bluuebunny/crossref_metadata_2025 huggingface dataset:
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

OBJECTIVESWe 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.
CDAO-Store: A New Vision in Data Integration
Authors: Chisham Brandon , Le Trung , Pontelli Enrico , Son Tran , Wright Ben
Published: October 2010

The 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

Recent 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.
A new phylogenetic comparative method: detecting niches and transitions with continuous characters
Authors: Boettiger Carl
Published: October 2010

Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples of these weaknesses using a classic data set on Anoles lizards. I describe a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes.
Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck. (Commelinaceae)
Authors: Nandikar M , Gurav R
Published: October 2010

Murdannia 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

Phylontal 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

Phenex 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

Regulation 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

For 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

Next 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

Melatonin 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

The 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

A 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

Systems 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

The 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

Last 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

It 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

The 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

Human 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.
In Silico Analysis To Explore Novel Inhibitors For Human Proto-oncogene Tyrosine Protein Kinase Src
Authors: Mahanandi Nagapriya , Pradhan Dibyabhaba , Umamaheswari Amineni
Published: October 2010

The first oncogene and the first non receptor tyrosine kinase, Src, plays a key role in cell morphology, motility, proliferation and survival. Over expression of Src kinase activity disrupts the RAS pathway in signaling pathway, where it loses its ability to hydrolyse GTP and thus, leads to cancer. A wide range of evidences indicated that Src-signaling was important in the oncogenesis of prostate cancer and other tumours. Src-signaling is involved in androgen-induced proliferation of prostate cancer in cancer tissue of patients having castration-refractory prostate cancer. Once prostate cancer becomes castration-resistant, bone metastases become significant problem for which treatment options are limited. As Src is involved in multiple signaling pathways, central to prostate cancer development, progression, and metastasis, in addition to normal and pathologic osteoclast activities, Src inhibition becomes a valid therapeutic strategy for investigation. Existing Src kinase inhibitors are less efficient towards prostate cancer and bone metastasis. Hence an in silico work was carried out to identify novel potent inhibitors. Three published inhibitors of human Src kinase those are currently under clinical trial such as AZDO530, bosutinib and dasatinib were subjected to high-throughput screening from more than million entries of Ligand.Info Meta-Database, based on the assumption that small molecules with similar structure have similar pharmacological properties. The ligand dataset of 1152 generated through this approach were prepared using LigPrep to generate possible conformations of each ligand molecule, and at the same time duplicate conformers, conformations with reactive functional group and ADME violaters were rejected. The human Src kinase co-crystal structure with AZDO530 was analyzed to find the inhibitor binding site. The crystal structure was optimized and energy was minimized applying OPLS force field in Maestro v9.0. Glide 5.5 docking was performed to predict the binding orientation of prepared ligand molecule into a grid of 20 x 20 x 20 Å created around the centroid of optimized human Src kinase. Ten lead molecules with good binding affinity with human Src were identified. In silico pharmacokinetics study for these ten lead molecules had shown no ADME violation. Analysis of Lead ‘1’ - human Src docking complex had revealed a XP Gscore of -11.56 kcal/mol with highly stabilized hydrogen bond network with Ala390, Asn391, Lys295, W543 and W640 and good Van der Waals interactions. The docking complex coincides well with the native co-crystallized human Sac and inhibitor AZDO530 complex. Thus, Fisetin, identified as Lead ‘1’ in the present study would be highly useful for developing potential drug molecules for treatment of advanced prostate cancer.
Deciphering the genome structure and paleohistory of Theobroma cacao
Authors: Chaparro Cristian , Murat Florent , Carlson John , Guignon Valentin , Tahi Mathias , Guiderdoni Emmanuel , Legavre Thierry , Fouet Olivier , Sallet Erika , Sabau Xavier , Akaza Joseph Moroh , Quetier Francis , Guiltinan Mark , Poulain Julie , T. Schiex , Axtell Michael , Pitollat Bertrand , Panaud Olivier , Maximova Siela , Ruiz Manuel , Dievart Anne , Ma Zhaorong , Gramacho Karina , Wincker Patrick , Roguet Yolande , Kramer Melissa , Zhang Yufan , D’Hont Angélique , Sidibe-Bocs Stephanie , Lanaud Claire , Argout Xavier , Rodier-Goud Maguy , Gelley Laura , Brown Spencer , Brunel Dominique , Infante Diogenes , Salse Jerome , Barbosa-Neto Jose Fernandes , Sh Zi , Bourge Mickael , Golser Wolfgang , Kebe Ismael , Aury Jean Marc , Sabot Francois , Bérard Aurélie , Viot Christopher , Song Xiang , Costet Pierre , Droc Gaetan , Kudrna Dave , Ammiraju Jetty Siva , Boccara Michel , Clement Didier , Wing Rod , Gouzy Jerome , Abrouk Michael , Schuster Stephan , Risterucci Ange Marie , Rivalan Ronan , McCombie W. Richard , Allegre Mathilde
Published: October 2010

