bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D model of amphioxus steroid receptor complexed with estradiol
Authors: Baker Michael , Chang David 
Published: July 2019

AbstractThe origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid binding to nuclear receptors.
The study of the umbilical system in planktonic foraminifera in relation with depth of the Ziarat-kola section at the Maastrichtian, Central Alborz, IRAN
Authors: Shafiee Ardestani Meysam , Balmaki Behnaz , Asgharian Massod 
Published: July 2019

AbstractThe main aim of this research is study of the planktonic foraminifera morphogroups distinction genus to perform by changing the umbilicus area in Ziarat-kola section to find novel results. Therefore, original objection at this research considers the cause of organizing umbilicus structures (Lip, Portici, Tegilla) at this protests. it seems that phylogeny trend entirely the changes of planktonic foraminifera changing from lip at primary morphogroup to tegilla at development shape which continued this phylogeny trend opening become entirely umbilicus that this trend accompanied to increasing deep. Therefore, the study of planktonic foraminifera morphotype, and recognizing, the obtained results from planktonic foraminifera analysis percent and their comparison with umbilicus structures area diagrams at this section indicats the increasing morphotype three accompany with increase in sea level that here dominated portici and tegilla structure with compressed opening and with decrease of morphotype three which showed decrease sea level, opening structure (lip) dominated. These trends follows the from Pascal law at Ziarat-kola section of the research.
Evolutionary game theory and the evolution of neuron populations, ring rates, and decisionmaking
Authors: Cohen Yosef , Cohen Jeremiah 
Published: July 2019

AbstractOurs, is the first application of dynamical evolutionary games to decision making in neuroscience. Firing neurons are the players. The strategy is their firing rate. Neurons with equal firing rates define a population. The neurons do not know the rules of the game, they do not know what the reward is, they are not required to be rational and they do not even know they are playing the game. Interactions are inhibitory. The theory confirms experimental data about decision making in vision: (i ) A parameter of the game model determines how many populations of neurons participate in the decision; (ii ) the solution of the game dictates how many loci in the brain participate in the decision; (iii ) the theory clarifies the difference between ultimate and proximate factors and predicts that quick decisions are associated with more errors and slow decision are associated with fewer errors.
Independent elaboration of steroid hormone signaling pathways in Metazoans
Authors: Markov Gabriel , Tavares Raquel , Dauphin-Villemant Chantal , Demeneix Barbara , Baker Michael , Laudet Vincent 
Published: July 2019

AbstractSteroid hormones regulate many physiological processes in vertebrates, nematodes and arthropods through binding to nuclear receptors (NR), a metazoan-specific family of ligand-activated transcription factors. The main steps controlling the diversification of this family are now well understood. In contrast, the origin and evolution of steroid ligands remain mysterious although this is crucial for understanding the emergence of modern endocrine systems. Using a comparative genomic approach, we analyzed complete metazoan genomes to provide a comprehensive view of the evolution of major enzymatic players implicated in steroidogenesis at the whole Metazoan scale. Our analysis reveals that steroidogenesis has been independently elaborated in the three main Bilaterian lineages, and that steroidogenic cytochrome P450 enzymes descended from those that detoxify xenobiotics.
Natural Biomolecules from Marine Snail Telescopium telescopium and structure of its sperm: A Phylogenetic Study
Authors: Datta Uttam , Hembram Manik Lal , Roy Subhasis , Mukherjee Prasenjit 
Published: July 2019

AbstractAbstract:Biochemical analysis of the cytosol fraction isolated from the ovotestis / spermatheca glands of marine mollusc Telescopium telescopium and it’s sperm microtubular structure revealed that relatively similar biomolecules like different enzymes, hormones, minerals and structures of the sperm are also exist in humans. Moreover, antiserum of the cytosol fraction was found to cross-react with the human sperm antigen indicated presence of a common sperm surface antigenicity between these two diversified species. These findings might support and / or hypothesize about the origin and diversification of the vertebrate molecules from its ancestral form (s) from the invertebrates, and basic physiological functions of these ancestral biomolecules including some of the cellular structures plausibly remain the same regardless their structural changes even after evolution.
Tap Water vs. Bottled Water in a Footprint Integrated Approach
Authors: Botto Stefano 
Published: July 2019

AbstractA Footprint Integrated approach was used to assess and compare the impact on the environment and on the resources of tap water (TW) and pet-bottled natural mineral water (BW). A set of BW from six Italian companies was analyzed. This set covers about the 10% (by volume) of the total marketed bottled waters in Italy. TW is the public water available in Siena (Italy). The functional unit is a volume of water of 1.5 L.An ad hoc Footprint methodology was defined, integrating Ecological Footprint (EF), Water Footprint (WF) and Carbon Footprint (CF). A Life Cycle Assessment (LCA) was performed, in order to derive the material and energy inputs and outputs of each upstream and downstream process required by the two ways of drinking water.In the comparison based on Ecological Footprint and Carbon Footprint, tap water showed about 300 times lower values than bottled water. On the contrary, Water Footprint values were quite similar: TW displayed the same value of the average BW. The Footprint Integrated results were used to assess the Footprint savings allowed by tap water drinking. Water Footprint reduction chances were also discussed, including a comparison between PET, PLA (polylactic acid) and glass in bottling practice. Tap water seemed to be able to reduce his water consumption and withdrawal more than bottled water.
Use of inadequate data and methodological errors lead to a dramatic overestimation of the water footprint of Jatropha curcas
Authors: Maes Wouter , Achten Wouter , Muys Bart 
Published: July 2019

