bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonmagnetic impurity chemistry substitution effects in zigzag silicon carbide nanoribbons
Authors: Lou Ping 
Published: April 2013

AbstractUsing first‐principles calculations based on density functional theory (DFT) and nonequilibrium Green's function method, we systematically investigated the electronic and magnetic structures, local structural distortion, and electronic spin transport property of a zigzag silicon carbide nanoribbon (ZSiC NR) containing one isolated nonmagnetic impurity [boron (B) or nitrogen (N)] at the inequivalent substitutional sites. Our calculated results reveal that by controlling the doping position without an applied electronic field, greatly enriched electronic and magnetic properties, e.g., semiconducting, half‐metallic, and metallic behaviors, as well as the ferrimagnetic–ferromagnetic conversion, can be achieved in both B‐ and N‐doped ZSiC NRs. Interestingly, all the doped ZSiC NRs of B substituting Si atom and N substituting C atom have 100% spin transport polarization around the Fermi level and exhibit spin filtering behavior. It is found that except for position at the edge C‐site, the boron at other sites suppresses the local magnetic moment at edge Si atoms and enhances the local magnetic moment at edge C atoms. On the contrary, except for position at the edge Si‐site and its nearest‐neighbor Si‐site, the nitrogen at other sites suppresses the local magnetic moment at edge C atoms and enhances the local magnetic moment at edge Si atoms. It is also found that when the impurity atom substitutes Si atom, visible local structural distortion occurs around the impurity atom, whereas when the impurity atom substitutes C atom, only a minor local structural distortion occurs. Additionally, the local structural distortion around impurity atom becomes more pronounced when the impurity moves from the edge toward the center. These doping effects are discussed by using the band structures, projected density of states (DOS), electronegativity, as well as Mulliken charge analysis.
Determination of kinetic parameters and structure–activity relationships of ginsenosides as inhibitors of cyclin‐dependent kinase 5/p25 using ultra‐pressure liquid chromatography with triple quadrupole tandem mass spectrometry
Authors: Chen Ning , Yang Hongmei , Niu Jun , Liu Shuying 
Published: April 2013

RATIONALECyclin‐dependent kinase 5 (cdk5) is a serine/threonine kinase that is reported to play an important role in the pathogenesis of Alzheimer's disease. Ginsenosides have beneficial effects on Alzheimer's disease in both in vivo and in vitro experiments, but the precise mechanisms are not yet entirely clear.METHODSIn the present study, an ultrahigh‐pressure liquid chromatography (UPLC) and triple quadrupole mass spectrometry (TQMS) assay was developed to study the activities of cdk5 for the first time.RESULTSThe calibration curves showed a good linear behavior over the range 0.04 μM to 10 μM (y = 0.934x + 0.045, R2 = 0.995) with product phosphorylated peptide (PKpTPKKAKKV). The screening results suggested that the inhibition activities of ginsenosides are related to their chemical structures.CONCLUSIONSThe developed UPLC/TQMS‐based method for determination of an inhibitor of cdk5/p25 is sensitive and reliable. The effect of ginsenosides on Alzheimer's disease may be involved with the regulation of activities of cdk5/p25. Copyright © 2013 John Wiley & Sons, Ltd.
Uncertainty in radar‐rainfall composite and its impact on hydrologic prediction for the eastern Iowa flood of 2008
Authors: Seo Bong‐Chul , Cunha Luciana K. , Krajewski Witold F. 
Published: April 2013

Key Points
A significant potential source of error exists in mosaicked radar‐rainfall maps.
Different radar calibration offsets lead to misestimation of rainfall amounts.
Systematic error in rainfall significantly affects hydrologic predictions.
First evaluation of the climatological calibration algorithm in the real‐time TMPA precipitation estimates over two basins at high and low latitudes
Authors: Yong Bin , Ren Liliang , Hong Yang , Gourley Jonathan J. , Tian Yudong , Huffman George J. , Chen Xi , Wang Weiguang , Wen Yixin 
Published: April 2013

Key Points
The crucial upgrade of TMPA‐RT effectively reduces the systematic errors.
This upgrade tends to perform worse at higher latitudes, especially in winter.
Future efforts include improved error structure and extension to high latitudes.
An elementary theory of product-line variations
Authors: Sampath Prahladavaradan 
Published: April 2013

