bluuebunny/crossref_metadata_2025_split huggingface dataset:
The eDAL Suite: Tools and Concepts for Primary Data Citation
Authors: Lange Matthias , Colmsee Christian , Flemming Steffen , Chen Jinbo , Klapperstück Matthias , Scholz Uwe 
Published: October 2010

AbstractRetrieval and citation of primary data is the important factor in the approaching age of “data science”. Digital data are easily shared, and just as easily wiped or lost. The problem of keeping on-line data accessible and retrievable is especially difficult for SME like plant breeders plant biotech companies as well as research projects in this domain.Intension of eDAL is the provisioning of an information retrieval and data citation infrastructure that meets the requirements of the “data science” age and implements a re-usable platform for data retrieval, data citation, and data publication. Like a shopping cart, the idea is to combine a search engine and a data cart, which retrieves, rank and collect query relevant data from crop plant data centers.
The biotechnological perspective of Beta-Glucosidases
Authors: Khan Israr , Akhtar Muhammad waheed 
Published: October 2010

AbstractBiotechnology is the art and science of making and technology to process biological materials for the welfare of human being. This discussion includes the beta glucosidase classification, its structure, application, and recent research interests in relation to its significance and comparison with eukaryotic Beta glucosidases including plant, animal and yeast as well. The study also comprise of the various stress factors and modifications thereby the organism to cope it. The focus of the study is on the various kinetics principles and their full potential exploitation to increase the activity of the enzyme. As such making the enzyme a potent vehicle for various industrial, pharmaceutical and research purposes. It also include the various glycosylhydrolases of families 1 and 3 that include beta-glucosidases.
Historical Trends in Annual Water Yields for the Okanagan Basin, British Columbia, Canada
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractThe Okanagan Basin in south-central British Columbia, Canada, includes the Okanagan River watershed upstream from the outlet of Osoyoos Lake, with a total area of 8,046 km^2^. Over the past century, the population of the Basin has grown rapidly, and this trend is expected to continue. Water management issues attract significant attention in the region, given projected declines in supply and increases in demand. Historical streamflow data was obtained for three hydrometric stations on the Okanagan River between the outlet of Okanagan Lake at Penticton and near the U.S. border at Oliver. Collectively, the historical data series indicate no temporal changes in regional annual water yields for the Okanagan Basin over the past century, despite large increases in population and agricultural activity over this time. Although rapid and extensive human settlement and development of the region, along with possible climate change signatures during the 20th century, has potentially altered the inflow hydrographs to tributary streams in the Basin, the overall water yield of the region appears to be stable and possibly increasing.
Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease
Authors: Fraser-Liggett Claire 
Published: October 2010

AbstractInflammatory bowel diseases (IBD), such as Crohn’s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. In this application, we propose to develop and demonstrate the ability to profile Crohn’s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will employ a multidisciplinary approach based on metagenomic and metaproteomic molecular tools to elucidate the composition of the commensal microbiota in monozygotic twins that are either healthy or exhibit Crohn’s disease (for concordant, both are diseased; for discordant, one is healthy and one is diseased). The central hypotheses of this proposal are (1) that specific members and/or functional activities of the gastrointestinal (GI) microbiota differ in patients with Crohn’s disease as compared to healthy individuals, and (2) that it will be possible to elucidate microbial signatures which correlate with the occurrence and progression of this disease by integration of data obtained from 16S rRNA based molecular fingerprinting, metagenomics, and metaproteomics approaches. To address these hypotheses, three specific aims are proposed: 1) Obtain data on community gene content (metagenome) in a subset of healthy twins and twins with Crohn’s Disease to assess potential differences in the metabolic capabilities of the gut microbiota associated with CD, 2) Obtain data on community protein content (metaproteome) in a subset of healthy twins and twins with Crohn’s Disease to assess the state of expressed proteins associated with CD, 3) Apply various statistical clustering and classification methods to correlate/associate microbial community composition, gene and protein content with patient metadata, including metabolite profiles and clinical phenotype. The ultimate goal of these efforts is to identify novel biomarkers for non-invasive diagnostics of CD and to eventually identify drug targets (i.e. bacterial strains) for cure or suppression of disease symptoms.
jlibSEDML - a Java library for working with SED-ML
Authors: Adams Richard , Moraru Ion , Lakshminaryana Anuradha 
Published: October 2010