AbstractIn their recent article, Gerbens-Leenes et al. (1) calculated the water footprint (WF, the amount of water required to produce 1 GJ of energy) of several bioenergy crops. One of the most remarkable findings of this study was the very high water footprint of this species, which has serious management consequences. However, these results are in apparent contrast with recent findings on this species. We present evidence that several errors were made by the authors when calculating the water footprint of jatropha, which has lead to a dramatic overestimation. These errors include weaknesses concerning the data used for the calculation of the water footprint, as well as flaws in the calculation method, as we demonstrate in the letter. Based on peer-reviewed data, we furthermore provide a more correct, still rough, first estimate for the water footprint of this species, which would place it amongst the more water efficient bioenergy crops.
A novel Drosophila post-genomic CNS drug discovery model detects tetraethylammonium chloride with therapeutic potential
Authors: Singh Priyanka , Mohammad* Farhan , Sharma Abhay 
Published: July 2019

AbstractA Drosophila behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was distinct from the other one consisting of PTZ, GBP, VGB and ETH. Further, like LEV and NaVP, TEA regulated genes overrepresented ribosomal and energy metabolic pathways. Also, TEA, like LEV and NaVP, ameliorated development of locomotor deficit in the chronic PTZ model. Both transcriptomic and behavioral analyses thus demonstrated LEV- and NaVP- like neuroprotective effect of TEA. Our results are consistent with earlier paradoxical evidence suggesting that TEA may be neuroprotective. Amenability of Drosophila model thus provides an excellent opportunity to understand long term mechanisms of action of centrally acting drugs in molecular details.
Cross-Product Extensions of the Gene Ontology
Authors: Mungall Christopher , Bada Michael , Berardini Tanya , Deegan Jennifer , Ireland Amelia , Harris Midori , Hill David , Lomax Jane 
Published: July 2019

AbstractThe Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries.
Modulation of the Nuclear Transcription Factor of Activated T Cells by Duck Hepatitis B Virus
Authors: Loscher Christine , Matschl Urte , Iwanski Alicja , Chang Schau-Feng , Bruns Michael 
Published: July 2019

AbstractDuring infection with hepadnaviruses besides the infectious agent a high number of subviral particles without nucleocapsids are produced, which are able to change the infection dramatically. In addition, it was observed that the activation of the nuclear factor of activated T cells, regulated usually in cells of the immune system, was strongly influenced after infection. When primary duck liver cells were infected with purified virions of duck hepatitis B virus the activation of this factor was reduced in a similar way as it was achieved by inhibition of calcineurin, a cellular phosphatase necessary to control the factor, whereas the addition of subviral particles inhibited this reduction. It was found that the large surface protein of the virus was responsible for the reduced activity. Although this protein was embedded in similar amounts into the envelopes of both particles, only virions were able to inhibit the activity of the nuclear factor. An explanation of the different performances of the particles in primary duck liver cells apparently depends on the individual mode of insertion of the large surface proteins into the viral membrane. Furthermore, the nuclear factor of activated T cells could only be detected in liver sinusoidal endothelial cells, which was shown being attracted by virions but not by subviral particles.
Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
Authors: Arjunan Satya , Tomita Masaru 
Published: July 2019

AbstractThe-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement.
Desiderata for an ontology of diseases for the annotation of biological datasets.
Authors: Bodenreider Olivier , Burgun Anita 
Published: July 2019

AbstractThere is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
Authors: Batchelor Colin , Bittner Thomas , Eilbeck Karen , Mungall Chris , Richardson Jane , Knight Rob , Stombaugh Jesse , Zirbel Craig , Westhof Eric , Leontis Neocles 
Published: July 2019

AbstractBiomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared structural features, especially when these can be linked to specific functions. The RNAO is being developed in line with the developing standards of the Open Biomedical Ontologies (OBO) Consortium.
Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera
Authors: Riju Aikkal , Arunachalam Vadivel 
Published: July 2019

