bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling of capillary RBC flow failure with neuronal depolarization
Authors: Tomita Minoru , Tomita Yutaka , Toriumi Haruki , Unekawa Miyuki , Suzuki Norihiro 
Published: July 2019

AbstractRBC (oxygen-carrier) behaviour in the cerebrocortical microvasculature during K^+^-induced cortical spreading depression (CSD) was examined in urethane-anesthetized male Wistar rats (n=10). The movements of FITC-labeled RBCs in single capillaries in the cortical region were traced with a high-speed camera laser scanning confocal fluorescence microscope and analyzed with Matlab domain software, KEIO-IS2, to obtain the velocities of all labeled RBCs appearing in local capillaries during CSD wave propagation. We found that CSD induced periodic decreases in both RBC number and velocity until RBCs halted or disappeared for 3.3 +/- 2.3 s, and then RBC flow was restored. The RBC flow stall was statistically significant (P < 0.05). During capillary flow failure in association with CSD spread, systemic arterial blood pressure remained unchanged. We conclude that RBCs are transiently sieved and stalled in capillaries during neuronal depolarization, and we suggest that this neuro-capillary coupling involves a hemorheological (viscosity-related) mechanism.
A conceptual framework for the evolutionary selection of biologically 'essential' elements
Authors: Conyers Mark 
Published: July 2019

AbstractStandard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential and nonessential nutrients for plants is not always clear. When animals and 'lower' organisms are considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of monovalent elements (bar H^+^) and divalent elements (bar O2^-^) involves a trade-off between low atomic mass and low ionic potential. The essentiality of Mo and non-essentiality of As remain a problem for this model. This conceptual framework provides a basis for re-evaluating the function of an element in the nutrition of plants, animals and 'lower' organisms.
An evolutionary approach to Function
Authors: Lord Phillip 
Published: July 2019

AbstractThe distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for applying these definitions in practice.
Developing ontologies in decentralised settings
Authors: Garcia Alexander , O’Neill Kieran , Garcia Leyla , Lord Phillip , Stevens Robert , Corcho Oscar , Gibson Frank 
Published: July 2019

AbstractThis paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.
Why are Male IQ Scores More Variable?
Authors: Strauss Bernard , Strauss Jacob 
Published: July 2019

AbstractThe male female difference in the variance of quantitative traits including IQ can be accounted for by the observation of the concentration of genes involved in brain development on the X chromosome and by the mechanism of sex determination in mammals. Females have two X chromosomes with one randomly inactivated. Males have a single X chromosome, which results in increased variance. It is shown that these factors are sufficient to account for the observed differences.
Ustilago and the accidental domestication of maize
Authors: Martinez-Soriano Juan Pablo , Avina-Padilla Katia 
Published: July 2019

AbstractMaize is the essential crop of the Americas. Maize appeared suddenly about 8,500 years ago as domesticated teosinte; however, there is no evidence (genetical, archaeological, linguistic or ethnobotanical) able to support a gradual transformation from the teosinte ear into the corn ear. Teosinte has never been cultivated by Americans, nor did they ever attempt to domesticate it. Its grains were not used as food, making unrealistic the assumption that prehispanics created something edible from seeds that were not so. Plant domestication is a slow process in almost every known crop but maize evolution might not be the case. Teosinte has a brittle cob, whereas maize forms solid ones that do not release their seeds 2. The latter are soft, while in teosinte they are enclosed in hard inedible cases. Why would the prehispanic natives even think of modifying those hard seeds, if they were not used as food in the first place?. The switch from teosinte to maize were due to important mutations, occurring in a relatively short period so that natives immediately noticed if they were well aware of the importance of teosinte (or its parasites) and rescued the resultant newborn maize.Teosinte-maize hybrids were highly susceptible to the fungus Ustilago maydis (known in Mexico as huitlacoche) under natural conditions. Consequently, this parasite was found to infect every part of the hybrid plant.Huitlacoche is well known as a food delicacy and it has been important to Mexicans since prehispanic times and it might have been very likely used as food taken from infected teosinte at the same time it was changing into maize. Ustilago maydis probably played a vital role on the domestication process of maize, since the change from teosinte to maize was noticed by humans, who then rescued it from nature
Variation in PNPLA3 is associated with outcomes in alcoholic liver disease
Authors: Tian Chao , Stokowski Renee , Kershenobich David , Ballinger Dennis , Hinds David 
Published: July 2019

