepeda, Karla; Rutland, Joshua

2012-01-01

Summary Background A key feature of factor IXa (fIXa) is its allosteric transformation from an enzymatically latent form into a potent procoagulant. Whilst several small molecules have been found capable of partially effecting fIXa function (i.e. ethylene glycol, calcium ion and LMWH), the resulting modest changes in peptidolytic activity have made the study of their mechanisms of action challenging. Since these effects yield hints into potential regulatory forces that may be operational in full expression of fIXa coagulant activity, their description remains of high interest. Studies of crystal structures have yielded insight into structural changes induced by these effectors, but there remains a paucity of information to correlate any given structural change with specific consequences on fIXa function. Objectives To correlate structural changes induced by these modulators with defined consequences in fIXa substrate discrimination and function. Methods A peptidomics-based MS approach was used to examine patterns of hydrolysis of four combinatorial chemistry-derived pentapeptide libraries by fIXa under various conditions in a soluble, active enzyme system. Results Ethylene glycol specifically alters the S3 subsite of fIXa to render it more tolerant to side chains at the P3 substrate position, while calcium enhances tolerance at the S2 subsite. In contrast, LMWH alters both S2 and S1' subsites. Conclusions These results demonstrate the role of plasticity in regulating fIXa function with respect to discrimination of extended substrate sequences, as well as provide crucial insight into active site modulations that may be capitalized upon by various physiological cofactors of fIXa and in future drug design. PMID:22212890

Structural characteristics of pumpkin pectin extracted by microwave heating.

PubMed

Yoo, Sang-Ho; Lee, Byeong-Hoo; Lee, Heungsook; Lee, Suyong; Bae, In Young; Lee, Hyeon Gyu; Fishman, Marshall L; Chau, Hoa K; Savary, Brett J; Hotchkiss, Arland T

2012-11-01

To improve extraction yield of pumpkin pectin, microwave heating was adopted in this study. Using hot acid extraction, pumpkin pectin yield decreased from 5.7% to 1.0% as pH increased from pH 1.0 to 2.0. At pH 2.5, no pectin was recovered from pumpkin flesh powder. After a pretreatment at pH 1.0 and 25 °C for 1 h, pumpkin powder was microwave-extracted at 120 °C for 3 min resulting in 10.5% of pectin yield. However, premicrowave treatment at 60 °C for 20 min did not improve extraction yield. When microwave heating at 80 °C for 10 min was applied after premicrowave treatment, final pectin yield increased to 11.3%. When pH was adjusted to 2.0, the yield dropped to 7.7% under the same extraction conditions. Molecular shape and properties as well as chemical composition of pumpkin pectin were significantly affected depending on extraction methods. Galacturonic acid content (51% to 58%) of pumpkin pectin was lower than that detected in commercial acid-extracted citrus pectin, while higher content of neutral sugars and acetyl esters existed in pumpkin pectin structure. Molecular weight (M(w) ) and intrinsic viscosity (η(w) ) determined for microwave-extracted pumpkin pectins were substantially lower than acid-extracted pectin, whereas polydispersity was greater. However, microwave-extracted pectin at pH 2.0 had more than 5 times greater M(w) than did the pectin extracted at pH 1.0. The η(w) of microwave-extracted pectin produced at pH 2.0 was almost twice that of other microwave-extracted pectins, which were comparable to that of acid-extracted pectin. These results indicate that extraction yield of pumpkin pectin would be improved by microwave extraction and different pectin structure and properties can be obtained compared to acid extraction. Pumpkin is a promising alternative source for pectin material. Pumpkin pectin has a unique chemical structure and physical properties, presumably providing different functional properties compared to conventional commercial pectin sources. Depending on the conditions to produce pumpkin pectin, diverse molecular structures can be obtained and utilized in various food applications. © 2012 Institute of Food Technologists®

A critical review on the interaction of substrate nutrient balance and microbial community structure and function in anaerobic co-digestion.

PubMed

Xu, Rong; Zhang, Kai; Liu, Pu; Khan, Aman; Xiong, Jian; Tian, Fake; Li, Xiangkai

2018-01-01

Anaerobic co-digestion generally results in a higher yield of biogas than mono-digestion, hence co-digestion has become a topic of general interest in recent studies of anaerobic digestion. Compared with mono-digestion, co-digestion utilizes multiple substrates. The balance of substrate nutrient in co-digestion comprises better adjustments of C/N ratio, pH, moisture, trace elements, and dilution of toxic substances. All of these changes could result in positive shifts in microbial community structure and function in the digestion processes and consequent augmentation of biogas production. Nevertheless, there have been few reviews on the interaction of nutrient and microbial community in co-digestions. The objective of this review is to investigate recent achievements and perspectives on the interaction of substrate nutrient balance and microbial community structure and function. This may provide valuable information on the optimization of combinations of substrates and prediction of bioreactor performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spectral methods for study of the G-protein-coupled receptor rhodopsin. II. Magnetic resonance methods

NASA Astrophysics Data System (ADS)

Struts, A. V.; Barmasov, A. V.; Brown, M. F.

2016-02-01

This article continues our review of spectroscopic studies of G-protein-coupled receptors. Magnetic resonance methods including electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) provide specific structural and dynamical data for the protein in conjunction with optical methods (vibrational, electronic spectroscopy) as discussed in the accompanying article. An additional advantage is the opportunity to explore the receptor proteins in the natural membrane lipid environment. Solid-state 2H and 13C NMR methods yield information about both the local structure and dynamics of the cofactor bound to the protein and its light-induced changes. Complementary site-directed spin-labeling studies monitor the structural alterations over larger distances and correspondingly longer time scales. A multiscale reaction mechanism describes how local changes of the retinal cofactor unlock the receptor to initiate large-scale conformational changes of rhodopsin. Activation of the G-protein-coupled receptor involves an ensemble of conformational substates within the rhodopsin manifold that characterize the dynamically active receptor.

Physical properties of PNe: what IFU spectrographs can do?

NASA Astrophysics Data System (ADS)

Costa, R.; Lago, P. J. A.; Faes, D., M.

2014-04-01

Structure, kinematics and physical parameters of planetary nebulae are related to their progenitor stars. A better understanding of these properties is essential to improve the knowledge of the late stages of evolution of intermediate-mass stars, as well as to better understand the chemical enrichment mechanisms that feed the interstellar medium with the nucleosynthesis yields from such stars. Integral Field Unit (IFU) spectrographs can provide valuable information from these objects, mapping such properties point-to-point over the projected nebulae. In this communication we present the results of a survey of physical properties for southern PNe. We have used IFU spectroscopy in order to derive the angular distribution of electron densities and ionic abundances, and also to map the ionization profiles. The aim is to characterize their physical properties and structures, and results can be used in morpho-kinematical models (such as SHAPE) or in photoionization models (such as CLOUDY) to describe in detail the 3D structure and evolution of these objects.

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE PAGES

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi; ...

2016-12-30

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

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

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Brain blood vessel segmentation using line-shaped profiles

NASA Astrophysics Data System (ADS)

Babin, Danilo; Pižurica, Aleksandra; De Vylder, Jonas; Vansteenkiste, Ewout; Philips, Wilfried

2013-11-01

Segmentation of cerebral blood vessels is of great importance in diagnostic and clinical applications, especially for embolization of cerebral aneurysms and arteriovenous malformations (AVMs). In order to perform embolization of the AVM, the structural and geometric information of blood vessels from 3D images is of utmost importance. For this reason, the in-depth segmentation of cerebral blood vessels is usually done as a fusion of different segmentation techniques, often requiring extensive user interaction. In this paper we introduce the idea of line-shaped profiling with an application to brain blood vessel and AVM segmentation, efficient both in terms of resolving details and in terms of computation time. Our method takes into account both local proximate and wider neighbourhood of the processed pixel, which makes it efficient for segmenting large blood vessel tree structures, as well as fine structures of the AVMs. Another advantage of our method is that it requires selection of only one parameter to perform segmentation, yielding very little user interaction.

Molecular genetics of the hair follicle: the state of the art.

PubMed

Van Steensel, M A; Happle, R; Steijlen, P M

2000-01-01

For those who are interested in the biology of skin and its derivatives, these are interesting times indeed. In a mere 5 years, the field has been revolutionized by the application of molecular genetics to human congenital skin disorders. Where dermatology first was limited to observation and empirics, there are now DNA-diagnostics, rational drug design, and perhaps even gene therapy available soon. In particular, the study of rare human syndromes involving abnormalities of hair growth and structure has yielded new insights into the regulation of cell growth and differentiation in the hair follicle. As this structure shows a cyclic pattern of differentiation, it may give new information concerning the regulation of cell differentiation in general. This review covers the recent developments in this fast-moving field. First, we will give a short introduction to (structural) hair biology. Next, we will try to fit these data into the framework of what is already known and attempt to present a unified model for hair follicle growth and differentiation.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Technical Reports Server (NTRS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-01-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced at NASA's Kepler observatory.

The maximum entropy production and maximum Shannon information entropy in enzyme kinetics

NASA Astrophysics Data System (ADS)

Dobovišek, Andrej; Markovič, Rene; Brumen, Milan; Fajmut, Aleš

2018-04-01

We demonstrate that the maximum entropy production principle (MEPP) serves as a physical selection principle for the description of the most probable non-equilibrium steady states in simple enzymatic reactions. A theoretical approach is developed, which enables maximization of the density of entropy production with respect to the enzyme rate constants for the enzyme reaction in a steady state. Mass and Gibbs free energy conservations are considered as optimization constraints. In such a way computed optimal enzyme rate constants in a steady state yield also the most uniform probability distribution of the enzyme states. This accounts for the maximal Shannon information entropy. By means of the stability analysis it is also demonstrated that maximal density of entropy production in that enzyme reaction requires flexible enzyme structure, which enables rapid transitions between different enzyme states. These results are supported by an example, in which density of entropy production and Shannon information entropy are numerically maximized for the enzyme Glucose Isomerase.

Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription.

