bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of additive isotropic site potential for exchange-repulsion energy, based on intermolecular perturbation theory
Authors: Yokogawa Daisuke , Sato Hirofumi , Gusarov Sergey , Kovalenko Andriy 
Published: December 2009

We have developed an additive spherical site potential for exchange-repulsion energy by applying the local density approximation in Hilbert space, the local-site approximation, and the s-type auxiliary basis set to the equation derived from intermolecular perturbation theory. The method efficiently addresses the decomposition of molecular interactions derived from quantum chemistry into additive spherical site potentials, required as force field input in a statistical-mechanical, reference interaction site model (RISM and 3D-RISM), molecular theory of solvation. The present method reproduces the exchange-repulsion energy between simple molecules obtained from quantum chemical calculations.
STREAM
Authors: Caspersen Michael E. , Kolling Michael 
Published: December 2009

Programming is recognized as one of seven grand challenges in computing education. Decades of research have shown that the major problems novices experience are composition-based---they may know what the individual programming language constructs are, but they do not know how to put them together. Despite this fact, textbooks, educational practice, and programming education research hardly address the issue of teaching the skills needed for systematic development of programs.
We provide a conceptual framework for incremental program development, called Stepwise Improvement, which unifies best practice in modern software development such as test-driven development and refactoring with the prevailing perspective of programming methodology, stepwise refinement. The conceptual framework enables well-defined characterizations of incremental program development.
We utilize the conceptual framework to derive a programming process, STREAM, designed specifically for novices. STREAM is a carefully down-scaled version of a full and rich agile software engineering process particularly suited for novices learning object-oriented programming. In using it we hope to achieve two things: to help novice programmers learn faster and better while at the same time laying the foundation for a more thorough treatment of more advanced aspects of software engineering. In this article, two examples demonstrate the application of STREAM.
The STREAM process has been taught in the introductory programming courses at our universities for the past three years and the results are very encouraging. We report on a small, preliminary study evaluating the learning outcome of teaching STREAM. The study indicates a positive effect on the development of students’ process competences.
p38 mitogen-activated protein kinase activation during platelet storage: consequences for platelet recovery and hemostatic function in vivo
Authors: Canault Matthias , Duerschmied Daniel , Brill Alexander , Stefanini Lucia , Schatzberg Daphne , Cifuni Stephen M. , Bergmeier Wolfgang , Wagner Denisa D. 
Published: December 2009

AbstractPlatelets undergo several modifications during storage that reduce their posttransfusion survival and functionality. One important feature of these changes, which are known as platelet storage lesion, is the shedding of the surface glycoproteins GPIb-α and GPV. We recently demonstrated that tumor necrosis factor-α converting enzyme (TACE/ADAM17) mediates mitochondrial injury-induced shedding of adhesion receptors and that TACE activity correlates with reduced posttransfusion survival of these cells. We now confirm that TACE mediates receptor shedding and clearance of platelets stored for 16 hours at 37°C or 22°C. We further demonstrate that both storage and mitochondrial injury lead to the phosphorylation of p38 mitogen-activated kinase (MAPK) in platelets and that TACE-mediated receptor shedding from mouse and human platelets requires p38 MAP kinase signaling. Protein kinase C, extracellular regulated-signal kinase MAPK, and caspases were not involved in TACE activation. Both inhibition of p38 MAPK and inactivation of TACE during platelet storage led to a markedly improved posttransfusion recovery and hemostatic function of platelets in mice. p38 MAPK inhibitors had only minor effects on the aggregation of fresh platelets under static or flow conditions in vitro. In summary, our data suggest that inhibition of p38 MAPK or TACE during storage may significantly improve the quality of stored platelets.
Hydroxychloroquine protects the annexin A5 anticoagulant shield from disruption by antiphospholipid antibodies: evidence for a novel effect for an old antimalarial drug
Authors: Rand Jacob H. , Wu Xiao-Xuan , Quinn Anthony S. , Ashton Anthony W. , Chen Pojen P. , Hathcock James J. , Andree Harry A. M. , Taatjes Douglas J. 
Published: December 2009

