bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era
Authors: Gao Feng , Ming Chen , Hu Wangjie , Li Haipeng 
Published: June 2016

AbstractGenetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR) that uses machine learning to estimate recombination rate ρ (=4Ner) from intraspecific DNA polymorphism data. When ρ&gt;10 and the number of sampled diploid individuals is large enough (≥50), the variance of ρFastEPRR remains slightly smaller than that of ρLDhat. The new estimate ρcomb (calculated by averaging ρFastEPRR and ρLDhat) has the smallest variance of all cases. When estimating ρFastEPRR, the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB) extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the ρFastEPRR and ρLDhat maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/) is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era.
Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?
Authors: Khedkar Supriya , Seshasayee Aswin Sai Narain 
Published: June 2016

Abstract
Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences.
TheDrosophila prageGene, Required for Maternal Transcript Destabilization in Embryos, Encodes a Predicted RNA Exonuclease
Authors: Cui Jun , Lai Yun Wei , Sartain Caroline V , Zuckerman Rebecca M , Wolfner Mariana F 
Published: June 2016

AbstractEgg activation, the transition of mature oocytes into developing embryos, is critical for the initiation of embryogenesis. This process is characterized by resumption of meiosis, changes in the egg’s coverings and by alterations in the transcriptome and proteome of the egg; all of these occur in the absence of new transcription. Activation of the egg is prompted by ionic changes in the cytoplasm (usually a rise in cytosolic calcium levels) that are triggered by fertilization in some animals and by mechanosensitive cues in others. The egg’s transcriptome is dramatically altered during the process, including by the removal of many maternal mRNAs that are not needed for embryogenesis. However, the mechanisms and regulators of this selective RNA degradation are not yet fully known. Forward genetic approaches in Drosophila have identified maternal-effect genes whose mutations prevent the transcriptome changes. One of these genes, prage (prg), was identified by Tadros et al. in a screen for mutants that fail to destabilize maternal transcripts. We identified the molecular nature of the prg gene through a combination of deficiency mapping, complementation analysis, and DNA sequencing of both extant prg mutant alleles. We find that prg encodes a ubiquitously expressed predicted exonuclease, consistent with its role in maternal mRNA destabilization during egg activation.
Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes
Authors: Kariuki Silvia N , Blischak John D , Nakagome Shigeki , Witonsky David B , Di Rienzo Anna 
Published: June 2016

AbstractThe active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25D), plays an important immunomodulatory role, regulating transcription of genes in the innate and adaptive immune system. The present study examines patterns of transcriptome-wide response to 1,25D, and the bacterial lipopolysaccharide (LPS) in primary human monocytes, to elucidate pathways underlying the effects of 1,25D on the immune system. Monocytes obtained from healthy individuals of African-American and European-American ancestry were treated with 1,25D, LPS, or both, simultaneously. The addition of 1,25D during stimulation with LPS induced significant upregulation of genes in the antimicrobial and autophagy pathways, and downregulation of proinflammatory response genes compared to LPS treatment alone. A joint Bayesian analysis enabled clustering of genes into patterns of shared transcriptional response across treatments. The biological pathways enriched within these expression patterns highlighted several mechanisms through which 1,25D could exert its immunomodulatory role. Pathways such as mTOR signaling, EIF2 signaling, IL-8 signaling, and Tec Kinase signaling were enriched among genes with opposite transcriptional responses to 1,25D and LPS, respectively, highlighting the important roles of these pathways in mediating the immunomodulatory activity of 1,25D. Furthermore, a subset of genes with evidence of interethnic differences in transcriptional response was also identified, suggesting that in addition to the well-established interethnic variation in circulating levels of vitamin D, the intensity of transcriptional response to 1,25D and LPS also varies between ethnic groups. We propose that dysregulation of the pathways identified in this study could contribute to immune-mediated disease risk.
Identification and Characterization of acis-Regulatory Element for Zygotic Gene Expression inChlamydomonas reinhardtii
Authors: Hamaji Takashi , Lopez David , Pellegrini Matteo , Umen James 
Published: June 2016

AbstractUpon fertilization Chlamydomonas reinhardtii zygotes undergo a program of differentiation into a diploid zygospore that is accompanied by transcription of hundreds of zygote-specific genes. We identified a distinct sequence motif we term a zygotic response element (ZYRE) that is highly enriched in promoter regions of C. reinhardtii early zygotic genes. A luciferase reporter assay was used to show that native ZYRE motifs within the promoter of zygotic gene ZYS3 or intron of zygotic gene DMT4 are necessary for zygotic induction. A synthetic luciferase reporter with a minimal promoter was used to show that ZYRE motifs introduced upstream are sufficient to confer zygotic upregulation, and that ZYRE-controlled zygotic transcription is dependent on the homeodomain transcription factor GSP1. We predict that ZYRE motifs will correspond to binding sites for the homeodomain proteins GSP1-GSM1 that heterodimerize and activate zygotic gene expression in early zygotes.
Saccharomyces cerevisiae Tti2 Regulates PIKK Proteins and Stress Response
Authors: Hoffman Kyle S , Duennwald Martin L , Karagiannis Jim , Genereaux Julie , McCarton Alexander S , Brandl Christopher J 
Published: June 2016

