bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational prediction and analysis of the DR6–NAPP interaction
Authors: Ponomarev Sergei Y. , Audie Joseph 
Published: December 2010

AbstractAlzheimer's disease (AD) is a progressive neurodegenerative disorder that involves a devastating clinical course and that lacks an effective treatment. A biochemical model for neuronal development, recently proposed by Nikolaev et al., that may also have implications for AD, hinges on a novel protein–protein interaction between the death cell receptor 6 (DR6) ectodomain and an N‐terminal fragment of amyloid precursor protein (NAPP), specifically, the growth factor‐like domain of NAPP (GFD NAPP). Given all of this, we used a pure computational work‐flow to dock a binding competent homology model of the DR6 ectodomain to a binding competent crystal structure of GFD NAPP. The DR6 homology model was built according to a template supplied by the neurotrophin p75 receptor. The best docked model was selected according to an empirical estimate of the binding affinity and represents a high quality model of probable structural accuracy, especially with respect to the residue‐level contribution of GFD NAPP. The final model was tested and verified against a variety of biophysical and theoretical data sets. Particularly, worth noting is the excellent observed agreement between the theoretically calculated DR6–GFD NAPP binding free energy and the experimental quantity. The model is used to provide a satisfying structural and energetic interpretation of DR6–GFD NAPP binding and to suggest the possibility of and a mechanism for spontaneous apoptosis. The evidence suggests that the DR6–NAPP model proposed here is of probable accuracy and that it will prove useful in future studies, modeling work, and structure‐based AD drug design. Proteins 2011. © 2010 Wiley‐Liss, Inc.
A natural and readily available crowding agent: NMR studies of proteins in hen egg white
Authors: Martorell Gabriel , Adrover Miquel , Kelly Geoff , Temussi Piero Andrea , Pastore Annalisa 
Published: December 2010

AbstractIn vitro studies of biological macromolecules are usually performed in dilute, buffered solutions containing one or just a few different biological macromolecules. Under these conditions, the interactions among molecules are diffusion limited. On the contrary, in living systems, macromolecules of a given type are surrounded by many others, at very high total concentrations. In the last few years, there has been an increasing effort to study biological macromolecules directly in natural crowded environments, as in intact bacterial cells or by mimicking natural crowding by adding proteins, polysaccharides, or even synthetic polymers. Here, we propose the use of hen egg white (HEW) as a simple natural medium, with all features of the media of crowded cells, that could be used by any researcher without difficulty and inexpensively. We present a study of the stability and dynamics behavior of model proteins in HEW, chosen as a prototypical, readily accessible natural medium that can mimic cytosol. We show that two typical globular proteins, dissolved in HEW, give NMR spectra very similar to those obtained in dilute buffers, although dynamic parameters are clearly affected by the crowded medium. The thermal stability of one of these proteins, measured in a range comprising both heat and cold denaturation, is also similar to that in buffer. Our data open new possibilities to the study of proteins in natural crowded media. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Biological characterization of sulfoxaflor, a novel insecticide
Authors: Babcock Jonathan M , Gerwick Clifford B , Huang Jim X , Loso Michael R , Nakamura Genta , Nolting Steven P , Rogers Richard B , Sparks Thomas C , Thomas James , Watson Gerald B , Zhu Yuanming 
Published: December 2010

