bluuebunny/crossref_metadata_2025_split huggingface dataset:
Support for the Dominance Theory inDrosophilaTranscriptomes
Authors: Llopart Ana , Brud Evgeny , Pettie Nikale , Comeron Josep M 
Published: October 2018

AbstractInteractions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here, we study genome-wide patterns of gene expression in females and males of Drosophila yakuba, Drosophila santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analyses also suggest a contribution of weakly deleterious regulatory mutations to gene expression divergence in genes with sex-biased expression, but only in the sex toward which the expression is biased (e.g., genes with female-biased expression when analyzed in females). In the opposite sex, we found stronger selective constraints on gene expression divergence. Although genes with a high degree of male-biased expression show a clear signal of faster-X evolution of gene expression, we also detected slower-X evolution in other gene classes (e.g., female-biased genes). This slower-X effect is mediated by significant decreases in cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with a high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts.
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes
Authors: Kim Woojin , Underwood Ryan S , Greenwald Iva , Shaye Daniel D 
Published: October 2018

Abstract
OrthoList, a compendium of Caenorhabditis elegans genes with human orthologs compiled in 2011 by a meta-analysis of four orthology-prediction methods, has been a popular tool for identifying conserved genes for research into biological and disease mechanisms. However, the efficacy of orthology prediction depends on the accuracy of gene-model predictions, an ongoing process, and orthology-prediction algorithms have also been updated over time. Here we present OrthoList 2 (OL2), a new comparative genomic analysis between C. elegans and humans, and the first assessment of how changes over time affect the landscape of predicted orthologs between two species. Although we find that updates to the orthology-prediction methods significantly changed the landscape of C. elegans–human orthologs predicted by individual programs and—unexpectedly—reduced agreement among them, we also show that our meta-analysis approach “buffered” against changes in gene content. We show that adding results from more programs did not lead to many additions to the list and discuss reasons to avoid assigning “scores” based on support by individual orthology-prediction programs; the treatment of “legacy” genes no longer predicted by these programs; and the practical difficulties of updating due to encountering deprecated, changed, or retired gene identifiers. In addition, we consider what other criteria may support claims of orthology and alternative approaches to find potential orthologs that elude identification by these programs. Finally, we created a new web-based tool that allows for rapid searches of OL2 by gene identifiers, protein domains [InterPro and SMART (Simple Modular Architecture Research Tool], or human disease associations ([OMIM (Online Mendelian Inheritence in Man], and also includes available RNA-interference resources to facilitate potential translational cross-species studies.
Spatiotemporal Gene Expression Analysis of theCaenorhabditis elegansGermline Uncovers a Syncytial Expression Switch
Authors: Tzur Yonatan B , Winter Eitan , Gao Jinmin , Hashimshony Tamar , Yanai Itai , Colaiácovo Monica P 
Published: October 2018

AbstractDevelopmental programs are executed by tightly controlled gene regulatory pathways. Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear amplification and sequencing) to generate a spatiotemporal gene expression map of the Caenorhabditis elegans syncytial germline from adult hermaphrodites and males. We found that over 6000 genes exhibit spatiotemporally dynamic expression patterns throughout the hermaphrodite germline, with two dominant groups of genes exhibiting reciprocal shifts in expression at late pachytene during meiotic prophase I. We found a strong correlation between restricted spatiotemporal expression and known developmental and cellular processes, indicating that these gene expression changes may be an important driver of germ cell progression. Analysis of the male gonad revealed a shift in gene expression at early pachytene and upregulation of subsets of genes following the meiotic divisions, specifically in early and late spermatids, mostly transcribed from the X chromosome. We observed that while the X chromosome is silenced throughout the first half of the gonad, some genes escape this control and are highly expressed throughout the germline. Although we found a strong correlation between the expression of genes corresponding to CSR-1-interacting 22G-RNAs during germ cell progression, we also found that a large fraction of genes may bypass the need for CSR-1-mediated germline licensing. Taken together, these findings suggest the existence of mechanisms that enable a shift in gene expression during prophase I to promote germ cell progression.
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data
Authors: Meisner Jonas , Albrechtsen Anders 
Published: October 2018