PubMed

Assenberg, R; Delmas, O; Morin, B; Graham, S C; De Lamballerie, X; Laubert, C; Coutard, B; Grimes, J M; Neyts, J; Owens, R J; Brandt, B W; Gorbalenya, A; Tucker, P; Stuart, D I; Canard, B; Bourhy, H

2010-08-01

Some mammalian rhabdoviruses may infect humans, and also infect invertebrates, dogs, and bats, which may act as vectors transmitting viruses among different host species. The VIZIER programme, an EU-funded FP6 program, has characterized viruses that belong to the Vesiculovirus, Ephemerovirus and Lyssavirus genera of the Rhabdoviridae family to perform ground-breaking research on the identification of potential new drug targets against these RNA viruses through comprehensive structural characterization of the replicative machinery. The contribution of VIZIER programme was of several orders. First, it contributed substantially to research aimed at understanding the origin, evolution and diversity of rhabdoviruses. This diversity was then used to obtain further structural information on the proteins involved in replication. Two strategies were used to produce recombinant proteins by expression of both full length or domain constructs in either E. coli or insect cells, using the baculovirus system. In both cases, parallel cloning and expression screening at small-scale of multiple constructs based on different viruses including the addition of fusion tags, was key to the rapid generation of expression data. As a result, some progress has been made in the VIZIER programme towards dissecting the multi-functional L protein into components suitable for structural and functional studies. However, the phosphoprotein polymerase co-factor and the structural matrix protein, which play a number of roles during viral replication and drives viral assembly, have both proved much more amenable to structural biology. Applying the multi-construct/multi-virus approach central to protein production processes in VIZIER has yielded new structural information which may ultimately be exploitable in the derivation of novel ways of intervening in viral replication. Copyright 2010 Elsevier B.V. All rights reserved.

The correlation between the SOS in trabecular bone and stiffness and density studied by finite-element analysis.

PubMed

Goossens, Liesbet; Vanderoost, Jef; Jaecques, Siegfried; Boonen, Steven; D'hooge, Jan; Lauriks, Walter; Van der Perre, Georges

2008-01-01

For the clinical assessment of osteoporosis (i.e., a degenerative bone disease associated with increased fracture risk), ultrasound has been proposed as an alternative or supplement to the dual-energy X-ray absorptiometry (DEXA) technique. However, the interaction of ultrasound waves with (trabecular) bone remains relatively poorly understood. The present study aimed to improve this understanding by simulating ultrasound wave propagation in 15 trabecular bone samples from the human lumbar spine, using microcomputed tomography-based finite-element modeling. The model included only the solid bone, without the bone marrow. Two structural parameters were calculated: the bone volume fraction (BV/TV) and the structural (apparent) elastic modulus (E(s)), and the ultrasound propagation parameter speed of sound (SOS). Relations between BV/TV and E(s) were similar to published experimental relations. At 1 MHz, correlations between SOS and the structural parameters BV/TV and Es were rather weak, but the results can be explained from the specific features of the trabecular structure and the intrinsic material elastic modulus E(i). In particular, the systematic differences between the three main directions provide information on the trabecular structure. In addition, at 1 MHz the correlation found between the simulated SOS values and those calculated from the simple bar equation was poor when the three directions are considered separately. Hence, under these conditions, the homogenization approach-including the bar equation-is not valid. However, at lower frequencies (50-300 kHz) this correlation significantly improved. It is concluded that detailed analysis of ultrasound wave propagation through the solid structure in various directions and with various frequencies, can yield much information on the structural and mechanical properties of trabecular bone.

Statistical Analysis of Large Simulated Yield Datasets for Studying Climate Effects

NASA Technical Reports Server (NTRS)

Makowski, David; Asseng, Senthold; Ewert, Frank; Bassu, Simona; Durand, Jean-Louis; Martre, Pierre; Adam, Myriam; Aggarwal, Pramod K.; Angulo, Carlos; Baron, Chritian;

Synthesis of Fullerenes in Low Pressure Benzene/Oxygen Diffusion Flames

NASA Technical Reports Server (NTRS)

Hebgen, Peter; Howard, Jack B.

1999-01-01

The interest in fullerenes is strongly increasing since their discovery by Kroto et al. in 1985 as products of the evaporation of carbon into inert gas at low pressure. Due to their all carbon closed-shell structure, fullerenes have many exceptional physical and chemical properties and a large potential for applications such as superconductors, sensors, catalysts, optical and electronic devices, polymers, high energy fuels, and biological and medical materials. This list is still growing, because the research on fullerenes is still at an early stage. Fullerenes can be formed not only in a system containing only carbon and an inert gas, but also in premixed hydrocarbon flames under reduced pressure and fuel rich conditions. The highest yields of fullerenes in flames are obtained under conditions of substantial soot formation. There is a need for more information on the yields of fullerenes under different conditions in order to understand the mechanisms of their formation and to enable the design of practical combustion systems for large-scale fullerene production. Little work has been reported on the formation of fullerenes in diffusion flames. In order to explore the yields of fullerenes and the effect of low pressure in diffusion flames, therefore we constructed and used a low pressure diffusion flame burner in this study.

Phase transformations and equation of state of praseodymium metal to 103 GPa

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

Chesnut, Gary N.; Vohra, Yogesh K.

2000-08-01

Pressure-induced structural phase transformations in a trivalent rare-earth metal praseodymium (Pr) were studied at room temperature in a diamond anvil cell to 103 GPa by energy dispersive x-ray diffraction using a synchrotron source. Our x-ray diffraction studies document the following crystal structure sequence: dhcp{yields}fcc{yields}distorted fcc(hR24 type){yields}monoclinic(C2/m){yields}{alpha}-uranium with increasing pressure. We measure a 16.7% volume collapse at the transition to the {alpha}-uranium phase at 20 GPa. The high-pressure {alpha}-uranium phase in Pr was found to be stable to the highest pressure of 103 GPa, which corresponds to a volume compression V/V{sub 0}=0.407. (c) 2000 The American Physical Society.

Prediction of β-turns in proteins from multiple alignment using neural network

PubMed Central

Kaur, Harpreet; Raghava, Gajendra Pal Singh

2003-01-01

A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033

Predicting protein crystallization propensity from protein sequence

PubMed Central

2011-01-01

The high-throughput structure determination pipelines developed by structural genomics programs offer a unique opportunity for data mining. One important question is how protein properties derived from a primary sequence correlate with the protein’s propensity to yield X-ray quality crystals (crystallizability) and 3D X-ray structures. A set of protein properties were computed for over 1,300 proteins that expressed well but were insoluble, and for ~720 unique proteins that resulted in X-ray structures. The correlation of the protein’s iso-electric point and grand average hydropathy (GRAVY) with crystallizability was analyzed for full length and domain constructs of protein targets. In a second step, several additional properties that can be calculated from the protein sequence were added and evaluated. Using statistical analyses we have identified a set of the attributes correlating with a protein’s propensity to crystallize and implemented a Support Vector Machine (SVM) classifier based on these. We have created applications to analyze and provide optimal boundary information for query sequences and to visualize the data. These tools are available via the web site http://bioinformatics.anl.gov/cgi-bin/tools/pdpredictor. PMID:20177794

Silver-induced reconstruction of an adeninate-based metal–organic framework for encapsulation of luminescent adenine-stabilized silver clusters† †Electronic supplementary information (ESI) available: Experimental details and additional structural, physicochemical and optical characterisation. See DOI: 10.1039/c6tc00260a Click here for additional data file.

PubMed Central

Jonckheere, Dries; Coutino-Gonzalez, Eduardo; Baekelant, Wouter; Bueken, Bart; Reinsch, Helge; Stassen, Ivo; Fenwick, Oliver; Richard, Fanny; Samorì, Paolo; Ameloot, Rob; Hofkens, Johan

2016-01-01

Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal–organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4′-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications. PMID:28496980

Taming Big Data: An Information Extraction Strategy for Large Clinical Text Corpora.

PubMed

Gundlapalli, Adi V; Divita, Guy; Carter, Marjorie E; Redd, Andrew; Samore, Matthew H; Gupta, Kalpana; Trautner, Barbara

2015-01-01

Concepts of interest for clinical and research purposes are not uniformly distributed in clinical text available in electronic medical records. The purpose of our study was to identify filtering techniques to select 'high yield' documents for increased efficacy and throughput. Using two large corpora of clinical text, we demonstrate the identification of 'high yield' document sets in two unrelated domains: homelessness and indwelling urinary catheters. For homelessness, the high yield set includes homeless program and social work notes. For urinary catheters, concepts were more prevalent in notes from hospitalized patients; nursing notes accounted for a majority of the high yield set. This filtering will enable customization and refining of information extraction pipelines to facilitate extraction of relevant concepts for clinical decision support and other uses.