AbstractBACKGROUND: The commercialization of new insecticides is important for ensuring that multiple effective product choices are available. In particular, new insecticides that exhibit high potency and lack insecticidal cross‐resistance are particularly useful in insecticide resistance management (IRM) programs. Sulfoxaflor possesses these characteristics and is the first compound under development from the novel sulfoxamine class of insecticides.RESULTS: In the laboratory, sulfoxaflor demonstrated high levels of insecticidal potency against a broad range of sap‐feeding insect species. The potency of sulfoxaflor was comparable with that of commercial products, including neonicotinoids, for the control of a wide range of aphids, whiteflies (Homoptera) and true bugs (Heteroptera). Sulfoxaflor performed equally well in the laboratory against both insecticide‐susceptible and insecticide‐resistant populations of sweetpotato whitefly, Bemisia tabaci Gennadius, and brown planthopper, Nilaparvata lugens (Stål), including populations resistant to the neonicotinoid insecticide imidacloprid. These laboratory efficacy trends were confirmed in field trials from multiple geographies and crops, and in populations of insects with histories of repeated exposure to insecticides. In particular, a sulfoxaflor use rate of 25 g ha−1 against cotton aphid (Aphis gossypii Glover) outperformed acetamiprid (25 g ha−1) and dicrotophos (560 g ha−1). Sulfoxaflor (50 g ha−1) provided a control of sweetpotato whitefly equivalent to that of acetamiprid (75 g ha−1) and imidacloprid (50 g ha−1) and better than that of thiamethoxam (50 g ha−1).CONCLUSION: The novel chemistry of sulfoxaflor, its unique biological spectrum of activity and its lack of cross‐resistance highlight the potential of sulfoxaflor as an important new tool for the control of sap‐feeding insect pests. Copyright © 2010 Society of Chemical Industry
Low pesticide rates may hasten the evolution of resistance by increasing mutation frequencies
Authors: Gressel Jonathan 
Published: December 2010

AbstractAt very low pesticide rates, a certain low proportion of pests may receive a sublethal dose, are highly stressed by the pesticide and yet survive. Stress is a general enhancer of mutation rates. Thus, the survivors are likely to have more than normal mutations, which might include mutations leading to pesticide resistance, both for multifactorial (polygenic, gene amplification, sequential allelic mutations) and for major gene resistance. Management strategies should consider how to eliminate the subpopulation of pests with the high mutation rates, but the best strategy is probably to avoid too low application rates of pesticides from the outset. Copyright © 2010 Society of Chemical Industry
Light‐induced degradation in compensated n‐type Czochralski silicon solar cells
Authors: Schutz‐Kuchly Thomas , Dubois Sébastien , Veirman Jordi , Veschetti Yannick , Heslinga Dick , Palais Olivier 
Published: December 2010

AbstractThis study focuses on the evolution under illumination of the electrical performances of solar cells made with n‐type boron–phosphorus compensated Czochralski silicon. First, we show via carrier lifetime measurements that this material is sensitive to light‐induced degradation (LID) effects due to the formation of BOi2 complexes. Solar cells were then processed with this compensated material. The cells performances were found to be dependent on the position of the wafer along the ingot height.This dependence is due to carrier lifetime variations along the ingot height and is not directly linked with the differences in concentration between boron and phosphorus. LID experiments were then performed on the same cells. Unlike what was suggested from previous studies, we highlighted a weak decrease of the cell performances under illumination, consistent with the electrical characterizations at the wafer level. These degradations have been quantified and linked with the chemical composition of the material.
A universal matrix‐assisted laser desorption/ionization cleavable cross‐linker for protein structure analysis
Authors: Müller Mathias Q. , Zeiser Johannes J. , Dreiocker Frank , Pich Andreas , Schäfer Mathias , Sinz Andrea 
Published: December 2010

AbstractThe concept of protein cross‐linking in combination with mass spectrometry holds great promise to derive structural information on protein conformation and protein‐protein interactions. We recently presented a dissociative amine‐reactive cross‐linker (NHS‐BuUrBu‐NHS) that is shown herein to be universally applicable to protein structure analysis under matrix‐assisted laser desorption/ionization tandem mass spectrometric (MALDI‐MS/MS) conditions, based on the examples of the peptides substance P, luteinizing hormone releasing hormone (LHRH), and the 32‐kDa ligand‐binding domain of peroxisome proliferator‐activated receptor alpha (PPARα). The characteristic fragment ion patterns and constant neutral losses of the cross‐linker greatly simplify the identification of different cross‐linked species from complex mixtures and drastically reduce the potential of identifying false‐positive cross‐links. Therefore, this cross‐linker holds an enormous potential for deriving structural information of proteins and protein complexes in a highly automated fashion. Copyright © 2010 John Wiley & Sons, Ltd.
Lyso‐form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids
Authors: Hou Weimin , Zhou Hu , Khalil Maroun Bou , Seebun Deeptee , Bennett Steffany A. L. , Figeys Daniel 
Published: December 2010