Abstract
The primary aim of a software product-line is to maximise reuse of software components by managing the variability in component functionalities and product configurations. Feature oriented domain analysis (FODA) diagrams are a formalism for modelling the variability in a software product-line, and are used as a tool for managing a product-line and planning its evolution. This paper presents an elementary theory of variations in a product-line, leading up to a technique for extracting FODA diagrams from legacy product-lines. The theory is elementary in the sense that it is built using very simple mathematical structures, making minimal assumptions on the structure of product-lines. Examples drawn from the automotive domain are used to illustrate the theoretical developments.
Discovery and characterization of a novel ATP/polyphosphate xylulokinase from a hyperthermophilic bacterium Thermotoga maritima
Authors: Martín del Campo Julia S , Chun You , Kim Jae-Eung , Patiño Rodrigo , Zhang Y-H Percival 
Published: April 2013

Abstract
Xylulokinase (XK, E.C. 2.7.1.17) is one of the key enzymes in xylose metabolism and it is essential for the activation of pentoses for the sustainable production of biocommodities from biomass sugars. The open reading frame (TM0116) from the hyperthermophilic bacterium Thermotoga maritima MSB8 encoding a putative xylulokinase were cloned and expressed in Escherichia coli BL21 Star (DE3) in the Luria–Bertani and auto-inducing high-cell-density media. The basic biochemical properties of this thermophilic XK were characterized. This XK has the optimal temperature of 85 °C. Under a suboptimal condition of 60 °C, the k cat was 83 s−1, and the K m values for xylulose and ATP were 1.24 and 0.71 mM, respectively. We hypothesized that this XK could work on polyphosphate possibly because this ancestral thermophilic microorganism utilizes polyphosphate to regulate the Embden–Meyerhof pathway and its substrate-binding residues are somewhat similar to those of other ATP/polyphosphate-dependent kinases. This XK was found to work on low-cost polyphosphate, exhibiting 41 % of its specific activity on ATP. This first ATP/polyphosphate XK could have a great potential for xylose utilization in thermophilic ethanol-producing microorganisms and cell-free biosystems for low-cost biomanufacturing without the use of ATP.
Dynamic elicited priors for updating covert networks
Authors: GILL JEFF , FREEMAN JOHN R. 
Published: April 2013

AbstractThe study of covert networks is plagued by the fact that individuals conceal their attributes and associations. To address this problem, we develop a technology for eliciting this information from qualitative subject-matter experts to inform statistical social network analysis. We show how the information from the subjective probability distributions can be used as input to Bayesian hierarchical models for network data. In the spirit of “proof of concept,” the results of a test of the technology are reported. Our findings show that human subjects can use the elicitation tool effectively, supplying attribute and edge information to update a network indicative of a covert one.
Xenon Neurotoxicity in Rat Hippocampal Slice Cultures Is Similar to Isoflurane and Sevoflurane
Authors: Brosnan Heather , Bickler Philip E. 
Published: April 2013

Abstract

Background:
Anesthetic neurotoxicity in the developing brain of rodents and primates has raised concern. Xenon may be a nonneurotoxic alternative to halogenated anesthetics, but its toxicity has only been studied at low concentrations, where neuroprotective effects predominate in animal models. An equipotent comparison of xenon and halogenated anesthetics with respect to neurotoxicity in developing neurons has not been made.

Methods:
Organotypic hippocampal cultures from 7-day-old rats were exposed to 0.75, 1, and 2 minimum alveolar concentrations (MAC) partial pressures (60% xenon at 1.2, 2.67, and 3.67 atm; isoflurane at 1.4, 1.9, and 3.8%; and sevoflurane at 3.4 and 6.8%) for 6 h, at atmospheric pressure or in a pressure chamber. Cell death was assessed 24 h later with fluorojade and fluorescent dye exclusion techniques.

Results:
Xenon caused death of hippocampal neurons in CA1, CA3, and dentate regions after 1 and 2 MAC exposures, but not at 0.75 MAC. At 1 MAC, xenon increased cell death 40% above baseline (P < 0.01; ANOVA with Dunnett test). Both isoflurane and sevoflurane increased neuron death at 1 but not 2 MAC. At 1 MAC, the increase in cell death compared with controls was 63% with isoflurane and 90% with sevoflurane (both P < 0.001). Pretreatment of cultures with isoflurane (0.75 MAC) reduced neuron death after 1 MAC xenon, isoflurane, and sevoflurane.