AbstractTwo recent genome-wide association studies have described associations of SNP variants in PNPLA3 with nonalcoholic fatty liver and plasma liver enzyme levels in population based cohorts. We investigated the contributions of these variants to clinical outcomes in Mestizo subjects with a history of excessive alcohol consumption. We show that non-synonymous variant rs738409[G] (I148M) in PNPLA3 is strongly associated with alcoholic liver disease and progression to alcoholic cirrhosis (unadjusted OR = 2.25, P = 1.7x10^-10^; ancestry-adjusted OR = 1.79, P = 1.9x10^-5^).
An assessment of organic solvent based equilibrium partitioning methods for predicting the bioconcentration behavior of perfluorinated sulfonic acids, carboxylic acids, and sulfonamides
Authors: Rayne Sierra , Forest Kaya 
Published: July 2019

AbstractSPARC, KOWWIN, and ALOGPS octanol-water partitioning (log K~ow~) and distribution (log D) constants were calculated for all C~1~ through C~8~ and the straight chain C~9~ through C~15~ perfluoroalkyl sulfonic acids (PFSAs) and carboxylic acids (PFCAs). Application of five established models for estimating bioconcentration factors (BCFs) were applied to the PFSA and PFCA log K~ow~ and log D data and compared to available field and laboratory BCF data. Wide variability was observed between the methods for estimating log K~ow~ and log D values, ranging up to several log units for particular congeners, and which was further compounded by additional variability introduced by the different BCF equations applied. With the exception of n-perfluorooctanecarboxylic acid (n-PFOA), whose experimental BCF was poorly modeled by all approaches, the experimental BCF values of the other PFSA and PFCA congeners were reasonably approximated by the ALOGPS log P values in combination with any of the five log K~ow~ based BCF equations. The SPARC and KOWWIN log K~ow~ and log D values provided generally less accurate BCF estimates regardless of the BCF equation applied. However, the SPARC K~ow~ values did provide BCF estimates for PFSA congeners with errors <0.3 log units using any of the five BCF equations. Model lipophilic and proteinophilic solvent based distribution constant calculations for the PFSA and PFCA congeners with experimental BCFs exhibited similar relationships with their corresponding BCF values. For longer chain PFCA and PFSA congeners, increasing hydrophobicity of the perfluoroalkyl chain appears to be driving corresponding increases in BCF values. Perfluorooalkyl sulfonamides are expected to display similar chain length and branching pattern influences on BCFs, but no experimental data are currently available upon which to validate the estimated values which range widely between the various approaches by up to 10 log units. The amidic proton acidity on primary and secondary perfluoroalkyl sulfonamides will play a significant role in the partitioning of these compounds with both abiotic and biotic organic matter, and will need to be taken into account when assessing their environmental and biological fate.
Rethinking Leucine Zipper – a ubiquitous signal transduction motif
Authors: Nikolaev Yaroslav , Pervushin Konstantin 
Published: July 2019

AbstractIn this essay we attempt to reconsider the concept of the “Leucine Zipper” (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended “Coiled Coil” motifs, on the functional level short and moderately stable “Leucine Zippers” might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended “Coiled Coils”. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we demonstrate how a simple set of rules, applied in the context of the universal coiled coil scaffold, creates a robust LZ interaction vocabulary. Owing to the high abundance of Leucine Zippers, this motif might account for coupling of distinct protein signalling pathways into a unified intracellular signalling network. In the last part of this essay we provide examples demonstrating prevalence of the LZ-mediated signal transduction and illustrate applicability of the “LZ code” formalism to interpret evidences of couplings between cytoplasmic and nuclear signalling networks.
Effect of Stimulating Magenetic Field on Plants
Authors: Charan R. V. K. 
Published: July 2019