AbstractIn this work we report the development of a novel methodology for the determination of stereospecificity of diacyl glycerophospholipids, including glycerophosphatidic acids (PA), glycerophosphoserines (PS), glycerophosphoglycerols (PG), glycerophosphoinositols (PI), and glycerophosphoethanolamines (PE), which can be conventionally ionized in negative ion mode. This methodology uses MS2 recorded on a hybrid quadrupole time‐of‐flight mass spectrometer to determine the stereospecificity of diacyl glycerophospholipids based on the lyso‐form fragment ions, attributed to the neutral loss of fatty acyl moieties. The fragmentation patterns of a variety of diacyl glycerophospholipid standards were first fully examined over a wide range of collision energy. We observed that lyso‐form fragment ions corresponding to the neutral loss of fatty acyl moieties attached to the sn2 position as free fatty acids ([M–Sn2]−) and as ketenes ([M–(Sn2‐H2O)]−) exhibited consistently higher intensity than their counterpart ions due to the neutral loss of fatty acyl moieties attached to the sn1 position ([M–Sn1]− and [M–(Sn1‐H2O)]−). Therefore, we concluded that an empirical fragmentation rule can be used to precisely determine the stereospecificity of diacyl glycerophospholipids, primarily on the basis of relative abundance of the lyso‐form fragment ions. We then examined the product ion spectra of diacyl glycerophospholipids recorded from lipid extracts of rat hepatoma cells, where the stereospecific information of these lipids was conclusively determined. Combining the novel methodology reported in this work with the currently widely practiced mass spectrometric techniques such as multiple precursor ion scans (MPIS), fatty acyl scans (FAS), and multidimensional mass spectrometry based shotgun lipidomics (MDMS‐SL), should enable a reliable and convenient platform for comprehensive glycerophospholipid profiling. Copyright © 2010 John Wiley & Sons, Ltd.
Detergent enhancement of on‐tissue protein analysis by matrix‐assisted laser desorption/ionization imaging mass spectrometry
Authors: Mainini Veronica , Angel Peggi M. , Magni Fulvio , Caprioli Richard M. 
Published: December 2010

AbstractMatrix‐Assisted Laser Desorption/Ionization (MALDI) Imaging Mass Spectrometry (IMS) is a molecular technology that allows simultaneous investigation of the content and spatial distribution of molecules within tissue. In this work, we examine different classes of detergents, the anionic sodium dodecyl sulfate (SDS), the nonionic detergents Triton X‐100, Tween 20 and Tween 80, and the zwitterionic 3‐[(3‐cholamidopropyl)dimethylammonio]‐1‐propanesulfonate (CHAPS) for use in MALDI IMS of analytes above m/z 4000. These detergents were found to be compatible with MALDI MS and did not cause signal suppression relative to non‐detergent applications and did not produce interfering background signals. In general, these detergents enhanced signal acquisition within the mass range m/z 4–40 000. Adding detergents into the matrix was comparable with the separate application of detergent and matrix. Evaluation of spectra collected from organ‐specific regions of a whole mouse pup section showed that different detergents perform optimally with different organs, indicating that detergent selection should be optimized on the specific tissue for maximum gain. These data show the utility of detergents towards enhancement of protein signals for on‐tissue MALDI IMS analysis. Copyright © 2010 John Wiley & Sons, Ltd.
Objectives and Indicators in Sustainable Development Strategies: Similarities and Variances across Europe
Authors: Steurer Reinhard , Hametner Markus 
Published: December 2010