AbstractOil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in E. guineensis species and in E. oleifera, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and Indel(4.1/kbp) frequency was higher in E. oleifera than E. guineensis species (16.8/kbp, 1.6/kbp). E. oleifera showed higher transition to transversion ratio (1.40) than in E. guineensis (1.02). The ratio of Ts vs Tv showed, the genetic divergence is occurring in this crops in different fashion and E. guineensis had diverged more than E. oleifera. We provide the results of the study as online database ("http://riju.byethost31.com/oilpalm/":http://riju.byethost31.com/oilpalm/) for use by oil palm breeders.
Using Ontology Fingerprints to evaluate genome-wide association study results
Authors: Tsoi Lam , Boehnke Michael , Klein Richard , Zheng W. Jim 
Published: July 2019

AbstractWe describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block. We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for LDL; and LPL, APOA1 and APOB for triglyceride. In addition, we identified some top ranked genes linking to lipid metabolism from the literature even in cases where such knowledge was not reflected in current annotation of these genes. These results demonstrate that ontology fingerprints can be used effectively to prioritize genes from GWA studies for experimental validation.
Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery Using Natural Polysaccharides
Authors: Jain Vikas , Singh Ranjit 
Published: July 2019

AbstractIn the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron microscopy. The colon specific formulations were prepared by compression coating of microsponges with pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data followed Higuchi matrix and the main mechanism of drug release from microsponges was diffusion. In vitro studies exhibited that compression coated colon specific tablet formulations started the release the drug at the 6th hour corresponding to the arrival time to proximal colon.
The Sonic Hedgehog Pathway Stimulates Prostate Tumor Growth by Paracrine Signaling and Recaptures Embryonic Gene Expression in Tumor Myofibroblasts
Authors: Shaw Aubie , Gipp Jerry , Bushman Wade 
Published: July 2019

AbstractThe Hedgehog (Hh) pathway contributes to prostate cancer growth and progression. The presence of robust Shh expression in both normal prostate and localized cancer challenged us to explain the unique growth promoting effect in cancer. We show here that paracrine Hh signaling exerts a non-cell autonomous effect on xenograft tumor growth and that Hh pathway activation in myofibroblasts alone is sufficient to stimulate tumor growth. Nine genes regulated by Hh in the mesenchyme of the developing prostate were found to be regulated in the stroma of Hh over-expressing xenograft tumors. Correlation analysis of gene expression in matched specimens of benign and malignant human prostate tissue revealed a partial 5 gene fingerprint of Hh-regulated expression in stroma of all cancers and the complete 9 gene fingerprint in the subset of tumors exhibiting a reactive stroma. No expression fingerprint was observed in benign tissues. We conclude that changes in the prostate stroma due to association with cancer result in an altered transcriptional response to Hh that mimics the growth promoting actions of the fetal mesenchyme. Patients with an abundance of myofibroblasts in biopsy tissue may comprise a sub-group that will exhibit a particularly good response to anti-Hedgehog therapy.
Cosmetic Use of Botulinum Toxin-A Affects Processing of Emotional Language
Authors: Havas David , Glenberg Arthur , Gutowski Karol , Lucarelli Mark , Davidson Richard 
Published: July 2019

AbstractLanguage can evoke powerful emotions and influence consequent actions in readers, but the mechanisms underlying interactions of language and emotion are largely unknown. Since Darwin, emotional expressions have been implicated in emotional cognition, experience and understanding, but the functional role of the affective periphery is difficult to test. In a first experiment, facial electromyography revealed that silent reading of emotional (angry, sad, and happy) sentences automatically elicits differential patterns of activity in facial muscles used in expression of corresponding emotions (smiling and frowning). In a second experiment, temporary paralysis of the facial muscle corrugator supercilli (responsible for producing a frown) hindered processing, relative to pre-injection baseline, for angry and sad sentences, while processing for happy sentences was unaffected. These findings suggest a bi-directional mechanism between emotion and language, offer new evidence for facial feedback theories of emotion, and report a novel effect of botulinum toxin-A on human cognition.
Evaluation of protein surface roughness index using its heat denatured aggregates
Authors: Mishra Hrishikesh , Lahiri Tapobrata 
Published: July 2019

AbstractRecent research works on potential of different protein surface describing parameters to predict protein surface properties gained significance for its possible implication in extracting clues on protein's functional site. In this direction, Surface Roughness Index, a surface topological parameter, showed its potential to predict SCOP-family of protein. The present work stands on the foundation of these works where a semi-empirical method for evaluation of Surface Roughness Index directly from its heat denatured protein aggregates (HDPA) was designed and demonstrated successfully. The steps followed consist, the extraction of a feature, Intensity Level Multifractal Dimension (ILMFD) from the microscopic images of HDPA, followed by the mapping of ILMFD into Surface Roughness Index (SRI) through recurrent backpropagation network (RBPN). Finally SRI for a particular protein was predicted by clustering of decisions obtained through feeding of multiple data into RBPN, to obtain general tendency of decision, as well as to discard the noisy dataset. The cluster centre of the largest cluster was found to be the best match for mapping of Surface Roughness Index of each protein in our study. The semi-empirical approach adopted in this paper, shows a way to evaluate protein's surface property without depending on its already evaluated structure.