bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensemble QSAR: A QSAR method based on conformational ensembles and metric descriptors
Authors: Pissurlenkar Raghuvir R. S. , Khedkar Vijay M. , Iyer Radhakrishnan P. , Coutinho Evans C. 
Published: April 2011

AbstractQuantitative structure–activity relationship (QSAR) is the most versatile tool in computer‐assisted molecular design. One conceptual drawback seen in QSAR approaches is the “one chemical–one structure–one parameter value” dogma where the model development is based on physicochemical description for a single molecular conformation, while ignoring the rest of the conformational space. It is well known that molecules have several low‐energy conformations populated at physiological temperature, and each conformer makes a significant impact on associated properties such as biological activity. At the level of molecular interaction, the dynamics around the molecular structure is of prime essence rather than the average structure. As a step toward understanding the role of these discrete microscopic states in biological activity, we have put together a theoretically rigorous and computationally tractable formalism coined as eQSAR. In this approach, the biological activity is modeled as a function of physicochemical description for a selected set of low‐energy conformers, rather than that's for a single lowest energy conformation. Eigenvalues derived from the “Physicochemical property integrated distance matrices” (PD‐matrices) that encompass both 3D structure and physicochemical properties, have been used as descriptors; is a novel addition. eQSAR is validated on three peptide datasets and explicitly elaborated for bradykinin‐potentiating peptides. The conformational ensembles were generated by a simple molecular dynamics and consensus dynamics approaches. The eQSAR models are statistically significant and possess the ability to select the most biologically relevant conformation(s) with the relevant physicochemical attributes that have the greatest meaning for description of the biological activity. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Adaptation of microplate‐based respirometry for hippocampal slices and analysis of respiratory capacity
Authors: Schuh Rosemary A. , Clerc Pascaline , Hwang Hyehyun , Mehrabian Zara , Bittman Kevin , Chen Hegang , Polster Brian M. 
Published: April 2011

AbstractMultiple neurodegenerative disorders are associated with altered mitochondrial bioenergetics. Although mitochondrial O2 consumption is frequently measured in isolated mitochondria, isolated synaptic nerve terminals (synaptosomes), or cultured cells, the absence of mature brain circuitry is a remaining limitation. Here we describe the development of a method that adapts the Seahorse Extracellular Flux Analyzer (XF24) for the microplate‐based measurement of hippocampal slice O2 consumption. As a first evaluation of the technique, we compared whole‐slice bioenergetics with previous measurements made with synaptosomes or cultured neurons. We found that mitochondrial respiratory capacity and O2 consumption coupled to ATP synthesis could be estimated in cultured or acute hippocampal slices with preserved neural architecture. Mouse organotypic hippocampal slices oxidizing glucose displayed mitochondrial O2 consumption that was well coupled, as determined by the sensitivity to the ATP synthase inhibitor oligomycin. However, stimulation of respiration by uncoupler was modest (<120% of basal respiration) compared with previous measurements in cells or synaptosomes, though enhanced slightly (to ∼150% of basal respiration) by acute addition of the mitochondrial complex I‐linked substrate pyruvate. These findings suggest a high basal utilization of respiratory capacity in slices and a limitation of glucose‐derived substrate for maximal respiration. The improved throughput of microplate‐based hippocampal respirometry over traditional O2 electrode‐based methods is conducive to neuroprotective drug screening. When coupled with cell type‐specific pharmacology or genetic manipulations, the ability to measure O2 consumption efficiently from whole slices should advance our understanding of mitochondrial roles in physiology and neuropathology. © 2011 Wiley‐Liss, Inc
Evaluation of three methods to estimate density and detectability from roadside point counts
Authors: Murray Les D. , Gates Robert J. , Spinola R. Manuel 
Published: April 2011

AbstractRoadside point counts are often used to estimate trends of bird populations. The use of aural counts of birds without adjustment for detection probability, however, can lead to incorrect population trend estimates. We compared precision of estimates of density and detectability of whistling northern bobwhites (Colinus virginianus) using distance sampling, independent double‐observer, and removal methods from roadside surveys. Two observers independently recorded each whistling bird heard, distance from the observer, and time of first detection at 362 call‐count stops in Ohio. We examined models that included covariates for year and observer effects for each method and distance from observer effects for the double‐observer and removal methods using Akaike's Information Criterion (AIC). The best model of detectability from distance sampling included observer and year effects. The best models from the removal and double‐observer techniques included observer and distance effects. All 3 methods provided precise estimates of detection probability (CV = 2.4–4.4%) with a range of detectability of 0.44–0.95 for a 6‐min survey. Density estimates from double‐observer surveys had the lowest coefficient of variation (2005 = 3.2%, 2006 = 1.7%), but the removal method also provided precise estimates of density (2005 CV = 3.4%, 2006 CV = 4.8%), and density estimates from distance sampling were less precise (2005 CV = 9.6%, 2006 CV = 7.9%). Assumptions of distance sampling were violated in our study because probability of detecting bobwhites near the observer was <1 or the roadside survey points were not randomly distributed with respect to the birds. Distances also were not consistently recorded by individual members of observer pairs. Although double‐observer surveys provided more precise estimates, we recommend using the removal method to estimate detectability and abundance of bobwhites. The removal method provided precise estimates of density and detection probability and requires half the personnel time as double‐observer surveys. Furthermore, the likelihood of meeting model assumptions is higher for the removal survey than with independent double‐observers. © 2011 The Wildlife Society.
Using a general index approach to analyze camera‐trap abundance indices
Authors: Bengsen Andrew J. , Leung Luke K.‐P. , Lapidge Steven J. , Gordon Iain J. 
Published: April 2011