AbstractEurope has positioned itself as a progressive global player in environmental and sustainable development (SD) policies, and SD strategies should play a key role in better coordinating policies horizontally across sectors and vertically across levels of government. This paper gives an overview of the objectives and indicators employed in 24 national SD strategies across Europe, covering five different welfare‐state models. After highlighting some structural features of SD strategies the paper explores how coherently they address environmental and social policies, measured against the objectives and indicators of the EU SD strategy. It is shown that environmental objectives and indicators are more coherent than social ones. Regarding the five socioeconomic models it was found that the significant variance regarding social policy objectives and indicators is mainly because some SD strategies from Mediterranean countries ignore this dimension of SD. The paper concludes that SD strategies in Europe (in particular the EU SD strategy) unfold only a fraction of their potential to better coordinate policies vertically across different levels of government. As this conclusion is confirmed by more qualitative research approaches, the European governance architecture for sustainable development is questioned in fundamental ways. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Upregulation of liprin‐α1 protein in the temporal neocortex of intractable epileptic patients and experimental rats
Authors: Yin Huan , Wang Linyuan , Xiao Fei , Huang Zuchun , Huang Yuanyuan , Zhou Chunlei , Han Yanbing , Tao Shuxin , Yang Hui , Wang Xuefeng 
Published: December 2010

AbstractIntractable epilepsy (IE) patients have synaptic dysfunction. However, the exact mechanism of synaptic function needs further elucidation. The aim of this study was to use immunohistochemistry, immunofluorescence, and Western blotting to investigate the expression of the Liprin‐α1 protein, one of the synapse‐associated proteins, in human IE brain tissues and experimental rats and to discuss the possible role of Liprin‐α1 in IE. We selected 30 temporal neocortical tissue samples from patients with intractable temporal lobe epilepsy (TLE) and 10 histologically normal temporal lobes from controls. Fifty‐six Sprague‐Dawley rats were divided randomly into seven groups; one control group and six groups with epilepsy induced by lithium‐pilocarpine administration. Temporal lobe tissues were taken from controls and from rats at 1, 3, 7, 14, 30, and 60 days postseizure. Liprin‐α1 was mainly expressed in neurons of human controls and TLE patients and was significantly higher in TLE patients than in controls. Liprin‐α1 was also expressed in neurons of control and experimental rats and it was significantly higher in experimental rats than in the control group. The expression of Liprin‐α1 in animals in the experimental group gradually increased from Days 1 to 30 postseizure induction and reached a stable level when spontaneous recurrent seizures (SRS) appeared. These results suggest that an increased expression of Liprin‐α1 in the brain may be associated with human IE. Synapse, 2011. © 2011 Wiley‐Liss, Inc.
The effect of size and density on the mean retention time of particles in the reticulorumen of cattle (Bos primigenius f. taurus), muskoxen (Ovibos moschatus) and moose (Alces alces)
Authors: Clauss Marcus , Lechner Isabel , Barboza Perry , Collins William , Tervoort Theo A. , Südekum Karl-Heinz , Codron Daryl , Hummel Jürgen 
Published: December 2010

Particle passage from the reticulorumen (RR) depends on particle density and size. Forage particle density and size are related and change over time in the RR. Particle density mainly influences sorting in the reticulum, whereas particle size influences particle retention in the fibre mat of stratified rumen contents (‘filter-bed’ effect). We investigated these effects independently, by inserting plastic particles of different sizes (1, 10 and 20 mm) and densities (1·03, 1·20 and 1·44 mg/ml) in the RR of cattle (Bos primigenius f. taurus) as a pilot study, and of muskoxen (Ovibos moschatus; n 4) and moose (Alces alces; n 2) both fed two diets (browse and grass). Faeces were analysed for plastic residues for 13 d after dosing to calculate mean retention times (MRT). The results confirmed previous findings of differences in absolute MRT between species. Comparing muskoxen with moose, there was no difference in the effect of particle density on the MRT between species but particle size had a more pronounced effect on the MRT in muskoxen than in moose. This indicated a stronger ‘filter-bed effect’ in muskoxen, in accord with the reports of stratified RR contents in this species v. the absence of RR content stratification in moose. Low-density particles were retained longer in both species fed on grass diets, indicating a contribution of forage type to the ‘filter-bed effect’. The results indicate that retention based on particle size may differ between ruminant species, depending on the presence of a fibre mat in the RR, whereas the density-dependent mechanism of sedimentation in the RR is rather constant across species.
MADS-box genes of maize: frequent targets of selection during domestication
Authors: ZHAO QIONG , WEBER ALLISON L. , MCMULLEN MICHAEL D. , GUILL KATHERINE , DOEBLEY JOHN 
Published: December 2010