AbstractMeisner and Albrechtsen present two methods for inferring population structure and admixture proportions in low depth next-generation sequencing (NGS). NGS methods provide large amounts of genetic data but are associated with statistical uncertainty, especially for low-depth...We here present two methods for inferring population structure and admixture proportions in low-depth next-generation sequencing (NGS) data. Inference of population structure is essential in both population genetics and association studies, and is often performed using principal component analysis (PCA) or clustering-based approaches. NGS methods provide large amounts of genetic data but are associated with statistical uncertainty, especially for low-depth sequencing data. Models can account for this uncertainty by working directly on genotype likelihoods of the unobserved genotypes. We propose a method for inferring population structure through PCA in an iterative heuristic approach of estimating individual allele frequencies, where we demonstrate improved accuracy in samples with low and variable sequencing depth for both simulated and real datasets. We also use the estimated individual allele frequencies in a fast non-negative matrix factorization method to estimate admixture proportions. Both methods have been implemented in the PCAngsd framework available at http://www.popgen.dk/software/.
Spatial Vulnerabilities of the Escherichia coli Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing
Authors: Zhang Xiaolong , Zhang Xuehong , Zhang Xia , Liao Yuwei , Song Luyao , Zhang Qingzheng , Li Peiying , Tian Jichao , Shao Yanyan , AI-Dherasi Aisha Mohammed , Li Yulong , Liu Ruimei , Chen Tao , Deng Xiaodi , Zhang Yu , Lv Dekang , Zhao Jie , Chen Jun , Li Zhiguang 
Published: October 2018

Abstract
Investigation of spontaneous mutations by next-generation sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long-term (possibly be years of) culturing, but not the freshly generated mutations that occur at very low frequencies. In this study, we established a molecularly barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 Escherichia coli cell culture samples were defined with a high confidence (P &lt; 0.01). We also developed a hotspot-calling approach based on the run-length encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra in a single expansion process without long-term culturing.
Activity Performance Curves of Individuals With Cerebral Palsy
Authors: van Gorp Marloes , Roebroeck Marij E. , Swan Tan Siok , de Groot Vincent , Gorter Jan Willem , Smits Dirk-Wouter , Schmidt Ann Katrin , Dallmeijer Annet J. ,   on behalf of the PERRIN DECADE Study Group
Published: October 2018

OBJECTIVES:
Describe development curves of motor and daily activity performance in individuals with cerebral palsy (CP).

METHODS:
Participants with CP aged 1 to 20 years at baseline (n = 421) and Gross Motor Functioning Classification System (GMFCS) levels I to V (27% of participants with intellectual disability [ID]) were longitudinally assessed up to a 13-year follow-up period. Motor and daily activity performance were assessed using the relevant subdomains of the Vineland Adaptive Behavior Scales survey. Nonlinear mixed effects analyses were used, estimating the limit (average maximal performance level) and the age by which individuals reached 90% of the limit (age90).

RESULTS:
Limits of motor performance decreased with each lower functional level. Age90 for motor performance was reached at ∼6 to 8 years of age in children with GMFCS levels I to III, and at younger ages in those with lower functional levels. Limits of daily activity performance did not differ between individuals without ID with GMFCS levels I to III. The age90s of daily activities were reached between 11 and 14 (personal), 26 and 32 (domestic), and 22 and 26 years of age (community). Individuals with ID reached lower daily activity performance limits earlier.

CONCLUSIONS:
Individuals with CP continue to develop motor performance after gross motor capacity limits are reached. For those without ID, daily activities continue to develop into their 20s. Individuals who are severely affected functionally have the least favorable development of motor performance, and those with ID have the least favorable development of daily activity performance.
Effectiveness and Eficiency of Educational Systems in a Context of Shifting Educational Paradigms
Authors: Želvys Rimantas , Dukynaitė Rita , Vaitekaitis Jogaila 
Published: October 2018