AbstractThe lack of variance estimates constrain the utility of abundance indices calculated from camera‐trap data. We adapted a General Index model, which allows variance estimation, to analyze camera‐trap observations of feral pigs (Sus scrofa) for population monitoring in a tropical rainforest. We tested whether the index would respond to population manipulation, and found that it decreased by 57% following removal of 24 pigs and remained low in the following period. Our method is useful for monitoring other large animals in difficult landscapes, and the model can be used to enhance the value of existing data sets. © 2011 The Wildlife Society.
Evaluating precision of cementum annuli analysis for aging mule deer from southern California
Authors: Asmus Jim , Weckerly Floyd W. 
Published: April 2011

AbstractWe evaluated the precision of age estimates produced by cementum annuli analysis (CAA) of blind‐duplicate specimens taken from 994 southern mule deer (Odocoileus hemionus) collected over 15 years. We found that the mean annual proportion of unreliably aged incisor pairs was greater for females (0.48, SD = 0.13) than for males (0.22, SD = 0.07). Most of the 308 unreliably aged tooth pairs disagreed by only 1 year. Sex, precipitation, and certainty codes assigned by Matson's Lab to the age estimates were the best predictors for agreement of estimated ages within incisor pairs. Our estimated overall age error rate of CAA (17%) was >2 times as large as estimated error rates from Montana and South Dakota, but less than half of error rates estimated for Mississippi and south Texas. Knowing the error rate of age estimates from a specific deer population allows wildlife managers to perform tasks requiring specific age class information such as monitoring the harvest rate of older female deer in a hunted population or performing population reconstruction. © 2011 The Wildlife Society.
A practical sampling design for acoustic surveys of bats
Authors: Rodhouse Thomas J. , Vierling Kerri T. , Irvine Kathryn M. 
Published: April 2011

AbstractAcoustic surveys are widely used for describing bat occurrence and activity patterns and are increasingly important for addressing concerns for habitat management, wind energy, and disease on bat populations. Designing these surveys presents unique challenges, particularly when a probabilistic sample is required for drawing inference to unsampled areas. Sampling frame errors and other logistical constraints often require survey sites to be dropped from the sample and new sites added. Maintaining spatial balance and representativeness of the sample when these changes are made can be problematic. Spatially balanced sampling designs recently developed to support aquatic surveys along rivers provide solutions to a number of practical challenges faced by bat researchers and allow for sample site additions and deletions, support unequal‐probability selection of sites, and provide an approximately unbiased local neighborhood‐weighted variance estimator that is efficient for spatially structured populations such as is typical for bats. We implemented a spatially balanced design to survey canyon bat (Parastrellus hesperus) activity along a stream network. The spatially balanced design accommodated typical logistical challenges and yielded a 25% smaller estimated standard error for the mean activity level than the usual simple random sampling estimator. Spatially balanced designs have broad application to bat research and monitoring programs and will improve studies relying on model‐based inference (e.g., occupancy models) by providing flexibility and protection against violations of the independence assumption, even if design‐based estimators are not used. Our approach is scalable and can be used for pre‐ and post‐construction surveys along wind turbine arrays and for regional monitoring programs. © 2011 The Wildlife Society.
Structural and biochemical investigation of two Arabidopsis shikimate kinases: The heat‐inducible isoform is thermostable
Authors: Fucile Geoffrey , Garcia Christel , Carlsson Jonas , Sunnerhagen Maria , Christendat Dinesh 
Published: April 2011

