bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Motivation: 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

Chemical 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

*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

Green 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

World 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

Intronic 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

Direct 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

The 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

RNase 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

Conservative 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

MRI 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

Written 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

Vein 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.
Spatiotemporal dynamics of complex ecological networks: Power-law scaling and implications for conservation planning
Authors: Wright Christopher
Published: July 2019

Spatial constraints on the topology of complex networks are just beginning to be appreciated, both theoretically^1-3^ and in concrete examples like the Internet^4^ and global air transportation network^5^. Ecological networks, composed of habitat patches connected by species dispersal, are intrinsically spatial and show promise as a tool for conservation planning; but while habitat-loss effects on ecological networks have been simulated, such effects have not been directly measured in ecological networks varying over time^6-8^. In this study, I used satellite remote sensing to study ecological networks composed of wetland habitat in the Prairie Pothole Region (PPR) of North America. I find power-law scaling of important topological properties as a function of dispersal ability and as wetland density varies with climate. Prairie wetland networks are 'meso-worlds' with mean topological distance increasing faster with network size than small-world networks^9^, but slower than regular lattices^10^. While similar dynamics have been shown in random spatial networks^1,3^, these results emphasize the importance of processes determining locations of nodes in a spatial network, with possible implications in other areas like wireless communication networks^11^ or disease transmission networks^12^. Wetland networks establish a climate envelope for landscape connectivity in the PPR, and I show that wetland-dependent species face a 'crisis of connectivity' with climate change. The global biodiversity crisis requires that conservation planners act quickly over large areas using limited resources^13,14^; a network-based approach to coarse-filter conservation planning in dynamic landscapes should be broadly applicable to this problem.
Second-Hand Stress: Neurobiological Evidence for a Human Alarm Pheromone
Authors: Mujica-Parodi Lilianne , Strey Helmut , Frederick Blaise , Savoy Robert , Cox David , Botanov Yevgeny , Tolkunov Denis , Rubin Denis , Weber Jochen
Published: July 2019

Alarm pheromones are airborne chemical signals, released by an individual into the environment, which transmit warning of danger to conspecifics via olfaction. Using fMRI, we provide the first neurobiological evidence for a human alarm pheromone. Individuals showed activation of the amygdala in response to sweat produced by others during emotional stress, with exercise sweat as a control; behavioral data suggest facilitated evaluation of ambiguous threat.
Parrot proventricular dilatation disease: a possible model of Guillain-Barré syndrome?
Authors: Rossi Giacomo , Crosta Lorenzo , Pesaro Stefano
Published: July 2019

Proventricular Dilatation Disease (PDD) affects parrots with clinico-pathological aspects similar to those of the Guillain-Barré syndrome (GBS), a human neurophathy. We observed that in sera of PPD-affected parrots antibodies to gangliosides were detectable, similarly to that observed for GBS, and that quantification of such antibodies could be diagnostic for PDD. Then, we proved that administration of purified gangliosides to parrots, elicited autoimmune response and a pathological outcome similar to that of natural PDD. We propose this model not only for better studying PDD, but also as the basis for developing a reliable animal model of GBS.
The Modified Pharaoh Approach: Stingless bees mummify beetle parasites alive
Authors: Greco Mark , Neumann Peter , Hoffmann Dorothee , Dollin Anne , Duncan Michael , Spooner-Hart Robert
Published: July 2019

Social insect colonies usually live in nests, which are often invaded by parasitic species^1^. Workers from these colonies use different defence strategies to combat invaders^1^. Nevertheless, some parasitic species are able to bypass primary colony defences due to their morphology and behaviour^1-3^. In particular, some beetle nest invaders cannot be killed or removed by workers of social bees^2-5^, thus creating the need for alternative social defence strategies to ensure colony survival. Here we show, using Diagnostic Radioentomology^6^, that stingless bee workers Trigona carbonaria, immediately mummify invading destructive nest parasites Aethina tumida alive, with a mixture of resin, wax and mud, thereby preventing severe damage to the colony. In sharp contrast to the responses of honeybee^7^ and bumblebee colonies^8^, the rapid live mummification strategy of T. carbonaria effectively prevents beetle parasite advancements and removes their ability to reproduce. The convergent evolution of live mummification by stingless bees and social encapsulation by honeybees^3^ suggests that colonies of social bees generally rely on, secondary defence mechanisms when harmful nest intruders cannot be killed or ejected easily. This process is analogous to immune responses in animals.
Evidence of novel type of ribosome in eukaryotic intermediate flatworm
Authors: Wang Haoran , Gao Mary , Kenzo Sato , Hirai Kazumitsu
Published: July 2019