AbstractAnnexin A5 (AnxA5) is a potent anticoagulant protein that crystallizes over phospholipid bilayers (PLBs), blocking their availability for coagulation reactions. Antiphospholipid antibodies disrupt AnxA5 binding, thereby accelerating coagulation reactions. This disruption may contribute to thrombosis and miscarriages in the antiphospholipid syndrome (APS). We investigated whether the antimalarial drug, hydroxychloroquine (HCQ), might affect this prothrombotic mechanism. Binding of AnxA5 to PLBs was measured with labeled AnxA5 and also imaged with atomic force microscopy. Immunoglobulin G levels, AnxA5, and plasma coagulation times were measured on cultured human umbilical vein endothelial cells and a syncytialized trophoblast cell line. AnxA5 anticoagulant activities of APS patient plasmas were also determined. HCQ reversed the effect of antiphospholipid antibodies on AnxA5 and restored AnxA5 binding to PLBs, an effect corroborated by atomic force microscopy. Similar reversals of antiphospholipid-induced abnormalities were measured on the surfaces of human umbilical vein endothelial cells and syncytialized trophoblast cell lines, wherein HCQ reduced the binding of antiphospholipid antibodies, increased cell-surface AnxA5 concentrations, and prolonged plasma coagulation to control levels. In addition, HCQ increased the AnxA5 anticoagulant activities of APS patient plasmas. In conclusion, HCQ reversed antiphospholipid-mediated disruptions of AnxA5 on PLBs and cultured cells, and in APS patient plasmas. These results support the concept of novel therapeutic approaches that address specific APS disease mechanisms.
Secondhand smoke inhibits both Cl- and K+ conductances in normal human bronchial epithelial cells
Authors: Savitski Amy N , Mesaros Clementina , Blair Ian A , Cohen Noam A , Kreindler James L 
Published: December 2009

AbstractSecondhand smoke (SHS) exposure is an independent risk factor for asthma, rhinosinusitis, and more severe respiratory tract infections in children and adults. Impaired mucociliary clearance with subsequent mucus retention contributes to the pathophysiology of each of these diseases, suggesting that altered epithelial salt and water transport may play an etiological role. To test the hypothesis that SHS would alter epithelial ion transport, we designed a system forin vitroexposure of mature, well-differentiated human bronchial epithelial cells to SHS. We show that SHS exposure inhibits cAMP-stimulated, bumetanide-sensitive anion secretion by 25 to 40% in a time-dependent fashion in these cells. Increasing the amount of carbon monoxide to 100 ppm from 5 ppm did not increase the amount of inhibition, and filtering SHS reduced inhibition significantly. It was determined that SHS inhibited cAMP-dependent apical membrane chloride conductance by 25% and Ba2+-sensitive basolateral membrane potassium conductance by 50%. These data confirm previous findings that cigarette smoke inhibits chloride secretion in a novel model of smoke exposure designed to mimic SHS exposure. They also extend previous findings to demonstrate an effect on basolateral K+conductance. Therefore, pharmacological agents that increase either apical membrane chloride conductance or basolateral membrane potassium conductance might be of therapeutic benefit in patients with diseases related to SHS exposure.
The zebrafish prospero homolog prox1 is required for mechanosensory hair cell differentiation and functionality in the lateral line
Authors: Pistocchi Anna , Feijóo Carmen G , Cabrera Pablo , Villablanca Eduardo J , Allende Miguel L , Cotelli Franco 
Published: December 2009

AbstractBackgroundThe lateral line system in zebrafish is composed of a series of organs called neuromasts, which are distributed over the body surface. Neuromasts contain clusters of hair cells, surrounded by accessory cells.ResultsIn this report we describe zebrafishprox1mRNA expression in the migrating primordium and in the neuromasts of the posterior lateral line. Furthermore, using an antibody against Prox1 we characterize expression of the protein in different cell types within neuromasts, and we show distribution among the supporting cells and hair cells.ConclusionFunctional analysis using antisense morpholinos indicates thatprox1activity is crucial for the hair cells to differentiate properly and acquire functionality, while having no role in development of other cell types in neuromasts.
Haplotypes of the porcine peroxisome proliferator-activated receptor delta gene are associated with backfat thickness
Authors: Meidtner Karina , Schwarzenbacher Hermann , Scharfe Maren , Severitt Simone , Blöcker Helmut , Fries Ruedi 
Published: December 2009

Abstract

Background
Peroxisome proliferator-activated receptor delta belongs to the nuclear receptor superfamily of ligand-inducible transcription factors. It is a key regulator of lipid metabolism. The peroxisome proliferator-activated receptor delta gene (PPARD) has been assigned to a region on porcine chromosome 7, which harbours a quantitative trait locus for backfat. Thus, PPARD is considered a functional and positional candidate gene for backfat thickness. The purpose of this study was to test this candidate gene hypothesis in a cross of breeds that were highly divergent in lipid deposition characteristics.

Results
Screening for genetic variation in porcine PPARD revealed only silent mutations. Nevertheless, significant associations between PPARD haplotypes and backfat thickness were observed in the F2 generation of the Mangalitsa × Piétrain cross as well as a commercial German Landrace population. Haplotype 5 is associated with increased backfat in F2 Mangalitsa × Piétrain pigs, whereas haplotype 4 is associated with lower backfat thickness in the German Landrace population. Haplotype 4 and 5 carry the same alleles at all but one SNP. Interestingly, the opposite effects of PPARD haplotypes 4 and 5 on backfat thickness are reflected by opposite effects of these two haplotypes on PPAR-δ mRNA levels. Haplotype 4 significantly increases PPAR-δ mRNA levels, whereas haplotype 5 decreases mRNA levels of PPAR-δ.

