bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pythoscape: a framework for generation of large protein similarity networks
Authors: Barber Alan E. , Babbitt Patricia C. 
Published: September 2012

Abstract
Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence–structure–function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.
Contact: babbitt@cgl.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ImgLib2—generic image processing in Java
Authors: Pietzsch Tobias , Preibisch Stephan , Tomančák Pavel , Saalfeld Stephan 
Published: September 2012

Abstract
Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.
Availability: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib.
Supplementary Information: Supplementary data are available at Bioinformatics Online.
Contact: saalfeld@mpi-cbg.de
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples
Authors: Cazier Jean-Baptiste , Holmes Chris C. , Broxholme John 
Published: September 2012

Abstract
Summary: GREVE has been developed to assist with the identification of recurrent genomic aberrations across cancer samples. The exact characterization of such aberrations remains a challenge despite the availability of increasing amount of data, from SNParray to next-generation sequencing. Furthermore, genomic aberrations in cancer are especially difficult to handle because they are, by nature, unique to the patients. However, their recurrence in specific regions of the genome has been shown to reflect their relevance in the development of tumors. GREVE makes use of previously characterized events to identify such regions and focus any further analysis.
Availability: GREVE is available through a web interface and open-source application (http://www.well.ox.ac.uk/GREVE).
FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma
Authors: Jiang Peiyong , Chan K. C. Allen , Liao Gary J. W. , Zheng Yama W. L. , Leung Tak Y. , Chiu Rossa W. K. , Lo Yuk Ming Dennis , Sun Hao 
Published: September 2012

Abstract
Motivation: The fractional fetal DNA concentration is one of the critical parameters for non-invasive prenatal diagnosis based on the analysis of DNA in maternal plasma. Massively parallel sequencing (MPS) of DNA in maternal plasma has been demonstrated to be a powerful tool for the non-invasive prenatal diagnosis of fetal chromosomal aneuploidies. With the rapid advance of MPS technologies, the sequencing cost per base is dramatically reducing, especially when using targeted MPS. Even though several approaches have been developed for deducing the fractional fetal DNA concentration, none of them can be used to deduce the fractional fetal DNA concentration directly from the sequencing data without prior genotype information.
Result: In this study, we implement a statistical mixture model, named FetalQuant, which utilizes the maximum likelihood to estimate the fractional fetal DNA concentration directly from targeted MPS of DNA in maternal plasma. This method allows the improved deduction of the fractional fetal DNA concentration, obviating the need of genotype information without loss of accuracy. Furthermore, by using Bayes’ rule, this method can distinguish the informative single-nucleotide polymorphism loci where the mother is homozygous and the fetus is heterozygous. We believe that FetalQuant can help expand the spectrum of diagnostic applications using MPS on DNA in maternal plasma.
Availability: Software and simulation data are available at http://sourceforge.net/projects/fetalquant/
Contact: haosun@cuhk.edu.hk
Supplementary Information: Supplementary data are available at Bioinformatics online.
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures
Authors: Walsh Ian , Sirocco Francesco G. , Minervini Giovanni , Di Domenico Tomás , Ferrari Carlo , Tosatto Silvio C. E. 
Published: September 2012

Abstract
Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure.
Results: Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q2 value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records.
Availability: The RAPHAEL web server is available with additional data at http://protein.bio.unipd.it/raphael/
Contact: silvio.tosatto@unipd.it
Supplementary information: Supplementary data are available at Bioinformatics online
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery
Authors: Athanasiadis Emmanouil , Cournia Zoe , Spyrou George 
Published: September 2012

Abstract
Summary: ChemBioServer is a publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. It provides researchers with the ability to (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply perfect match substructure search, (iv) cluster compounds according to their physicochemical properties providing representative compounds for each cluster, (v) build custom compound mining pipelines and (vi) quantify through property graphs the top ranking compounds in drug discovery procedures. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.
Availability: The ChemBioServer web application is available at: http://bioserver-3.bioacademy.gr/Bioserver/ChemBioServer/.
Contact: gspyrou@bioacademy.gr
Comparing clustering and pre-processing in taxonomy analysis
Authors: Bonder Marc J. , Abeln Sanne , Zaura Egija , Brandt Bernd W. 
Published: September 2012