We sequenced and assembled the genome of Theobroma cacao, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for T. cacao disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. The T. cacao genome can be considered as a simple living relic of higher plant evolution.
The activating receptors 2B4 and NTB-A, but not CRACC are subject to ligand-induced down-regulation on human natural killer cells
Authors: Meinke Stephan , Böhm Carolin , Durlanik Sibel , Watzl Carsten
Published: October 2010

Activation of natural killer cells can be mediated by different receptors. Stimulation of the receptors 2B4, NTB-A and CRACC, members of the SLAM-related receptor family, induces cytotoxicity and cytokine production. The surface expression of 2B4 and other activating natural killer cell receptors is down-modulated after receptor engagement, which results in a weaker response to consecutive stimulation. We tested whether this regulatory mechanism applies to all SLAM-related receptors expressed by primary human natural killer cells. After co-culture with target cells expressing the respective ligands different effects on receptor surface expression were observed. While 2B4 ex-pression was strongly reduced, NTB-A showed less prominent down-modulation and the expression level of CRACC remained unchanged. The expression levels of the receptor-proximal signaling molecules SAP, EAT-2 and FynT did not change after receptor engagement. Co-culture with target cells expressing the ligands for NTB-A or CRACC had no impact on subsequent NTB-A or CRACC-mediated NK cell activation.
Diabetes and kidney cancer: A direct or indirect association?
Authors: Ojha Rohit , Evans Eva , Powell Tabatha , Nuwayhid Bahij , Mulla Zuber
Published: October 2010

A positive association between diabetes and kidney cancer has been reported in several investigations, but it is unclear whether diabetes or its complications account for this association. Recent advances in estimating direct associations may be useful for elucidating the association between diabetes and kidney cancer. Therefore, we performed a case-control analysis to evaluate whether the direct association between diabetes and kidney cancer is the primary concern in this exposure-outcome relation. Discharge data (with International Classification of Diseases – 9 codes) from 2001 for hospitals throughout Florida were used to construct a case-control population of inpatients aged ≥45 years. Cases (n=1,909) were inpatients with malignant kidney cancer and controls (n=6,451) were inpatients with motor vehicle injuries. Diabetes status was ascertained for cases and controls. Covariates that required adjustment to estimate the total (age, gender, ethnicity, obesity, and smoking) and direct (age, gender, ethnicity, obesity, smoking, hypertension, and kidney disease) associations were identified in a directed acyclic graph. Binary logistic regression was used to estimate the adjusted total and direct odds ratios (ORs) and corresponding 95% confidence intervals (CIs) of kidney cancer for diabetics. The odds of kidney cancer were higher for inpatients with diabetes than inpatients without diabetes when estimating the total association (OR=1.27, 95%CI: 1.10, 1.47) but attenuated when estimating the direct association (OR=1.08, 95%CI: 0.93, 1.25). Our findings provide preliminary insight that the direct association between diabetes and kidney cancer may not be the primary concern in this exposure-outcome relation; indirect pathways (i.e. diabetic complications) may have greater influence on this relation. A similar analysis using longitudinal data with appropriately measured covariates may provide more definitive conclusions and could have implications for kidney cancer prevention among diabetics.
PERSPECTIVES OF NANODIAMOND FORMATION FROM THE ORGANIC MATTER AT LOW P-T PARAMETERS
Authors: Simakov Sergei
Published: October 2010

The perspectives of nanosized diamond particles formation at metastable P-T parameters from organic matter at hydrothermal conditions is discussed. From the known data it’s possible to conclude that we could provide the hydrothermal syntheses of nanodiamonds from the water-oil or water-alcohol-oil solutions.
SC1/PRDM4 recruits PRMT5 to control the timing of neural precursor differentiation in developing neural stem cells
Authors: Chittka Alexandra , Grazini Ursula
Published: October 2010