Conclusion
This study provides evidence for an association between PPARD and backfat thickness. The association is substantiated by mRNA quantification. Further studies are required to clarify, whether the observed associations are caused by PPARD or are the result of linkage disequilibrium with a causal variant in a neighbouring gene.
Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey
Authors: Seidl Verena , Song Lifu , Lindquist Erika , Gruber Sabine , Koptchinskiy Alexeji , Zeilinger Susanne , Schmoll Monika , Martínez Pedro , Sun Jibin , Grigoriev Igor , Herrera-Estrella Alfredo , Baker Scott E , Kubicek Christian P 
Published: December 2009

AbstractBackgroundCombating the action of plant pathogenic microorganisms by mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since two decades. The fungal genusTrichodermaincludes a high number of taxa which are able to recognize, combat and finally besiege and kill their prey. Only fragments of the biochemical processes related to this ability have been uncovered so far, however.ResultsWe analyzed genome-wide gene expression changes during the begin of physical contact betweenTrichoderma atrovirideand two plant pathogensBotrytis cinereaandRhizoctonia solani, and compared with gene expression patterns of mycelial and conidiating cultures, respectively. About 3000 ESTs, representing about 900 genes, were obtained from each of these three growth conditions. 66 genes, represented by 442 ESTs, were specifically and significantly overexpressed during onset of mycoparasitism, and the expression of a subset thereof was verified by expression analysis. The upregulated genes comprised 18 KOG groups, but were most abundant from the groups representing posttranslational processing, and amino acid metabolism, and included components of the stress response, reaction to nitrogen shortage, signal transduction and lipid catabolism. Metabolic network analysis confirmed the upregulation of the genes for amino acid biosynthesis and of those involved in the catabolism of lipids and aminosugars.ConclusionThe analysis of the genes overexpressed during the onset of mycoparasitism inT. atroviridehas revealed that the fungus reacts to this condition with several previously undetected physiological reactions. These data enable a new and more comprehensive interpretation of the physiology of mycoparasitism, and will aid in the selection of traits for improvement of biocontrol strains by recombinant techniques.
Novel Tn4371-ICE like element in Ralstonia pickettiiand Genome mining for comparative elements
Authors: Ryan Michael P , Pembroke J Tony , Adley Catherine C 
Published: November 2009

Abstract

Background
Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements.
A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element.

Results
Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type.

Conclusion
All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.
Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Authors: Yuan JF , Zhang SJ , Jafer O , Furlong RA , Chausiaux OE , Sargent CA , Zhang GH , Affara NA 
Published: December 2009

Abstract

Background
Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult.

Results
In this report, we have analyzed native host (piglets) gene expression changes in response to acute pseudorabies virus infection of the brain and lung using a printed human oligonucleotide gene set from Illumina. A total of 210 and 1130 out of 23,000 transcript probes displayed differential expression respectively in the brain and lung in piglets after PRV infection (p-value < 0.01), with most genes displaying up-regulation. Biological process and pathways analysis showed that most of the up-regulated genes are involved in cell differentiation, neurodegenerative disorders, the nervous system and immune responses in the infected brain whereas apoptosis, cell cycle control, and the mTOR signaling pathway genes were prevalent in the infected lung. Additionally, a number of differentially expressed genes were found to map in or close to quantitative trait loci for resistance/susceptibility to pseudorabies virus in piglets.

Conclusion
This is the first comprehensive analysis of the global transcriptional response of the native host to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to be of interest for the further study and understanding of host viral gene interactions.
Non-receptor tyrosine kinase Src is required for ischemia-stimulated neuronal cell proliferation via Raf/ERK/CREB activation in the dentate gyrus
Authors: Tian He-Ping , Huang Bao-Sheng , Zhao Jie , Hu Xiao-Han , Guo Jun , Li Li-Xin 
Published: December 2009

Abstract

Background
Neurogenesis in the adult mammalian hippocampus may contribute to repairing the brain after injury. However, Molecular mechanisms that regulate neuronal cell proliferation in the dentate gyrus (DG) following ischemic stroke insult are poorly understood. This study was designed to investigate the potential regulatory capacity of non-receptor tyrosine kinase Src on ischemia-stimulated cell proliferation in the adult DG and its underlying mechanism.