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

PubMed

Qian, Lunwen; Hickey, Lee T; Stahl, Andreas; Werner, Christian R; Hayes, Ben; Snowdon, Rod J; Voss-Fels, Kai P

2017-01-01

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

Nanoindentation of Electropolished FeCrAl Alloy Welds

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

Weaver, Jordan; Aydogan, Eda; Mara, Nathan Allan

The present report summarizes Berkovich nanoindentation modulus and hardness measurements on two candidate FeCrAl alloys (C35M and C37M) on as-received (AR) and welded samples. In addition, spherical nanoindentation stress-strain measurements were performed on individual grains to provide further information and demonstrate the applicability of these protocols to mechanically characterizing welds in FeCrAl alloys. The indentation results are compared against the reported tensile properties for these alloys to provide relationships between nanoindentation and tensile tests and insight into weldsoftening for these FeCrAl alloys. Hardness measurements revealed weld-softening for both alloys in good agreement with tensile test results. C35M showed a largermore » reduction in hardness at the weld center from the AR material compared to C37M; this is also consistent with tensile tests. In general, nanohardness was shown to be a good predictor of tensile yield strength and ultimate tensile stress for FeCrAl alloys. Spherical nanoindentation measurements revealed that the fusion zone (FZ) + heat affected zone (HAZ) has a very low defect density typical of well-annealed metals as indicated by the frequent pop-in events. Spherical nanoindentation yield strength, Berkovich hardness, and tensile yield strength measurements on the welded material all show that the C37M welded material has a higher strength than C35M welded material. From the comparison of nanoindentation and tensile tests, EBSD microstructure analysis, and information on the processing history, it can be deduced that the primary driver for weld-softening is a change in the defect structure at the grain-scale between the AR and welded material. These measurements serve as baseline data for utilizing nanoindentation for studying the effects of radiation damage on these alloys.« less

Non-invasive Geophysical Surveys in Search of the Roman Temple of Augustus Under the Cathedral of Tarragona (Catalonia, Spain): A Case Study

NASA Astrophysics Data System (ADS)

Casas, Albert; Cosentino, Pietro L.; Fiandaca, Gianluca; Himi, Mahjoub; Macias, Josep M.; Martorana, Raffaele; Muñoz, Andreu; Rivero, Lluís; Sala, Roger; Teixell, Imma

2018-04-01

An integrated geophysical survey has been conducted at the Tarragona's Cathedral (Catalonia, NE Spain) with the aim to confirm the potential occurrence of archaeological remains of the Roman Temple dedicated to the Emperor Augustus. Many hypotheses have been proposed about its possible location, the last ones regarding the inner part of the Cathedral, which is one of the most renowned temples of Spain (twelfth century) evolving from Romanesque to Gothic styles. A geophysical project including electrical resistivity tomography (ERT) and ground probing radar (GPR) was planned over 1 year considering the administrative and logistic difficulties of such a project inside a cathedral of religious veneration. Finally, both ERT and GPR have been conducted during a week of intensive overnight surveys that provided detailed information on subsurface existing structures. The ERT method has been applied using different techniques and arrays, ranging from standard Wenner-Schlumberger 2D sections to full 3D electrical imaging with the advanced Maximum Yield Grid array. Electrical resistivity data were recorded extensively, making available many thousands of apparent resistivity data to obtain a complete 3D image after a full inversion. In conclusion, some significant buried structures have been revealed providing conclusive information for archaeologists. GPR results provided additional information about shallowest structures. The geophysical results were clear enough to persuade religious authorities and archaeologists to conduct selected excavations in the most promising areas that confirmed the interpretation of geophysical data. In conclusion, the significant buried structures revealed by geophysical methods under the cathedral were confirmed by archaeological digging as the basement of the impressive Roman Temple that headed the Provincial Forum of Tarraco, seat of the Concilium of Hispania Citerior Province.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Macromolecular diffractive imaging using imperfect crystals

PubMed Central

Ayyer, Kartik; Yefanov, Oleksandr; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Lourdu Xavier, Paulraj; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

2016-01-01

The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7. PMID:26863980

Image restoration and superresolution as probes of small scale far-IR structure in star forming regions

NASA Technical Reports Server (NTRS)

Lester, D. F.; Harvey, P. M.; Joy, M.; Ellis, H. B., Jr.

1986-01-01

Far-infrared continuum studies from the Kuiper Airborne Observatory are described that are designed to fully exploit the small-scale spatial information that this facility can provide. This work gives the clearest picture to data on the structure of galactic and extragalactic star forming regions in the far infrared. Work is presently being done with slit scans taken simultaneously at 50 and 100 microns, yielding one-dimensional data. Scans of sources in different directions have been used to get certain information on two dimensional structure. Planned work with linear arrays will allow us to generalize our techniques to two dimensional image restoration. For faint sources, spatial information at the diffraction limit of the telescope is obtained, while for brighter sources, nonlinear deconvolution techniques have allowed us to improve over the diffraction limit by as much as a factor of four. Information on the details of the color temperature distribution is derived as well. This is made possible by the accuracy with which the instrumental point-source profile (PSP) is determined at both wavelengths. While these two PSPs are different, data at different wavelengths can be compared by proper spatial filtering. Considerable effort has been devoted to implementing deconvolution algorithms. Nonlinear deconvolution methods offer the potential of superresolution -- that is, inference of power at spatial frequencies that exceed D lambda. This potential is made possible by the implicit assumption by the algorithm of positivity of the deconvolved data, a universally justifiable constraint for photon processes. We have tested two nonlinear deconvolution algorithms on our data; the Richardson-Lucy (R-L) method and the Maximum Entropy Method (MEM). The limits of image deconvolution techniques for achieving spatial resolution are addressed.

Comparative genomic analysis of oil spill impacts on deep water shipwreck microbiomes in the northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Damour, M.; McGown, C.; Figan, C.; Kassahun, Z.; Blackwell, K.; Horrell, C.; Gillevet, P.

2014-12-01

Shipwrecks serve as artificial reefs in the deep ocean. Because of their inherent diversity compared to their surrounding environment and their random distribution, shipwrecks are ideal ecosystems to study pollution impacts and microbial distribution patterns in the deep biosphere. This study provides a comparative assessment of Deepwater Horizon spill impacts on shipwreck and local sedimentary microbiomes and the synergistic effects of contaminants on these communities and the physical structures that support them. For this study, microbiomes associated with wooden 19th century shipwrecks and World War II era steel shipwrecks in the northern Gulf of Mexico were investigated using next generation sequencing. Samples derived from in situ biofilm monitoring platforms deployed adjacent to 5 shipwrecks for 4 months, and sediment collected from distances ranging from 2-200m from each shipwreck were evaluated for shifts in microbiome structure and gene function relative to proximity to the spill, and oil spill related contaminants in the local environment. The goals of the investigation are to determine impacts to recruitment and community structure at sites located within and outside of areas impacted by the spill. Taxonomic classification of dominant and rare members of shipwreck microbiomes and metabolic information extracted from sequence data yield new understanding of microbial processes associated with site formation. The study provides information on the identity of microbial inhabitants of shipwrecks, their role in site preservation, and impacts of the Deepwater Horizon spill on the primary colonizers of artificial reefs in the deep ocean. This approach could inform about the role of microorganisms in establishment and maintenance of the artificial reef environment, while providing information about ecosystem feedbacks resulting from spills.

Mechanical forces as information: an integrated approach to plant and animal development

PubMed Central

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R.; Benítez, Mariana

2014-01-01

Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes. PMID:24959170

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System

PubMed Central

Röcker, Carlheinz; Nagy, Julia; Michaelis, Jens

2017-01-01

Single-molecule Förster Resonance Energy Transfer (smFRET) can be used to obtain structural information on biomolecular complexes in real-time. Thereby, multiple smFRET measurements are used to localize an unknown dye position inside a protein complex by means of trilateration. In order to obtain quantitative information, the Nano-Positioning System (NPS) uses probabilistic data analysis to combine structural information from X-ray crystallography with single-molecule fluorescence data to calculate not only the most probable position but the complete three-dimensional probability distribution, termed posterior, which indicates the experimental uncertainty. The concept was generalized for the analysis of smFRET networks containing numerous dye molecules. The latest version of NPS, Fast-NPS, features a new algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering that allows for the analysis of large smFRET networks in a comparably short time. Moreover, Fast-NPS allows the calculation of the posterior by choosing one of five different models for each dye, that account for the different spatial and orientational behavior exhibited by the dye molecules due to their local environment. Here we present a detailed protocol for obtaining smFRET data and applying the Fast-NPS. We provide detailed instructions for the acquisition of the three input parameters of Fast-NPS: the smFRET values, as well as the quantum yield and anisotropy of the dye molecules. Recently, the NPS has been used to elucidate the architecture of an archaeal open promotor complex. This data is used to demonstrate the influence of the five different dye models on the posterior distribution. PMID:28287526

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System.

PubMed

Dörfler, Thilo; Eilert, Tobias; Röcker, Carlheinz; Nagy, Julia; Michaelis, Jens

2017-02-09

Single-molecule Förster Resonance Energy Transfer (smFRET) can be used to obtain structural information on biomolecular complexes in real-time. Thereby, multiple smFRET measurements are used to localize an unknown dye position inside a protein complex by means of trilateration. In order to obtain quantitative information, the Nano-Positioning System (NPS) uses probabilistic data analysis to combine structural information from X-ray crystallography with single-molecule fluorescence data to calculate not only the most probable position but the complete three-dimensional probability distribution, termed posterior, which indicates the experimental uncertainty. The concept was generalized for the analysis of smFRET networks containing numerous dye molecules. The latest version of NPS, Fast-NPS, features a new algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering that allows for the analysis of large smFRET networks in a comparably short time. Moreover, Fast-NPS allows the calculation of the posterior by choosing one of five different models for each dye, that account for the different spatial and orientational behavior exhibited by the dye molecules due to their local environment. Here we present a detailed protocol for obtaining smFRET data and applying the Fast-NPS. We provide detailed instructions for the acquisition of the three input parameters of Fast-NPS: the smFRET values, as well as the quantum yield and anisotropy of the dye molecules. Recently, the NPS has been used to elucidate the architecture of an archaeal open promotor complex. This data is used to demonstrate the influence of the five different dye models on the posterior distribution.

Mechanical forces as information: an integrated approach to plant and animal development.

PubMed

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R; Benítez, Mariana

2014-01-01

Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes.

Radiochemistry and the Study of Fission

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

Rundberg, Robert S.

These are slides from a lecture given at UC Berkeley. Radiochemistry has been used to study fission since its discovery. Radiochemical methods are used to determine cumulative mass yields. These measurements have led to the two-mode fission hypothesis to model the neutron energy dependence of fission product yields. Fission product yields can be used for the nuclear forensics of nuclear explosions. The mass yield curve depends on both the fuel and the neutron spectrum of a device. Recent studies have shown that the nuclear structure of the compound nucleus can affect the mass yield distribution. The following topics are covered:more » In the beginning: the discovery of fission; forensics using fission products: what can be learned from fission products, definitions of R-values and Q-values, fission bases, K-factors and fission chambers, limitations; the neutron energy dependence of the mass yield distribution (the two mode fission hypothesis); the influence of nuclear structure on the mass yield distribution. In summary: Radiochemistry has been used to study fission since its discovery. Radiochemical measurement of fission product yields have provided the highest precision data for developing fission models and for nuclear forensics. The two-mode fission hypothesis provides a description of the neutron energy dependence of the mass yield curve. However, data is still rather sparse and more work is needed near second and third chance fission. Radiochemical measurements have provided evidence for the importance of nuclear states in the compound nucleus in predicting the mass yield curve in the resonance region.« less

Validation of the Unthinned Loblolly Pine Plantation Yield Model-USLYCOWG

Treesearch

V. Clark Baldwin; D.P. Feduccia

1982-01-01

Yield and stand structure predictions from an unthinned loblolly pine plantation yield prediction system (USLYCOWG computer program) were compared with observations from 80 unthinned loblolly pine plots. Overall, the predicted estimates were reasonable when compared to observed values, but predictions based on input data at or near the system's limits may be in...