AbstractThe expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental stress and developmental requirements in an isoform‐specific manner. Despite their important physiological role, experimental structures of plant SKs have not been determined and the biochemical nature of plant SK regulation is unknown. The Arabidopsis thaliana genome encodes two SKs, AtSK1 and AtSK2. We demonstrate that AtSK2 is highly unstable and becomes inactivated at 37°C whereas the heat‐induced isoform, AtSK1, is thermostable and fully active under identical conditions at this temperature. We determined the crystal structure of AtSK2, the first SK structure from the plant kingdom, and conducted biophysical characterizations of both AtSK1 and AtSK2 towards understanding this mechanism of thermal regulation. The crystal structure of AtSK2 is generally conserved with bacterial SKs with the addition of a putative regulatory phosphorylation motif forming part of the adenosine triphosphate binding site. The heat‐induced isoform, AtSK1, forms a homodimer in solution, the formation of which facilitates its relative thermostability compared to AtSK2. In silico analyses identified AtSK1 site variants that may contribute to AtSK1 stability. Our findings suggest that AtSK1 performs a unique function under heat stress conditions where AtSK2 could become inactivated. We discuss these findings in the context of regulating metabolic flux to competing downstream pathways through SK‐mediated control of steady state concentrations of shikimate.
Impact of InGaN growth conditions on structural stability under high temperature process in InGaN/GaN multiple quantum wells
Authors: Hikosaka Toshiki , Shioda Tomonari , Harada Yoshiyuki , Tachibana Koichi , Sugiyama Naoharu , Nunoue Shin‐ya 
Published: April 2011

AbstractThe influence of InGaN growth conditions on the structural instability of green light‐emitting InGaN quantum wells (QWs) is investigated. The multiple quantum wells (MQWs) were grown by metal‐organic chemical vapor deposition (MOCVD), varying the growth rate of InGaN well layers. It is found that the structural deterioration of MQWs attributable to high‐temperature post‐growth of GaN on MQWs is suppressed by decreasing the growth rate. Atomic force microscope measurement reveals the reduction of In‐rich clusters that are fragile under high‐temperature process on the surface of MQWs grown at low growth rates. It is demonstrated that the suppression of the formation of these In‐rich clusters at the lower growth rates lead to the improvement of the thermal stability and the enhancement of optical properties of green light‐emitting diodes. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Process Simulation and Economic Feasibility Analysis for a Hydrogen‐Based Novel Suspension Ironmaking Technology
Authors: Pinegar Haruka K. , Moats Michael S. , Sohn H. Y. 
Published: April 2011

AbstractA novel gas‐solid suspension ironmaking process is under development at the University of Utah, which would greatly reduce energy consumption and carbon dioxide emission compared with current blast furnace technology. The proposed process is based on the flash reduction of iron ore concentrate using a gaseous reagent, such as hydrogen, syngas, natural gas or a combination of thereof.A process flow sheet of the proposed ironmaking process using purchased hydrogen was constructed and then simulations were performed at several potential operating conditions. Ironmaking was simulated using two different process configurations. The simulation results show that the required fresh hydrogen would increase with higher excess driving force and operating temperature, but not greatly when hydrogen is preheated. Compared with the average blast furnace process, the proposed process would reduce energy consumption by 57 ‐ 60%, using the higher heating value of hydrogen (71 – 73%, if the lower heating value is used), when hydrogen and coal are considered as the starting materials in the respective processes. The economic feasibility analysis using net present value (NPV) indicates that the proposed process could be economically feasible at elevated hot metal prices and/or if reduction in carbon dioxide emissions has a significant value in a cap and trade scenario.
Spline‐Interpolation and Calculation of Machine Parameters for the Three‐Roll‐Pushbending of Spline‐Contours
Authors: Engel B. , Kersten S. , Anders D. 
Published: April 2011

AbstractToday, bending tasks become more and more complex. Not even constant bending radii are required in the industrial practice. There is a growing demand for bending spline‐contours, too. Such geometries are often produced with Freeform‐Bending procedures like Three‐Roll‐Pushbending.This paper presents a method to interpolate a given spline bending‐contour (by CAD data), in order to calculate its radii distribution, which is needed to determine the machine parameters in certain points for the Three‐Roll‐Pushbending. For the determination of the machine parameters one has to consider the different influences on the bending process. The material springback and the deflection of the bending machine per radius need to be compensated to reach a near net shape bending result. Nevertheless deviations cannot be avoided. To improve the results, a possibility to adjust the pre‐calculated machine parameters is shown.For the investigations tube profiles with constant wall thicknesses were considered. The corresponding plasticity calculations refer to tube cross‐sections. The results were validated by bending a representative spline contour on the bending machine of the Chair of Forming Technology at the University of Siegen.
Neurodevelopment following fetal growth restriction and its relationship with antepartum parameters of placental dysfunction
Authors: Baschat A. A. 
Published: April 2011