In all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm Spirometra erinaceiuropaei. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms Diphyllobothrium hottai and Diphyllobothrium Nipponkaiizeme. Relevant to this finding, in flatworm Paragonimus westermani, 18S rRNAs were found much more numerous than 28S rRNAs. Moreover, consistent with this biochemical finding, transmission electron microscopy examinations show that the ribosomes isolated from Spirometra erinaceiuropaei are composed of either one ball or two similar size subunits (balls), while the structure of ribosomes isolated from control liver tissue exactly match the conventional large and small subunit ribosome model. Our study provides direct biochemical and biophysical evidence of structurally distinct novel type of ribosomes in intermediate eukaryotic flatworms. These finding may be important for re-recognition of biological protein synthesis and evolutionary process of living things.
Design and Implementation of the UniProt Website
Authors: Jain Eric , Phan Isabelle , Duvaud Severine , Gasteiger Elisabeth , Redaschi Nicole , Martin Maria , McGarvey Peter , Bairoch Amos
Published: July 2019

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.
Breast Cancer Associated Metastasis is Significantly Increased in a Model of Autoimmune Arthritis
Authors: Das Roy Lopamudra , Pathangey Latha , Tinder Teresa , Mukherjee Pinku
Published: July 2019

Chronic inflammation is known to play a role in cancer initiation, promotion,and metastasis. However, the mechanism by which inflammation promotes metastasis is still unclear. We evaluated if chronic inflammation induced by autoimmune arthritis may contribute to increased breast cancer-associated metastasis. We report a three-fold increase in lung metastasis and a significant increase in the incidence of bone metastasis in the pro-arthritic mice compared to control mice. The metastatic breast tumors in turn augment the severity of arthritis resulting in a vicious cycle that increases both bone destruction and metastasis. Enhanced neutrophilic and granulocytic infiltration in lungs and bone of the pro-arthritic mice and subsequent increase in circulating levels of proinflammatory cytokines, such as IL-17, IL-6, VEGF, and TNF-&x03B1; were the underlying factors contributing to the increased metastasis. The data clearly has important clinical implications for patients diagnosed with metastatic breast cancer.
Genetically modified Cotton species detection by LISS-III satellite data
Authors: Mukherjee Saumitra , Shashtri Satyanarayan , Kumar Singh Chander , Kumari Bindu , Kumari Reena , Avatar Ram , Mukherjee Anita , Singh Bhoop
Published: July 2019

It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showing R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton has reasonably acceptable correlation with Total Dissolved Solids (TDS) of soil and water also.
Assortative human pair-bonding for partner ancestry and allelic variation of the dopamine receptor D4 (DRD4) gene
Authors: Eisenberg Dan , Apicella Coren , Campbell Benjamin , Dreber Anna , Garcia Justin , Lum J. Koji
Published: July 2019

The 7R allele of the dopamine receptor D4 gene has been associated with attention-deficit hyperactivity disorder and risk taking. On the cross-population scale, 7R allele frequencies have been shown to be higher in populations with more of a history of long-term migrations. It has also been shown that the 7R allele is associated with individuals having multiple-ancestries. Here we conduct a replication of this latter finding with two independent samples. Measures of subjects’ ancestry are used to examine past reproductive bonds. The individuals’ history of inter-racial/ancestral dating and their feelings about this are also assessed. Tentative support for an association between multiple ancestries and the 7R allele were found. These results are dependent upon the method of questioning subjects about their ancestries. Inter-racial dating and feelings about inter-racial pairing were not related to the presence of the 7R allele. This might be accounted for by secular trends that might have substantively altered the decision-making process employed when considering relationships with individuals from different groups. This study provides continued support for the 7R allele playing a role in migration and/or mate choice patterns. However, replications and extensions of this study are needed and must carefully consider how ancestry/race is assessed.
Strategies for identifying exact structure of neural circuits with broad light microscopy connectivity probes
Authors: Mishchenko Yuriy
Published: July 2019