Polymorphism, population structure, and multivariate relationships among secondary traits in open-pollinated corn heterotic groups

USDA-ARS?s Scientific Manuscript database

Plant, ear and kernel traits directly or indirectly associated with grain yield in corn (Zea mays) were suggested as "secondary" traits to select for larger grain yield, especially in open-pollinated corn varieties (OPVs) and their hybrids (OPVhs). Thirty-four secondary traits, besides grain yield, ...

Rice Crop Monitoring and Yield Assessment with MODIS 250m Gridded Vegetation Products: A Case Study of Sa Kaeo Province, Thailand

NASA Astrophysics Data System (ADS)

Wijesingha, J. S. J.; Deshapriya, N. L.; Samarakoon, L.

2015-04-01

Billions of people in the world depend on rice as a staple food and as an income-generating crop. Asia is the leader in rice cultivation and it is necessary to maintain an up-to-date rice-related database to ensure food security as well as economic development. This study investigates general applicability of high temporal resolution Moderate Resolution Imaging Spectroradiometer (MODIS) 250m gridded vegetation product for monitoring rice crop growth, mapping rice crop acreage and analyzing crop yield, at the province-level. The MODIS 250m Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) time series data, field data and crop calendar information were utilized in this research in Sa Kaeo Province, Thailand. The following methodology was used: (1) data pre-processing and rice plant growth analysis using Vegetation Indices (VI) (2) extraction of rice acreage and start-of-season dates from VI time series data (3) accuracy assessment, and (4) yield analysis with MODIS VI. The results show a direct relationship between rice plant height and MODIS VI. The crop calendar information and the smoothed NDVI time series with Whittaker Smoother gave high rice acreage estimation (with 86% area accuracy and 75% classification accuracy). Point level yield analysis showed that the MODIS EVI is highly correlated with rice yield and yield prediction using maximum EVI in the rice cycle predicted yield with an average prediction error 4.2%. This study shows the immense potential of MODIS gridded vegetation product for keeping an up-to-date Geographic Information System of rice cultivation.

Application of a rising plate meter to estimate forage yield on dairy farms in Pennsylvania

USDA-ARS?s Scientific Manuscript database

Accurately assessing pasture forage yield is necessary for producers who want to budget feed expenses and make informed pasture management decisions. Clipping and weighing forage from a known area is a direct method to measure pasture forage yield, however it is time consuming. The rising plate mete...

Harvesting number and timing effects on shoot yield and flavonoid content in American skullcap (Scutellaria lateriflora)

USDA-ARS?s Scientific Manuscript database

Information on optimal management practices for high dry matter and flavonoid yield in American skullcap is lacking. A field experiment was conducted in central Alabama to determine the effect of timing and frequency of harvest on shoot yield and flavonoid content of American skullcap. In the first ...

Measurement of airborne ultrasonic slow waves in calcaneal cancellous bone.

PubMed

Strelitzki, R; Paech, V; Nicholson, P H

1999-05-01

Measurements of an airborne ultrasonic wave were made in defatted cancellous bone from the human calcaneus using standard ultrasonic equipment. The wave propagating under these conditions was consistent with a decoupled Biot slow wave travelling in the air alone, as previously reported in gas-saturated foams. Reproducible measurements of phase velocity and attenuation coefficient were possible, and an estimate of the tortuosity of the trabecular framework was derived from the high frequency limit of the phase velocity. Thus the method offers a new approach to the acoustic characterisation of bone in vitro which, in contrast to existing techniques, has the potential to yield information directly characterising the trabecular structure.

Phase lag deduced information in photo-thermal actuation for nano-mechanical systems characterization

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

Bijster, R. J. F., E-mail: roy.bijster@tno.nl; Vreugd, J. de; Sadeghian, H.

2014-08-18

In photo-thermal actuation, heat is added locally to a micro-cantilever by means of a laser. A fraction of the irradiation is absorbed, yielding thermal stresses and deformations in the structure. Harmonic modulation of the laser power causes the cantilever to oscillate. Moreover, a phase lag is introduced which is very sensitive to the spot location and the cantilever properties. This phase lag is theoretically predicted and experimentally verified. Combined with thermo-mechanical properties of the cantilever and its geometry, the location of the laser spot, the thermal diffusivity, and the layer thicknesses of the cantilever can be extracted.

Simulation of organismic morphology and behavior by synthetic poly-alpha-amino acids.

PubMed

Fox, S W; McCauley, R; Joseph, D; Windsor, C R; Yuyama, S

1966-01-01

Experiments imitating spontaneous geothermal occurrences have yielded most of the amino acids found in protein. All of the amino acids found in protein are simultaneously condensed, by heating in a range of appropriate conditions, to polymers which have many of the properties of proteins. These properties include molecular weights of many thousand, digestibility by proteolytic enzymes, and catalytic activities. One of the other properties is the tendency to form structured units; these units have many of the attributes of biocells. The processes indicated, and others, comprise a conceptual continuum which, according to accumulated information, must have occurred under the conditions existing in regions of the primitive Earth.

An electron diffraction study of alkali chloride vapors

NASA Technical Reports Server (NTRS)

Mawhorter, R. J.; Fink, M.; Hartley, J. G.

1985-01-01

A study of monomers and dimers of the four alkali chlorides NaCl, KCl, RbCl, and CsCl in the vapor phase using the counting method of high energy electron diffraction is reported. Nozzle temperatures from 850-960 K were required to achieve the necessary vapor pressures of approximately 0.01 torr. Using harmonic calculations for the monomer and dimer 1 values, a consistent set of structures for all four molecules was obained. The corrected monomer distances reproduce the microwave values very well. The experiment yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Directional x-ray dark-field imaging of strongly ordered systems

NASA Astrophysics Data System (ADS)

Jensen, Torben Haugaard; Bech, Martin; Zanette, Irene; Weitkamp, Timm; David, Christian; Deyhle, Hans; Rutishauser, Simon; Reznikova, Elena; Mohr, Jürgen; Feidenhans'L, Robert; Pfeiffer, Franz

2010-12-01

Recently a novel grating based x-ray imaging approach called directional x-ray dark-field imaging was introduced. Directional x-ray dark-field imaging yields information about the local texture of structures smaller than the pixel size of the imaging system. In this work we extend the theoretical description and data processing schemes for directional dark-field imaging to strongly scattering systems, which could not be described previously. We develop a simple scattering model to account for these recent observations and subsequently demonstrate the model using experimental data. The experimental data includes directional dark-field images of polypropylene fibers and a human tooth slice.

Comprehensive Genetic Characterization of Intraprostatic Chronic Inflammation and Prostate Cancer in African American Men

DTIC Science & Technology

2017-09-01

with new methodologies of intratumoral phylogenetic analyses, will yield pivotal information in elucidating the key genes involved evolution of PCa...combined with both clinical and experimental genetic data produced by this study may empower patients and doctors to make personalized treatment decisions...sequencing, paired with new methodologies of intratumoral phylogenetic analyses, will yield pivotal information in elucidating the key genes involved

Naval Weapons Station Earle Reassessment

DTIC Science & Technology

2013-12-01

property, or site is understood and its meaning (and ultimately its significance) within prehistory or history is made clear” (NPS 1991). A historic...components may lack individual distinction; or D. Information Potential—yielded, or is likely to yield, information important in prehistory or history...period in history or prehistory . Feeling Feeling is a property’s expression of the aesthetic or historic sense of a particular time period. Association

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

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

Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp; Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011; Ohta, Keisuke

2011-07-08

Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweetmore » taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.« less

Investigation of the structure and lithology of bedrock concealed by basin fill, using ground-based magnetic-field-profile data acquired in the San Rafael Basin, southeastern Arizona

USGS Publications Warehouse

Bultman, Mark W.

2013-01-01

Data on the Earth’s total-intensity magnetic field acquired near ground level and at measurement intervals as small as 1 m include information on the spatial distribution of nearsurface magnetic dipoles that in many cases are unique to a specific lithology. Such spatial information is expressed in the texture (physical appearance or characteristics) of the data at scales of hundreds of meters to kilometers. These magnetic textures are characterized by several descriptive statistics, their power spectrum, and their multifractal spectrum. On the basis of a graphical comparison and textural characterization, ground-based magnetic-field profile data can be used to estimate bedrock lithology concealed by as much as 100 m of basin fill in some cases, information that is especially important in assessing and exploring for concealed mineral deposits. I demonstrate that multifractal spectra of ground-based magnetic-field-profile data can be used to differentiate exposed lithologies and that the shape and position of the multifractal spectrum of the ground-based magnetic-field-profile of concealed lithologies can be matched to the upward-continued multifractal spectrum of an exposed lithology to help distinguish the concealed lithology. In addition, ground-based magnetic-field-profile data also detect minute differences in the magnetic susceptibility of rocks over small horizontal and vertical distances and so can be used for precise modeling of bedrock geometry and structure, even when that bedrock is concealed by 100 m or more of nonmagnetic basin fill. Such data contain valuable geologic information on the bedrock concealed by basin fill that may not be so visible in aeromagnetic data, including areas of hydrothermal alteration, faults, and other bedrock structures. Interpretation of these data in the San Rafael Basin, southeastern Arizona, has yielded results for estimating concealed lithologies, concealed structural geology, and a concealed potential mineral-resource target.

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Stochastic metallic-glass cellular structures exhibiting benchmark strength.

