bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a complete model of radial growth in Pinus edulis: the effects of CO2 and prior years
Authors: Tysor C. Susannah , Whipple Amy , Koch George 
Published: October 2010

AbstractPinus edulis (piñon pine) is found across 35% of the Colorado Plateau and is a foundation species in the piñon-juniper woodlands of the Southwest. Piñon pine mortality in the recent drought has been high and climate change models forecast a warmer future for the region, which will increase piñon pine water stress. In order to predict the fate of piñon pine, we must understand how various climatic factors influence piñon growth. Tree rings provide a climate sensitive record of growth ideal for exploring the relationship between growth and climate. We used 78 piñon pine trees cored at Red Mountain in northern Arizona in 1998 to predict tree ring width and piñon pine mortality, using variables including available moisture, growing season length, tree age, growth in prior years, and [CO~2~] in a hierarchical Bayes modeling structure. As a first step towards the full model, tree ring width in the prior year and [CO~2~] was considered in a lag 1 year autoregressive model of mean yearly ring width with [CO~2~] as a linear covariate.As a linear covariate, [CO~2~] is related to tree ring width with slope 0.019 (95% Credible Interval (CI) 0.015 to 0.024) and intercept -5.5 (95% CI -6.88 to -4.07). Tree ring width increases with [CO~2~] and [CO~2~] explains the overall increasing trend in average yearly ring width better than available moisture (as Palmer Drought Severity Index values) or growing season length (as the number of days/year with an average of 5°C or higher). The autocorrelation coefficient is 0.49 (95% CI 0.30 to 0.68), suggesting a strong effect of growth in the prior year on growth in the subsequent year. The model successfully predicts yearly average ring width, though ring width is overestimated in extremely dry years. As other factors and more data are incorporated into the model, ring width predictions should improve along with our understanding of piñon growth. We plan to consider the ramifications of various climate change scenarios for piñon pine with this model and compare the responses of trees that have survived to those that have died in the recent drought. As recent experiments indicate that piñon pine mortality can arise from drought-induced carbon starvation, the contribution of increasing [CO~2~] to growth could be very important to predicting piñon pine survival.
Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research
Authors: Samwald Matthias 
Published: October 2010

AbstractKey assertions are extracted from “conclusions” sections of PubMed abstracts andconverted into Semantic Web / Linked Data format. The results are made accessible viafiles, a SPARQL endpoint, and a faceted search interface. Conclusion sections areidentified as valuable resources for machine-augmented key assertion identification andintegration in the biomedical domain. Results are discussed and opportunities for futurework and cooperation are highlighted.
BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations
Authors: Woycicki Rafal , Gutman Wojciech , Przybecki Zbigniew 
Published: October 2010

AbstractAnalyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much of the homologies as we can, to proper molecular function, biological process and cellular component (as its proposed by widely accepted Gene Ontology Consortium annotations or MapMan mappings by Max-Planc-Institute).To facilitate fast retrieval of interesting Blast homologies and making right deductions about the biological role of sequences, in big sequencing projects, the new Perl script BRAGOMAP was written. The program make use of some of BioPerl modules as well as the power of regex text-mining in the Perl itself.The script gives us the possibility to find interesting sequence similarities by using keywords and giving points for each one found. It collects all important information from the GenBank data and puts it in different columns of tab-delimited file for further use. If we were interested (for example) in flower differentiation genes we could use the keywords (flower, ovule, anther, etc.) and/or filter all the homologies isolated from flower tissues in a special development stage. We can also filter results by choosing similarities to interesting genes or protein products. This script retrieve also all standard information from the Blast and GenBank files as Description, ACC no., E-value, Similarity positions, Query Length, Percent of Similarity etc. Automatic GO and MapMan annotations are done by looking for genes, protein products and /or DB references in the proper mappings files. Here we present the usefulness of the script in analyzing sequence similarities and annotations mapping of 3855 BAC ends obtained from the HindIII BAC genomic library of cucumber (Cucumis sativus L., line B10).
Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Authors: Spirov Alexander , Holloway David 
Published: October 2010

AbstractA new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Authors: Gu Jin 
Published: October 2010

AbstractTranscription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true motifs when noise is high and shows higher specificity for predicting the tissue-specific functions of CRRs.
Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Authors: Dirnagl Ulrich , Group Members of the MCAO-SOP 
Published: October 2010

AbstractRecently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System
Authors: Denny Ellen , Miller-Rushing Abraham , Haggerty Brian , Wilson Bruce , Weltzin Jake , USA-NPN Protocol Development Team the rest of the 
Published: October 2010

