bluuebunny/crossref_metadata_2025_split huggingface dataset:
CDAO-Store: A New Vision in Data Integration
Authors: Chisham Brandon , Le Trung , Pontelli Enrico , Son Tran , Wright Ben 
Published: October 2010

AbstractThe Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by NESCent, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic trees and associated character data matrices. CDAO-store is a repository providing a rich set of API’s for querying and visualizing phyloinformatics data. It is a triple-store encoding data as RDF triples constructed according to the CDAO concept vocabulary. CDAO-store provides three classes of services: a service for importing data in CDAO format, a PhyloWS interface supporting an advanced set of queries for other external applications, and a web-interface for visualizing and interacting with data in the store.
Bio::Phylo - Phyloinformatic Analysis Using Perl
Authors: Vos Rutger 
Published: October 2010

AbstractRecent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps often need to be redone by the researcher multiple times anyway and are too error-prone, tedious and time-consuming to do by hand. Hence, phyloinformatic analyses benefit from increased automation. The Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from a variety of commonly used data formats. In addition, it allows researchers to read and write data formats for which no Perl support has existed so far (e.g. NeXML, “Pagel format”), compute heretofore unimplemented topological indices (various measures for tree balancee.g. , branchinesse.g. and phylogenetic distinctivenesse.g. ), apply heretofore unavailable sampling and resampling algorithms and visualize the results in publication-ready (PDF) or web (SVG, SWF, PNG) graphics. Because of its compatibility with BioPerl it can be easily integrated in larger bioinformatic workflows. The toolkit is available from the Comprehensive Perl Archive Network under the same licensing conditions as perl itself, i.e. the dual Artistic License / GPL scheme. The toolkit is thoroughly documented, with usage examples for all public methods and classes and a 15-page “birds eye view” manual.
Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck. (Commelinaceae)
Authors: Nandikar M , Gurav R 
Published: October 2010

AbstractMurdannia lanuginosa (C. B. Cl.) Brucek. (Commelinaceae), an endemic plant to Western Ghats of Peninsular India. It is categorized as regionally endangered taxon owing to its restricted habitat and low population status in ateritic plateaus of Maharashtra and Karnataka. It is observed in higher abundance in lateritic plateaus and hilly slopes at an altitude range of 900 to 1600 m. M. lanuginosa found on open grassy plateaus along with herbs like M. simplex, M. versicolor, Ischaemum impressum, Glyphochloa forficulata, Paspalum canarae, Smithia bigemina, S. purpurea, Rotala densiflora, Pogostemon deccanensis, etc. Extent of occurrence of M. lanuginosa estimated to be 4,000 sq. km and found only at few locations. This paper presents morphological, anatomical, palynological as well as cytological studies on Murdannia lanuginosa (Wall.ex C. B. Cl.).
Phylontal: Using Phylogenies to Align Phenotype Ontologies
Authors: Midford Peter 
Published: October 2010

AbstractPhylontal is a simple approach to generating alignments of ontologies or constructs based on controlled vocabularies that correspond to tips on a phylogeny. The method requires only a downpass (tips to root) and thus constructing alternative alignments from multiple or uncertain phylogenies may be relatively inexpensive.
Phenex: Ontological Annotation of Phenotypic Diversity
Authors: Balhoff James , Dahdul Wasila , Kothari Cartik , Lapp Hilmar , Lundberg John , Mabee Paula , Midford Peter , Westerfield Monte , Vision Todd 
Published: October 2010

AbstractPhenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge.
Modulation of iron responsive gene expression and enzymatic activities in response to changes of the iron nutritional status in _Cucumis sativus_ L.
Authors: De Nisi Patrizia , Vigani Gianpiero , Zocchi Graziano 
Published: October 2010