Dissecting the structure of neural circuits in the brain is one of the central problems of neuroscience. Until present day, the only way to obtain complete and detailed reconstructions of neural circuits was thought to be the serial section Electron Microscopy, which could take decades to complete a small circuit. In this paper, we develop a mathematical framework that allows performing such reconstructions much faster and cheaper with existing light microscopy and genetic tools. In this framework, a collection of genetically targeted light probes of connectivity is prepared from different animals and then used to systematically deduce the circuit's connectivity. Each measurement is represented as mathematical constraint on the circuit architecture. Such constraints are then computationally combined to identify the detailed connectivity matrix for the probed circuit. Connectivity here is understood broadly, such as that between different identifiable neurons or identifiable classes of neurons, etc. This paradigm may be applied with connectivity probes such as ChR2-assisted circuit mapping, GRASP or transsynaptic viruses, and genetic targeting techniques such as Brainbow, MARCM/MADM or UAS/Gal4, in model organisms such as C. Elegans, Drosophila, zerbafish, mouse, etc. In particular, we demonstrate how, by using this paradigm, the wiring diagram between all neurons in C. Elegans may be reconstructed with GRASP and Brainbow and off-the-shelf light microscopy tools in the time span of one week or less. Described approach allows recovering exact connectivity matrix even if neurons may not be targeted individually in ~Np*log(N) time (Np is the number of nonzero entries and N is the size of the connectivity matrix). For comparison, the minimal time that would be necessary to determine connectivity matrix directly by probing connections between individual neurons when one knows a-priory which pairs should be tested, e.g. with whole-cell patches, is ~Np.
Cross-modal facilitation of visual and tactile motion
Authors: Burr David , Sandini Giulio , Gori Monica
Published: July 2019

Robust and versatile perception of the world is augmented considerably when information from our five separate sensory systems is combined. Much recent evidence has demonstrated near-optimal integration across senses, but it remains unclear at what level the integration occurs, at a "sensory" or "decisional" level. Here we show that non-informative "pedestal" motion stimuli in one sensory modality (vision or touch) selectively lowers thresholds in the other, to the same degree as pedestals in the same modality: strong evidence for functionally important cross-sensory integration at early levels of sensory processing.
Capsaicin protects neuromuscular junctions from the inhibitory effects of botulinum neurotoxin A
Authors: Thyagarajan Baskaran , Garcia Carmen , Potian Joseph , Krivitskaya Natalia , Hognason Kormakur , McArdle Joseph
Published: July 2019

Within 24 hrs after injecting botulinum neurotoxin A (BoNT/A) into the hindlimb, mice lost the toe spread reflex and developed progressive muscle weakness. At the same time, the compound muscle action potential amplitude decreased. Injection of capsaicin before BoNT/A significantly reduced these affects and protected the muscle twitch tension of the Extensor digitorum longus (EDL) nerve muscle preparation. Acute in vitro exposure of isolated nerve muscle preparations, as well as Neuro 2a cells, to capsaicin prevented uptake of Alexa 647 BoNT/A. Motor nerve endings as well as Neuro 2a cells express the capsaicin receptor, a transient receptor potential channel of the vanilloid family (TRPV1). Capsaicin as well as disruption of clathrin coated pits (CCPs) reduced Neuro 2a cell uptake of BoNT/A. FM1-43 uptake indicated that exocytosis persists for BoNT/A treated Neuro 2a cells pretreated with capsaicin. Pre-injection of wortmannin (WMN), a PI3Kinase inhibitor, also protected mice from the paralytic effects of BoNT/A. When applied alone, either WMN or capsaicin selectively reduced stimulus-evoked transmitter release from motor nerve endings. We hypothesize that TRPV1 activation reduces PI(4,5)P2 level within the membrane. This prevents CCP formation and uptake of BoNT/A.
The Hepatocellular Hypoxia Criteria:2’Nitroimidazole Effect on Hepatocyte Carbohydrate Metabolizing Enzymes
Authors: Sharma Rakesh
Published: July 2019

Aim: to understand the 2’-nitroimidazole induced hypoxia and liver cell interaction, we proposed a “Hapatocellular Hypoxia Criteria”. Hypothesis: The nitroimidazole induced metabolic energy loss and oxygen depletion (hypoxia) in liver cell mitochondria causes the phagocytosis. Based on it, ten control subjects with 2’-nitroimidazole therapy were studied for their carbohydrate metabolizing enzymes in serum and hepatocellular enzymes in liver biopsy tissues.

Materials and Methods:

Proven ten control subjects were studied for hypoxia by enzyme assays. The 2’nitroimidazole treated paired ten subjects were studied for hypoxia using enzyme assays and hepatocellular cytomorphology by electron microscopy.