Conclusion:
Xenon causes neuronal cell death in an in vitro model of the developing rodent brain at 1 MAC, as does isoflurane and sevoflurane at similarly potent concentrations. Preconditioning with a subtoxic dose of isoflurane eliminates this toxicity.
Neither Xenon nor Fentanyl Induces Neuroapoptosis in the Newborn Pig Brain
Authors: Sabir Hemmen , Bishop Sarah , Cohen Nicki , Maes Elke , Liu Xun , Dingley John , Thoresen Marianne 
Published: April 2013

Abstract

Background:
Some inhalation anesthetics increase apoptotic cell death in the developing brain. Xenon, an inhalation anesthetic, increases neuroprotection when combined with therapeutic hypothermia after hypoxic-ischemic brain injury in newborn animals. The authors, therefore, examined whether there was any neuroapoptotic effect of breathing 50% xenon with continuous fentanyl sedation for 24 h at normothermia or hypothermia on newborn pigs.

Methods:
Twenty-six healthy pigs (<24-h old) were randomized into four groups: (1) 24 h of 50% inhaled xenon with fentanyl at hypothermia (Trec = 33.5°C), (2) 24 h of 50% inhaled xenon with fentanyl at normothermia (Trec = 38.5°C), (3) 24 h of fentanyl at normothermia, or (4) nonventilated juvenile controls at normothermia. Five additional nonrandomized pigs inhaled 2% isoflurane at normothermia for 24 h to verify any proapoptotic effect of inhalation anesthetics in our model. Pathological cells were morphologically assessed in cortex, putamen, hippocampus, thalamus, and white matter. To quantify the findings, immunostained cells (caspase-3 and terminal deoxynucleotidyl transferase–mediated deoxyuridine-triphosphate nick-end labeling) were counted in the same brain regions.

Results:
For groups (1) to (4), the total number of apoptotic cells was less than 5 per brain region, representing normal developmental neuroapoptosis. After immunostaining and cell counting, regression analysis showed that neither 50% xenon with fentanyl nor fentanyl alone increased neuroapoptosis. Isoflurane caused on average a 5- to 10-fold increase of immunostained cells.

Conclusion:
At normothermia or hypothermia, neither 24 h of inhaled 50% xenon with fentanyl sedation nor fentanyl alone induces neuroapoptosis in the neonatal pig brain. Breathing 2% isoflurane increases neuroapoptosis in neonatal pigs.
Arabidopsis 3-Ketoacyl-Coenzyme A Synthase9 Is Involved in the Synthesis of Tetracosanoic Acids as Precursors of Cuticular Waxes, Suberins, Sphingolipids, and Phospholipids
Authors: Kim Juyoung , Jung Jin Hee , Lee Saet Buyl , Go Young Sam , Kim Hae Jin , Cahoon Rebecca , Markham Jennifer E. , Cahoon Edgar B. , Suh Mi Chung 
Published: April 2013

AbstractVery-long-chain fatty acids (VLCFAs) with chain lengths from 20 to 34 carbons are involved in diverse biological functions such as membrane constituents, a surface barrier, and seed storage compounds. The first step in VLCFA biosynthesis is the condensation of two carbons to an acyl-coenzyme A, which is catalyzed by 3-ketoacyl-coenzyme A synthase (KCS). In this study, amino acid sequence homology and the messenger RNA expression patterns of 21 Arabidopsis (Arabidopsis thaliana) KCSs were compared. The in planta role of the KCS9 gene, showing higher expression in stem epidermal peels than in stems, was further investigated. The KCS9 gene was ubiquitously expressed in various organs and tissues, including roots, leaves, and stems, including epidermis, silique walls, sepals, the upper portion of the styles, and seed coats, but not in developing embryos. The fluorescent signals of the KCS9::enhanced yellow fluorescent protein construct were merged with those of BrFAD2::monomeric red fluorescent protein, which is an endoplasmic reticulum marker in tobacco (Nicotiana benthamiana) epidermal cells. The kcs9 knockout mutants exhibited a significant reduction in C24 VLCFAs but an accumulation of C20 and C22 VLCFAs in the analysis of membrane and surface lipids. The mutant phenotypes were rescued by the expression of KCS9 under the control of the cauliflower mosaic virus 35S promoter. Taken together, these data demonstrate that KCS9 is involved in the elongation of C22 to C24 fatty acids, which are essential precursors for the biosynthesis of cuticular waxes, aliphatic suberins, and membrane lipids, including sphingolipids and phospholipids. Finally, possible roles of unidentified KCSs are discussed by combining genetic study results and gene expression data from multiple Arabidopsis KCSs.
Dynamic Transcriptomic Profiles between Tomato and a Wild Relative Reflect Distinct Developmental Architectures
Authors: Chitwood Daniel H. , Maloof Julin N. , Sinha Neelima R. 
Published: April 2013