SummaryMADS-box genes encode transcription factors that are key regulators of plant inflorescence and flower development. We examined DNA sequence variation in 32 maize MADS-box genes and 32 randomly chosen maize loci and investigated their involvement in maize domestication and improvement. Using neutrality tests and a test based on coalescent simulation of a bottleneck model, we identified eight MADS-box genes as putative targets of the artificial selection associated with domestication. According to neutrality tests, one additional MADS-box gene appears to have been under selection during modern agricultural improvement of maize. For random loci, two genes were indicated as targets of selection during domestication and four additional genes were indicated to be candidate-selected loci for maize improvement. These results suggest that MADS-box genes were more frequent targets of selection during domestication than genes chosen at random from the genome.
Trauma, identity and mental health in UK military veterans
Authors: Brewin C. R. , Garnett R. , Andrews B. 
Published: December 2010

BackgroundMilitary service can lead to profound changes in identity, both in servicemen's perception of themselves and in their relationship to the world, but the significance of these changes for psychopathology is unclear. We investigated whether the extent and valence of identity change was related to the degree of military trauma exposure or to post-traumatic stress disorder (PTSD) and suicide attempts. We further sought to describe the nature of such changes using qualitative analysis.MethodA total of 153 veterans in receipt of a war pension for PTSD or physical disability were identified. Interviews established retrospectively DSM-IV diagnoses of PTSD and reports of suicidal ideation or behaviour since enlistment were examined.ResultsTrauma exposure alone was unrelated to any measure of identity change. By contrast, PTSD was associated with a relationship to the world that had changed in a negative direction. It was also associated with a changed perception of self, which could be either positive or negative. After controlling for trauma exposure and PTSD, suicidal behaviours were associated with more negative perceptions of the world. These perceptions of the world included disillusionment about human nature and a more specific rejection of civilian life.ConclusionsPTSD and suicidal behaviours in veterans seem not to be associated with significantly more negative views of the self but rather with more alienation from civilian life. This has serious consequences for engaging veterans in National Health Service (NHS) mental health services and for the provision of effective treatment.
Clinical Study and Molecular Genetic Analyses of Malaysian GEFS+ Patients
Authors: Tan Emmilia , Abdul Razak Salmi , Mohamed Yusoff Abdul Aziz , Abdullah Jafri Malin 
Published: December 2010

AbstractGeneralized epilepsy with febrile seizure plus (GEFS+) is a familial epilepsy syndrome characterized by phenotypic and genetic heterogeneity. Neuronal voltage gated sodium channel α-1 subunit gene, SCN1A is the most clinically relevant and associated with GEFS+. The objective was to study the clinical presentations of GEFS+ and analyze the SCN1A gene associated with Malaysian GEFS+ patients. Blood samples were collected from 30 unrelated GEFS+ patients and genomic DNA was obtained using the Qiagen DNA Blood Mini Kit following the manufacturer’s instructions. The 26 exons of SCN1A genes were analyzed by polymerase chain reaction (PCR) and denaturing high performance liquid chromatography (DHPLC). The aberrant profile peak from DHPLC analysis was confirmed by direct sequencing. The spectrum of phenotypes observed in Malaysian GEFS+ patients included febrile seizure (FS), febrile seizure plus (FS+) and afebrile generalized tonic clonic seizure (AGTCS). Direct sequencing of SCN1A revealed seven sequence variants including one novel SCN1A mutation that was associated with GEFS+. This suggests that mutation of the SCN1A gene is one of the prevalent causes of GEFS+ in Malaysia.
PE-Assembler: de novo assembler using short paired-end reads
Authors: Ariyaratne Pramila Nuwantha , Sung Wing-Kin 
Published: December 2010

Abstract
Motivation: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.
Result: We present a method that eschews the traditional graph-based approach in favor of a simple 3′ extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods.
Availability: The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request.
Contact: ksung@comp.nus.edu.sg; sungk@gis.a-star.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.