bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleosome-mediated cooperativity between transcription factors
Authors: Mirny Leonid 
Published: July 2019

AbstractCooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated cooperativity is mathematically identical to the Monod-Wyman-Changeux (MWC) model of cooperativity in hemoglobin. This surprising parallel provides deep insights, with parallels between heterotropic regulation of hemoglobin (e.g. Bohr effect) and roles of nucleosome-positioning sequences and chromatin modifications in gene regulation. Characterized mechanism is consistent with numerous experimental results, allows substantial flexibility in and modularity of CRRs, and provides a rationale for a broad range of genomic and evolutionary observations. Striking parallels between cooperativity in hemoglobin and in transcription regulation point at a new design principle that may be used in range of biological systems.
Emergence and Fixing of Antiviral Resistance in Influenza A Via Recombination and Hitch Hiking
Authors: Niman Henry 
Published: July 2019

AbstractThe dramatic rise of oseltamivir resistance in the H1N1 serotype in the 2007/2008 season and the fixing of H274Y in the 2008/2009 season has raised concerns regarding individuals at risk for seasonal influenza, as well as development of similar resistance in the H5N1 serotype. Previously, oseltamivir resistance produced changes in H1N1 and H3N2 at multiple positions in treated patients. In contrast, the recently reported resistance involved patients who had not recently taken oseltamivir. Moreover, the resistance was limited to the H1N1 which had acquired H274Y. Using phylogenetic analysis I show that the fixing of H274Y was due to hitch hiking on a genetic background that acquired key changes from another circulating sub-clade. H274Y jumped from clade 2C (Hong Kong/2562/2006-like) to clade 1 (New Caledonia/20/1999-like) to clade 2B (Brisbane/59/2007-like) which included multiple introductions. Sub-clades that had acquired key changes on the neuramindase and hemagglutinin genes expanded and fixed of H274Y on H1N1. These changes led to the spread of adamantane resistance on clade 2C outside of Asia, followed by the spread of oseltamivir resistance in 2007/2008 and the fixing of H274Y in 2008/2009. The hemagglutinin change, A193T, was a key component and the coincident polymorphism, S193F, was linked to the fixing of adamantane resistance in H3N2. The aggregation of key polymorphisms onto different genetic backgrounds supports a mechanism of homologous recombination between co-circulating influenza sub-clades, and provides a rationale for the prediction of vaccine targets and emergence of antiviral resistance.
Predictability engenders more efficient neural responses
Authors: Eagleman David , Pariyadath Vani , Churchill Sara 
Published: July 2019

AbstractThe neural response to a stimulus diminishes with repeated presentations, a phenomenon known as repetition suppression. We here use neuroimaging to demonstrate that repetition suppression appears to be a special case of "prediction suppression"--that is, the brain shows diminishing activity when subsequent stimuli in a train are predictable. This demonstration supports the hypothesis that the brain dynamically leverages prediction to minimize energy consumption.
Cognitive epidemiology of ethnic health and the CHRM2 vagal vigour hypothesis
Authors: Frye Roy 
Published: July 2019

AbstractEthnic populations representing areas throughout California were compared regarding cognitive ability, socioeconomic position, and mortality. Cognition and socioeconomic position were inversely correlated with mortality. The single nucleotide polymorphism rs8191992 in the M2 muscarinic receptor gene (CHRM2) was previously linked to IQ and modulation of vagal tone. The CHRM2 vagal vigour hypothesis posits that variation at rs8191992 alters the binding site for a brain-expressed microRNA (hsa-mir-383) thereby changing expression of brain M2 muscarinic receptors to cause pleiotropic effects on cognition and vagus nerve signalling which then affects health via the vagal cholinergic anti-inflammatory pathway. This may help explain ethnic health differences, including the Hispanic Health Paradox, since ethnic differences in rs8191992 allele frequencies correspond to ethnic differences in systemic inflammation and mortality. The rs8191992 A-allele may contribute to the clustering of low IQ and low vagal tone with higher substance abuse, externalizing psychopathology, depression, systemic inflammation, metabolic syndrome, and cardiovascular disease.
The Necessity of Darwin
Authors: Sessions Stanley , Macgregor Herbert 
Published: July 2019

AbstractFebruary 12th, 2009 was Charles Darwin's 200th birthday, and November 2009 represents the 150th anniversary of the publication of his transformative book, The Origin of Species. It seems a good time to look back and assess Darwin's legacy within the perspective of current knowledge of genetics, cytogenetics, and molecular biology in general. Although a comprehensive understanding of evolution would no doubt have emerged eventually, it is difficult to imagine how anyone could have matched Darwin’s prodigious and sustained efforts, as well as his talent for explaining things in simple terms.
Contaminant Trapping Behind Large Dams: A Mini-Review
Authors: Rayne Sierra , Friesen Ken 
Published: July 2019

