bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CALBC RDF Triple store: retrieval over large literature content
Authors: Croset Samuel 
Published: April 2011

AbstractIntegration of the scientific literature into a biomedical research infrastructure requires the processing of the literature, identification of the contained named entities (NEs) and concepts, and to represent the content in a standardised way.The CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions (Silver Standard Corpus, SSC). The four semantic groups were chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). The content of the SSC has been fully integrated into RDF Triple Store (4,568,678 triples) and has been aligned with content from the GeneAtlas (182,840 triples), UniProtKb (12,552,239 triples for human) and the lexical resource LexEBI (BioLexicon). RDF Triple Store enables querying the scientific literature and bioinformatics resources at the same time for evidence of genetic causes, such as drug targets and disease involvement.
Systems Biology Graphical Notation: Process Description language Level 1
Authors: Moodie Stuart , Le Novere Nicolas , Demir Emek , Mi Huaiyu , Villeger Alice 
Published: April 2011

AbstractStandard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven 
Published: April 2011

AbstractThe molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargoes inside cells.During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and unbinding rates for kinesin and thus offers a tool to specifically probe those steps. We will report the effects of different osmolytes on microtubule speed and other observables in the gliding motility assay.Kinesin’s kinetic core cycle hydrolyzes ATP with the help of a water molecule. Any modification to the water molecules the kinesin is in will change how ATP hydrolyzes and will ultimately affect how kinesin moves along microtubules. We will report preliminary results showing how kinesin is affected when the solvent it is in is changed from light water to heavy water.When used in a surface assay or in devices, the kinesin and microtubule system is also dependent on substrate passivation. Kinesin motor domains do not transport microtubules in the gliding motility assay if kinesin is added to a glass microscope slide that has not been functionalized. Functionalization of the glass slides and slips is typically performed with bovine milk proteins called caseins. Bovine casein is a globular protein that can be broken up into four constituents: αs1, αs2, β, and κ. Each casein constituent affects how kinesin adheres to the glass and ultimately the speed at which microtubules are observed to glide at. Building on the work of Verma et.al., we have found that each constituent individually produces different outcomes in gliding assays. We will present these findings and discuss implications they have for the use of gliding assays to study kinesin and the use of the kinesin-microtubule system in microdevices.[1] Chaen, S, N Yamamoto, I Shirakawa, and H Sugi. 2001. Effect of deuterium oxide on actomyosin motility in vitro. Biochimica et biophysica acta 1506, no. 3: 218-23.[2] Vivek Verma, William O Hancock, Jeffrey M Catchmark, "The role of casein in supporting the operation of surface bound kinesin," J. Biol. Eng. 2008; 2: 14.
Acknowledgements:
This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008.CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I've edited the poster to correct for this. Thanks, Erik!
(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Authors: Koch Steven , Maloney Andy , Herskowitz Lawrence 
Published: April 2011

AbstractThe osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule gliding speeds from image series. We will also show our preliminary analyses of the changes seen in gliding assays when done in heavy water (either heavy-hydrogen or heavy-oxygen) or osmolytes (betaine). We will discuss whether osmotic stress and isotopes, particularly heavy-oxygen water, might be an important tool for probing effects of water on binding interactions between kinesin and microtubules. We will also discuss potential applications of deuterium water for stabilizing microtubules and kinesin for lab or device applications.[1] Parsegian, V. A., Rand, R. P., & Rau, D. C. (1995). Macromolecules and water: probing with osmotic stress. Methods in Enzymology, 259.This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008 in collaboration with Dr. Susan Atlas lab (UNM).CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I’ve edited the poster to correct for this. Thanks, Erik!2011 March Correction: Using temperature stabilization and much-improved technique, Andy has taken higher-quality data for the heavy-hydrogen and heavy-oxygen experiments. See the added slides, 6-7.
Structure and function prediction of human homologue hABH5 of E. coli ALKB5 using in silico approach
Authors: Shankaracharya  , Das Saibal , Vidyarthi Ambarish Sharan 
Published: April 2011