PubMed

Demetriou, Marios D; Veazey, Chris; Harmon, John S; Schramm, Joseph P; Johnson, William L

2008-10-03

By identifying the key characteristic "structural scales" that dictate the resistance of a porous metallic glass against buckling and fracture, stochastic highly porous metallic-glass structures are designed capable of yielding plastically and inheriting the high plastic yield strength of the amorphous metal. The strengths attainable by the present foams appear to equal or exceed those by highly engineered metal foams such as Ti-6Al-4V or ferrous-metal foams at comparable levels of porosity, placing the present metallic-glass foams among the strongest foams known to date.

The imprint of proper motion of nonlinear structures on the cosmic microwave background

NASA Technical Reports Server (NTRS)

Tuluie, Robin; Laguna, Pablo

1995-01-01

We investigate the imprint of nonlinear matter condensations on the cosmic microwave background (CMB) in an Omega = 1, cold dark matter (CDM) model universe. Temperature anisotropies are obtained by numerically evolving matter inhomogeneities and CMB photons from the beginning of decoupling until the present epoch. The underlying density field produced by the inhomogeneities is followed from the linear, through the weakly clustered, into the fully nonlinear regime. We concentrate on CMB temperature distortions arising from variations in the gravitational potentials of nonlinear structures. We find two sources of temperature fluctuations produced by time-varying potentials: (1) anisotropies due to intrinsic changes in the gravitational potentials of the inhomogeneities and (2) anisotropies generated by the peculiar, bulk motion of the structures across the microwave sky. Both effects generate CMB anisotropies in the range of 10(exp -7) approximately less than or equal to (Delta T/T) approximately less than or equal to 10(exp -6) on scales of approximately 1 deg. For isolated structures, anisotropies due to proper motion exhibit a dipole-like signature in the CMB sky that in principle could yield information on the transverse velocity of the structures.

Evaluation of crack status in a meter-size concrete structure using the ultrasonic nonlinear coda wave interferometry.

PubMed

Legland, Jean-Baptiste; Zhang, Yuxiang; Abraham, Odile; Durand, Olivier; Tournat, Vincent

2017-10-01

The field of civil engineering is in need of new methods of non-destructive testing, especially in order to prevent and monitor the serious deterioration of concrete structures. In this work, experimental results are reported on fault detection and characterization in a meter-scale concrete structure using an ultrasonic nonlinear coda wave interferometry (NCWI) method. This method entails the nonlinear mixing of strong pump waves with multiple scattered probe (coda) waves, along with analysis of the net effect using coda wave interferometry. A controlled damage protocol is implemented on a post-tensioned, meter-scale concrete structure in order to generate cracking within a specific area being monitored by NCWI. The nonlinear acoustic response due to the high amplitude of acoustic modulation yields information on the elastic nonlinearities of concrete, as evaluated by two specific nonlinear observables. The increase in nonlinearity level corresponds to the creation of a crack with a network of microcracks localized at its base. In addition, once the crack closes as a result of post-tensioning, the residual nonlinearities confirm the presence of the closed crack. Last, the benefits and applicability of this NCWI method to the characterization and monitoring of large structures are discussed.

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

PubMed Central

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease. PMID:26526043

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens.

PubMed

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10-20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

An inventory of reasons for sperm donation in formal versus informal settings.

PubMed

Bossema, Ercolie R; Janssens, Pim M W; Treucker, Roswitha G L; Landwehr, Frieda; van Duinen, Kor; Nap, Annemiek W; Geenen, Rinie

2014-03-01

The shortage of sperm donors in formal settings (i.e., assisted reproduction clinics) and the availability of sperm donors in informal settings (such as through contacts on the internet) motivated us to investigate why men may prefer either a formal or an informal setting for sperm donation. Interviews with ten sperm donors and non-sperm donors yielded 55 reasons for sperm donation in the two settings. These reasons were categorized according to similarity by 14 sperm donors and non-sperm donors. These categorizations were then structured by means of hierarchical cluster analysis. Reasons favouring formal settings included being legally and physically protected, evading paternal feelings or social consequences, and having a simple, standardized procedure in terms of effort and finances. Reasons favouring informal settings related to engagement, the possibility to choose a recipient, lack of rules and regulations, having contact with the donor child, and having an (intimate) bond with the recipient. The overview of reasons identified may help potential sperm donors decide on whether to donate in a formal or informal setting, and may fuel discussions by professionals about the most appropriate conditions and legislation for sperm donation in formal settings.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

PubMed

Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C; Nir, Eyal

2018-06-01

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Remotely sensed rice yield prediction using multi-temporal NDVI data derived from NOAA's-AVHRR.

PubMed

Huang, Jingfeng; Wang, Xiuzhen; Li, Xinxing; Tian, Hanqin; Pan, Zhuokun

2013-01-01

Grain-yield prediction using remotely sensed data have been intensively studied in wheat and maize, but such information is limited in rice, barley, oats and soybeans. The present study proposes a new framework for rice-yield prediction, which eliminates the influence of the technology development, fertilizer application, and management improvement and can be used for the development and implementation of provincial rice-yield predictions. The technique requires the collection of remotely sensed data over an adequate time frame and a corresponding record of the region's crop yields. Longer normalized-difference-vegetation-index (NDVI) time series are preferable to shorter ones for the purposes of rice-yield prediction because the well-contrasted seasons in a longer time series provide the opportunity to build regression models with a wide application range. A regression analysis of the yield versus the year indicated an annual gain in the rice yield of 50 to 128 kg ha(-1). Stepwise regression models for the remotely sensed rice-yield predictions have been developed for five typical rice-growing provinces in China. The prediction models for the remotely sensed rice yield indicated that the influences of the NDVIs on the rice yield were always positive. The association between the predicted and observed rice yields was highly significant without obvious outliers from 1982 to 2004. Independent validation found that the overall relative error is approximately 5.82%, and a majority of the relative errors were less than 5% in 2005 and 2006, depending on the study area. The proposed models can be used in an operational context to predict rice yields at the provincial level in China. The methodologies described in the present paper can be applied to any crop for which a sufficient time series of NDVI data and the corresponding historical yield information are available, as long as the historical yield increases significantly.

Remotely Sensed Rice Yield Prediction Using Multi-Temporal NDVI Data Derived from NOAA's-AVHRR

PubMed Central

Huang, Jingfeng; Wang, Xiuzhen; Li, Xinxing; Tian, Hanqin; Pan, Zhuokun

2013-01-01

Grain-yield prediction using remotely sensed data have been intensively studied in wheat and maize, but such information is limited in rice, barley, oats and soybeans. The present study proposes a new framework for rice-yield prediction, which eliminates the influence of the technology development, fertilizer application, and management improvement and can be used for the development and implementation of provincial rice-yield predictions. The technique requires the collection of remotely sensed data over an adequate time frame and a corresponding record of the region's crop yields. Longer normalized-difference-vegetation-index (NDVI) time series are preferable to shorter ones for the purposes of rice-yield prediction because the well-contrasted seasons in a longer time series provide the opportunity to build regression models with a wide application range. A regression analysis of the yield versus the year indicated an annual gain in the rice yield of 50 to 128 kg ha−1. Stepwise regression models for the remotely sensed rice-yield predictions have been developed for five typical rice-growing provinces in China. The prediction models for the remotely sensed rice yield indicated that the influences of the NDVIs on the rice yield were always positive. The association between the predicted and observed rice yields was highly significant without obvious outliers from 1982 to 2004. Independent validation found that the overall relative error is approximately 5.82%, and a majority of the relative errors were less than 5% in 2005 and 2006, depending on the study area. The proposed models can be used in an operational context to predict rice yields at the provincial level in China. The methodologies described in the present paper can be applied to any crop for which a sufficient time series of NDVI data and the corresponding historical yield information are available, as long as the historical yield increases significantly. PMID:23967112

A compilation of nuclear weapons test detonation data for U.S. Pacific ocean tests.

PubMed

Simon, S L; Robison, W L

1997-07-01

Prior to December 1993, the explosive yields of 44 of 66 nuclear tests conducted by the United States in the Marshall Islands were still classified. Following a request from the Government of the Republic of the Marshall Islands to the U.S. Department of Energy to release this information, the Secretary of Energy declassified and released to the public the explosive yields of the Pacific nuclear tests. This paper presents a synopsis of information on nuclear test detonations in the Marshall Islands and other locations in the mid-Pacific including dates, explosive yields, locations, weapon placement, and summary statistics.

Measuring heterogenous stress fields in a 3D colloidal glass

NASA Astrophysics Data System (ADS)

Lin, Neil; Bierbaum, Matthew; Bi, Max; Sethna, James; Cohen, Itai

Glass in our common experience is hard and fragile. But it still bends, yields, and flows slowly under loads. The yielding of glass, a well documented yet not fully understood flow behavior, is governed by the heterogenous local stresses in the material. While resolving stresses at the atomic scale is not feasible, measurements of stresses at the single particle level in colloidal glasses, a widely used model system for atomic glasses, has recently been made possible using Stress Assessment from Local Structural Anisotropy (SALSA). In this work, we use SALSA to visualize the three dimensional stress network in a hard-sphere glass during start-up shear. By measuring the evolution of this stress network we identify local-yielding. We find that these local-yielding events often require only minimal structural rearrangement and as such have most likely been ignored in previous analyses. We then relate these micro-scale yielding events to the macro-scale flow behavior observed using bulk measurements.

(I Can’t Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research

PubMed Central

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: “random chance,” which is based on probability sampling, “minimal information,” which yields at least one new code per sampling step, and “maximum information,” which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario. PMID:28746358

A sub-canopy structure for simulating oil palm in the Community Land Model: phenology, allocation and yield

NASA Astrophysics Data System (ADS)

Fan, Y.; Roupsard, O.; Bernoux, M.; Le Maire, G.; Panferov, O.; Kotowska, M. M.; Knohl, A.