Results and Discussion:

Out of ten subjects on 2’-nitroimidazole, nine showed elevated carbohydrate metabolizing and lysosomal enzyme levels in serum. The enzymes glucokinase (in 80% samples), aldolase (in 80% samples), phosphofructokinase (in 80% samples), malate dehydrogenase (in 75% samples), isocitrate dehydrogenase (ICDH) (in 60% patients) were elevated while succinate dehydrogenase and lactate dehydrogenase (LDH) levels remained unaltered. Lysosomal enzymes β-glucuronidase, alkaline phosphatase, acid phosphatase, showed enhanced levels in the serum samples. In control ten liver biopsies, the hepatocytes and Kupffer cell preparations showed altered enzyme levels. Hepatocytes showed lowered glucokinase (in 80%), LDH (in 80%), and higher content of aldolase (in 80%), pyruvate kinase (in 100%), malate dehydrogenase (in 80%), ICDH (in 80%), citrate dehydrogenase (in 70%), phosphogluconate dehydrogenase (in 80%). Kupffer cells showed higher enzyme levels of β-glucuroronidase (in 80%), leucine aminopeptidase (in 70%), acid phosphatase (in 80%) and aryl sulphatase (in 88%). In these 10 biopsy samples from subjects on 2’-nitronidazole clinical trial, the electron microscopy cytomorphology observations showed swollen bizarre mitochondria, proliferative endoplasmic reticulum, and anisonucleosis after 2’-Nitroimidazole effect in liver cell damage.

Conclusion:

The proposed “Hepatocellular Hypoxia Criteria” served to define origin of liver hypoxia and showed altered hepatic enzyme activities with active phagocytosis and cytotoxicity in subjects after 2’-nitroimidazole treatment. The study suggests the enzyme based evaluation of nitroimidazole induced hypoxia monitoring and treatment of hepatic tumors and infected liver.
Narrow genetic and apparent phenetic diversity in Jatropha curcas: initial success with generating low phorbol ester interspecific hybrids
Authors: Popluechai Siam , Breviario Diego , Mulpuri Sujatha , Makkar Harinder , Raorane Manish , Reddy Attipalli , Palchetti Enrico , Gatehouse Angharad , Syers Keith , O'Donnell Anthony , Kohli Ajay
Published: July 2019

Due to the increasing popularity of Jatropha curcas as a feedstock for biodiesel, generating non-toxic and high yielding varieties of the plant requires genotypic characterization towards identifying breeding lines. There is little information on the phylogenetic relationships between its global accessions and species. Assessing genetic variation by RAPD, AFLP and combinatorial tubulin based polymorphism (cTBP) in 38 J. curcas accessions from 13 countries on 3 continents revealed narrow genetic diversity. However, 6 different species of Jatropha from India exhibited pronounced genetic diversity indicating possibilities of improving J. curcas by interspecific breeding. The relatively unexplored cTBP approach we used was a highly efficient and cost effective genotyping tool. Using such tools towards breeding J. curcas for low phorbol ester (PE) content is highly desirable because of the co-carcinogenic nature of the PEs present in all the commercially relevant parts such as seeds, seed-cake and biodiesel. We report initial success in obtaining interspecific F1 and back cross (BC1) plants with low PE and improved agronomic traits.Further efforts will lead to generating varieties with targeted traits. Despite the limited genetic diversity within J. curcas accessions, appreciable variability was noticed in important phenotypic, physiological and biochemical traits such as seed size, water use efficiency and seed oil content respectively. This implicates fundamental epigenetic regulatory mechanisms and posits J. curcas as a unique system to study them.
Palaeobathymetry of the Abderaz Formation using foraminifera, Iran
Authors: Shafiee Ardestani Meysam , Ghasemi-Nejad Ebrahim
Published: July 2019

Abderaz Formation at its type section with an age of Turonian-early Campanian and a thickness of 300 m contains light grey shale and marl. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation. Also the planktonic to benthic ratio was calculated using Depth = e^(3.58718 + (0.03534 × %*p)^ equilibrium which explains that at the deposits 400 meter at total part of in this Formation. This study was intended to explore the marine sedimentation of Abderaz Formation in (outer neritic-upper bathyal) restrict and the provided curves from morphotypes changes are in full agreement with the curves of the sea level changes and planktonic foraminifer to epifauna benthic ratio.
Reaction time to judge the temporal inequality of digits numbers
Authors: Vicario Carmelo
Published: July 2019