AbstractNewly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. The predicted and validated model of human homologue hABH5 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate research on designing appropriate inhibitors, aiding in chemotherapy and cancer related diseases.
Integrative analysis of large-scale biological data sets
Authors: Glaab Enrico , Garibaldi Jonathan , Krasnogor Natalio 
Published: April 2011

AbstractWe present two novel web-applications for microarray and gene/protein set analysis, ArrayMining.net and TopoGSA. These bioinformatics tools use integrative analysis methods, including ensemble and consensus machine learning techniques, as well as modular combinations of different analysis types, to extract new biological insights from experimental transcriptomics and proteomics data. They enable researchers to combine related algorithms and datasets to increase the robustness and accuracy of statistical analyses and exploit synergies of different computational methods, ranging from statistical learning to optimization and topological network analysis.
The effect of abiotic factors on asymbiotic nitrogen fixation in dead roots from the Pacific Northwest
Authors: Hicks William , Chen Hua 
Published: April 2011

AbstractHigh rates of asymbiotic nitrogen fixation have been observed in dead roots. However, little is known about how biotic and abiotic factors influence asymbiotic nitrogen fixation in dead roots. The objective of this study was to examine how nitrogen fixation in dead roots responded to three abiotic factors: temperature, oxygen concentration, and moisture content by measuring acetylene reduction rates in dead roots. For measuring the response to temperature and oxygen, we collected dead roots of Douglas-fir (Pseudotsuga menziesii) from one site in western Oregon, while the effect of moisture content was tested with samples from three species including Douglas-fir, western hemlock (Tsuga heterophylla), and Ponderosa pine (Pinus ponderosa) from three sites in western Oregon. We measured acetylene reduction rates at 5, 13, 20, 30, and 40°C and at oxygen concentrations of 0, 1, 2, 4, 8, and 21% in dead root samples that had been previously wetted. Unaltered root samples with different moisture contents were used to measure the effect of moisture content on acetylene reduction. The optimal temperature for acetylene reduction in roots was 20°C with an acetylene reduction rate of 9.6 nmol/g/d and a standard error of 3.2 nmol/g/d. Asymbiotic nitrogen fixation was greatly reduced above and below this temperature with acetylene reduction rates of 1.2 ± 0.6 nmol/g/d at 5°C and 0.2 ± 0.2 nmol/g/d at 40°C. The highest acetylene reduction rates (13.8 ± 4.2 nmol/g/d) occurred at an oxygen concentration of 2%. Rates dropped sharply under no oxygen condition (3.0 ± 2.8 nmol/g/d) and at an oxygen concentration of 21% (3.0 ± 0.8 nmol/g/d). Optimal acetylene reduction activity occurred above 60% root moisture content and activity was near zero below 60%. These abiotic factors have a similar influence on asymbiotic nitrogen fixation activity in other substrates like dead wood. In the Pacific Northwest, annual nitrogen fixation activity in dead roots tends to be primarily controlled by temperature while above-ground substrates like dead wood can have reduced activity during the dry summer months when lower moisture contents and higher oxygen concentrations can reduce activity.
Getting The Most Out of Your Research
Authors: Erogbogbo Folarin 
Published: April 2011

AbstractResearch is the cornerstone of invention, facilitator of innovation, and mother of discovery. Even though many students are competent in advancing through the class room and getting good grades, excellent research requires a different set of attitudinal and academic skills. This workshop, "Get the most out of your research" is an outstanding program developed from extensive time spent with brilliant scientists and a wide variety of mentored students. Familiarize yourself with the fine points of this workshop and arm yourself for a successful research career.
SNPxGE2: a database for human 3-way SNP-expression associations
Authors: Wang Yupeng , Joseph Sandeep , Liu Xinyu , Kelly Michael , Rekaya Romdhane 
Published: April 2011