Abstract
The TTT complex is composed of the three essential proteins Tel2, Tti1, and Tti2. The complex is required to maintain steady state levels of phosphatidylinositol 3-kinase-related kinase (PIKK) proteins, including mTOR, ATM/Tel1, ATR/Mec1, and TRRAP/Tra1, all of which serve as regulators of critical cell signaling pathways. Due to their association with heat shock proteins, and with newly synthesized PIKK peptides, components of the TTT complex may act as cochaperones. Here, we analyze the consequences of depleting the cellular level of Tti2 in Saccharomyces cerevisiae. We show that yeast expressing low levels of Tti2 are viable under optimal growth conditions, but the cells are sensitive to a number of stress conditions that involve PIKK pathways. In agreement with this, depleting Tti2 levels decreased expression of Tra1, Mec1, and Tor1, affected their localization and inhibited the stress responses in which these molecules are involved. Tti2 expression was not increased during heat shock, implying that it does not play a general role in the heat shock response. However, steady state levels of Hsp42 increase when Tti2 is depleted, and tti2L187P has a synthetic interaction with exon 1 of the human Huntingtin gene containing a 103 residue polyQ sequence, suggesting a general role in protein quality control. We also find that overexpressing Hsp90 or its cochaperones is synthetic lethal when Tti2 is depleted, an effect possibly due to imbalanced stoichiometry of a complex required for PIKK assembly. These results indicate that Tti2 does not act as a general chaperone, but may have a specialized function in PIKK folding and/or complex assembly.
Binding Sites in theEFG1Promoter for Transcription Factors in a Proposed Regulatory Network: A Functional Analysis in the White and Opaque Phases ofCandida albicans
Authors: Pujol Claude , Srikantha Thyagarajan , Park Yang-Nim , Daniels Karla J , Soll David R 
Published: June 2016

AbstractIn Candida albicans the transcription factor Efg1, which is differentially expressed in the white phase of the white-opaque transition, is essential for expression of the white phenotype. It is one of six transcription factors included in a proposed interactive transcription network regulating white-opaque switching and maintenance of the alternative phenotypes. Ten sites were identified in the EFG1 promoter that differentially bind one or more of the network transcription factors in the white and/or opaque phase. To explore the functionality of these binding sites in the differential expression of EFG1, we generated targeted deletions of each of the 10 binding sites, combinatorial deletions, and regional deletions using a Renillareniformis luciferase reporter system. Individually targeted deletion of only four of the 10 sites had minor effects consistent with differential expression of EFG1, and only in the opaque phase. Alternative explanations are considered.
Poner en palabras lo traumático: mujeres sobrevivientes del abuso sexual
Authors: Fridman Irene 
Published: June 2016

<p>En este trabajo se profundiza acerca de las consecuencias psíquicas de haber sido víctima de incesto en la infancia, comparando la situación traumática de la violencia sexual incestuosa con los efectos psíquicos de las víctimas de violencia política. Junto con esto se realiza un análisis crítico acerca de los puntos de la teoría psicoanalítica problemáticos para poder entender las vivencias de las mujeres que son víctimas de violencia.</p><p> </p>
Avaliação de um Módulo de Reconhecimento de Fala na Plataforma Arduino
Authors: Andrade Carlos Alberto , Ramos Silva Gustavo , Cavalcante da Silva Daniella Dias , Vasconcelos César Rocha 
Published: June 2016

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>O grande avanço tecnológico gerado pela globalização tornou urgente a busca por dispositivos eletrônicos que sejam viáveis, ágeis e práticos. Uma ferramenta poderosa e que cingi todo esse cunho fundamental é a possibilidade de realizar a interação com tais dispositivos por meio do reconhecimento da fala. O objetivo deste trabalho foi avaliar um módulo de reconhecimento de fala compatível com a plataforma Arduino, identificando seus recursos como também suas limitações. A metodologia adotada incluiu testes de reconhecimento em um ambiente com ruído e uma análise de SNR (Signal-to-Noise Ratio) para o microfone que acompanha o módulo. Ao longo deste artigo são apresentados os principais conceitos relacionados ao reconhecimento de fala, sobre a plataforma Arduino e funcionamento do módulo analisado. </span></p></div></div></div>
O enfermeiro e o ensino na assistência às doenças sexualmente transmissíveis: revisão integrativa
Authors: Santos Joao Carlos Alves dos 
Published: June 2016