During cortical development, neural stem cells (NSCs) switch from proliferative to neuron-generating asymmetric divisions. Here we investigated the role of Schwann cell factor 1 (SC1/PRDM4), a transcriptional repressor highly expressed in the developing nervous system, during NSCs development. We found that SC1 protein levels were down-regulated in newly differentiating neurons, while remaining high in undifferentiated NSCs, suggesting an asymmetric inheritance of SC1. Knockdown of SC1 in the NSCs led to precocious differentiation of neurons and its overexpression led to an increase in Nestin-expressing precursors. We found that SC1, through its amino-terminus, recruits the chromatin modifier PRMT5, a histone arginine methyltransferase that catalyses histone H4R3 symmetric dimethylation (H4R3me2s). Mutations disrupting SC1/PRMT5 interaction resulted in loss of SC1-mediated increase in undifferentiated neural precursor cells. Our data demonstrate that SC1 and PRMT5 are components of an epigenetic regulatory complex that provides an epigenetic signature of a “stem-like” cellular state in the NSCs and which may be asymmetrically inherited during neurogenic divisions.
Molecular evidence for Toxoplasma gondii in the brain of striped dolphins (Stenella coeruleoalba) stranded along the Ligurian Sea coast of Italy
Authors: Traversa Donato , Di Cesare Angela , Casalone Cristina , Iulini Barbara , Mignone Walter , Tittarelli Cristiana , Proietto Umberto , Meloni Silvana , Buffatello Giulia , Forster Fiona , Kennedy Seamus , Di Guardo Giovanni
Published: October 2010

Toxoplasma gondii is a protozoan agent of increasing concern for both free-ranging and captive cetaceans. Nonetheless, information on epidemiology, biology, genetics and pathogenic potential of T. gondii for aquatic mammals is incomplete. This work provides molecular evidence for T. gondii in the brain tissue from five striped dolphins (Stenella coeruleoalba) found stranded in 2007-2008 along the Ligurian Sea coast of Italy. These animals showed a more or less severe, subacute to chronic, non purulent, multifocal meningo-encephalitis. Additionally, the cerebral parenchyma of 3 animals harboured protozoan cysts and zoites which were immunohistochemically linked to T. gondii. Consequently, a preliminary molecular investigation was undertaken to confirm the presence of the protozoan in these dolphins. Genomic DNA was extracted from the brain tissue of the animals and the extracts were examined with a nested PCR specific for the B1 gene of T. gondii. Three out of the 5 animals scored positive upon B1-PCR. Sequences were subsequently searched against the GenBankTM Database using the Basic Local Alignment Search Tool. The three sequences were identical to each other and showed 100% homology with the corresponding B1 sequence of T. gondii, with no insertions/deletions nor substitutions. The other 2 dolphins were negative upon B1-specific PCRs and also upon PCRs targeting other T. gondii genes (i.e. GRA and UPRT). To explore more in depth the genetic make-up of this protozoan, complementary studies are presently ongoing on GRA and UPRT genes of the 3 animals which were molecularly confirmed (i.e. B1-PCR) as infected by T. gondii. In conclusion, further studies are needed to elucidate a number of epidemiological and biological features of T. gondii infection in free-ranging cetaceans, with special emphasis on “pelagic” species such as striped dolphins.
A unique avenue to control drug resistant pathogens: Experimental evidences
Authors: Sen Sribir
Published: October 2010

Drug resistant bacterial pathogens are increasing in the environment due to multiple reasons. If any drug resistant pathogen grows in a host, the host will face death treat because there is no way to resist their growth in the host system. Eventuality is death in almost all cases. Reports on the mechanisms of drug resistance in bacteria are many. However, there is no solution for these cases. The present work is providing an important understanding to fight against drug resistant pathogens and that can be used in gastrointestinal diseases.
Cluster Analysis of Breast Cancer Microarray Data
Authors: Dave Kirtan
Published: October 2010