AbstractIt appears likely that the installation of many large dams on major rivers worldwide over the past century has led to large and complex contaminant loadings becoming trapped in the sediments behind these dams. Future planned large dam removal efforts or unintentional breaches may result in substantial contaminant releases downstream. We review the current state of the art regarding knowledge of contaminant loadings behind large dams and potential downstream impacts following dam breaches.
Geometric bionics: Lotus effect helps polystyrene nanotube films get good blood compatibility
Authors: Mao Chun , Zhao Wen-Bo , Luo Wen-Ping , Liang Cun-Xia , Hou Xiao-Mei , Huang Xiao-Hua , Liu Hong-Ke , Xiao Ying-Hong , Bao Jian-Chun , Shen Jian 
Published: July 2019

AbstractVarious biomaterials have been widely used for manufacturing biomedical applications including artificial organs, medical devices and disposable clinical apparatus, such as vascular prostheses, blood pumps, artificial kidney, artificial hearts, dialyzers and plasma separators, which could be used in contact with blood^1^. However, the research tasks of improving hemocompatibility of biomaterials have been carrying out with the development of biomedical requirements^2^. Since the interactions that lead to surface-induced thrombosis occurring at the blood-biomaterial interface become a reason of familiar current complications with grafts therapy, improvement of the blood compatibility of artificial polymer surfaces is, therefore a major issue in biomaterials science^3^. After decades of focused research, various approaches of modifying biomaterial surfaces through chemical or biochemical methods to improve their hemocompatibility were obtained^1^. In this article, we report that polystyrene nanotube films with morphology similar to the papilla on lotus leaf can be used as blood-contacted biomaterials by virtue of Lotus effect^4^. Clearly, this idea, resulting from geometric bionics that mimicking the structure design of lotus leaf, is very novel technique for preparation of hemocompatible biomaterials.
Learning alters theta-nested gamma oscillations in inferotemporal cortex
Authors: Kendrick Keith , Zhan Yang , Fischer Hanno , Nicol Alister , Zhang Xuejuan , Feng Jianfeng 
Published: July 2019

AbstractHow coupled brain rhythms influence cortical information processing to support learning is unresolved. Local field potential and neuronal activity recordings from 64- electrode arrays in sheep inferotemporal cortex showed that visual discrimination learning increased the amplitude of theta oscillations during stimulus presentation. Coupling between theta and gamma oscillations, the theta/gamma ratio and the regularity of theta phase were also increased, but not neuronal firing rates. A neural network model with fast and slow inhibitory interneurons was developed which generated theta nested gamma. By increasing N-methyl-D-aspartate receptor sensitivity similar learning-evoked changes could be produced. The model revealed that altered theta nested gamma could potentiate downstream neuron responses by temporal desynchronization of excitatory neuron output independent of changes in overall firing frequency. This learning-associated desynchronization was also exhibited by inferotemporal cortex neurons. Changes in theta nested gamma may therefore facilitate learning-associated potentiation by temporal modulation of neuronal firing.
Enhanced display of scientific articles using extended metadata
Authors: Page Roderic 
Published: July 2019

AbstractAlthough the Web has transformed science publishing, scientific papers themselves are still essentially "black boxes", with much of their content intended for human readers only. Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical coordinates, publishers could greatly increase the scientific value of their digital content. At the same time this will provide novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic citation.As a proof of concept, my entry in the Elsevier Grand Challenge extracted extended metadata from a set of articles from the journal Molecular Phylogeny and Evolution and used it to populate a entity-attribute-value database. A simple web interface to this database enables an enhanced display of the content of an article, including a map of localities mentioned either explicitly or implicitly (through links to geotagged data), taxonomic coverage, and both data and citation links. Metadata extraction was limited to information listed in tables in the articles (such as GenBank sequences and specimen codes), the body of the article wasn't used. This restriction was deliberate, in order to demonstrate that making extended metadata available doesn't require a journal's publisher to make the full-text freely available (although this is desirable for other reasons).
Dung beetles can eat acorns to increase their fitness
Authors: Verdu Jose R. , Casas Jose L. , Lobo Jorge , Numa Catherine 
Published: July 2019