Several studies had consistently lighted mechanisms about the relation between spatial and numerical cognition; parallel to this, a separate research line begin to document similar relationships for the representation of time and quantity as well. However there are still few studies that explore cognitive mechanisms subserving this relation. Starting from the evidence of the SNARC effect (Dehaene et al., 1993), here we investigate about the presence of similar effect in the processing of temporal and numerical information. We studied the effects of numerical exposure when participants are asked to perform a visual detection task in which temporal information is explicitly or implicitly conveyed. The main result shows that, during explicit timing, low digits exposure improve reaction time in the judgment of shorter duration whereas big digits exposure improve reaction time in judgment of longer duration. No interaction between temporal and numerical information is documented when participants perform implicit timing task. Results suggest a role quantity exposure for timing task-dependent attentional orientation.
Inhibition of pteridine reductase 1 (PTR1) expression in Leishmania promastigotes using a full-length antisense construct
Authors: Kheirandish Farnaz , Bandehpour Mojgan , Davoudi Nushin , Mosaffa Nariman , Mahboudi Fereydoun , Kazemi Bahram , Haghighi Ali , Mohebali Mehdi
Published: July 2019

Leishmania exhibit many unusual features, one of which is the pteridine metabolic pathway essential for the growth for these parasites. Leishmania have evolved a complex and versatile pteridine salvage network capable of scavenging a wide array of conjugated and unconjugated pteridines. The L. major PTR1 gene was cloned into pcDNA3 digested with KpnI and BamHI. The gene was cloned antiparallel to the promoter and named pcDNA-Rptr. L. major promastigotes were divided into two groups. One group was transfected with 50 &x03BC;g of pcDNA-Rptr, whereas the other group was electroporated with pcDNA3. Mentioned cells were cultured and plated onto semi-solid media.Western blotting was performed on extracts from transfected promastigotes of L. major using an leishmania major PTR1 antibody. The PTR1 protein was not expressed in pcDNA-Rptr-tansfected promastigotes, 'Our results indicate that our system may be useful for studying the pteridine salvage pathway in Leishmania as a possible drug target.
The Feasibility of Neuroimaging Methods in Marketing Research
Authors: Lee Nick , Senior Carl , Butler Michael , Fuchs Ricardo
Published: July 2019

On July 17, 1990, President George Bush issued “Proclamation 6158” which boldly declared the following ten years would be called the “Decade of the Brain” (Bush, 1990). Accordingly, the research mandates of all US federal biomedical institutions worldwide were redirected towards the study of the brain in general and cognitive neuroscience specifically. In 2008, one of the greatest legacies of this “Decade of the Brain” is the impressive array of techniques that can be used to study cortical activity. We now stand at a juncture where cognitive function can be mapped in the time, space and frequency domains, as and when such activity occurs. These advanced techniques have led to discoveries in many fields of research and clinical science, including psychology and psychiatry. Unfortunately, neuroscientific techniques have yet to be enthusiastically adopted by the social sciences. Market researchers, as specialized social scientists, have an unparalleled opportunity to adopt cognitive neuroscientific techniques and significantly redefine the field and possibly even cause substantial dislocations in business models. Following from this is a significant opportunity for more commercially-oriented researchers to employ such techniques in their own offerings. This report examines the feasibility of these techniques.
Intestinal Electric Stimulation Accelerates Whole Gut Transit and Promotes Fat Excrement in Conscious Rats
Authors: Sun Ying , Chen Jiande
Published: July 2019

*Introduction:* Intestinal electric stimulation (IES) is proposed as a potential tool for the treatment of morbid obesity. Our previous study showed that IES with one pair of electrodes accelerated intestinal transit and decreased fat absorption in a segment of the jejunum in the anesthetized rats. The aims of this study were to assess the effects of IES on the whole gut transit and fat absorption in conscious rats, to examine the effects of multi-channel IES, and to explore the cholinergic mechanism behind the effects of IES. *Methods:* Thirty-eight male rats implanted with serosal electrodes were randomized into five groups: control without IES, 2/3 channel IES with short pulses, atropine and atropine plus IES. The whole gut transit and fat remained and emptied from the gut were analyzed after continuous 2-hour IES.

*Results:*

Two and three channel IES significantly accelerated phenol red (marker used for transit) excretion (ANOVA, P < 0.001). No significant difference was found between two and three channel IES. Two channel IES significantly increased the excretion of fat (P < 0.05). Atropine significantly blocked the accelerated transit induced by IES (ANOVA, P < 0.001). Correlation was found between the percentage of phenol red and fat retained in the whole gut (r = 0.497, P < 0.01).