Abstract
Motivation: Massively parallel sequencing allows for rapid sequencing of large numbers of sequences in just a single run. Thus, 16S ribosomal RNA (rRNA) amplicon sequencing of complex microbial communities has become possible. The sequenced 16S rRNA fragments (reads) are clustered into operational taxonomic units and taxonomic categories are assigned. Recent reports suggest that data pre-processing should be performed before clustering. We assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data.
Results: The number of clusters varied up to two orders of magnitude depending on pre-processing. Pre-processing using both denoising and chimera checking resulted in a number of clusters that was closest to the number of species in the mock dataset (25 versus 15). Based on run time, purity and normalized mutual information, we could not identify a single best clustering algorithm. The differences in clustering accuracy among the algorithms after the same pre-processing were minor compared with the differences in accuracy among different pre-processing steps.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: bonder.m.j@gmail.com or b.brandt@acta.nl
The origins of formal education in sub-Saharan Africa: was British rule more benign?
Authors: Frankema Ewout H.P. 
Published: September 2012

Abstract
British colonial rule has often been praised for its comparatively benign features, such as its support of local educational development. This study argues that the impact of British educational policies and investments on the supply of schooling in British Africa should not be overstated. Until 1940, mission schools, mainly run by African converts, provided the bulk of education at extremely low costs. Given the limited financial capacity of missionary societies, the Africanization of the mission was a prerequisite for rising enrolment rates and this only occurred in areas where the demand for Western education was high. The British happened to control most of these “fertile” areas.
Utility of lung ultrasound in predicting pulmonary and cardiac pressures
Authors: Platz Elke , Lattanzi AnnMarie , Agbo Chioma , Takeuchi Madoka , Resnic Frederic S. , Solomon Scott D. , Desai Akshay S. 
Published: September 2012

AimsQuantification of linear lung ultrasound (LUS) artefacts (B‐lines) represents a novel, non‐invasive approach to assess pulmonary congestion. We investigated the relationship between the number of B‐lines (vertical artefacts arising from the pleural line) and intracardiac pressures.Methods and resultsPrior to scheduled right heart catheterization (RHC), 100 subjects underwent LUS of eight zones. A reviewer blinded to the haemodynamic data quantified the number of sonographic B‐lines. Of 92 subjects who completed RHC, 79 had adequate LUS data of all zones [median age 61 years, 26 women, median left ventricular ejection fraction (LVEF) 58%, 35 with history of heart failure; 22 postcardiac transplantation]. The number of B‐lines correlated with measured right atrial (r = 0.32), pulmonary artery diastolic (PADP) (r = 0.34), mean pulmonary artery (mPAP) (r = 0.43), pulmonary artery systolic (PASP) (r = 0.48) pressures, and pulmonary vascular resistance (PVR) (r = 0.51) (P < 0.005 for all), but not with pulmonary capillary wedge pressure. There was a graded association between tertiles of B‐line number and increasing PADP, mPAP, PASP, and PVR (P for trend ≤0.001 for all). Each additional B‐line was associated with an increase in PASP of 1 mmHg and an increase in PVR of 0.1 Wood units. These associations remained robust after multivariable adjustment (P = 0.002). Assessment of two inferior lateral zones resulted in similar correlations to the eight‐zone method.ConclusionsEasily obtainable, LUS may be useful in the estimation of right‐sided cardiac pressures and PVR. Further evaluation of lung ultrasound as an adjunct to heart failure diagnosis, monitoring, and prognosis is warranted.
The p35 human invariant chain in transgenic mice restores mature B cells in the absence of endogenous CD74
Authors: Genève Laetitia , Ménard Catherine , Labrecque Nathalie , Thibodeau Jacques 
Published: September 2012

