bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogenetic role of tissue factor in graft-versus-host disease
Authors: Quan Li , Weiming Li , Jian Zhang , Ping Zou 
Published: July 2019

AbstractGraft-versus-host disease (GVHD) is a serious complication after allogeneic stem cell transplantation, the mechanism of it is still not elucidated. Recent findings suggest that host endothelial cells are a target of alloreactive donor cytotoxic T lymphocytes in GVHD and tissue factor (TF) plays an important role not only in coagulation-inflammation cycle, but also in transplant immunology. We postulate TF expression in vascular endothelial cells(VEC) may play an pivotal role in the pathogenesis of GVHD. TF gene andprotein expression in target organs of GVHD in aGVHD mice was significantly elevated compared to that of controls as determined by real-time PCR and Western blotting. Allogeneic CD4^+^T cell and CD8^+^T cells enhanced TF, VCAM-1, TNF-[alpha], IFN-[gamma] and IL-6 expression in TNF-[alpha] prestimulated HUVECs compared to controls as determined by flowcytometry and real-time PCR. JNK and p38MAPK mediated allogeneic T cells-induced TF expression in HUVECs. These effects were largely prevented by monoclonal antibody against TF, SB203580 and SP600125. In concert, these data provide strong evidence that upregulated TF expression is related to tissue damage caused by GVHD, TF isthe key factor in GVHD mediated by endothelial cells and allogeneic T cells-induced TF and consecutive proinflammatory cytokines expression in VEC contribute to the pathogenesis of GVHD.
Treatment of Alzheimer's Disease with Anti-Homocysteic acid Antibody
Authors: Hasegawa Tohru , Mikoda Nobuyuki , Kitazawa Masashi , LaFerla Frank 
Published: July 2019

AbstractHomocysteic acid (HA) may play an important role in Alzhiemer disease (AD) as we previously reported that HA induced accumulation of intraneuronal A[beta]42. In this study, we first analyzed HA levels in a mouse model of AD. 4-month old pre-pathologic 3xTg-AD mice exhibited higher levels of HA in the hippocampus as compared to age-matched nontransgenic, suggesting that HA accumulation may precede both A[beta] and tau pathologies. To further determine the pathogenic role of HA in AD, we treated young 3xTg-AD mice with vitamin B6-deficient food for 3 weeks to induce the production of HA in the brain. Concominantly, mice received either saline or anti-HA antibody intraventricularly using a guide cannula every 3 days. Mice received anti-HA antibody significantly rescued cognitive impairment induced by vitamin B6 deficiency. Pathologically, 3-week treatment with vitamin B-6 deficient food resulted in strong neurodegeneration in the hippocampal CA1 zone and decreased hippocampal volume. In contrast, anti-HA antibody treatment attenuated these pathological changes. Taken together, we conclude that increased brain HA triggers memory impairment whose condition was deteriorated by amyloid and subsequent neurodegeneration and reduction of neurogenesis. Our results indicate a pathogenic role of HA in AD.
Archaebacterial Whole-Genome Duplication and Origin of Eukaryots
Authors: Stupar Milanko 
Published: July 2019

AbstractDivision of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of archaeal ancestor of eukaryots. Second, the double-strand break can be repaired intergenomically by complementary strands invasion. Third, this duplicated genome can be fissioned into two compartments by reciprocal genetic recombination. Scenario is accomplished by aberrant fission of the inner membrane surrounding separately those two compartments.
Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics
Authors: Dumontier Michel , Green James , Golshani Ashkan , Smith Myron , Mir-Rashed Nadereh , Alamgir Md , Eroukova Veronika , Dehne Frank , Cheetham James 
Published: July 2019

Abstract
Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures.

Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.

Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™
Authors: Goldsmith Elizabeth , Mendiratta Saurabh , Akella Radha , Dahlgren Kathleen 
Published: July 2019

AbstractMotivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result:
Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com.
GO faster ChEBI with Reasonable Biochemistry
Authors: Hull Duncan 
Published: July 2019

AbstractChemical Entities of Biological Interest (ChEBI) is a database and ontology that represents biochemical knowledge about small molecules. Recent changes to the ontology have created new opportunities for automated reasoning with description logic, that have not previously been fully exploited in Chemistry. These changes open up the possibility of building an improved chemical semantic web, by making more use of necessary and sufficient conditions, allowing reasoning about chemical structure, highlighting ambiguous inconsistencies and improving alignment with the Gene Ontology (GO). This paper briefly discusses some of the problems with reasoning over the current version of ChEBI, to tackle these issues, and their potential solutions.
FDserver: A web service for protein folding research
Authors: Ma Bin-Guang , Chen Ling-Ling , Zhang Hong-Yu 
Published: July 2019

Abstract*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.*Availability:* http://sdbi.sdut.edu.cn/FDserver
China is on the track tackling Enteromorpha spp forming green tide
Authors: Ye Naihao , Zhuang Zhimeng , Jin Xianshi , Wang Qingyin , Zhang Xiaowen , Li Demao , Wang Hongxia , Mao Yuze , Jiang Zengjie , Li Bin , Xue Zhixin 
Published: July 2019

AbstractGreen tide management is supposed to be a long term fight rather than an episode during the 29th Olympic Games for China, since it has been gaining in scale and frequency during the past 3 decades in both marine and estuary environment all over the world. A number of rapid-responding studies including oceanographic comprehensive surveys along the coastline have been conducted during the bloom and post-bloom periods in 2008 by Chinese marine scientists. The preliminary results are as below: (1) phylogenetic analysis indicates that the bloom forming alga forms a clade with representatives of the green seaweed Enteromorpha linza, though, the alga has been identified as E. proliera by means of morphological; (2) the present data suggest that the bloom was originated from south of Yellow Sea, but not the severely affected area near Qingdao City; (3) pathways of reproduction for E. prolifera have approved to be multifarious, including sexual, asexual and vegetative propagation; (4) somatic cells may act as a propagule bank, which is supposed to be a very dangerous transmitting way for its marked movability, adaptability and viability; (5) pyrolysis of the alga showed that three stages appeared during the process, which are dehydration (18–20^o^C), main devolatilization (200–450^o^C) and residual decomposition (450–750^o^C), and activation energy of the alga was determined at 237.23 KJ•mol^-1^. Although the scarce knowlegde on E. prolifera not yet allow a fully understanding of the green tide, some of the results suggests possible directions in further green tide research and management.
Nitrogen Fixation and Translocation in Sugarcane
Authors: Ohyama Takuji , Momose Atsushi , Ohtake Norikuni , Sueyoshi Kuni , Sato Takashi , Nakanishi Yasuhiro , Akao Shoichiro 
Published: July 2019

AbstractWorld sugarcane production is increasing rapidly as a biofuel. In some areas in Brazil, sugarcane has been grown continually over very long periods without N fertiliser inputs. Therefore, the occurrence of N fixation has been suspected. However, quantitative studies seeking to identify the N~2~ fixation sites in the plant and to record the translocation of fixed N around the plant have not yet established. A ^15^N~2~ gas tracer experiment was conducted using young sugarcane plants to investigate the sites of N~2~ fixation and also to explore the possibility of translocation of the fixed N among the plant's major organs. Young sugarcane plants (Saccharum officinarum L.) about 40 cm high and some 14 days after sprouting from a stem cutting were exposed to ^15^N~2~ labeled air in a 500 mL plastic cylinder for 7 days. Following the 7-day ^15^N~2~ feeding, some plants were potted and grown on in normal air for a further chase period. The incorporation of ^15^N into the shoot, roots, and stem cutting was analysed at day-3, and day-7 of the labeling period and at day-14, and day-21 during the chase period. After 3 days of ^15^N~2~ feeding, the % of N derived from the ^15^N labeled air in the shoot, roots and stem cutting were 0.027%, 2.22% and 0.271%, respectively. The roots showed the highest N fixing activity followed by the stem cutting, while the incorporation of ^15^N into the shoot was very low. After 21 days about a half of the N originating in the stem cutting had been transported to the shoot and the roots. However, the ^15^N fixed either in the roots or in the stem cutting remained in the original parts and was not appreciably transported to the shoot.
Autism-associated SNPs in the clock genes npas2, per1 and the homeobox gene en2 alter DNA sequences that show characteristics of microRNA genes.
Authors: Nicholas Brad , Owen Michael , Wimpory Dawn , Caspari Thomas 
Published: July 2019