*Conclusions:*

IES accelerates whole gut transit and promotes fat excrement in conscious rats, and these effects are mediated through the cholinergic nerves. These findings are in support of the concept that IES may be a promising treatment option for obesity.
The maximum sustainable yield leads to extinction of species in most single and multispecies fisheries
Authors: Legović Tarzan , Klanjšček Jasminka , Geček Sunčana
Published: July 2019

The Commission of the European Communities passed a resolution in 2006 to implement sustainability in EU fisheries through application of the maximum sustainable yield (MSY) based policy. It is shown here that attempts to reach MSY will lead towards extinction of species for every fishery that includes fishing of at least one trophic level which is directly or indirectly used as food for a higher trophic level. Because this condition is met by most single and multispecies fisheries, attempts to reach MSY should be discouraged instead of being legally prescribed as a goal. Based upon above result advice is given on how to manage a fishery which will not drive species to extinction.
Stress impairs decision-making in rats
Authors: Jones Lauren , Yoon Taejib , Kim Jeansok
Published: July 2019

Stress influences various types of memory, but its effects on other cognitive functions are relatively unknown. We investigated the effects of uncontrollable stress on subsequent decision-making in rats, using a computer vision-based water foraging choice task. Stress impaired the animals' ability to bias their responses toward the larger reward when transitioning from equal to unequal quantities, and this stress effect was dependent on the amygdala.
Molecular phylogenies and evolutionary behavior of AhR (aryl hydrocarbon receptor) pathway genes in aquatic animals
Authors: Zhou Hailong , Qu Ying , Xue Qinzhao
Published: July 2019

Phylogenetic analysis of AhR pathway genes and their evolutionary rate variations were studied on aquatic animals. The gene sequences for the proteins involved in this pathway were obtained from major phylogenetic groups of mollusc, amphibian, fish and aquatic mammal. These genes were distributed under four major steps of toxicology regulation: formation of cytosolic complex, translocation of AhR, heterodimerization of AhR and induction of CYP1A. The NJ, MP and ML algorithm were used on protein coding DNA sequences to deduce the evolutionary relationship for the respective AhR pathway gene among different aquatic animals. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d~N~) and synonymous nucleotide substitutions per synonymous site (d~S~) were calculated for different clade of the respective phylogenetic tree for each AhR pathway gene. The phylogenetic analysis suggests that evolutionary pattern of AhR pathway genes in aquatic animals is characterized mainly by gene duplication events. The d~N~ values indicate that AhR pathway genes are well conserved in aquatic animals, except for CYP1A gene. Furthermore, the d~N~ value indicates that AhR pathway genes are less conserved in fish than in any other aquatic animals, and they likely go through an adaptive evolution within aquatic animals.
ADME/Tox WEB in silico predictions of longer chain perfluoroalkyl carboxylic acid pKa values are more accurate than other computational methods
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

Perfluoroalkyl carboxylates are contaminants whose environmental fate and toxicological effects are of broad interest within the academic, industrial, and governmental science and regulatory communities. In addition, coupled perfluoroalkyl and carboxylate moieties are often used in medicinal chemistry as part of the drug design process. However, to date there has been a notable absence of reliable acidity constant estimation programs for these compounds. Here we report that the ADME/Tox WEB method for in silico pKa value predictions is more accurate than the PM6, SPARC, and COSMOtherm methods for the longer chain perfluoroalkyl carboxylic acids, suggesting this may be a good general acidity constant estimation approach for these compounds.
Dissociation of Alzheimer's morphological pathology from cognitive impairment
Authors: Hasegawa Tohru , Mikoda Nobuyuki
Published: July 2019

We observed the Alzheimer's morphological pathology, amyloid production induces Alzheimer's cognitive impairment, was dissociated from the cognitive impairment. The earlier Alzheimer's pathological changes can be induced in normal C57BL mice, by B6 deficient feeding 4 months with no amyloid, and this cognitive and memory impairments were completely inhibited by anti-homocysteic acid antibody. According to Koch's postulate, if a pathogen of Alzheimer's disease is administrated to the normal animal, we would observe the Alzheimer's cognitive impairment in the normal animal. We actually have observed this cognitive impairment in normal C57BL male mice with no amyloid. From our observations, it is suggested the dissociation of Alzheimer's morphological pathology may be possible from the cognitive impairment.