Abstract
The invariant chain (Ii; CD74) has pleiotropic functions and Ii-deficient mice show defects in MHC class II (MHC II) transport and B cell maturation. In humans, but not in mice, a minor Iip35 isoform of unknown function includes an endoplasmic reticulum-retention motif that is masked upon binding of MHC II molecules. To gain further insight into the roles of Ii in B cell homeostasis, we generated Iip35 transgenic mice (Tgp35) and bred these with mice deficient for Ii (Tgp35/mIiKO). Iip35 was shown to compete with mIi for the binding to I-Ab . In addition, classical endosomal degradation products (p20/p10) and the class II-associated invariant chain peptide (CLIP) fragment were detected. Moreover, Iip35 favored the formation of compact peptide–MHC II complexes in the Tgp35/mIiKO mice. I-Ab levels were restored at the plasma membrane of mature B cells but Iip35 affected the fine conformation of MHC II molecules as judged by the increased reactivity of the AF6-120.1 antibody in permeabilized cells. However, the human Iip35 cannot fully replace the endogenous Ii. Indeed, most immature B cells in the bone marrow and spleen of transgenic mice had reduced surface expression of MHC II molecules, demonstrating a dominant-negative effect of Iip35 in Tgp35 mice. Interestingly, while maturation to follicular B cells was normal, Iip35 expression appeared to reduce the proportions of marginal zone B cells. These results emphasize the importance of Ii in B cell homeostasis and suggest that Iip35 could have regulatory functions.
Regulation of intestinal homeostasis by innate and adaptive immunity
Authors: Kayama Hisako , Takeda Kiyoshi 
Published: September 2012

Abstract
The intestine is a unique tissue where an elaborate balance is maintained between tolerance and immune responses against a variety of environmental factors such as food and the microflora. In a healthy individual, the microflora stimulates innate and adaptive immune systems to maintain gut homeostasis. However, the interaction of environmental factors with particular genetic backgrounds can lead to dramatic changes in the composition of the microflora (i.e. dysbiosis). Many of the specific commensal-bacterial products and the signaling pathways they trigger have been characterized. The role of T h 1, T h 2 and T h 17 cells in inflammatory bowel disease has been widely investigated, as has the contribution of epithelial cells and subsets of dendritic cells and macrophages. To date, multiple regulatory cells in adaptive immunity, such as regulatory T cells and regulatory B cells, have been shown to maintain gut homeostasis by preventing inappropriate innate and adaptive immune responses to commensal bacteria. Additionally, regulatory myeloid cells have recently been identified that prevent intestinal inflammation by inhibiting T-cell proliferation. An increasing body of evidence has shown that multiple regulatory mechanisms contribute to the maintenance of gut homeostasis.
Characterization of a Viral Synergism in the MonocotBrachypodium distachyonReveals Distinctly Altered Host Molecular Processes Associated with Disease
Authors: Mandadi Kranthi K. , Scholthof Karen-Beth G. 
Published: September 2012

AbstractPanicum mosaic virus (PMV) and its satellite virus (SPMV) together infect several small grain crops, biofuel, and forage and turf grasses. Here, we establish the emerging monocot model Brachypodium (Brachypodium distachyon) as an alternate host to study PMV- and SPMV-host interactions and viral synergism. Infection of Brachypodium with PMV+SPMV induced chlorosis and necrosis of leaves, reduced seed set, caused stunting, and lowered biomass, more than PMV alone. Toward gaining a molecular understanding of PMV- and SPMV-affected host processes, we used a custom-designed microarray and analyzed global changes in gene expression of PMV- and PMV+SPMV-infected plants. PMV infection by itself modulated expression of putative genes functioning in carbon metabolism, photosynthesis, metabolite transport, protein modification, cell wall remodeling, and cell death. Many of these genes were additively altered in a coinfection with PMV+SPMV and correlated to the exacerbated symptoms of PMV+SPMV coinfected plants. PMV+SPMV coinfection also uniquely altered expression of certain genes, including transcription and splicing factors. Among the host defenses commonly affected in PMV and PMV+SPMV coinfections, expression of an antiviral RNA silencing component, SILENCING DEFECTIVE3, was suppressed. Several salicylic acid signaling components, such as pathogenesis-related genes and WRKY transcription factors, were up-regulated. By contrast, several genes in jasmonic acid and ethylene responses were down-regulated. Strikingly, numerous protein kinases, including several classes of receptor-like kinases, were misexpressed. Taken together, our results identified distinctly altered immune responses in monocot antiviral defenses and provide insights into monocot viral synergism.
Impaired Auxin Biosynthesis in the defective endosperm18 Mutant Is Due to Mutational Loss of Expression in the ZmYuc1 Gene Encoding Endosperm-Specific YUCCA1 Protein in Maize
Authors: Bernardi Jamila , Lanubile Alessandra , Li Qin-Bao , Kumar Dibyendu , Kladnik Ale¡ , Cook Sam D. , Ross John J. , Marocco Adriano , Chourey Prem S. 
Published: September 2012