AbstractRecently, gene co-expression relationships have been found to be often conditional and dynamic. Besides, many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE2 database contains the computationally predicted human 3-way SNP-expression associations, that is, the differential co-expression between 2 genes is associated with a genotype/SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 701,202 SNPs and 15,000 gene expression profiles. Two models of 3-way SNP-expression associations were considered: gap/substitution and on/off. The implementation was carried out using 64 Linux cluster nodes in ~30 days and assessed SNP-expression combinations. The results, including 4,713 on/off associations and 36,170 gap/substitution associations at a p-value cutoff of 0.001, can be queried in the SNPxGE2 database via either gene name or reference SNP ID. For each reported association, a detailed information page is provided. The SNPxGE2 database can be freely accessed at http://tunisia.ads.uga.edu/SNPxGE2/index.php.
DNA Sequence Evolution through Integral Value Transformations
Authors: Hassan Sk Sarif , Pal Choudhury Pabitra , Guha Ranita , Chakraborty Shantanav , Goswami Arunava 
Published: April 2011

AbstractIn deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database. This problem motivated us to study the DNA evolutions from a more fundamental point of view. Parallel to the CA paradigm we have devised an enriched set of discrete transformations which have been named as Integral Value Transformations (IVT). Interestingly, on applying the IVT systematically, we have been able to show that each of the DNA sequences at various discrete time instances in IVT evolutions can be directly mapped to a specific DNA sequence existing in the database. This has been possible through our efforts of getting quantitative mathematical parameters of the DNA sequences involving Fractals. Thus we have at our disposal some transformational mechanism between one DNA to another.
Characterization of a pig skeletal muscle microarray to study pork quality: the GenmascqChip 15K
Authors: Damon Marie , Herault Frédéric , Vincent Annie , Le Roy Pascale , Cherel Pierre 
Published: April 2011

AbstractPork quality is highly variable and availability of relevant predictors of fresh meat quality at slaughter is critical to optimize carcass use and improve its valuation. High throughput gene expression studies have been widely used to describe biological mechanisms underlying variation of several traits but data are scarce regarding their use as tools for development of biomarkers. The GENMASCQ (GENomics enabled Marker Assisted Selection and Certification of Quality in Pork products ) research program was set up to select, using high-throughput gene expression screening, markers of the biological variation mostly appropriate to describe, and ultimately forecast, the sensory quality of an important meat product, accounting for nearly 40 % of meat protein sources in human food. This report describes the characterization of a porcine skeletal muscle microarray, the GenmascqChip 15K, as a new tool to study pig meat quality. This microarray is annotated at nearly 90 % and permits to explore a list of 9169 unique genes.
Quantitative detection of cereal geminiviruses
Authors: Drechsler Nadine , Habekuß Antje , Thieme Thomas , Schubert Jörg 
Published: April 2011