AbstractIntronic single nucleotide polymorphisms (SNPs) in the clock genes npas2 and per1 and the homeobox gene en2 are reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated SNPs rs1861972 and rs1861973 in en2, rs1811399 in npas2, and rs885747 in per1, shows that these regions encode RNA transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted in silico by the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated in autism (gabrb3, shank3) and genes causative of diseases co-morbid with autism (mecp2 and rai1). The inheritance of the AC haplotype of rs1861972 - rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 in per1 may contribute to the causes of autism by affecting microRNA genes that are co-expressed along with the homeobox gene en2 and the circadian genes npas2 and per1.
Nucleotide repeats in mitochondrial genome determine human lifespan
Authors: Popadin Konstantin , Bazykin Georgii 
Published: July 2019

AbstractDirect nucleotide repeats can facilitate deletions of segments of mitochondrial genome1, leading to a wide range of neuromuscular disorders1,2 as well as aging2,3 in humans. We hypothesized that the number of the direct perfect repeats in human mitochondrial genomes influences longevity through the formation of harmful mtDNA deletions in the somatic cells. The analysis of the complete mitochondrial genomes of 762 unrelated Japanese individuals4-6 reveals a negative correlation between the abundance of the direct perfect repeats and the expected longevity. This association is largely due to the disruption of the common repeat (8470,13447) by a point mutation 8473C which occurred at the origin of the D4a haplogroup characterized by extreme longevity in Japan7. Our results provide the first evidence for correlation between the number of nucleotide repeats and the lifespan on intraspecific level.
Principal basis for enzyme power
Authors: Foigel Alexander 
Published: July 2019

AbstractThe reaction rate enhancement that enzymes produce had not been fully appreciated. The object of the article is to present the mechanism of the enormous catalytic power of the enzymes. I conclude that during substrate conversion to product the enzyme transfers firstly some additional small reactant group that must be initially presented in the active site of the enzyme to bound substrate (i) ; the enzyme regenerates during second substrate group transfer (ii); the active enzyme acts as a reactant of the enzymatic reaction (iii). The detailed chemical mechanisms of enzymatic reactions, such as a the well-studied reaction of the serine proteases family, the peptide bond hydrolysis catalyzed by α-chymotrypsin, and the glyceraldehyde-3-phosphate interconversion step in glycolysis, are in accordance with my conclusion.
Decrease in gyrase A protein expression in E. coli cells inhibited by antisense ribozymes
Authors: Sainath Rao Shilpakala , Raghunathan Malathi 
Published: July 2019

AbstractRNase P complexed with external guide sequence (EGS) represents a novel nucleic-acid-based gene interference approach to modulate gene expression. Nucleic acid-based gene interference technologies represent promising strategies for specific inhibition of mRNA sequences of choice. Recently, small interfering RNAs have been implicated in inducing endogenous RNase of the RNA-induced silencing complex in the RNA interference pathway to inhibit gene expression and growth of several human viruses. We report down regulation of protein expression of E. coli gyrase A, an essential gene for DNA supercoiling and antibiotic susceptibility in BL21 (DE3) strain of E. coli, using Ribonuclease P based external guide sequence (EGS) technique. EGS directed against gyrase A gene that was cloned into pUC vector, which contains the ampicillin (Amp) resistance gene. The recombinant plasmid pT7EGyrA was transformed into BL21 (DE3) and inductions were performed using IPTG. Western blot was done to investigate the downregulation of gyrase A protein. The results showed a significant decrease of gyrase A suggesting the utility of EGS RNAs in gene therapy applications, by inhibiting the expression of essential proteins.
Facial Expression Processing Varies with Political Affiliation
Authors: Vigil Jacob 
Published: July 2019