AbstractAnimals eat different foods in proportions that yield a more favourable balance of nutrients. In spite of known examples of these behaviours across different taxa, the ecological and physiological benefits remain unknown. We identified a surprising dietary shift that confers ecophysiological advantages in a dung beetle species. Thorectes lusitanicus, a Mediterranean ecosystem species adapted to eat dung, is also actively attracted to oak acorns - consuming and burying them. Acorn consumption appears to confer advantages over beetles that do not eat acorns: acorn-fed beetles showed important improvements in fat body mass, haemolymph composition, and ovary development. Beetles incorporating acorns into their diets should have greatly improved resistance to low-temperature conditions and improved reproductive success. In addition to enhancing understanding of the relevance of dietary plasticity to the evolutionary biology of dung beetles, these results open the way to a more general understanding of the ecophysiological implications of differential dietary selection in the context of fitness.
The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Authors: Filler Aaron 
Published: July 2019

AbstractA steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Enhanced anti-tumor effects of combined MDR1 RNA interference and human sodium/iodide symporter (NIS) radioiodine gene therapy using an adenoviral system in a colon cancer model
Authors: Ahn Sohn Joo , Jeon Yong Hyun , Lee Yong Jin , Lee You La , Lee Sang-Woo , Ahn Byeong-Cheol , Ha Jeoung-Hee , Lee Jaetae 
Published: July 2019

AbstractUsing an adenoviral system as a delivery mediator of therapeutic gene, we investigated the therapeutic effects of the use of combined MDR1 shRNA and human NIS (hNIS) radioiodine gene therapy in a mouse colon xenograft model. In vitro uptake of Tc-99m sestamibi was increased approximately two-fold in cells infected with an adenovirus vector that expressed MDR1 shRNA (Ad-shMDR) and I-125 uptake was 25-fold higher in cells infected with an adenovirus vector that expressed human NIS (Ad-hNIS) as compared to control cells. As compared with doxorubicin or I-131 treatment alone, the combination of doxorubicin and I-131 resulted in enhanced cytotoxicity for both Ad-shMDR and Ad-hNIS infected cells but not for control cells. In vivo uptake of Tc-99m sestamibi and Tc-99m pertechnetate was two-fold and 10-fold higher for Ad-shMDR and Ad-hNIS-infected tumors as compared to tumors infected with a control adenovirus construct that expressed [beta]-galactrosidase (Ad-LacZ), respectively. In mice treated with either doxorubicin or I-131 alone, there was a slight delay in tumor growth as compared to mice treated with Ad-LacZ. However, combination therapy with doxorubicin and I-131 induced further significant inhibition of tumor growth as compared with mice treated with Ad-LacZ. We have demonstrated successful therapeutic efficacy of combined MDR shRNA and hNIS radioiodine gene therapy using an adenoviral vector system in a mouse colon cancer model. Adenovirus-mediated cancer gene therapy using MDR1 shRNA and hNIS would be a useful tool for the treatment of cancer cells expressing multi-drug resistant genes.
Female Scent Signals Enhances Male Resistance to Influenza
Authors: Litvinova Ekaterina , Goncharova Elena , Zaidman Alla , Zenkova Marina , Moshkin Mikhail 
Published: July 2019

AbstractScent of receptive females as signal to reproduction stimulate male mice to olfactory search of a potential breeding partner^1, 2^. This searching behavior is coupled with infection risk due to bacterial contamination of the fecal and urine scent marks^4^. The theoretical consideration of host evolution under inevitable parasitic pressures, including helminthes, bacteria, virus etc., predicts adaptations that help protect against parasites associated with breeding^7^. In this study, we propose that acceptation of female signals by male mice leads to adaptive redistribution of immune defense directed to protection against respiratory infection risks. Our results reveal migration of macrophages and neutrophils to upper airways upon exposure to female odor stimulus resulting in increased resistance to influenza virus in male mice. Contrary to widely accepted immunosuppressive function of female sexual signals, our data provide the first demonstration of the adaptive immunological response to female odor stimulus through induction of nonspecific immune response in upper airways.
Connectivity reflects coding: A model of voltage-based spike-timing-dependent-plasticity with homeostasis
Authors: Clopath Claudia , Büsing Lars , Vasilaki Eleni , Gerstner Wulfram 
Published: July 2019