AbstractA plant's metabolism contains 90-95 percent of diamagnetic water and rest contains several apra, ferro and dia metals and non-metals.The present work is to study stimulating magnetic effect on plants. In result I find abrupt rising of the pulse rate which may enhance the growth of the plant resulting in removing of necessity of using fertilizers and chemicals for plant growth if it is for human consumption. A relation can also be established in between plant pulsation and the applied field.
Reconstruction of an in silico metabolic model of Arabidopsis thaliana through database integration
Authors: Radrich Karin , Tsuruoka Yoshimasa , Dobson Paul , Gevorgyan Albert , Swainston Neil , Schwartz Jean-Marc 
Published: July 2019

AbstractThe number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant Arabidopsis thaliana, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a core metabolic model containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an intermediate metabolic model attempts to fill gaps and provides better continuity. Third, a complete metabolic model contains the full set of known metabolic reactions and compounds in Arabidopsis thaliana.We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry.
Systems level analysis of transgenerational spermatogenic inheritance predicts biomarkers and underlying pathways
Authors: Sharma Abhay 
Published: July 2019

AbstractTransgenerational spermatogenic inheritance of adult male acquired CNS gene expression characteristics has recently been discovered using a Drosophila systems model. In this novel mode of inheritance, transcriptomic alteration induced by the neuroactive drug pentylenetetrazole (PTZ) has been found to leak to future generations. Here, the available microarray gene expression data pertaining to CNS and/or testis of exposed F0 and the resulting F1 and F2 generations has been pooled and analyzed in an unbiased manner at four levels, namely, biological processes and pathways, protein interactome networks, miRNA-targets, and microarray expression profile similarities. Enrichment for processes related to translation, energy metabolism, cell proliferation, cell differentiation, secretion, central nervous system development, germ cell development, gamete generation, wing development, nutrition etc. was observed. Also, ribosome, oxidative phosphorylation and, to a lesser extent, wingless signaling pathway showed overrepresentation. In the proteomic interactome map, the cell cycle gene Ras85D exhibited overinteraction. In miRNA-target network, the fly transgenerational genes showed overrepresentation of mir-315 targets. Transcriptomic matching revealed overlap of transgenerational set with genes related to epigenetic drug treatment, stem cells, Myc targets and miRNA targets. Many of the findings were consistent with the existing epigenetic evidence in complex mammalian traits. Converging evidence suggests that ribosomal RNA and proteins may serve as candidate biomarkers of transgenerational environmental effect. A compelling systems biology frame-work integrative of transgenerational epigenetic inheritance is suggested. Nutrient, circulating peptide hormone, Myc, Wnt, and stem cell signaling pathways constitute the frame-work. The analysis has implications in explaining missing heritability in complex traits including common human disorders. The fly model offers an excellent opportunity to understand somatic and germline communication, and epigenetic memory formation and its retention across generations in molecular details.
Polymorphisms of CYP1A1 I462V and GSTM1 genotypes and lung cancer susceptibility in Mongolian
Authors: Chang Fuhou , Zhang Zhi-Xie , Ma Jia , QI Jun , Wang Min-jie , Yin Qin , Wang Guang 
Published: July 2019