AbstractRegulation exerted by the iron status of the plant on the iron deficiency responses was investigated in cucumber roots (Cucumis sativus L.) both at the biochemical and molecular level. Absence of iron induced the expression of the CsFRO1, CsIRT1, CsHA1 and the Cspepc1 transcripts that was followed by an increase in the corresponding enzymatic activities. Supply of iron repressed gene expression, in particular those of the Fe(III)-chelate reductase and for the high affinity iron transporter and reduce the enzymatic activities. Our results confirm and extend the hypothesis of a coordinate regulation of these responses. Besides these two activities strictly correlated with iron deficiency adaptation, we considered also the H+-ATPase and the phosphoenolpyruvate carboxylase, that have been shown to be involved in this response.
Lightning Talk: Biopython (bio) Geography Module
Authors: Matzke Nicholas 
Published: October 2010

AbstractFor Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython. The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank. Application of the tool to a historical biogeography study on bivalves will be illustrated.As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:"http://www.biopython.org/DIST/LICENSE":http://www.biopython.org/DIST/LICENSEThe module is described, and a tutorial is presented, on the Biopython wiki:http://biopython.org/wiki/BioGeographyThe page contains links to the source hosted on Github; here is the direct link:"http://github.com/nmatzke/biopython/tree/Geography":http://github.com/nmatzke/biopython/tree/Geography
Identifying Copy Number Variations based on Next Generation Sequencing Data by a Mixture of Poisson Model
Authors: Schwarzbauer Karin , Klambauer Günter , Mayr Andreas , Hochreiter Sepp 
Published: October 2010

AbstractNext generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more popular due to cost effectiveness and their speed. NGS can be utilized to identify DNA structural variants, namely copy number variations (CNVs) which showed association with diseases like HIV, diabetes II, or cancer.There have been first approaches to detect CNVs in NGS data, where most of them detect a CNV by a significant difference of read counts within neighboring windows at the chromosome. However these methods suffer from systematical variations of the underlying read count distributions along the chromosome due to biological and technical noise. In contrast to these global methods, we locally model the read count distribution characteristics by a mixture of Poissons which allows to incorporate a linear dependence between copy numbers and read counts. Model selection is performed in a Bayesian framework by maximizing the posterior through an EM algorithm. We define a CNV call which indicates a deviation of the Poisson mixture parameters from the null hypothesis represented by the prior which is a model for constant copy number across the samples. A CNV call requires sufficient information in the data to push the model away from the null hypothesis given by the prior.We test our approach on the HapMap cohort where we rediscovered previously found CNVs which validates our approach. It is then tested on the tumor genome data set where we are able to considerably increase the detection while reducing the false discoveries.
Concentrations and profiles of melatonin and serotonin in fruits and vegetables during ripening: A mini-review
Authors: Rayne Sierra 
Published: October 2010

AbstractMelatonin and serotonin are important phytochemicals with hormonal, antioxidant, immunoactive, and neuroactive biological properties, and have been identified and quantitated in a broad range of fruits, vegetables, and derivative products. Relatively little is known about the temporal profiles of these compounds during fruit and vegetable development. Improved knowledge in this area would help guide our understanding of fundamental plant physiology, as well as potentially facilitate better control of melatonin and serotonin concentrations and relative abundances in functional foods. The current work synthesizes the current state-of-the-art regarding the presence and trends of these compounds during fruit and vegetable development. The literature reflects sometimes conflicting conclusions regarding the temporal profiles of melatonin and serotonin during fruit and vegetable ripening. At present, it is unclear whether consistent trends can be identified within a particular species, and the direction and magnitude of effects from different geographic locations and management practices.
Long-term impacts of tropical storms and earthquakes on human population growth in Haiti and Dominican Republic
Authors: Klose Christian D. , Webersik Christian 
Published: October 2010

AbstractThe two Caribbean states, Haiti and the Dominican Republic, have experienced similar natural forces since the 18th century, including hurricanes and earthquakes. Although, both countries seem to be two of the most prone of all Latin American and Caribbean countries to natural hazard events, historically, Haiti tends to be more vulnerable to natural forces. The purpose of this article is to understand to what extent geohazards shape demographic changes. Research findings of this study show that neither atmospheric nor seismic hazards that directly hit the territory of Haiti have significant impacts on population densities and growth rates. Quantitative evidence is provided, that between 1850 to 2009 urbanization processes have exposed more people to natural forces. Thus, Haiti is willing to take an increasing risk, because, finally, it matters where people settle.
Human-triggered earthquakes and their impacts on human security
Authors: Klose Christian D. 
Published: October 2010