AbstractThe USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise—from backyard naturalists to professional scientists—to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify specific single dates at which individual phenological events are observed, but the scientific usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that directs observers to record each day that they observe an individual plant, and to assess and report the state of specific life stages (or phenophases) as occurring or not occurring on that plant for each observation date. Observations of animal phenophases are similarly recorded, although for a species as a whole rather than for a specific individual. Evaluation is phrased in terms of simple, easy-to-understand, questions (e.g. “Do you see open flowers?”) which makes it appropriate for a broad audience. From this method, a rich dataset of phenological metrics can be extracted, including the duration of a phenophase (e.g. open flowers), the beginning and end points of a phenophase (e.g. traditional phenological events such as first flower and end flowering), multiple distinct occurrences of phenophases within a single growing season (e.g multiple flowering events, common in drought-prone regions), as well as quantification of sampling frequency and observational uncertainties. The system also includes a mechanism for translation of phenophase start and end points into standard traditional phenological events to facilitate comparison of contemporary data collected with this new “phenophase status” monitoring approach to historical datasets collected with the “phenological event” monitoring approach. These features greatly enhance the utility of the resulting data for statistical analyses addressing questions such as how phenological events vary in time and space, and in response to global change.
Crinumin, a novel substitute of chymotrypsin, may control pancreatic insufficiency and inflammation: Purification and characterization
Authors: Singh Kunwar Awaneesh , Singh Chandan , Rao G.R.K. , Jagannatham M.V. 
Published: October 2010

AbstractCrinumin, a glycosylated serine protease with chymotrypsin like catalytic specificity was purified from a medicinally important plant Crinum asiaticum of family Amaryllidaceae. Ethno-botanical information and Pharmacological studies confirming about the presence of active bio- molecules in the Crinum played crucial role in injury, inflamed joint, local pain and arthritis. Biomedical research suggests chymotrypsin was not only used as digestive aid but also helpful in the above disease. These findings support towards the crinumin may be the active bio-molecule. Crinumin shows activity over a wide range of pH (4.5-11.5 and optimum at 8.5), temperature (75 °C and optimum at 70 °C) and is also functional against chaotrophs, organic solvents, and detergents even after prolonged exposure. The molecular mass (67.7kDa), extinction coefficient (17.7) and isoelectric point (6.9) were also estimated. The denatured natural substrates, such as casein, azocasein, azoalbumin and haemoglobin were hydrolysed by crinumin with very high specific activity. The enzyme also showed amidolytic activity against synthetic substrates, N-succinyl-Phe-p-nitroanilide and α-leucine-pnitroanilide. The apparent Km, Vmax and Kcat values obtained from the Lineweaver–Burk plot were 5 × 104 μM, 0.316 μM/min and 0.73 with N-succinyl-L-phenylalanine-p-nitroanilide as substrate. The proteolytic activity of the enzyme is inhibited by PMSF but not by SBTI make it more special and useful than other serine proteases being used in the food industry. Easy and economic purification with high yield (33%), stability and activity in adverse conditions with chymotrypsin like functioning make it better among known chymotrypsin enzymes from different sources.
Nuisance Signal in Resting-State fMRI Study
Authors: Zuo Xi-Nian , Milham Michael 
Published: October 2010

AbstractWe systematically presented various nuisance signals in resting-state fMRI (R-fMRI) dataset. First, we examined the impact of different extraction methods on the default-mode pattern seeded by posterior cingulate cortex (PCC). Second, we compared their differences in test-retest reliability. Finally, we speculated the equivalence of removing global mean signal to removing gray matter mean signal.
Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and Cosmology: Graphene, Boron Nitride and Coronene
Authors: Heyrovska Raji , Atchison Lakshmi , Narayan Sara 
Published: October 2010

AbstractNanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and thereby their precise atomic structures, for the first time. Considered here are three nanomaterials with hexagonal structures, but of quite different properties, namely, graphene (an electrical conductor), boron nitride (an insulator) and coronene (indicators of life in the Universe).
A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Authors: Muetzelfeldt Robert 
Published: October 2010

AbstractThe aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.
Gas phase carbon acidity and correlations with aqueous pK~a~ values: A comparison of B3LYP/6-311++G(d,p), Gaussian-4 (G4), and experimental approaches
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractGas phase standard state (298.15 K, 1 atm) calculations were conducted at the B3LYP/6-311++G(d,p) density functional and the Gaussian-4 (G4) composite method levels of theory to estimate the acidity of various carbon acids. Excellent agreement was found between the G4 gas phase enthalpies and free energies of carbon acid dissociation and corresponding experimental values. The B3LYP/6-311++G(d,p) level of theory displayed a significantly lower accuracy for gas phase acidity prediction, but with similar qualitative trends as the G4 calculations. Good correlations using both theoretical methods were found with corresponding carbon acid aqueous pK~a~ values. However, the pK~a~ prediction accuracy of carbon acids based on correlations with theoretical gas phase acidities appears lower than previously reported. Some carbon acid moieties may be outliers in general aqueous pK~a~ versus gas phase acidity quantitative structure-property relationships (QSPRs), warranting further investigative efforts on broader training sets.
Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision
Authors: Tsuchiya Masa , Piras Vincent , Tomita Masaru , Giuliani Alessandro , Selvarajoo Kumar 
Published: October 2010