AbstractAim: To study the genotype of cytochrome P450 1A1(CYP1A1) I462V and glutathions S-transferase M1( GSTM1) and the relationship of the genetic polymorphism of them with the susceptibility of lung cancer in Mongolia of China. Methods: Allele-specific PCR and a multiplex PCR were employed to identify the genotypes of I462V of CYP1A1 and GSTM1 in a case-control study of 210 lung cancer patients with bronchoscopy diagnosis and 210 matched controls free of malignancy.
Results:
The frequencies of the variant CYP1A1(Val/Val) genotypes and GSTM1(-) in lung cancer groups were higher than that in control groups (15.24% vs 7.4% and 56.67% vs 40.95% ). The individuals who carried with CYP1A1(Val/Val) or GSTM1(-) genotype had a significantly higher risk of lung cancer, the OR is 2.56 and 1.89 respectively. Stratified histologically the relative risk increased to 2.6 - fold when the patients carried with two valine alleles than the ones carried one valine allele in cases of SCC. GSTM1(-) genotype is the risk factor of SCC (OR=2.39) and AC(OR=2.16). The presence of at least one Val allele of CYP1A1 and GSTM1(-), the risk of lung cancer was increased, the OR was 4.15 for one Val allele and GSTM1(-) and 2.67 for two Val alleles and GSTM1 Considering ages and smoking status, the risk of lung cancer increased when the age less than 50 who carried with CYP1A1 valine (one or two) alleles or the age during the 51 to 65 who carried with GSTM1(-) genotype. The light smokers with CYP1A1 valine alleles and GSTM1(-) have a high risk for lung cancer. No association was found between the light and heavy drinkers with the susceptibility of lung cancer and the genetic polymorphisms of CYP1A1 I462V and GSTM1(-). Conclusion: The valine allele of CYP1A1 was the risk factors of lung cancer especially for SCC and GSTM1(-) also was the risk factor of lung cancer and especially for SCC and AC of Mongolian, China. Light smoking has a influence each other with genotype of CYP1A1 I462V and GSTM1(-) and susceptibility of lung cancer. No relationship was found between the susceptibility of lung cancer and drinkers with genetic polymorphisms of CYP1A1 I462V and GSTM1(-). The influence of genotypes on the susceptibility of lung cancer may depend on the ages. There may be a synergetic interaction between CYP1A1 valine allele and GSTM1(-) genotypes on the elevated susceptibility of lung cancer. So do those genotypes with light smokers. Key words polymorphism; genotype; lung cancer; cytochrome P450&xFF1B;glutathione S-transferase Abbreviations: SCC, squamous cell carcinoma; AC, adenocarcinoma; SCLC, small cell lung cancer; LCLC, large cell lung cancer
Small critical RNAs in the scrapie agent
Authors: Simoneau Steve , Ruchoux Marie-Madeleine , Vignier Nicolas , Lebon Pierre , Freire Sophie , Comoy Emmanuel , Deslys Jean-Philippe , Fournier Jean-Guy 
Published: July 2019

AbstractUnconventional infectious agents cause transmissible spongiform encephalopathy (TSE) diseases including scrapie and bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease in humans. The protein only hypothesis claims that the TSE agent is composed solely of the protein called prion (PrP^sc^)^1^. This protein is the misfolded form of a host-encoded cellular protein, PrP^c^ exerting presumably a vital role at the synapse^2^. Even though now widely accepted, the prion concept fails to provide in certain circumstances^3-6^, a satisfying interpretation of the infectious phenomenon. Using the 263K scrapie-hamster model, we conducted a transmission study to search for a putative prion-associated factor indispensable for infectivity. Here we show that innocuous recombinant prion protein (recPrP) was capable, in a reproducible manner, of transmitting scrapie disease when the protein was [beta]–sheet converted in a solution containing PrP^sc^-derived RNA material. Analysis of the PrP-RNA mixture revealed the association of recPrP with two prominent populations of small RNA molecules having an average length of about ~27 and ~55 nucleotides. We conclude that the nature of the TSE agent seems to be composed of a nucleoprotein molecular complex, in which informative RNA molecules of small sizes are associated with the misfolded prion protein (PrP^sc^).
Averaging Transformations of Synaptic Potentials on Networks
Authors: Noori Hamid Reza 
Published: July 2019

AbstractThe problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is introduced that simulates the internal information processing of brain compartments. Synaptic potentials are integrated over small number of realistically coupled neurons to obtain macroscopic quantities. The striatal complex, an important part of the basal ganglia circuit in the brain for regulating motor activity, has been investigated as an example for the validation of the model.
Progression of Parkinson’s disease pathology is reproduced by intragastric administration of rotenone in mice
Authors: Pan-Montojo Francisco , Anichtchik Oleg , Dening Yanina , Knells Lilla , Pursche Stefan , Jung Roland , Gille Gabriele , Spillantini Maria Grazia , Reichmann Heinz , Funk Richard 
Published: July 2019

AbstractIn Parkinson’s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic blood or the central nervous system (CNS) (detection limit [rotenone]<20nM), suggesting that rotenone is detoxified by the liver. These alterations are sequential, appearing only in synaptically connected nervous structures, treatment time-dependent and accompanied by inflammatory signs and motor dysfunctions. These results strongly suggest that the local effect of pesticides on the ENS might be sufficient to induce PD progression and to reproduce the neuroanatomical and neurochemical features of PD staging. Thus, providing new insight into how environmental factors could trigger PD and suggesting a transsynaptic mechanism by which PD might propagate to and through the CNS.