AbstractA comprehensive understanding of earthquake risks in urbanized regions requires an accurate assessment of both urban vulnerabilities and earthquake hazards. Socioeconomic risks associated with human-triggered earthquakes are often misconstrued and receive little scientific, legal, and public attention. However, more than 200 damaging earthquakes, associated with industrialization and urbanization, were documented since the 20th century. This type of geohazard has impacts on human security on a regional and national level. For example, the 1989 Newcastle earthquake caused 13 deaths and US$3.5 billion damage (in 1989). The monetary loss was equivalent to 3.4 percent of Australia’s national income (GDI) or 80 percent of Australia’s GDI per capita growth of the same year. This article provides an overview of global statistics of human-triggered earthquakes. It describes how geomechanical pollution due to large-scale geoengineering activities can advance the clock of earthquakes or trigger new seismic events. Lastly, defense-oriented strategies and tactics are described, including risk mitigation measures such as urban planning adaptations and seismic hazard mapping.
Waveomics: bringing experimental data to online collaboration
Authors: Swainston Neil 
Published: October 2010

AbstractSystems biology offers an interdisciplinary approach to scientific research that typically involves the collaboration of teams of experimentalists and mathematical modellers. While the importance of data standards has been recognised in facilitating exchange of data between the parties, challenges still remain regarding the practicalities of disseminating experimental data.The introduction of novel web-based tools aimed at promoting collaborative work has provided a platform upon which scientific applications can be built. The recently released Google Wave protocol provides a facility for real-time collaboration between teams of researchers.This work introduces a customized Robot that automatically scans text in Google Waves for experimental data identifiers, extracts corresponding experimental data from remote resources associated with such identifiers, and appends charts showing this experimental data to the Wave.
Behavioral origins of metabolic syndrome disorders
Authors: Watve Milind , Jog Maithili , Belsare Prajakta 
Published: October 2010

AbstractThe metabolic syndrome disorders (MSD) including type 2 diabetes, hypertension, hypercholesterolemia, atherosclerosis and cardiovascular disease are known to be triggered by lifestyle change. We state and support a hypothesis here that changes in behavior rather than changes in diet and metabolism are central to MSD. We provide and discuss evidence in support of the following sequence of arguments. (i) Diet, thriftiness and obesity centered paradigm is inadequate to explain most of the physiological and immunological changes associated with metabolic syndrome disorders (MSD). (ii) Comparative studies show that relative obesity rather than absolute obesity is strongly associated with various parameters of MSD and further perception of calories without actual change in intake of calories can induce physiological changes. (iii) Alternative behavioral strategies co-exist in animal populations which are associated with characteristic metabolic states and some of these states show close resemblance with MSD in humans. (iv) Obesity and MSD are strongly and cross culturally associated with certain behavioral traits. (v) Deficiencies of certain behaviors that evolved with hunter gatherer life as adaptive behaviors but that are deficient in modern life lead to corresponding dysfunctions of neuro-endocrine mechanisms. Through a meta-analysis study we show that deficiency of physical aggression is strongly associated with MSD as seen by neuro-endocrine mechanisms as well as epidemiological data. This raises a possibility that the effects of behavioral deficiencies may be reversed by behavioral supplementation. (vi) On a pilot scale, behavioral interventions substantially ameliorated many components of MSD without significantly changing body weights. All the evidence collectively indicates that MSD originates due to behavioral deficiencies rather than metabolic thriftiness and therefore behavioral supplementation may be effective in reversing the chronic conditions.
Diet of Northern Map Turtles (Graptemys geographica): Relationship to Sexual Dimorphism and Potential Impacts of an Altered River System in Maryland
Authors: Richards-Dimitrie Teal , Seigel Richard 
Published: October 2010