2015-06-01

Land surface modelling has been widely used to characterize the two-way interactions between climate and human activities in terrestrial ecosystems such as deforestation, agricultural expansion, and urbanization. Towards an effort to quantify the effects of forests to oil palm conversion occurring in the tropics on land-atmosphere carbon, water and energy fluxes, we introduce a new perennial crop plant functional type (PFT) for oil palm. Due to the modular and sequential nature of oil palm growth (around 40 stacked phytomers) and yield (fruit bunches axillated on each phytomer), we developed a specific sub-canopy structure for simulating palm's growth and yield within the framework of the Community Land Model (CLM4.5). In this structure each phytomer has its own prognostic leaf growth and fruit yield capacity like a PFT but with shared stem and root components among all phytomers. Phenology and carbon and nitrogen allocation operate on the different phytomers in parallel but at unsynchronized steps, so that multiple fruit yields per annum are enabled in terms of carbon and nitrogen outputs. An important phenological phase is identified for the palm PFT - the storage growth period of bud and "spear" leaves which are photosynthetically inactive before expansion. Agricultural practices such as transplanting, fertilization, and leaf pruning are represented. Parameters introduced for the new PFT were calibrated and validated with field measurements of leaf area index (LAI) and yield from Sumatra, Indonesia. In calibration with a mature oil palm plantation, the cumulative yields from 2005 to 2014 matched perfectly between simulation and observation (mean percentage error = 4 %). Simulated inter-annual dynamics of PFT-level and phytomer-level LAI were both within the range of field measurements. Validation from eight independent oil palm sites shows the ability of the model to adequately predict the average leaf growth and fruit yield across sites but also indicates that seasonal dynamics and site-to-site variability of yield are driven by processes not yet implemented in the model. The new sub-canopy structure and phenology and allocation functions now allow exploring the effects of tropical land use change, from natural ecosystems to oil palm plantations, on carbon, water and energy cycles and regional climate.

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

Spatially-explicit modeling of multi-scale drivers of aboveground forest biomass and water yield in watersheds of the Southeastern United States.

PubMed

Ajaz Ahmed, Mukhtar Ahmed; Abd-Elrahman, Amr; Escobedo, Francisco J; Cropper, Wendell P; Martin, Timothy A; Timilsina, Nilesh

2017-09-01

Understanding ecosystem processes and the influence of regional scale drivers can provide useful information for managing forest ecosystems. Examining more local scale drivers of forest biomass and water yield can also provide insights for identifying and better understanding the effects of climate change and management on forests. We used diverse multi-scale datasets, functional models and Geographically Weighted Regression (GWR) to model ecosystem processes at the watershed scale and to interpret the influence of ecological drivers across the Southeastern United States (SE US). Aboveground forest biomass (AGB) was determined from available geospatial datasets and water yield was estimated using the Water Supply and Stress Index (WaSSI) model at the watershed level. Our geostatistical model examined the spatial variation in these relationships between ecosystem processes, climate, biophysical, and forest management variables at the watershed level across the SE US. Ecological and management drivers at the watershed level were analyzed locally to identify whether drivers contribute positively or negatively to aboveground forest biomass and water yield ecosystem processes and thus identifying potential synergies and tradeoffs across the SE US region. Although AGB and water yield drivers varied geographically across the study area, they were generally significantly influenced by climate (rainfall and temperature), land-cover factor1 (Water and barren), land-cover factor2 (wetland and forest), organic matter content high, rock depth, available water content, stand age, elevation, and LAI drivers. These drivers were positively or negatively associated with biomass or water yield which significantly contributes to ecosystem interactions or tradeoff/synergies. Our study introduced a spatially-explicit modelling framework to analyze the effect of ecosystem drivers on forest ecosystem structure, function and provision of services. This integrated model approach facilitates multi-scale analyses of drivers and interactions at the local to regional scale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using coordinate-based meta-analyses to explore structural imaging genetics.

PubMed

Janouschek, Hildegard; Eickhoff, Claudia R; Mühleisen, Thomas W; Eickhoff, Simon B; Nickl-Jockschat, Thomas

2018-05-05

Imaging genetics has become a highly popular approach in the field of schizophrenia research. A frequently reported finding is that effects from common genetic variation are associated with a schizophrenia-related structural endophenotype. Genetic contributions to a structural endophenotype may be easier to delineate, when referring to biological rather than diagnostic criteria. We used coordinate-based meta-analyses, namely the anatomical likelihood estimation (ALE) algorithm on 30 schizophrenia-related imaging genetics studies, representing 44 single-nucleotide polymorphisms at 26 gene loci investigated in 4682 subjects. To test whether analyses based on biological information would improve the convergence of results, gene ontology (GO) terms were used to group the findings from the published studies. We did not find any significant results for the main contrast. However, our analysis enrolling studies on genotype × diagnosis interaction yielded two clusters in the left temporal lobe and the medial orbitofrontal cortex. All other subanalyses did not yield any significant results. To gain insight into possible biological relationships between the genes implicated by these clusters, we mapped five of them to GO terms of the category "biological process" (AKT1, CNNM2, DISC1, DTNBP1, VAV3), then five to "cellular component" terms (AKT1, CNNM2, DISC1, DTNBP1, VAV3), and three to "molecular function" terms (AKT1, VAV3, ZNF804A). A subsequent cluster analysis identified representative, non-redundant subsets of semantically similar terms that aided a further interpretation. We regard this approach as a new option to systematically explore the richness of the literature in imaging genetics.

Composite Films Formed by Cellulose nanocrystals and Latex Nanoparticles: Optical, Structural, and Mechanical Properties

NASA Astrophysics Data System (ADS)

Vollick, Brandon McRae

This thesis describes the preparation of iridescent, birefringent, composite films composed of cellulose nanocrystals (CNCs), latex nanoparticles (NPs) and a NP crosslinker; hexanediamine (HDA). First, aqueous suspensions were prepared with varying quantities of CNCs, NPs and HDA before equilibrating for one week. The cholesteric (Ch) phase was then cast and dried into a film. The optical, structural and mechanical properties of the film was analyzed. Second, films with identical compositions of CNCs, NPs, and HDA were fabricated in three different ways to yield films of different morphology, (i) fast drying of an isotropic suspension, yielding an isotropic film, (ii) slow drying of an isotropic suspension, yielding a partially Ch films, (iii) slow drying of an equilibrated suspension, yielding a highly Ch film. The optical and mechanical properties of the films was analyzed.

Fertilizing growth: Agricultural inputs and their effects in economic development.

PubMed

McArthur, John W; McCord, Gordon C

2017-07-01

This paper estimates the role of agronomic inputs in cereal yield improvements and the consequences for countries' processes of structural change. The results suggest a clear role for fertilizer, modern seeds and water in boosting yields. We then test for respective empirical links between agricultural yields and economic growth, labor share in agriculture and non-agricultural value added per worker. The identification strategy includes a novel instrumental variable that exploits the unique economic geography of fertilizer production and transport costs to countries' agricultural heartlands. We estimate that a half ton increase in staple yields generates a 14 to 19 percent higher GDP per capita and a 4.6 to 5.6 percentage point lower labor share in agriculture five years later. The results suggest a strong role for agricultural productivity as a driver of structural change.

Synthesis and characterization of poly (dihydroxybiphenyl borate) with high char yield for high-performance thermosetting resins

NASA Astrophysics Data System (ADS)

Wang, Shujuan; Xing, Xiaolong; Li, Jian; Jing, Xinli

2018-01-01

The objective of the current work is to synthesize novel boron-containing polymers with excellent thermal resistance, and reveal the structure and the reason for the high char yield. Thus, poly (dihydroxybiphenyl borate) (PDDB) with a more rigid molecular chain, was successfully synthesized using 4,4‧-dihydroxybiphenyl and boric acid. Structural characterizations of the prepared PDDB were performed via NMR, FTIR, XPS, and XRD analyses. The results reveal that PDDB consists of aromatic, Phsbnd Osbnd B and Bsbnd Osbnd B structures as well as a small number of boron hydroxyl and phenolic hydroxyl groups. PDDB shows good solubility in strong polar solvents, which is of great importance for the modification of thermosetting resins. TGA combined with DSC were employed to evaluate the thermal properties of PDDB, and increases in the glass transition temperature (Tg) and char yield were observed with increased boron content. Tg and char yield of PDDB (800 °C, nitrogen atmosphere) reached up to 219 °C and 66.5%, respectively. PDDB was extensively characterized during pyrolysis to reveal the high char yield of PDDB. As briefly discussed, the boron oxide and boron carbide that formed during pyrolysis play a crucial role in the high char yield of PDDB, which reduces the release of volatile carbon dioxide and carbon. This research suggests that PDDB has great potential as a novel modified agent for the improvement of the comprehensive performance of thermosetting resins to broaden their applicability in the field of advanced composites.

Study of charge symmetry breaking in dd collisions with WASA-at-COSY

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

Wronska, Aleksandra

2011-10-24

Charge symmetry is an approximate symmetry of the strong interaction. Studies of its breaking can yield information on the u and d quark mass difference. A theoretical collaboration is currently working on the description of charge symmetry breaking mechanisms for dd{yields}{alpha}{pi}{sup 0} and np{yields}d{pi}{sup 0} within Chiral Perturbation Theory, using the data from TRI-UMF and IUCF. One of the items in the program of the WASA-at-COSY collaboration is to extend the data base for the dd{yields}{alpha}{pi}{sup 0} reaction to higher energies, which would allow the extraction of the information on the p-wave. Status of the analysis of experimental data alongmore » with the preliminary results from the pilot run will be presented here.« less

CROMAX : a crosscut-first computer simulation program to determine cutting yield

Treesearch

Pamela J. Giese; Jeanne D. Danielson

1983-01-01

CROMAX simulates crosscut-first, then rip operations as commonly practiced in furniture manufacture. This program calculates cutting yields from individual boards based on board size and defect location. Such information can be useful in predicting yield from various grades and grade mixes thereby allowing for better management decisions in the rough mill. The computer...

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

Early lactation production, health, and welfare characteristics of cows selected for extended lactation.