Results
Src kinase activated continuously in the DG 24 h and 72 h after transient global ischemia, while SU6656, the Src kinase inhibitor significantly decreased the number of bromodeoxyuridine (BrdU) labeling-positive cells of rats 7 days after cerebral ischemia in the DG, as well as down-regulated Raf phosphorylation at Tyr(340/341) site, and its down-stream signaling molecules ERK and CREB expression followed by 24 h and 72 h of reperfusion, suggesting a role of Src kinase as an enhancer on neuronal cell proliferation in the DG via modifying the Raf/ERK/CREB cascade. This hypothesis is supported by further findings that U0126, the ERK inhibitor, induced a reduction of adult hippocampal progenitor cells in DG after cerebral ischemia and down-regulated phospho-ERK and phospho-CREB expression, but no effect was detected on the activities of Src and Raf.

Conclusion
Src kinase increase numbers of newborn neuronal cells in the DG via the activation of Raf/ERK/CREB signaling cascade after cerebral ischemia.
Coding of shape from shading in area V4 of the macaque monkey
Authors: Arcizet Fabrice , Jouffrais Christophe , Girard Pascal 
Published: December 2009

AbstractBackgroundThe shading of an object provides an important cue for recognition, especially for determining its 3D shape. However, neuronal mechanisms that allow the recovery of 3D shape from shading are poorly understood. The aim of our study was to determine the neuronal basis of 3D shape from shading coding in area V4 of the awake macaque monkey.ResultsWe recorded the responses of V4 cells to stimuli presented parafoveally while the monkeys fixated a central spot. We used a set of stimuli made of 8 different 3D shapes illuminated from 4 directions (from above, the left, the right and below) and different 2D controls for each stimulus. The results show that V4 neurons present a broad selectivity to 3D shape and illumination direction, but without a preference for a unique illumination direction. However, 3D shape and illumination direction selectivities are correlated suggesting that V4 neurons can use the direction of illumination present in complex patterns of shading present on the surface of objects. In addition, a vast majority of V4 neurons (78%) have statistically different responses to the 3D and 2D versions of the stimuli, while responses to 3D are not systematically stronger than those to 2D controls. However, a hierarchical cluster analysis showed that the different classes of stimuli (3D, 2D controls) are clustered in the V4 cells response space suggesting a coding of 3D stimuli based on the population response. The different illumination directions also tend to be clustered in this space.ConclusionTogether, these results show that area V4 participates, at the population level, in the coding of complex shape from the shading patterns coming from the illumination of the surface of corrugated objects. Hence V4 provides important information for one of the steps of cortical processing of the 3D aspect of objects in natural light environment.
Modulation of auditory evoked responses to spectral and temporal changes by behavioral discrimination training
Authors: Draganova Rossitza , Wollbrink Andreas , Schulz Matthias , Okamoto Hidehiko , Pantev Christo 
Published: December 2009

Abstract

Background
Due to auditory experience, musicians have better auditory expertise than non-musicians. An increased neocortical activity during auditory oddball stimulation was observed in different studies for musicians and for non-musicians after discrimination training. This suggests a modification of synaptic strength among simultaneously active neurons due to the training. We used amplitude-modulated tones (AM) presented in an oddball sequence and manipulated their carrier or modulation frequencies. We investigated non-musicians in order to see if behavioral discrimination training could modify the neocortical activity generated by change detection of AM tone attributes (carrier or modulation frequency). Cortical evoked responses like N1 and mismatch negativity (MMN) triggered by sound changes were recorded by a whole head magnetoencephalographic system (MEG). We investigated (i) how the auditory cortex reacts to pitch difference (in carrier frequency) and changes in temporal features (modulation frequency) of AM tones and (ii) how discrimination training modulates the neuronal activity reflecting the transient auditory responses generated in the auditory cortex.

Results
The results showed that, additionally to an improvement of the behavioral discrimination performance, discrimination training of carrier frequency changes significantly modulates the MMN and N1 response amplitudes after the training. This process was accompanied by an attention switch to the deviant stimulus after the training procedure identified by the occurrence of a P3a component. In contrast, the training in discrimination of modulation frequency was not sufficient to improve the behavioral discrimination performance and to alternate the cortical response (MMN) to the modulation frequency change. The N1 amplitude, however, showed significant increase after and one week after the training. Similar to the training in carrier frequency discrimination, a long lasting involuntary attention to the deviant stimulus was observed.

Conclusion
We found that discrimination training differentially modulates the cortical responses to pitch changes and to envelope fluctuation changes of AM tones. This suggests that discrimination between AM tones requires additional neuronal mechanisms compared to discrimination process between pure tones. After the training, the subjects demonstrated an involuntary attention switch to the deviant stimulus (represented by the P3a-component in the MEG) even though attention was not prerequisite.