Abstract
Developmental differences between species commonly result from changes in the tissue-specific expression of genes. Clustering algorithms are a powerful means to detect coexpression across tissues in single species but are not often applied to multidimensional data sets, such as gene expression across tissues in multiple species. As next-generation sequencing approaches enable interspecific analyses, methods to visualize and explore such data sets will be required. Here, we analyze a data set comprising gene expression profiles across six different tissue types in domesticated tomato (Solanum lycopersicum) and a wild relative (Solanum pennellii). We find that self-organizing maps are a useful means to analyze interspecies data, as orthologs can be assigned to independent levels of a “super self-organizing map.” We compare various clustering approaches using a principal component analysis in which the expression of orthologous pairs is indicated by two points. We leverage the expression profile differences between orthologs to look at tissue-specific changes in gene expression between species. Clustering based on expression differences between species (rather than absolute expression profiles) yields groups of genes with large tissue-by-species interactions. The changes in expression profiles of genes we observe reflect differences in developmental architecture, such as changes in meristematic activity between S. lycopersicum and S. pennellii. Together, our results offer a suite of data-exploration methods that will be important to visualize and make biological sense of next-generation sequencing experiments designed explicitly to discover tissue-by-species interactions in gene expression data.
ACYL-LIPID DESATURASE2Is Required for Chilling and Freezing Tolerance inArabidopsis
Authors: Chen Mingjie , Thelen Jay J. 
Published: April 2013

AbstractFatty acid desaturation of membrane lipids is a strategy for plants to survive chilling or freezing temperature. To further characterize enzymes involved in this stress response pathway, ACYL-LIPID DESATURASE2 (ADS2; Enzyme Commission 1.14.99) was studied using genetic, cell, and biochemical approaches. ads2 mutant plants appear similar to the wild type under standard growth conditions but display a dwarf and sterile phenotype when grown at 6°C and also show increased sensitivity to freezing temperature. Fatty acid composition analysis demonstrated that ads2 mutant plants at 6°C have reduced levels of 16:1, 16:2, 16:3, and 18:3 and higher levels of 16:0 and 18:0 fatty acids compared with the wild type. Lipid profiling revealed that 34C species of phosphatidylglycerol (PG) and monogalactosyl diacylglycerol (MGDG) content in ads2 mutants were lower and phosphatidic acid, phosphatidylinositol, phosphatidylethanolamine, phosphatidylcholine, lyso-phosphatidylcholine, and phosphatidylserine were higher than the wild type. Subcellular localization of C- and N-terminal enhanced fluorescence fusion proteins indicated that ADS2 localized primarily to the endoplasmic reticulum, although signal was also confirmed in Golgi and plastids. A double mutation with a putative plastid ADS3 paralog exacerbates the growth defects of ads2 mutant plants under low temperature. These observations suggest that ADS2 encodes a 16:0 desaturase of MGDG and PG. We hypothesize that a low temperature–induced shift from the plastid to endoplasmic reticulum pathway for membrane lipid biosynthesis is required for the cold stress response in Arabidopsis thaliana, and ADS2 is essential to adjust the acyl composition of organelle membrane lipid composition in response to cold stress.
Herbivory differentially alters litter dynamics of two functionally contrasted grasses
Authors: Ibanez Sébastien , Bernard Lionel , Coq Sylvain , Moretti Marco , Lavorel Sandra , Gallet Christiane 
Published: April 2013

Summary

Herbivores can have contrasted impacts on litter quality and litter decomposition, through an alteration of leaf chemistry and leaf senescence. Depending on the context, herbivores can induce defensive secondary compounds and thus slow down litter decomposition or accelerate decomposition by short‐cutting nutrient resorption.

Almost nothing is known for grasses, which contain smaller amounts of secondary compounds than forbs and trees. Because grasses span a gradient from exploitative species having a low C : N ratio and induced defences, to conservative species having a high C : N ratio and constitutive defences, we hypothesize that the litter dynamics of functionally contrasted grasses may be differentially altered by herbivores.

In a mesocosm experiment, we assessed the litter decomposition rate of two subalpine grasses, the more exploitative Dactylis glomerata and the conservative Festuca paniculata, in the presence of two grasshopper species, Chorthippus scalaris and Euthystira brachyptera. We hypothesized that decomposition patterns depending on grass species and herbivory could be explained by the C : N ratio and the total phenolic content of fresh, senescent and decomposed leaves.