AbstractCells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors. However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density distributions resulted in the emergence of distinct high density localizations from non-localized low density spread distributions, forming attractor cores for both atRA and DMSO. These attractor cores overlapped, pointing to the existence of a neutrophil cell fate attractor. Notably, we found the localizations of correlation distributions for the majority of lowly expressed genes (LEGs) ensembles overlapped with the whole genome attractor cores, while the remaining genomes’ localizations did not overlap. Therefore, we postulate the existence of genetic vehicle, made up mainly of LEGs, for the guidance of cell fate.
Creating and improving detoxification pathways for interpretation of toxicogenomics data
Authors: Giesbertz Pieter , Hummel Jonas , Gaj Stan , Jennen Danyel , Kelder Thomas , Evelo Chris , van Delft Joost , Kleinjans Jos 
Published: October 2010

AbstractCurrent high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of these pathway databases contain rather aspecific information about which genes are involved in reactions. A single identifier, like an Enzyme Code, may correspond to a full family of enzymes, whereas only one family member is responsible for the reaction in the given biological context. Another problem arises in the availability of relevant biological pathways for both rodents and humans. This is especially true in the field of toxicology, where many pathways are still lacking. The focus of this project was to create phase I and phase II detoxification pathways using PathVisio, the pathway editor of WikiPathways. New pathway content was generated using information obtained from several trusted resources: a) handbooks, b) manual/automated PubMed literature searches; c) online pathway resources; d) UniProt Knowledgebase; e) EnsEMBL; f) GeneCards. In addition, the content of some existing toxicology pathways was improved. To illustrate the usefulness of the new pathways data from experiments with carcinogenic compounds were retrieved from the main online microarray data repositories Gene Expression Omnibus (GEO) and ArrayExpress. The resulting data were visualized on the new pathways using PathVisio. All these pathways are made available to the community at WikiPathways, where they can be further used for statistical pathway analysis and visualization in the (toxico)genomics field.
Chopped Arms & Big Macs: ERP Correlates of Viewing and Imagining Aversive and Food Photos
Authors: Comeau Amy , Yeh Wei-Hsien , Abizaid Alfonso , Hellemans Kim , D'Angiulli Amedeo 
Published: October 2010

AbstractOBJECTIVESWe investigated the Event-Related Potential (ERP) correlates of perceived and imagined food photos and their relation to the perception and imagery of unpleasant emotional photos. Our aim was to determine whether similar or different patterns of neural activity were associated with viewing and imagining food photos versus emotional photos. METHODS Nine volunteers with prescreened normal mood and anxiety levels wore a 32 channel Cap with embedded electrodes (10/20 international system) connected to a high-density low-noise Neuroscan EEG system. Participants were tested during two different blocks: a hunger block (containing 25 neutral and food photos) and an emotional block (containing 3 sets of 20 neutral, unpleasant and pleasant photos). The photos were selected from the International Affective Picture System (Lang, Bradley, & Cuthbert, 1999). In both blocks, each trial began with a blank screen followed by presentation of a centered fixation point, displayed for 1 second. A photo was displayed for 3 seconds followed by a 1-second blank mask. For the next 3 seconds, participants were asked to form a mental image of the photo they had just viewed and then rate its vividness (i.e., the self-reported imagery intensity, D’Angiulli & Reeves, 2002) on a 5-point rating scale (1 = no image, 5 = very vivid). RESULTSGrand averages of ERPs recorded during perception of unpleasant and food photos revealed an early negative deflection (150-250 milliseconds post-stimulus) in the anterior areas (Centro-Frontal electrodes) followed by a late positive waveform (850-950 milliseconds post-stimulus) in the posterior areas (Parietal and Occipital electrodes). A similar pattern was observed for the ERPs recorded during the imagery of unpleasant photos, except that it was observed across the entire scalp and at significantly lower amplitudes. For food imagery, we found a negative deflection (450-550 milliseconds post-stimuli) followed by a late positive waveform for all anterior and posterior areas. Importantly, unpleasant imagery was rated as less vivid than food imagery. CONCLUSION These results suggest that unpleasant and food photos involve similar top-down EEG activation patterns during perception, but not during imagery. Indeed, the vividness data strongly suggest that the negative deflection may indicate suppression of unpleasant imagery. Our findings may have important application for desensitization and conditioning in the treatment of eating disorders.