AbstractThe Geminiviruses _Wheat dwarf virus_ (WDV) and _Barley dwarf virus_ (BDV) cause symptoms such as dwarfing, stunting and yellowing in infected cereals and can lead to reduced yield and even death of the plant. Both viruses are transmitted by the leafhopper _Psammotettix alienus_ Dahlb. in a persistent non propagative manner. WDV is reported in Germany since the early 1990s. In the future an increase of infections is predicted due to global warming which leads to prolonged active periods of the vector in autumn. Furthermore infected plants can hibernate and serve as source of infection in spring.For the first time quantitative PCR assays were developed which allow the sensitive detection and quantification of WDV and BDV both in plants and vectors. Both viruses are detected with primers located in conserved regions of the viral genome. Taqman® Hydrolysis probes were designed for differentiating detection of WDV and BDV. The absolute quantification of viral copies is done by a standard dilution series of cloned viral DNA. The sensitivity of the method was compared to DAS-ELISA. For this purpose, sap of heavily infected plants was diluted with sap of healthy plants. With qPCR, virus was detectable in dilutions of 10-8 whereas the ELISA reaches the limit of detection at dilutions of 10-4.Field plants were analyzed to investigate how many viral copies can be found under natural infection conditions in late spring. ELISA and rating of symptoms were performed in parallel. It could be shown that viral copy number does not correlate with severity of disease symptoms.Winter barley cultivar ‘Rubina’ was inoculated with viruliferous _P. alienus_ under greenhouse conditions to monitor spatial development of infection. Virus titre increased continuously over 4 weeks. The virus was unequally distributed in the plant; the highest amounts were detected in the youngest leaf.Body and head of _P. alienus_ were analyzed separately to quantify virus content. The viruliferous leafhoppers were kept on plants for 7 days to infect them. It became evident that virus content of the vector does not correlate with its ability to infect plants.These highly sensitive and specific PCR assays allow a wide range of applications, e.g. investigations of the development of virus infection in the plant, vector transmission studies and comparisons of virus content of different cultivars for resistance breeding purposes.
Stir Bar Sorptive Extraction – A method for detection of volatiles from potato plants?
Authors: Beyer Katrin , Ziegler Angelika , Ulrich Detlef , Weiß Kirsten , Grünwald René , Wilhelm Ralf 
Published: April 2011

AbstractThe application of Stir Bar Sorptive Extraction (SBSE) as a method for extraction of emitted volatile compounds of potato leaves using GC/MS will be studied. A suitable efficient method shall be developed to describe differences in the spectrum of volatile compounds of potato varieties. It was shown that SBSE yields results similar to other established methods but with less effort. The method will be optimized further. The use of the spectrum of volatile compounds as a parameter for variety assessment (e.g.: plant health, plant protection, biosafety) is planned.
Copper and other heavy metals in specialized crops and their effects on soil coenosis
Authors: Steindl Anna , Strumpf Thomas , Riepert Frank 
Published: April 2011

AbstractThe background of the project are claims of the EU regulation to generate reliable data considering the extent of copper contamination in soils of specialized crops in order to decide about copper restrictions in organic farming.2522 single soil samples were collected on 85 vineyard and 13 hop areas with different management histories. Samples were taken from sites presently under cultivation, formerly cultivated, and sites without anthropogenic copper contamination as control, indicating natural background values. In addition to Aqua Regia extraction for determining total copper contents, available plant copper content was analyzed in NH~4~NO~3~ extraction. Soil parameters such as pH-value, C/N ratio, soil type etc. were also analyzed. The correlation between plant-available and total copper contents is not very high, probably due to the broad range of relevant values e.g. soil parameters or cultivation measurements. An ongoing biological survey about the present status of earthworm populations will give information about possible impairments of soil coenosis.
Organic Control of Oilseed Rape Pests through Natural Pesticides and Mixed Cultivation with Turnip Rape
Authors: Ludwig Tobias , Jansen Eva , Trost Benjamin , Mayer Julia , Kühne Stefan , Böhm Herwart 
Published: April 2011

AbstractA mixed cropping system of rapeseed and 10 % turnip rape as trap crop was compared with oilseed rape in pure stand to demonstrate the reduction of infestation by insect pests. Furthermore the application of bio-pesticides like pyrethrum/rape oil (Spruzit® Neu), spinosad (SpinTor), diatomeen earth (SiO~2~) /sunflower-oil and rock powder/water was tested. Oilseed rape showed a higher infestation by stem weevils (Ceutorhynchus spp.) in the mixed cropping system compared to rapeseed in pure stand. The reduction of the pollen beetle (Meligethes aeneus) on the rapeseed buds resulted from higher attractiveness of turnip rape as a consequence of advanced growth. The faster development of turnip rape seems to be the important key of successful pollen beetle regulation. The application of pyrethrum and spinosad against Ceutorhynchus spp. had no effect, spinosad was the only agent that caused a reduction of the pollen beetle.