Neoliberal conceptions are pervading educational context worldwide. Lithuania is not an exception. Originally conceived as a sociocultural educational paradigm is being rapidly replaced by an economical paradigm. Constrained and short-sighted preoccupation with labour market needs is a sharp shift from humanistic and cultural vision of education as social good per se.
Effectiveness and efficiency as an important endeavour of The New Public Management today permeates our education system. Data from international surveys show clear links between investment in education and student learning outcomes, yet, as EBPO PISA 2015 demonstrates, science classrooms in Lithuanian schools come short of laboratory equipment, leaving teachers with traditional chalk and talk methods, significantly lagging behind the international ones. We ask rhetorically “outputs without inputs”?
Despite the criticism of narrow input-output mindset growing numbers of educational efficiency studies are observed. Moving away from economical concerns to focus on the educational process educational effectiveness research includes such variables as classroom microclimate, student motivation, socioeconomic and cultural status, which is proven to have tremendous influence on student learning outcomes and overall wellbeing. Effectiveness and efficiency research though seemingly complement each other but still rarely merge.
Our most important educational documents – Lithuania’s progress strategy “Lithuania 2030”, National Education Strategy, Education Act, The Good School Concept are characterized by humanistic rhetoric stressing the importance of social and cultural aspects of education, but more than often indicators of success are oriented towards the implementation of the neoliberal economic education paradigm which leaves a lot to be desired.
Association of Soluble TNFR-1 Concentrations with Long-Term Decline in Kidney Function: The Multi-Ethnic Study of Atherosclerosis
Authors: Bhatraju Pavan K. , Zelnick Leila R. , Shlipak Michael , Katz Ronit , Kestenbaum Bryan 
Published: October 2018

BackgroundTNF receptor-1 (TNFR-1), which plays a causative role in endothelial cell dysfunction and inflammation, is expressed on the cell surface in glomerular and peritubular capillary endothelium of the kidneys. Higher soluble TNF receptor-1 (sTNFR-1) concentrations are associated with kidney disease progression among persons with established diabetic kidney disease. However, no studies have assessed sTNFR-1’s role in long-term kidney function changes in a multiethnic population without cardiovascular disease at baseline.MethodsWe tested associations between baseline sTNFR-1 concentrations and 10-year decline in eGFR (incident ≥40% decline and annual proportional decline) among 2548 participants in the Multi-Ethnic Study of Atherosclerosis (MESA), a prospective cohort study. Serum creatinine concentrations were determined at enrollment and study years 3, 5, and 10.ResultsMean age of participants was 61 years old, 53% were women, and mean baseline eGFR was 79 ml/min per 1.73 m2. Serum sTNFR-1 was inversely associated with baseline eGFR. Over median follow-up of 9.3 years, 110 participants developed ≥40% decline in eGFR; each SD higher concentration of sTNFR1 was associated with higher risk of 40% eGFR decline (adjusted hazard ratio, 1.43; 95% confidence interval [95% CI], 1.16 to 1.77;P<0.001). The highest sTNFR-1 tertile was associated with adjusted annualized decline in eGFR of 1.94% (95% CI, 1.79 to 2.09). Associations persisted across subgroups defined by demographics, hypertension, diabetes, and baseline CKD status.ConclusionsElevated serum sTNFR-1 concentrations are associated with faster declines in eGFR over the course of a decade in a multiethnic population, independent of previously known risk factors for kidney disease progression.
BAKÜ BELEDİYE BİNASINDAKİ FİGÜRLÜ ARMALARIN İKONOGRAFİK YORUMU
Authors: AKTEMUR Alimurat 
Published: October 2018

Özet

İstiklaliyet caddesi’nde
yer alan 1870 tarihli Belediye Binasının mimarı aslen Polonyalı olan İ.V. Goslavski’dir.

Meclis Binası, Belediye
Binası gibi adlarla anılan bu yapı, genel olarak değerlendirildiğinde,
Neo-Barok ve Art-Nouveau üsluplarında ve XIX. yüzyılda Bakü’ye hakim olmaya
başlayan Avrupai tarzda yapıldığı görülür.