PubMed

Lehmann, J O; Mogensen, L; Kristensen, T

2017-02-01

Some cows are able to achieve relatively high milk yields during extended lactations beyond 305 d in milk, and farmers may be able to use this potential by selecting the most suitable cows for an extended lactation. However, the decision to postpone insemination has to rely on information available in early lactation. The main objectives of this study were, therefore, to assess the association between the information available in early lactation and the relative milk production of cows on extended lactation, and to investigate if this information can be used to differentiate time of first insemination between cows. Data came from 4 Danish private herds practicing extended lactation in which some cows are selected to have a delayed time of planned first insemination. Average herd size varied from 93 to 157 cows, and milk yield varied from 7,842 to 12,315 kg of energy-corrected milk (ECM) per cow per year across herds. The analysis was based on 422 completed extended lactations (427 ± 87 d), and each lactation was assigned to 1 of 3 (low, medium, and high) milk performance groups (MPG) within parity group within herd based on a standardized lactation yield. For cows in the high MPG, peak ECM yield, and ECM yield at dry off were significantly greater, the relative reduction in milk yield between 60 and 305 d in milk was significantly smaller, and a smaller proportion had a body condition score (scale: 1-5) at dry off of 3.5 or greater compared with cows in low MPG. Previous lactation days in milk at peak ECM yield and ECM yield at dry off were higher, the relative reduction in milk yield between 60 and 305 d in milk was smaller, and the number of inseminations per conception was higher for multiparous cows in high MPG compared with low. Current lactation ECM yield at second and third milk recording were greater for cows in high MPG compared with low. A principal component analysis indicated that variables related to fertility, diseases, and milk yield explained most of the total variation between primiparous cows, whereas variables related to milk yield, fertility, and days in milk at peak yield were the most dominating for multiparous cows. Our study indicated that milk yields in previous lactation and at second and third milk recording correlate well with milk production potential, and therefore, may be promising indicators when selecting the most suitable cows for extended lactation. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Comparison of /sup 125/I-labeled and /sup 14/C-Labeled peptides of the major outer membrane protein of Chlamydia Trachomatis Strain L2/434 separated by high-performance liquid chromatography

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

Judd, R.C.; Caldwell, H.D.

1985-01-01

The objective of this study was to determine if in-gel chloramine-T radioiodination adequately labels OM proteins to allow for accurate and precise structural comparison of these molecules. Therefore, intrinsically /sup 14/C-amino acid labeled proteins and /sup 125/I-labeled proteins were cleaved with two endopeptidic reagents and the peptide fragments separated by HPLC. A comparison of retention times of the fragments, as determined by differential radiation counting, thus indicated whether /sup 125/Ilabeling identified of all the peptide peaks seen in the /sup 14/Clabeled proteins. Results demonstrated that radioiodination yields complete and accurate information about the primary structure of outer membrane proteins. Inmore » addition, it permits the use of extremely small amounts of protein allowing for method optimization and multiple separations to insure reproducibility.« less

The limits of life on Earth and searching for life on Mars

NASA Technical Reports Server (NTRS)

Nealson, K. H.

1997-01-01

Considerations of basic properties of bacteria such as size, structure, and metabolic versatility allow one to understand how these remarkable life-forms are so adaptable to environments previously thought to be uninhabitable. It is now appreciated that bacteria on Earth can utilize almost any redox couple that yields energy, taking advantage of this energy, while transforming the elements during metabolism. The ability to grow at the expense of inorganic redox couples allows the microbes to occupy niches not available to the more metabolically constrained eukaryotes. Furthermore, the simplicity of the bacterial structure allows them considerably more resistance to environmental variables (pH, salinity, temperature) that are toxic or lethal to more complex organisms. This information can be used to explain the predominance of prokaryotes in extreme environments on Earth, and to speculate as to simple types of metabolism and biogeochemical cycles that may exist on this planet, Mars, and perhaps other non-Earth environments.

The Effects of Caregiving Resources on Perceived Health among Caregivers

PubMed Central

Hong, Michin; Harrington, Donna

2016-01-01

This study examined how various types of resources influence perceived health of caregivers. Guided by the conservation of resources theory, a caregiver health model was built and tested using structural equation modeling. The caregiver health model consisted of caregiving situations (functional limitations and cognitive impairments of older adults and caregiving time), resources (financial resources, mastery, social support, family harmony, and service utilization), caregiver burden, and perceived health of caregivers. The sample included 1,837 unpaid informal caregivers drawn from the 2004 National Long-Term Caregiver Survey. The model fit indices indicated that the first structural model did not fit well; however, the revised model yielded an excellent model fit. More stressful caregiving situations were associated with fewer resources and higher burden, whereas greater resources were associated with lower burden and better perceived health of caregivers. The results suggest explicit implications for social work research and practice on how to protect the health of caregivers. PMID:29206951

Astragalar Morphology of Selected Giraffidae.

PubMed

Solounias, Nikos; Danowitz, Melinda

2016-01-01

The artiodactyl astragalus has been modified to exhibit two trochleae, creating a double pullied structure allowing for significant dorso-plantar motion, and limited mediolateral motion. The astragalus structure is partly influenced by environmental substrates, and correspondingly, morphometric studies can yield paleohabitat information. The present study establishes terminology and describes detailed morphological features on giraffid astragali. Each giraffid astragalus exhibits a unique combination of anatomical characteristics. The giraffid astragalar morphologies reinforce previously established phylogenetic relationships. We find that the enlargement of the navicular head is a feature shared by all giraffids, and that the primitive giraffids possess exceptionally tall astragalar heads in relation to the total astragalar height. The sivatheres and the okapi share a reduced notch on the lateral edge of the astragalus. We find that Samotherium is more primitive in astragalar morphologies than Palaeotragus, which is reinforced by tooth characteristics and ossicone position. Diagnostic anatomical characters on the astragalus allow for giraffid species identifications and a better understanding of Giraffidae.

Theoretical model to explain the problem-solving process in physics

NASA Astrophysics Data System (ADS)

Lopez, Carlos

2011-03-01

This work reports a theoretical model developed with the aim to explain the mental mechanisms of knowledge building during the problem-solving process in physics using a hybrid approach of assimilation- formation of concepts. The model has been termed conceptual chains and represents graphic diagrams of conceptual dependency, which have yielded information about the background knowledge required during the learning process, as well as about the formation of diverse structures that correspond to distinct forms of networking concepts Additionally, the conceptual constructs of the model have been classified according to five types of knowledge. Evidence was found about the influence of these structures, as well as of the distinct types of knowledge about the degree of difficulty of the problems. I want to be grateful to Laureate International Universities, Baltimore M.D., USA, for the financing granted for the accomplishment of this work.

Acousto-ultrasonic nondestructive evaluation of materials using laser beam generation and detection. M.S. Thesis

NASA Technical Reports Server (NTRS)

Huber, Robert D.; Green, Robert E., Jr.

1990-01-01

The acousto-ultrasonic method has proven to be a most interesting technique for nondestructive evaluation of the mechanical properties of a variety of materials. Use of the technique or a modification thereof, has led to correlation of the associated stress wave factor with mechanical properties of both metals and composite materials. The method is applied to the nondestructive evaluation of selected fiber reinforced structural composites. For the first time, conventional piezoelectric transducers were replaced with laser beam ultrasonic generators and detectors. This modification permitted true non-contact acousto-ultrasonic measurements to be made, which yielded new information about the basic mechanisms involved as well as proved the feasibility of making such non-contact measurements on terrestrial and space structures and heat engine components. A state-of-the-art laser based acousto-ultrasonic system, incorporating a compact pulsed laser and a fiber-optic heterodyne interferometer, was delivered to the NASA Lewis Research Center.

Inkjet printing-based volumetric display projecting multiple full-colour 2D patterns

NASA Astrophysics Data System (ADS)

Hirayama, Ryuji; Suzuki, Tomotaka; Shimobaba, Tomoyoshi; Shiraki, Atsushi; Naruse, Makoto; Nakayama, Hirotaka; Kakue, Takashi; Ito, Tomoyoshi

2017-04-01

In this study, a method to construct a full-colour volumetric display is presented using a commercially available inkjet printer. Photoreactive luminescence materials are minutely and automatically printed as the volume elements, and volumetric displays are constructed with high resolution using easy-to-fabricate means that exploit inkjet printing technologies. The results experimentally demonstrate the first prototype of an inkjet printing-based volumetric display composed of multiple layers of transparent films that yield a full-colour three-dimensional (3D) image. Moreover, we propose a design algorithm with 3D structures that provide multiple different 2D full-colour patterns when viewed from different directions and experimentally demonstrate prototypes. It is considered that these types of 3D volumetric structures and their fabrication methods based on widely deployed existing printing technologies can be utilised as novel information display devices and systems, including digital signage, media art, entertainment and security.

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Fortmann-Grote, C.; Bielecki, J.; Jurek, Z.; Santra, R.; Ziaja-Motyka, B.; Mancuso, A. P.

2017-08-01

We employ start-to-end simulations to model coherent diffractive imaging of single biomolecules using x-ray free electron lasers. This technique is expected to yield new structural information about biologically relevant macromolecules thanks to the ability to study the isolated sample in its natural environment as opposed to crystallized or cryogenic samples. The effect of the solvent on the diffraction pattern and interpretability of the data is an open question. We present first results of calculations where the solvent is taken into account explicitly. They were performed with a molecular dynamics scheme for a sample consisting of a protein and a hydration layer of varying thickness. Through R-factor analysis of the simulated diffraction patterns from hydrated samples, we show that the scattering background from realistic hydration layers of up to 3 Å thickness presents no obstacle for the resolution of molecular structures at the sub-nm level.

Stability and dynamics of membrane-spanning DNA nanopores

NASA Astrophysics Data System (ADS)

Maingi, Vishal; Burns, Jonathan R.; Uusitalo, Jaakko J.; Howorka, Stefan; Marrink, Siewert J.; Sansom, Mark S. P.

2017-03-01

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

The limits of life on Earth and searching for life on Mars.