AbstractjlibSEDML is an open-source Java library to support the emerging SED-ML standard to record the operations needed to run simulations and other operations on biochemical models. It is compatible with level 1 version 1 of the specification and is available from http://sourceforge.net/projects/jlibsedml
BioPAX: next steps for Semantic Web / CV workgroup
Authors: Splendiani Andrea 
Published: October 2010

AbstractOutline of the next steps which will be proposed as actions in the Semantic Web/ Linking/ CV workgroup of BioPAX.One main focus will be to clean the RDF representation and adopt some basic relations, in order to address use cases in data-integration, pathway analysis and simple ontology/pathway integration.
Workspaces, exposures, and multiscale modelling
Authors: Nickerson David 
Published: October 2010

AbstractHere I present technical details on the software package PMR2, which is the software running the CellML and Physiome Project model repositories. In particular, the use of mercurial repositories to define workspaces for collaborative model development, creating modular hierarchies of embedded workspaces, and defining exposures as a means to provide permanent links to specific revisions of model workspaces. I also briefly mention the use of OpenCMISS to link CellML models into large scale, spatially distributed field modeling and simulation.
SBGN-ED - a tool for editing, validating, and translating of SBGN maps
Authors: Czauderna Tobias , Klukas Christian , Junker Astrid , Schreiber Falk 
Published: October 2010

AbstractThe recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.We present methods for these tasks, the tool SBGN-ED, and an application example. SBGN-ED allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG and MetaCrop databases into SBGN, and to export SBGN maps into several file and image formats.
Effect of Crohn's Disease Risk Alleles on Enteric Microbiota Marker Paper
Authors: Pace Norman , Mayer Lloyd , Zhu Wei , Dietz David , Boedeker Edgar , Sartor R. Balfour , Li Ellen , Sodergren Erica , Weinstock George , Stappenbeck Thaddeus , Frank Daniel , Tarr Phillip , Robertson Charles 
Published: October 2010

AbstractThis UH2/UH3 demonstration project entitled “Effects of Crohn’s disease risk alleles on enteric microbiota” is focused on characterizing intestinal associated microbiota in patients with ileal Crohn’s disease (ileal CD), ulcerative colitis (UC) and control patients without inflammatory bowel diseases (non-IBD). We hypothesize that genetic factors that affect Paneth cell function, contribute to compositional changes in intestinal microbiota. These changes in microbiota may lead to reduction of protective commensal organisms and increased numbers of aggressive organisms that incite intestinal inflammation. This hypothesis is being tested by high throughput 16S rRNA sequence analysis of de-identified ileal and colonic tissues that have been archived at Washington University St. Louis, University of North Carolina, Mount Sinai Hospital and the Cleveland Clinic. Multivariate analysis of the metagenomic data will be conducted with genotyping metadata (highly reproducible CD risk alleles, including NOD2 and ATG16L1) and phenotyping metadata (e.g. age, gender, race, body mass index, medications and smoking). Shotgun sequencing will be performed on selected fecal specimens linked to ileal tissues to identify additional, or auxiliary, or synergistic pathogenic factors or other functional changes in the microbiome. Because members of this research team have observed that a chronic viral infection is required for the Paneth cell defect in Atg16l1 hypomorphic mice, a major focus of these studies will be towards identifying potential viral triggers for the defective Paneth cell phenotype in individuals harboring the ATG16L1 risk allele. Novel genetic probes for protective and aggressive organisms will be developed by mining bacterial genome and shotgun sequencing data. Genomic sequences will be produced for candidate protective and aggressive strains (e.g. adherent-invasive strains of E. coli) isolated from human intestinal tissues where there is limited existing genome information. Quantitative qPCR assays using the novel as well as established genetic probes will be conducted to test the hypothesis that an imbalance between protective and aggressive organisms is associated with genetic factors that affect Paneth cell function.Our combined expertise in multiple disciplines across multiple institutions, our demonstrated ability to collect a large number of well-phenotyped samples with longitudinal clinical information that will be linked to host response and morphologic studies, and our consortium’s capacity for high-throughput sequencing will be used to investigate how alterations in human microbiome relate to CD risk alleles and CD pathogenesis.
TreeRipper: towards a fully automated optical tree recognition software
Authors: Hughes Joseph 
Published: October 2010

AbstractRelationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century.TreeRipper is a command line c++ program for the fully-automated recognition of multifurcating phylogenetic trees. The program accepts a range of input image formats (PNG, JPG/JPEG, GIF, TIFF or PDF ). Then follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves.Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software.
Recent trends in US patent grants and issues to be considered
Authors: Garrity George , Parker Charles 
Published: October 2010

AbstractThe life sciences have changed radically since the Convention on Biological Diversity first opened for signatures in 1992. Traditional organism-based approaches to discovery and use of genetic resources have been supplanted by molecular approaches. Biodiversity prospecting is more likely to be a programmatic bioinformatics activity rather than an activity conducted by field scientists. Access to genetic resources is no longer centered on a hunt for novel species. Rather, the hunt is for novel genes and metabolic pathways that can be cloned into well-understood expression systems and readily scaled-up for industrial production. Information about contemporary research, development, and manufacturing practices needs to be addressed, especially when those genes do not need to be associated with their native host at the time of discovery. Information about the research organizations participating in all phases of the discovery and development process also needs to be considered, especially when it involves partnerships between academic and industrial organizations.We present a high-level view of recent trends in the issuance of US patent grants to commercial and non-commercial research organizations, and introduce a technology that is already in place which can be applied to monitoring the use of genetic materials by various stakeholders in an open and transparent manner, as intended under the International Regime for Access and Benefit Sharing (ABS).
The SBML Level 3 Annotation package: an initial proposal
Authors: Swainston Neil 
Published: October 2010

AbstractThe SBML Level 3 Annotation package proposal intends to extend the current Level 3 Core annotations by increasing the range of RDF features supported.Such an extension will support RDF Reification, annotation of SBML attributes, specification of relationships between annotations, negation of annotations and cross-references and cross-element annotations.
Essay: On the close relationship between speciation, inbreeding and recessive mutations.
Authors: Joly Etienne 
Published: October 2010

AbstractWhilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a process of separation allowing two populations to diverge sufficiently to become infertile with one another. I do, however, take the view that, if so much speciation has occurred, and still occurs around us, it cannot be a consequence of passive drift but must result from a selection process, whereby it is advantageous for groups of individuals to reproduce preferentially with one another and reduce their breeding with the rest of the population.In this essay, I propose a model whereby new species arise by “budding” from an ancestral stock, via a process of inbreeding among small numbers of individuals, driven by the occurrence of advantageous recessive mutations. Since the phenotypes associated to such mutations can only be retained in the context of inbreeding, it is the pressure of the ancestral stock which will promote additional reproductive barriers, and ultimately result in complete separation of a new species. I thus contend that the phenomenon of speciation would be driven by mutations resulting in the advantageous loss of certain functions, whilst adaptive evolution would correspond to gains of function that would, most of the time be dominant.A very important further advantage of inbreeding is that it reduces the accumulation of recessive mutations in genomes. A consequence of the model proposed is that the existence of species would correspond to a metastable equilibrium between inbreeding and outbreeding, with excessive inbreeding promoting speciation, and excessive outbreeding resulting in irreversible accumulation of recessive mutations that could ultimately only lead to the species extinction.
The C-terminal basic residues contribute to the chemical- and voltage-dependent activation of TRPA1
Authors: Samad Abdul , Sura Lucie , Benedikt Jan , Ettrich Rudiger , Minofar Babak , Teisinger Jan , Vlachova Viktorie 
Published: October 2010

The ankyrin transient receptor potential channel TRPA1 is a non-selective cationic channel that is expressed by sensory neurons, where it can be activated by pungent chemicals, such as AITC (allyl isothiocyanate), cinnamon or allicin, by deep cooling (&lt;18 °C) or highly depolarizing voltages (&gt;+100 mV). From the cytoplasmic side, this channel can be regulated by negatively charged ligands such as phosphoinositides or inorganic polyphosphates, most likely through an interaction with as yet unidentified positively charged domain(s). In the present study, we mutated 27 basic residues along the C-terminal tail of TRPA1, trying to explore their role in AITC- and voltage-dependent gating. In the proximal part of the C-terminus, the function-affecting mutations were at Lys969, Arg975, Lys988 and Lys989. A second significant region was found in the predicted helix, centred around Lys1048 and Lys1052, in which single alanine mutations completely abolished AITC- and voltage-dependent activation. In the distal portion of the C-terminus, the charge neutralizations K1092A and R1099A reduced the AITC sensitivity, and, in the latter mutant, increased the voltage-induced steady-state responses. Taken together, our findings identify basic residues in the C-terminus that are strongly involved in TRPA1 voltage and chemical sensitivity, and some of them may represent possible interaction sites for negatively charged molecules that are generally considered to modulate TRPA1.
Schizophrenia costs and treatment cost‐effectiveness
Authors: Knapp Martin 
Published: October 2010