AbstractPlacental dysfunction leading to fetal growth restriction (FGR) is an important risk factor for neurodevelopmental delay. Recent observations clarify that FGR evolves prenatally from a preclinical phase of abnormal nutrient and endocrine milieu to a clinical phase that differs in characteristics in preterm and term pregnancies. Relating childhood neurodevelopment to these prenatal characteristics offers potential advantages in identifying mechanisms and timing of critical insults. Based on available studies, lagging head circumference, overall degree of FGR, gestational age, and umbilical artery (UA), aortic and cerebral Doppler parameters are the independent prenatal determinants of infant and childhood neurodevelopment. While head circumference is important independent of gestational age, overall growth delay has the greatest impact in early onset FGR. Gestational age has an overriding negative effect on neurodevelopment until 32–34 weeks' gestation. Accordingly, the importance of Doppler status is demonstrated from 27 weeks onward and is greatest when there is reversed end‐diastolic velocity in the UA or aorta. While these findings predominate in early‐onset FGR, cerebral vascular impedance changes become important in late onset FGR. Abnormal motor and neurological delay occur in preterm FGR, while cognitive effects and abnormalities that can be related to specific brain areas increase in frequency as gestation advances, suggesting different pathophysiology and evolving vulnerability of the fetal brain. Observational and management studies do not suggest that fetal deterioration has an independent impact on neurodevelopment in early‐onset FGR. In late‐onset FGR further research needs to establish benefits of perinatal intervention, as the pattern of vulnerability and effects of fetal deterioration appear to differ in the third trimester. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Energy security in a developing world
Authors: Kuik Onno J. , Lima Mairon Bastos , Gupta Joyeeta 
Published: April 2011

AbstractEnergy security, a fuzzy concept, has traditionally been used to justify state control over energy and a reluctance to deal with energy issues at global level. However, over time, the concept is acquiring different meanings that are applicable at different levels of governance. Many of the elements of the new definitions also imply a number of inherent contradictions. Against this background, this article explores the dimensions of energy security with a special focus on the developing world. It argues that (1) within developing countries (DCs), energy security implies both access to modern energy services by the poorest as well as access by the rapidly developing industrial, services, and urban sectors. Lack of adequate resources has implied trade‐offs in terms of who gets access and in terms of taking into account the social and ecological consequences of specific energy sources. Furthermore, (2) the growing DCs' need for energy is impacted by industrialized country perceptions of the various dimensions of energy security—recognizing the need for access to the poorest; industrialized countries are increasingly implicitly questioning the right of DCs to use fossil fuels because of its implications for climate change; or to build large dams because of ecological and social security concerns or expand nuclear energy because of its potential security implications. The development of reliable, continuous, affordable, and environmentally sound provision of energy services combined with a focus on energy efficiency and conservation is the only way of alleviating the various multi‐level dimensions of energy security. WIREs Clim Change 2011 2 627–634 DOI: 10.1002/wcc.118This article is categorized under:

Climate and Development > Social Justice and the Politics of Development
Emerging roles for the Ro 60‐kDa autoantigen in noncoding RNA metabolism
Authors: Sim Soyeong , Wolin Sandra L. 
Published: April 2011

AbstractAll cells contain an enormous variety of ribonucleoprotein (RNP) complexes that function in diverse processes. Although the mechanisms by which many of these RNPs contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. A member of this latter category, the Ro 60‐kDa protein and its associated noncoding Y RNAs, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases systemic lupus erythematosus and Sjögren's syndrome. Recent studies have shown that Ro is ring shaped, binds the single‐stranded ends of misfolded noncoding RNAs in its central cavity, and may function in noncoding RNA quality control. Although Ro is not present in yeast, many bacterial genomes contain potential Ro orthologs. In the radiation‐resistant eubacterium Deinococcus radiodurans, the Ro ortholog functions with exoribonucleases during stress‐induced changes in RNA metabolism. Moreover, in both D. radiodurans and animal cells, Ro is involved in the response to multiple types of environmental stress. Finally, Y RNAs can influence the subcellular location of Ro, inhibit access of the central cavity to other RNAs, and may also act as binding sites for proteins that influence Ro function. WIREs RNA 2011 2 686–699 DOI: 10.1002/wrna.85This article is categorized under:

RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution
RNA Processing > Processing of Small RNAs
RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
Crystal Structure Refinement of M(NCNH)2 (M = Fe, Co) Based on Combined Neutron and X‐ray Diffraction Data
Authors: Tang Xiaojuan , Houben Andreas , Liu Xiaohui , Stork Ludwig , Dronskowski Richard 
Published: April 2011

AbstractThe crystal structures of Fe(NCNH)2 and Co(NCNH)2, isotypical with Ni(NCNH)2, have been refined by means of combined X‐ray and neutron powder diffraction data (SPODI, FRM II). The lattice parameters are a = 6.6655(7), b = 8.7923(8), c = 3.3304(3) Å for Fe(NCNH)2 and a = 6.5696(2), b = 8.8058(2), c = 3.2622(1) Å for Co(NCNH)2 in the orthorhombic system Pnmm (no. 58). The positions of the hydrogen atoms have been clearly resolved.