<p>As doenças sexualmente transmissíveis e a síndrome da imunodeficiência humana são doenças de alta prevalência, além de ser um problema de política pública de saúde do país. O objetivo deste estudo foi analisar na literatura nacional estudos a respeito da formação do enfermeiro docente e o seu ensino por meio de métodos e práticas pedagógicas na assistência a essas doenças. Trata-se de um estudo de revisão integrativa. A busca foi realizada na base de dados Literatura Latino-Americana e do Caribe em Ciências da Saúde, mediante a combinação dos descritores: Síndrome da Imunodeficiência Adquirida, Docentes, Ensino, Enfermagem entre o ano 2000 à 2014. Foram encontrados cinco artigos após a aplicação dos critérios de inclusão pré-definidos. Observou-se o relato de experiência e a valorização da percepção pessoal e profissional como instrumentos que alicerçam o ensino ao tema pelos docentes de enfermagem. Portanto, sugere-se a ampliação de pesquisas sobre o contexto docente e as estratégias de ensino, pois estudos com esse enfoque são fundamentais para uma percepção reflexiva do ensino em enfermagem e contribui para a melhoria de sua ação como educador.</p><p align="center"><strong><em>Nurses and teaching in assistance for sexually transmitted diseases: a integrative review </em></strong></p><p><strong>ABSTRACT</strong> - Sexually transmitted diseases and human immunodeficiency syndrome are highly prevalent diseases. Also, they are a public policy issue of health of the country. The aim of this study was to analyze in the national literature studies on the training of teaching nurses and their education through educational methods and practices in the care of these diseases. This is a study of integrative review. The search was performed in the database Latin American and Caribbean Health Sciences. Through the combination of descriptors: Human Immunodeficiency Syndrome, Teachers, Education, Nursing between 2000 and 2014. Five articles were found after application of predefined inclusion criteria. We observed a report of experience and the enhancement of personal and professional perception as instruments that support teaching on the subject by nursing professors. Therefore, we suggest the expansion of research on the teaching context and teaching strategies, because studies with this approach are key to a reflexive perception of nursing education and they contribute to the improvement of its action as an educator.</p>
La jerarquía de monedas nacionales y los problemas financieros actuales
Authors: Piqué Pilar 
Published: June 2016

Este artículo desarrolla el concepto de jerarquía de monedas nacionales para contextualizar la estructura monetaria y financiera mundial y su relación con los rasgos centrales del capitalismo actual. Examina los desequilibrios permanentes de cuenta corriente, los cambios en los objetivos de los bancos centrales, los problemas del sistema financiero actual y los límites de las instituciones financieras para formular un programa de reformas estructurales.
Discriminación y diferenciales de salarios en el mercado laboral
Authors: Nieto Fabio David 
Published: June 2016

Este artículo presenta un modelo de determinación de salarios que usa ecuaciones de réplica para representar las regularidades sociales que originan las preferencias de discriminación de los empleadores. La hipótesis básica es que esas preferencias están sujetas a la interacciónentre oferentes y demandantes de trabajo en un escenario de pleno empleo. El trabajo es un aporte teórico a la discusión sobre la discriminación de salarios, tema en el que predominan los estudios empíricos sobre las diferencias de salarios.
LOGOS I SPOZNAJA U HERAKLITOVOJ FILOZOFIJI
Authors: MILJEVIĆ ANA 
Published: June 2016

Rad preispituje temeljne pojmove Heraklitove filozofije kroz komparativnu analizu fragmenata, koji svojom hijastičkom strukturom, paralelizmom delova unutar svakog fragmenta, te ritmičkom i etimološkom igrom grade paradokse. Kako se Heraklit koristi paradoksima pri izgradnji osnovnih ontoloških pojmova, nameće se pitanje da li ovako izražena logosnost bivstvovanja, ima unapred određen metod. Heraklitov prvi fragment, koga mnogi autori nazivaju još i programskim fragmentom posmatran je u radu kao takav i u metodskom smislu. Ono što analiza ovog fragmenta donosi jeste to da Heraklit koristi etimološki i analitički metod kojima se u saznajnom smislu gradi, a u ontološkom smislu pokazuje paradoksalnost unutar pojmova. U tom kontekstu rad utvrđuje povezanost pojma <em>λόγος </em>(<em>logos</em>) sa pojmom <em>φρόνησις </em>(razboritost) i <em>τὸ σοφόν </em>kroz Heraklitov izraz <em>ἓν τὸ σοφόν </em>(Jedno-mudro).
"MEDIUM DUHA" VERSUS "KUĆA BITKA". HEGELOV SPEKULATIVNI POJAM JEZIKA
Authors: PEROVIĆ MILENKO A. 
Published: June 2016