Objective: The paper sets out to summarize evidence on the costs of schizophrenia and on the cost‐effectiveness of three broad treatment areas. Method: Evidence from a number of countries was examined, both published and unpublished, and systematic reviews and meta‐analyses were consulted. Results: The costs of schizophrenia are high and wide‐ranging. They fall not only to health‐care agencies but also to other parts of the public sector, to families, to sufferers themselves and to the wider society. However, there are interventions — a counselling intervention to address non‐compliance with medication, family interventions to reduce levels of expressed emotion, and atypical antipsychotic drugs — that have been found to be not only effective (improving patient outcomes) but also appear to be cost‐effective. Conclusion: Resource constraints and policy pressures make it increasingly common for economic as well as clinical questions to be asked about new modes of treatment. This is the new reality of mental health practice. Reliable evidence is now available to address these economic questions and can be factored into decision‐making processes.
A Radiographic Stress Technique for Evaluation of Coxofemoral Joint Laxity in Dogs
Authors: Flüaduckiger Mark A. , Friedrich G. Anne , Binder Heinrich 
Published: October 2010

Objective—To develop a radiographic stress technique to quantify hip joint laxity in dogs.Study Design—Prospective study on client‐owned dogs presented for hip dysplasia screening.Animal Population—302 nonselected dogs (63 breeds).Methods—Dogs were sedated and placed in dorsal recumbency. During pelvic radiography, the femoral heads were displaced manually in a craniodorsal direction. On these stress radiographs, the degree of lateral displacement of the femoral heads was assessed in terms of a subluxation index (SI) and compared with the degree of femoral head subluxation and the severity of hip dysplasia found on conventional extended hindlimb radiographs.Results—The degree of subluxation on stress radiographs was significantly greater than on conventional radiographs. Correlation between the severity of canine hip dysplasia (CHD), graded according to conventional techniques, and the degree of subluxation, induced by radiographic stress technique, was positive (r= .57; P < .0001). Two critical SI values were noted. Of the dogs with an SI value of 0.3 or less, 99% were classified as CHD grade normal, borderline, or mildly dysplastic. In dogs with an SI value between 0.3 and 0.5, CHD grading ranged from normal to severely dysplastic. Of the dogs with an SI value greater than 0.5, 95% had dysplastic hip joints.Conclusions—Hip joint laxity cannot be quantified precisely on standard position radiographs. The proposed stress technique yields significantly higher degrees of femoral head subluxation than the standard position.
The Effect of a Surgically Created Shunt Between the Corpus Cavernosum Penis and Corpus Spongiosum Penis of Stallions on Erectile and Ejaculatory Function
Authors: Schumacher Jim , Varner Dickson D. , Crabill Mark R. , Blanchard Terry L. 
Published: October 2010

Objective—To evaluate the effect of a shunt created between the corpus cavernosum penis (CCP) and corpus spongiosum penis (CSP) on erectile and ejaculatory function of normal stallions and to verify persistence of the shunt.Study Design—The capability of stallions to develop an erection and to ejaculate was evaluated before and after creation of a corporeal shunt. Persistence of the shunt was determined by dye injection into the CCP at necropsy.Animals—Six stallions.Methods—A CCP‐CSP shunt was created in five stallions. Semen was collected before and 4 to 14 weeks after surgery, before the horses were euthanatized. Dye was injected into the CCP to determine persistence of the shunt. Dye was also injected into the CCP of a control stallion.Results—All stallions had normal erectile and ejaculatory function before and after surgery. Dye, injected into the CCP, entered the CSP in three of five treated stallions, demonstrating persistence of the shunt, whereas in two stallions, dye was found only in the CCP, indicating closure of the shunt. No dye was detected in the CSP of the control stallion.Conclusions—Creation of a corporeal shunt does not interfere with normal erection and ejaculation of stallions. Shunt closure is not necessary for stallions to retain normal erectile and ejaculatory function.Clinical Relevance—Failure of a stallion affected by priapism to achieve normal erection or to ejaculate after creation of a corporeal shunt would likely be because of damage to corporeal tissue than from an effect of the shunt.