PubMed

Nealson, K H

1997-10-25

Considerations of basic properties of bacteria such as size, structure, and metabolic versatility allow one to understand how these remarkable life-forms are so adaptable to environments previously thought to be uninhabitable. It is now appreciated that bacteria on Earth can utilize almost any redox couple that yields energy, taking advantage of this energy, while transforming the elements during metabolism. The ability to grow at the expense of inorganic redox couples allows the microbes to occupy niches not available to the more metabolically constrained eukaryotes. Furthermore, the simplicity of the bacterial structure allows them considerably more resistance to environmental variables (pH, salinity, temperature) that are toxic or lethal to more complex organisms. This information can be used to explain the predominance of prokaryotes in extreme environments on Earth, and to speculate as to simple types of metabolism and biogeochemical cycles that may exist on this planet, Mars, and perhaps other non-Earth environments.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Mixed cropping regimes promote the soil fungal community under zero tillage.

PubMed

Silvestro, L B; Biganzoli, F; Stenglein, S A; Forjan, H; Manso, L; Moreno, M V

2018-07-01

Fungi of yield soils represent a significant portion of the microbial biomass and reflect sensitivity to changes in the ecosystem. Our hypothesis was that crops included in cropping regimes under the zero tillage system modify the structure of the soil fungi community. Conventional and molecular techniques provide complementary information for the analysis of diversity of fungal species and successful information to accept our hypothesis. The composition of the fungal community varied according to different crops included in the cropping regimes. However, we detected other factors as sources of variation among them, season and sampling depth. The mixed cropping regimes including perennial pastures and one crop per year promote fungal diversity and species with potential benefit to soil and crop. The winter season and 0-5 cm depth gave the largest evenness and fungal diversity. Trichoderma aureoviride and Rhizopus stolonifer could be used for monitoring changes in soil under zero tillage.

Bioanalytical applications of SERS (surface-enhanced Raman spectroscopy).

PubMed

Hudson, Stephen D; Chumanov, George

2009-06-01

Surface-enhanced Raman scattering (SERS) is a powerful technique for analyzing biological samples as it can rapidly and nondestructively provide chemical and, in some cases, structural information about molecules in aqueous environments. In the Raman scattering process, both visible and near-infrared (NIR) wavelengths of light can be used to induce polarization of Raman-active molecules, leading to inelastic light scattering that yields specific molecular vibrational information. The development of surface enhancement has enabled Raman scattering to be an effective tool for qualitative as well as quantitative measurements with high sensitivity and specificity. Recent advances have led to many novel applications of SERS for biological analyses, resulting in new insights for biochemistry and molecular biology, the detection of biological warfare agents, and medical diagnostics for cancer, diabetes, and other diseases. This trend article highlights many of these recent investigations and provides a brief outlook in order to assess possible future directions of SERS as a bioanalytical tool.

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

PubMed Central

Roux, Benoît; Weare, Jonathan

2013-01-01

An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method. PMID:23464140

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

Yield Potential of Sugar Beet – Have We Hit the Ceiling?

PubMed Central

Hoffmann, Christa M.; Kenter, Christine

2018-01-01

The yield of sugar beet has continuously increased in the past decades. The question arises, whether this progress will continue in the future. A key factor for increasing yield potential of the crop is breeding progress. It was related to a shift in assimilate partitioning in the plant toward more storage carbohydrates (sucrose), whereas structural carbohydrates (leaves, cell wall compounds) unintendedly declined. The yield potential of sugar beet was estimated at 24 t sugar ha-1. For maximum yield, sufficient growth factors have to be available and the crop has to be able to fully utilize them. In sugar beet, limitations result from the lacking coincidence of maximum irradiation rates and full canopy cover, sink strength for carbon assimilation and high water demand, which cannot be met by rainfall alone. After harvest, sugar losses during storage occur. The paper discusses options for a further increase in yield potential, like autumn sowing of sugar beet, increasing sink strength and related constraints. It is prospected that yield increase by further widening the ratio of storage and structural carbohydrates will come to its natural limit as a certain cell wall stability is necessary. New challenges caused by climate change and by prolonged processing campaigns will occur. Thus breeding for improved pathogen resistance and storage properties will be even more important for successful sugar beet production than a further increase in yield potential itself. PMID:29599787

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries.

PubMed

Godin, Bruno; Nagle, Nick; Sattler, Scott; Agneessens, Richard; Delcarte, Jérôme; Wolfrum, Edward

2016-01-01

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In this work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib ( bmr ) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

DOE PAGES

Godin, Bruno; Nagle, Nick; Sattler, Scott; ...

2016-11-21

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

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

Godin, Bruno; Nagle, Nick; Sattler, Scott

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

Resonating group method as applied to the spectroscopy of α-transfer reactions

NASA Astrophysics Data System (ADS)

Subbotin, V. B.; Semjonov, V. M.; Gridnev, K. A.; Hefter, E. F.

1983-10-01

In the conventional approach to α-transfer reactions the finite- and/or zero-range distorted-wave Born approximation is used in liaison with a macroscopic description of the captured α particle in the residual nucleus. Here the specific example of 16O(6Li,d)20Ne reactions at different projectile energies is taken to present a microscopic resonating group method analysis of the α particle in the final nucleus (for the reaction part the simple zero-range distorted-wave Born approximation is employed). In the discussion of suitable nucleon-nucleon interactions, force number one of the effective interactions presented by Volkov is shown to be most appropriate for the system considered. Application of the continuous analog of Newton's method to the evaluation of the resonating group method equations yields an increased accuracy with respect to traditional methods. The resonating group method description induces only minor changes in the structures of the angular distributions, but it does serve its purpose in yielding reliable and consistent spectroscopic information. NUCLEAR STRUCTURE 16O(6Li,d)20Ne; E=20 to 32 MeV; calculated B(E2); reduced widths, dσdΩ extracted α-spectroscopic factors. ZRDWBA with microscope RGM description of residual α particle in 20Ne; application of continuous analog of Newton's method; tested and applied Volkov force No. 1; direct mechanism.

Seismic attribute analysis for reservoir and fluid prediction, Malay Basin

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

Mansor, M.N.; Rudolph, K.W.; Richards, F.B.

1994-07-01

The Malay Basin is characterized by excellent seismic data quality, but complex clastic reservoir architecture. With these characteristics, seismic attribute analysis is a very important tool in exploration and development geoscience and is routinely used for mapping fluids and reservoir, recognizing and risking traps, assessment, depth conversion, well placement, and field development planning. Attribute analysis can be successfully applied to both 2-D and 3-D data as demonstrated by comparisons of 2-D and 3-D amplitude maps of the same area. There are many different methods of extracting amplitude information from seismic data, including amplitude mapping, horizon slice, summed horizon slice, isochronmore » slice, and horizon slice from AVO (amplitude versus offset) cube. Within the Malay Basin, horizon/isochron slice techniques have several advantages over simply extracting amplitudes from a picked horizon: they are much faster, permit examination of the amplitude structure of the entire cube, yield better results for weak/variable signatures, and aid summation of amplitudes. Summation in itself often yields improved results because it incorporates the signature from the entire reservoir interval, reducing any effects due to noise, mispicking, or waveform variations. Dip and azimuth attributes have been widely applied by industry for fault identification. In addition, these attributes can also be used to map signature variations associated with hydrocarbon contacts or stratigraphic changes, and this must be considered when using these attributes for structural interpretation.« less

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA).

PubMed

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T; Marzilli, Luigi G

2012-09-01

The reaction of an aminopolycarboxylate ligand, as partic- N - m onoacetic a cid (ASMA), with [Re(CO) 3 (H 2 O) 3 ] + was examined. The tridentate coordination of ASMA to this Re I tricarbonyl precursor yielded fac -Re(CO) 3 (ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the Tc I tricarbonyl complex, which yields fac - 99m Tc(CO) 3 (ASMA) under similar conditions. The formation, structure, and isomerization of fac -Re(CO) 3 (ASMA) products were characterized by HPLC, 1 H NMR spectroscopy, and X-ray crystallography. The two major fac -Re(CO) 3 (ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac -Re(CO) 3 (ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99m Tc(CO) 3 (ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99m Tc radiopharmaceuticals.

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA)

PubMed Central

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T.; Marzilli, Luigi G.

2013-01-01

The reaction of an aminopolycarboxylate ligand, aspartic-N-monoacetic acid (ASMA), with [Re(CO)3(H2O)3]+ was examined. The tridentate coordination of ASMA to this ReI tricarbonyl precursor yielded fac-Re(CO)3(ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the TcI tricarbonyl complex, which yields fac-99mTc(CO)3(ASMA) under similar conditions. The formation, structure, and isomerization of fac-Re(CO)3(ASMA) products were characterized by HPLC, 1H NMR spectroscopy, and X-ray crystallography. The two major fac-Re(CO)3(ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac-Re(CO)3(ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99mTc(CO)3(ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99mTc radiopharmaceuticals. PMID:24273448

Identification of emotional intonation evaluated by fMRI.

PubMed

Wildgruber, D; Riecker, A; Hertrich, I; Erb, M; Grodd, W; Ethofer, T; Ackermann, H

2005-02-15

During acoustic communication among human beings, emotional information can be expressed both by the propositional content of verbal utterances and by the modulation of speech melody (affective prosody). It is well established that linguistic processing is bound predominantly to the left hemisphere of the brain. By contrast, the encoding of emotional intonation has been assumed to depend specifically upon right-sided cerebral structures. However, prior clinical and functional imaging studies yielded discrepant data with respect to interhemispheric lateralization and intrahemispheric localization of brain regions contributing to processing of affective prosody. In order to delineate the cerebral network engaged in the perception of emotional tone, functional magnetic resonance imaging (fMRI) was performed during recognition of prosodic expressions of five different basic emotions (happy, sad, angry, fearful, and disgusted) and during phonetic monitoring of the same stimuli. As compared to baseline at rest, both tasks yielded widespread bilateral hemodynamic responses within frontal, temporal, and parietal areas, the thalamus, and the cerebellum. A comparison of the respective activation maps, however, revealed comprehension of affective prosody to be bound to a distinct right-hemisphere pattern of activation, encompassing posterior superior temporal sulcus (Brodmann Area [BA] 22), dorsolateral (BA 44/45), and orbitobasal (BA 47) frontal areas. Activation within left-sided speech areas, in contrast, was observed during the phonetic task. These findings indicate that partially distinct cerebral networks subserve processing of phonetic and intonational information during speech perception.