Abstract
The phytohormone auxin (indole-3-acetic acid [IAA]) plays a fundamental role in vegetative and reproductive plant development. Here, we characterized a seed-specific viable maize (Zea mays) mutant, defective endosperm18 (de18) that is impaired in IAA biosynthesis. de18 endosperm showed large reductions of free IAA levels and is known to have approximately 40% less dry mass, compared with De18. Cellular analyses showed lower total cell number, smaller cell volume, and reduced level of endoreduplication in the mutant endosperm. Gene expression analyses of seed-specific tryptophan-dependent IAA pathway genes, maize Yucca1 (ZmYuc1), and two tryptophan-aminotransferase co-orthologs were performed to understand the molecular basis of the IAA deficiency in the mutant. Temporally, all three genes showed high expression coincident with high IAA levels; however, only ZmYuc1 correlated with the reduced IAA levels in the mutant throughout endosperm development. Furthermore, sequence analyses of ZmYuc1 complementary DNA and genomic clones revealed many changes specific to the mutant, including a 2-bp insertion that generated a premature stop codon and a truncated YUC1 protein of 212 amino acids, compared with the 400 amino acids in the De18. The putative, approximately 1.5-kb, Yuc1 promoter region also showed many rearrangements, including a 151-bp deletion in the mutant. Our concurrent high-density mapping and annotation studies of chromosome 10, contig 395, showed that the De18 locus was tightly linked to the gene ZmYuc1. Collectively, the data suggest that the molecular changes in the ZmYuc1 gene encoding the YUC1 protein are the causal basis of impairment in a critical step in IAA biosynthesis, essential for normal endosperm development in maize.
DNA barcodes identify marine fishes of São Paulo State, Brazil
Authors: Ribeiro Amanda de Oliveira , Caires Rodrigo Antunes , Mariguela Tatiane Casagrande , Pereira Luiz Henrique Garcia , Hanner Robert , Oliveira Claudio 
Published: September 2012

AbstractAnthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp ‘barcode’ fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour‐joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43‐fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species‐pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna – extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation.
DPP‐4 Inhibition Attenuates Cardiac Dysfunction and Adverse Remodeling Following Myocardial Infarction in Rats with Experimental Diabetes
Authors: Connelly Kim Alexander , Zhang Yanling , Advani Andrew , Advani Suzanne L. , Thai Kerri , Yuen Darren A. , Gilbert Richard E. 
Published: September 2012

SummaryAimsFollowing myocardial infarction (MI), individuals with diabetes have a two‐fold increase in the risk of heart failure, due in part to excessive loss of cardiac microvasculature. Endothelial integrity and restitution are mediated in part by stromal cell–derived factor‐1α (SDF‐1α), a chemokine that is elaborated by ischemic tissue but rapidly degraded by dipeptidyl peptidase‐4 (DPP‐4). Accordingly, we hypothesized that inhibiting this enzyme may confer benefit following myocardial infarction in the diabetic setting beyond its effect on glycemia.Methods and ResultsFischer F344 rats with streptozotocin (STZ)‐diabetes were randomized to receive vehicle or the DPP‐4 inhibitor, sitagliptin (300 mg/kg/day). Two weeks later, animals underwent experimental MI, induced by ligation of the left anterior descending coronary artery. Cardiac function was assessed by conductance catheterization and echocardiography along with cardiac structure 4 weeks post‐MI. Following MI, untreated diabetic rats developed both systolic and diastolic cardiac dysfunction, in association with endothelial cell loss, fibrosis, and myocyte hypertrophy. Without affecting plasma glucose, sitagliptin treatment led to an improvement in passive left ventricular compliance, increased endothelial cell density, reduced myocyte hypertrophy, and a reduction in the abundance of collagen 1 (all P < 0.05). Systolic function was unchanged.ConclusionsThis study shows that DPP‐4 inhibition attenuates several, but not all, aspects of cardiac dysfunction and adverse remodeling in the post‐MI setting.