Herbivory by grasshoppers induced the accumulation of phenolics in the fresh leaves of D. glomerata, but most of these compounds were lost during senescence. The decomposition rate of D. glomerata senescent leaves did not depend on herbivory, phenolics and N content or C : N ratio. In contrast, herbivory did not induce any phenolic accumulation in the grazed leaves of F. paniculata, but during senescence, phenolics disappeared in greater proportions in grazed leaves than in ungrazed leaves, probably due to the physical alteration of grazed leaves. Herbivory slowed down the decomposition rate of F. paniculata, which was correlated to the phenolic concentration of senescent leaves, but not to the C : N ratio or N content.

Herbivory by grasshoppers differentially altered the litter decomposition rate of the two functionally contrasted grasses, having no effect on D. glomerata and slowing down F. paniculata. Thus, the combination of chemical and physical modifications of leaves by grazing and their interaction with grass traits may have either accelerating or decelerating effects on litter decomposition, with potentially complex outcomes at the ecosystem level.
Inadvertent consequences of fishing: the case of the sex‐changing shrimp
Authors: Côté Isabelle M. 
Published: April 2013

The Hokkai shrimp Pandalus latirostris starts life as a male, but eventually turns into a female given the right size and social conditions. The traps used in the fishery targeting this species selectively retain the larger females, leaving a severely male‐biased sex ratio in nature and social conditions that bear no resemblance to those that prompted (or prevented) sex change. Photo: Susumu ChibaimageThe Hokkai shrimp Pandalus latirostris starts life as a male, but eventually turns into a female given the right size and social conditions. The traps used in the fishery targeting this species selectively retain the larger females, leaving a severely male‐biased sex ratio in nature and social conditions that bear no resemblance to those that prompted (or prevented) sex change. Photo: Susumu Chiba

Chiba, S., Yoshino, K., Kanaiwa, M., Kawajiri, T. & Goshima, S. (2013) . Journal of Animal Ecology, 82, 631–640.
Fishing can have many unintended consequences. In this issue, Chiba et al. (2013) demonstrate that size‐selective harvesting of a sex‐changing shrimp effectively voids their normally adaptive adjustments to population sex ratio. The shrimp's ‘decision’ to change sex depends largely on the relative abundance of mature males and females in early summer, before fishing begins. However, fishing traps selectively retain females, leading to heavily male‐biased sex ratios at the onset of autumn breeding that are different from the ratios that influenced sex‐change decisions. Although this phenomenon is not yet expressed in catch trends, maladaptive sex‐change decisions could ultimately affect population productivity and persistence.
Competent in evidence‐based practice (EBP): validation of a measurement tool that measures EBP self‐efficacy and task value in speech–language therapy students
Authors: Spek B. , Wieringa‐de Waard M. , Lucas C. , van Dijk N. 
Published: April 2013

AbstractBackgroundWorldwide speech–language therapy (SLT) students are educated in evidence‐based practice (EBP). For students to use EBP in their future day‐to‐day clinical practice, they must value EBP as positive and must feel confident in using it. For curricula developers it is therefore important to know the impact their teaching has on these aspects of students’ motivational beliefs.AimsTo develop and validate a measurement tool to assess EBP task value and self‐efficacy in SLT students.Methods & ProceduresA 20‐item questionnaire was developed based on a review of the literature and an additional group interview with speech–language therapists. Face validity of the questionnaire was established using a Delphi panel consisting of six EBP lecturers. Dutch bachelor SLT students (n = 149) with a different level of EBP knowledge and skills filled in the newly developed questionnaire. Reliability (internal consistency) was assessed using Cronbach's alpha and internal validity using a principal component analysis (PCA). Construct validity was assessed by comparing the bachelor SLT student scores with a group of m students (n = 15) who were highly experienced in EBP.Outcomes & ResultsThe PCA showed that the questionnaire consists of two components, representing EBP task value and self‐efficacy, both with good reliability (Cronbach's α = 0.83 and 0.79, respectively). The hypothesis that master's students would score significantly higher on both components than bachelor SLT students was met.Conclusions & ImplicationsThe study provides evidence on the internal consistency and construct validity of this questionnaire to evaluate EBP task value and self‐efficacy in SLT students. As is common with new measures, more research is needed to evaluate further its psychometric properties.