AbstractLast recorded in Maryland in the early 1990’s, the Northern Map Turtle (Graptemys geographica) is listed as state endangered and is currently only known in the lower Susquehanna River drainage. This river is divided by a hydroelectric dam, used for recreation, and has increasing shoreline development, all of which may negatively impact this population. Knowing this population’s diet and if alterations to the river affect their prey base is important to understanding the species’ current status. Northern Map Turtles are mostly molluscivorous but will also consume other invertebrates. Studies have shown that map turtle species will subsidize their diet with invasive mussels, potentially decreasing dietary diversity. The Susquehanna River contains both native and nonnative mollusks species. Recently, Zebra Mussels (Dreissena polymorpha), an invasive species known to have large effects on aquatic food webs and nutrient cycling, have been found in the lower Susquehanna. Given the absence of basic data on Northern Map Turtle diet in Maryland, fecal samples of 32 turtles were examined. Three operational taxanomic units predominated across samples: gastropods, trichopteran larvae, and Corbicula fluminea. Pronounced sexual differences occurred for these taxa, as adult males (n=14) fed primarily on trichoptera, a small unidentified gastropod species (~2 mm), and Corbicula sp. while the females (n=18) fed almost exclusively on Pleurocerid snails. This research has provided us baseline data on Northern Map Turtle diet and monitoring of the diet will allow us to not only understand impacts of dam operations on composition of their prey base, but the potential shift to zebra mussels as well.
Quadruple context-free L-System mathematical tools as origin of biological evolution
Authors: Goswami Arunava , Pal Choudhury Pabitra , Singh Rajneesh , Hassan Sk. Sarif 
Published: October 2010

AbstractIt is well known that A, T, G, C annealed together early in evolution and the long stretch of DNA was found which ultimately resulted into chromosomes of different organisms. But it is unclear till date how exons, introns, conserved protein domains was formed. Using the DNA sequences of the largest known gene-family present in human genome, i.e., olfactory receptors and simplest possible quadruple context-free L-Systems, we show that conserved protein domains and intergenic regions which lies at the heart of the biological evolution started with a sixteen base-pairs stretch of DNA.
Performance of the major semiempirical, ab initio, and density functional theory methods in evaluating isomerization enthalpies for linear to branched heptanes
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractThe gas phase standard state (298.15 K, 1 atm) isomerization enthalpy prediction performance of the major semiempirical, ab initio, and density functional levels of theory was investigated using the linear to branched heptanes. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are best suited for thermodynamic studies of alkane derivative isomerizations expected during the processing of petroleum, biomass, coal, or other fuels. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise. Non-M062X density functionals are not recommended for theoretical studies of alkane derivative isomerizations.
Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules
Authors: Jaya Sai Karuna , Pradhan Dibyabhaba , Umamaheswari Amineni 
Published: October 2010

AbstractHuman proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES crystal structural data, the three dimensional structure of human YES was constructed based on template structure (PDB ID: 2H8H) obtained through homology search using MODELLER 9V7. The model was refined, energy minimized and assessed through PROCHECK. Active site residues of human YES were identified from the homology model in complex with template ligand AZD0530 and were further confirmed using CASTp. Five published inhibitors of YES family (Dasatinib, Bosutinib, SU6656, AZD0530 and CGP77675) were identified through literature search. High throughput virtual screening method at Ligand.Info was applied for these five inhibitors to establish a library of 1932 structural analogs. LigPrep was used to generate possible conformations of each ligand molecules from structural analog library. The ligand duplicates conformers, ligands having reactive functional group and poor ADME properties were rejected from the prepared dataset. Glide 5.5 was used to generate a grid box by picking the active site residues of human YES protein. Through sequential applications of stringent mode glide docking procedures from Glide HTVS to SP to XP respectively, 13 potential inhibitors were proposed. The docking complexes of each inhibitor with human YES protein were analyzed and lead ‘1’ molecule was identified to have higher binding affinity to human YES protein (XP Gscore: -12.07 Kcal/mol) compared to existing published inhibitors and other 12 lead molecules. The lead ‘1’ - human YES docking complex was highly stabilized through hydrogen bond network with amino acid residues Thr348, Asp358, Asp414 and Phe415. Moreover, from the results obtained we could decipher that lead ‘1’ molecule can be raised into potential inhibitors after binding assays, substantiated experimental investigations and passing several phases of clinical trials.