AbstractElectrophysiological connectivity patterns in cortex often show a few strong connections in a sea of weak connections. In some brain areas a large fraction of strong connections are bidirectional, in others they are mainly unidirectional. In order to explain these connectivity patterns, we use a model of Spike-Timing-Dependent Plasticity where synaptic changes depend on presynaptic spike arrival and the postsynaptic membrane potential. The model describes several nonlinear effects in STDP experiments, as well as the voltage dependence of plasticity under voltage clamp and classical paradigms of LTP/LTD induction. We show that in a simulated recurrent network of spiking neurons our plasticity rule leads not only to receptive field development, but also to connectivity patterns that reflect the neural code: for temporal coding paradigms strong connections are predominantly unidirectional, whereas they are bidirectional under rate coding. Thus variable connectivity patterns in the brain could reflect different coding principles across brain areas.
mRNA diffusion explains protein gradients in Drosophila early development
Authors: Dilao Rui , Murro Daniele 
Published: July 2019

AbstractWe propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of Drosophila. In this model, we consider that bicoid mRNA diffuses along the antero-posterior axis of the embryo and the protein is produced in the ribosomes localized near the syncytial nuclei. Bicoid protein stays localized near the syncytial nuclei as observed in experiments.We calibrate the parameters of the mathematical model with experimental data taken during the cleavage stages 11 to 14 of the developing embryo of Drosophila. We obtain good agreement between the experimental and the model gradients, with relative errors in the range 5-8%. The inferred diffusion coefficient of bicoid mRNA is in the range 4.6 x 10^-12^ - 1.5 x10^-11^ m^2^s^-1^, in agreement with the theoretical predictions and experimental measurements for the diffusion of macromolecules in the cytoplasm. We show that the model based on the mRNA diffusion hypothesis is consistent with the known observational data, supporting the recent experimental findings of the gradient of bicoid mRNA in Drosophila [Spirov et al. (2009) Development 136:605-614].
In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome
Authors: Shanker Arun , Maheswari M , Yadav S , Ventateswarlu B 
Published: July 2019

AbstractExpression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270–15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology model was constructed and verified using Anolea, Gromos and Verify3D. Scanning the motif for possible activation sites revealed that there was a protein kinase C phosphorylation site between 15th and 20th residue. The study indicates the possibility of the presence of a DNA binding transcription factor in chromosome 6 of Sorghum bicolor with 60 percent similarity to that of Arabidopsis hrd DNA binding transcription factor.
Automated ocular artifact removal: comparing regression and component-based methods
Authors: Schloegl Alois , Ziehe Andreas , Müller Klaus-Robert 
Published: July 2019

Abstract
Objective:
The aim is to compare various fully automated methods for reducing ocular artifacts from EEG recordings.

Methods:
Seven automated methods including regression, six component-based methods for reducing ocular artifacts have been applied to 36 data sets from two different labs. The influence of various noise sources is analyzed and the ratio between corrected and uncorrected EEG spectra, has been used to quantify the distortion. Results: The results show that not only regression but also component-based methods are vulnerable to over- or under-compensation and can cause significant distortion of EEG. Despite common belief, component-based methods did not demonstrate an advantage over the simple regression method. Conclusion: The newly proposed evaluation criterion showed to be an effective approach to evaluate 252 results from 36 data sets and 7 different methods. Significance: Currently, the regression method provides the most robust and stable results and is therefore the state-of-the-art-method for fully automated reduction of ocular artifacts.
Dating the cyanobacterial ancestor of the chloroplast
Authors: Falcon Luisa , Magallon Susana , Castillo Amanda 
Published: July 2019

AbstractCyanobacteria have played a pivotal role in the history of life on Earth being the first organism to carry out oxygenic photosynthesis, which changed atmospheric chemistry and allowed the evolution of Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which photosynthesis is conducted. Although the initial suggestion from Mereschkowsky (1905) that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks, because until now, the long-standing question of, from which, among the vast diversity of cyanobacteria, did chloroplasts evolve, has not been resolved. We found that chloroplasts form a monophyletic lineage, are most closely related to subsection I, N2-fixing unicellular cyanobacteria (Order Chroococcales), and heterocyst-forming Order Nostocales cyanobacteria are their sister group. The appearance of Nostocales and of Chroococcales occurred during the Paleoproterozoic, and chloroplasts appeared in the mid-Proterozoic. The capability of N2-fixation in cyanobacteria appeared once during the late Archaen and early Proterozoic eons. Furthermore, we found that oxygen-evolving cyanobacteria could have appeared in the Archean. Our results suggest that a free-living cyanobacterium with the capacity to store starch via oxygenic CO2 fixation, and to fix atmospheric N2, would be a very important intracellular acquisition, which, as can be recounted today from several lines of evidence, would have become the chloroplast by endosymbiosis.