High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. The recent development gene expression microarray and related technology provide to an opportunity to perform more detail profiling of the disease However, whole-genome approaches are still relatively new and critics have been quick to highlight, non-overlapping results from groups testing similar hypotheses. In this canopy, cluster analysis helps to reduce complex multivariate data and may be used to devise in the development of classification systems or taxonomies by gene ontology.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Authors: Smith Lucian , Wilkinson Darren , Hucka Michael , Bergmann Frank , Hoops Stefan , Keating Sarah , Sahle Sven , Schaff James
Published: October 2010

This is the final specification for Release 1 of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.More information about SBML and this specification is available online at "http://sbml.org/Documents/Specifications/":http://sbml.org/Documents/Specifications/.
Metabolic Network Representation in SBGN PD: EC and Identity Gate
Authors: Mazein Alexander
Published: October 2010

This presentations describes proposed changes in SBGN PD that would allow this language to be better adopted for representing metabolic network.
Context-based generation of kinetic equations with SBMLsqueezer 1.3
Authors: Dräger Andreas , Nitschmann Sandra , Dörr Alexander , Eichner Johannes , Ziller Michael , Zell Andreas
Published: October 2010

The development of predictive, quantitative models constitutes a common task in today‘s systems biology. To obtain a mathematical model description for the simulation of gene-regulatory, signaling, and metabolic networks, kinetic equations are required for each reaction within the network. Deriving and assembling these formulas is a complicated, time-consuming, and error-prone process that requires knowledge about the structure of interactions, consistently choosing a rate law for each type of reaction, and assignment of appropriate units to all parameters. In many cases, thermodynamic dependencies between the parameters have to be taken into account. For multi compartment models, the concentration units of reacting species have to be converted into molecular amounts. Here we present version 1.3 of the program SBMLsqueezer that generates kinetic equations for SBML models based on the definition of the network's topology and annotations of the elements therein, i.e., Systems Biology Ontology (SBO) and Minimal Information Requested In the Annotation of Models (MIRIAM) annotations.
JSBML
Authors: Rodriguez Nicolas , Dräger Andreas
Published: October 2010

The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.
Phantom Pain Reduction by Non-ionizing Electromagnetic Treatment
Authors: Bokkon Istvan
Published: October 2010

Based on our years of experience testing a technique called non-ionizing Electromagnetic-Own-Signal-Treatment (EMOST), here, we present our preliminary results for phantom pain reduction by this method under clinical circumstances. Our preliminary results showed not only a reduction in phantom pain in patients but also a marked improvement in their sleep and mood quality after the treatments. Here, we also suggest that some of the important effects of our method may be achieved via the redox balance of the body and redox-related neural plasticity. However, low-frequency and intensity electromagnetic fields can potentially provide useful methods for the treatment of various problematic disorders and can play important roles in public health of the 21st century medicine.
Update on libSBML status
Authors: Keating Sarah
Published: October 2010

Update on the current status of the stable 4.2.0 release and the developmental 5.0.0 release of libSBML; an API library for reading/writing and manipulating SBML.
Towards reproducible MSMS data preprocessing, quality control and quantification
Authors: Gatto Laurent , Lilley Kathryn
Published: October 2010

The development of MSnbase aims at providing researchers dealing with labelled quantitative proteomics data with a transparent, portable, extensible and open-source collaborative framework to easily manipulate and analyse MS2-level raw tandem mass spectrometry data. The implementation in R gives users and developers a great variety of powerful tools to be used in a controlled and reproducible way. Furthermore, MSnbase has been developed following an object-oriented programming paradigm: all information that is manipulated by the user is encapsulated in ad hoc data containers to hide it's underlying complexity. We illustrate the usage and achievements of our software using a published spiked-in data set in which varying quantities of test proteins have been labelled with four different iTRAQ tags. In addition to providing raw MSMS data, MSnbase also stores meta-data and logs processing steps in the data object itself for optimal traceability. We provide graphics on how to inspect precursor data for quality control and how individual or merged MSMS spectra can subsequently be processed, plotted and extracted using a variety of methods. We also demonstrate how reporter ions (or any peaks of interest defined by the user) can easily be quantified and normalised using several build-in alternative strategies and how the effect of each transformation can be recorded, examined and reproduced. MSnbase constitutes a unique versatile working and development environment to process labelled MSMS data and provides in turn important feedback for data acquisition optimisation. We conclude by presenting future extensions of MSnbase and highlight its usage in reproducible proteomics research.