Rasprava o Hegelovom shvatanju jezika postavljena je kroz implicitni polemički odnos prema Hajdegerovoj koncepciji jezika, analitičkoj tradiciji shvatanja jezika, kao i prema De Sosirovom lingvističkom razumijevanju jezika. Hegel na spekulativni način – posve drugačije od tradicije filozofskog mišljenja o jeziku (Haman, Herder, Kant, Humbolt i Fihte), kao i potonje povijesti razumijevanja jezika u okviru koncepcija filozofije jezika i savremene lingvistike – shvata jezik kao spekulativnu intelektualnu strukturu. Ontološko porijeklo jezika nije u transcendenciji, nego u ljudskoj imanenciji, u evoluciji produktivne uobrazilje u produktivno pamćenje. Hegelov pojam jezika autor dokučuje antropologijskim, fenomenologijskim i psihologijskim pitanjem o jeziku.
Portuguese Studium and Portuguese Scholars in the Middle Ages: Some Remarks on a Research Strand and its Databases = Studium y académicos portugueses en la Edad Media: algunas aportaciones sobre una línea de investigación y sus bases de datos
Authors: Fernandes Hermenegildo , Norte Armando , Oliveira Leitão André de 
Published: June 2016

Abstract:This paper aims to present an existing research strand at the Centro de História da Universidade de Lisboa (CH-ULisboa), which is based on several resources related to digital humanities. This broader research strand has three main axes: the study of the University of Lisbon per se, the mobility of Portuguese scholars in the medieval and early modern periods, and the funding and management of the medieval Portuguese studium, which together can help generate a general picture of the history of the universityin Portugal. These three axes are based on different field of digital humanities, such as databases and GIS, which we intend to merge and make available online in the near future. Two of these databases (the Magistri Database and the Peregrinatio Database) are presented here as case studies to discuss different issues derived from the use of the prosopographical method, as well as to address several technical issues.Keywords: Portugal, University, peregrination academica, Middle Ages and Early Modern Age, digital humanities.Resumen: El presente artículo tiene como objetivo la presentación de una línea de investigación existente en el Centro de História da Universidade de Lisboa (CH-ULisboa) basada en varios recursos relacionados con las humanidades digitales. Esta línea de investigación más amplia tiene tres ejes principales: el estudio de la Universidad de Lisboa, la movilidad de los estudiantes portugueses en las épocas medieval y moderna, y la financiación y gestión del studium medieval portugués, todos entrelazados con el fin de obtener una imagen de la historia de la universidad en Portugal. Estos tres ejes se basan en diferentes campos de las humanidades digitales, tales como las bases de datos y los SIG, que tenemos la intención de fusionar y hacer disponibles en línea en un futuro próximo. Dos de estas bases de datos (Magistri y Peregrinatio) se presentan aquí como casos de estudio que permiten examinar las cuestiones derivadas de la utilización de una metodología basada en la prosopografía, así como intentar aclarar problemas técnicos relacionados con ella.Palabras clave: Portugal, Universidad, peregrinatio academica, Edades Media y Moderna, humanidades digitales.
Anti Corrosion Ability and Biocidal Efficiency of Surfactants on Mild Steel in Aqueous Environment
Authors: Manonmani K. N. , Manjula P. , Vennila T. 
Published: June 2016

<div><p><em>The inhibition efficiency of DMBP (Diethyl-4-methyl benzyl phosphonate) along with Biocidal action of CTAB and SDS on corrosion of mild steel in neutral aqueous medium has been evaluated by mass loss method, both in absence and presence of Zn<sup>2+</sup>. It is observed that DMBP exhibits 65% IE individually at ambient temperature. Synergistic influence of Zn<sup>2+</sup> increases IE of DMBP to 71%. Addition of surfactants CTAB (N-Cetyl-N,N,N-Trimethyl Ammonium Bromide) and SDS ( Sodium dodecyl Benzene sulphonate) enhances the inhibition efficiency of DMBP from 65% to 96% and 92% respectively. The inhibitor system consisting of DMBP (200 ppm) + Zn<sup>2+</sup> (90 ppm)+ CTAB (50 ppm) / SDS (40 ppm) offered maximum Biocidal efficiency (BE %) of 100% after killing of microbial bacteria present in aqueous system. FTIR spectra indicates the protective film consist of Fe<sup>2+</sup>-DMBP and Zn(OH)<sub>2</sub>.</em></p></div>