AbstractConservative political beliefs have been linked to heightened stress reactivity and protective cognitive biases. Using a facial discrimination task designed to measure perceptions of threat (vs. non threat) and dominance (vs. submissiveness), I show that Republicans demonstrate a greater tendency to interpret ambiguous facial stimuli as expressing more threatening and more dominant emotions than do Democrats. The findings suggest the political ideology may be associated with basic social perceptual sensitivities.
'Magnetized' brains are slower: The cognitive effects of fMRI
Authors: Foucher Jack , Gounot Daniel , Pham Bich-Thuy , Marrer Corinne , Dufour Andre 
Published: July 2019

AbstractMRI is generally thought to have no impact on cognition. Although safety experiments have shown that MRI is not harmful, its finer effects have not been investigated. Because we repeatedly observed delayed response time during functional MRI (fMRI), we designed an experiment to confirm this effect and to identify its causal factor(s), including environment, noise, static magnetic field and/or gradient switch. Here we show that the participants had increased response times of +70 ms (up to +30%) in two different detection tasks, with most of this effect due to the 2 Tesla static magnetic field. The latter also specifically accounted for the longer time interval needed to detect two stimuli as occurring successively rather than simultaneously. These observations demonstrate that brain processes are slowed during fMRI, and that this slowing is caused by the static magnetic field. This may be the behavioral counterpart of the effects of static magnetic fields on neuronal excitability. Consequences on fMRI data should be taken into account especially considering the forthcoming very high field MRI. The ability of magnetic fields to modify brain activity suggest that they may be used for therapeutic purposes.
Why overlearned sequences are special: distinct neural networks in the right hemisphere for ordinal sequences
Authors: Pariyadath Vani , Churchill Sara , Eagleman David 
Published: July 2019

AbstractWritten and spoken words activate left hemisphere areas involved in language processing. However, we here show that overlearned sequences (e.g. letters, numbers, weekdays, months) involve an unexpected right hemispheric activation in both the middle temporal gyrus and temporoparietal junction. Our findings offer a framework for understanding neuropsychological patterns seen in conditions such as synesthesia, in which anomalous perceptual experiences are triggered by overlearned sequences, and also in semantic dementia, in which left hemisphere damage disrupts word knowledge even while sequences can be spared.
Gene Transfer of Calcitonin Gene-Related Peptide Inhibits Macrophages and Inflammatory Mediators in Vein Graft Disease
Authors: Zhang Xiaoning , Zhuang Jian , Wu Hongsui , Chen Zhihong , Su Jian , Chen Shiliang , Chen Jianguang , Zheng Yuhui , Yang Huanxin 
Published: July 2019

AbstractVein graft disease is a chronic inflammatory disease and limits the late results of coronary revascularization. Calcitonin gene-related peptide (CGRP) inhibits macrophages infiltrated and inflammatory mediators, we hypothesized that transfected CGRP gene inhibits macrophages infiltrated and inflammatory mediators in vein graft disease. Autologous rabbit jugular vein grafts were incubated ex vivo in a solution of mosaic adeno-associated virus vectors containing CGRP gene (AAV2/1.CGRP) &x3001;escherichia coli lac Z gene (AAV2/1.LacZ) or saline and then interposed in the carotid artery. Intima/media ratio were evaluated at postoperative 4 weeks, Macrophages were marked with CD68 antibody by immunocytochemistry. Inflammatory mediators were mensurated with real-time PCR. Neointimal thickening was significantly suppressed in AAV2/1.CGRP group. Macrophages infiltrated and inflammatory mediators monocyte chemoattractant protein-1 (MCP-1)&x3001;tumor necrosis factor&x03B1;(TNF-&x03B1;)&x3001;inducible nitricoxide synthase (iNOS)&x3001;matrix metalloproteinase-9 (MMP-9) was significantly suppressed in AAV2/1.CGRP group.Gene transfected AAV2/1.CGRP suppressed neointimal hyperplasia in vein graft disease by suppressed macrophages infiltrated and inflammatory mediators.