Pencere alınlıklarındaki
kabartma şeklinde işlenmiş armaların ikonografisine genel olarak baktığımızda;
sağlık ve tıbbın, işgücü ve üretimin,
eğitim ve ilmi araştırmaların, dünyayı ilmi araştırmalarla tanımanın, doğanın
önemine vurgu yapıldığı, tüm bunların insan yaşamı ve medeniyeti için
vazgeçilmez olduğunun üzerinde durulduğu görülür.

Anahtar
Kelimeler: Bakü, Belediye Binası, Arma, İkonografi
ÇANKIRI-ÇORUM-AMASYA HATTI ÜZERİNDEKİ HİTİT YERLEŞİMLERİNİN LOKALİZASYON SORUNLARIYLA İLGİLİ GENEL BİR DEĞERLENDİRME
Authors: SİR GAVAZ Özlem 
Published: October 2018

Son
yıllarda Hititler Dönemi Anadolu’nun tarihi coğrafyası ile ilgili değerli araştırmalar
yapılmış ve bu yöndeki çalışmalar artış göstermiştir. Bu çalışmalarda ortaya
konulan yeni görüşler ve isabetli lokalizasyon önerileri, özellikle günümüzde
Çankırı, Çorum ve Amasya İllerini kapsayan bölgenin tarihi coğrafyasını
aydınlatmada yol gösterici olmuştur. Fakat yapılan yeni teklifler bir takım sorunları
da beraberinde getirmiştir. Zira zaten tarihi coğrafya açısından problemli olan
bu bölge, kuzeydeki Kaška sorunsalı ile de büsbütün çıkmaza girmektedir.

Çalışmada Hititçe metinlerde geçen bazı
önemli yerleşimler ve bu yerleşimler için yapılan farklı lokalizasyon
tekliflerinin yol açtığı tartışmalar değerlendirilecektir. Özellikle Hititlerin başkenti
Boğazkale/Hattuša, Ortaköy/Šapinuwa, Maşathöyük/Tapigga ve Oymaağaç/Nerik
eşitlikleri esas alınarak yerleşimler için yapılan farklı görüşler
karşılaştırmalı olarak sunulacaktır.
Estimativas de recarga aquífera com uso de filtros digitais em sub-bacias hidrográficas do Sistema Aquífero Serra Geral no estado do Rio Grande do Sul
Authors: Bortolin Taison Anderson , Reginato Pedro Antonio Roehe , Presotto Marco Antonio , Schneider Vania Elisabete 
Published: October 2018

A estimativa de recarga aquífera possui grande relevância nos estudos de águas subterrâneas e cálculo de disponibilidade hídrica em diferentes regiões. Este estudo teve por objetivo estimar a recarga de águas subterrâneas a partir de 3 diferentes métodos através da estimativa de parâmetros de escoamento de base em 11 sub-bacias, inseridas no Sistema Aquífero Serra Geral localizadas no estado do Rio Grande do Sul a partir de dados diários de 30 anos de vazão (1977/2006). Para tal foram utilizados filtros recursivos digitais como métodos de separação de escoamento de base como o proposto por Eckhardt, onde é possível obter o fluxo de base nos cursos d’água através da separação da vazão em dois elementos: escoamento superficial (direto) e escoamento de base (indireto). O resultado dessa separação é definido por um índice de escoamento de base (BFI), sempre restringido a um valor máximo (BFImax). Para este fim, foram aplicados 3 valores de BFImax: um predefinido por Eckhardt conforme geologia local, um obtido através da razão das vazões de permanência Q90/Q50 e outro através da utilização de um filtro inverso proposto por Collischonn e Fan (2013). Após, calculou-se as taxas de recarga (TR), relacionando os valores da vazão de base média obtidos em cada estação fluviométrica analisada e as áreas de drenagem de cada sub-bacia. Pode-se constatar que para a região de estudo os parâmetros predefinidos de Eckhardt apresentam valores mais baixos na maior parte das bacias se comparado aos outros. Os resultados encontrados demonstraram que há diferenças estatisticamente significativas no emprego de diferentes métodos. Para as 11 sub-bacias do Sistema Aquífero Serra Geral, foram encontradas recargas que variaram entre 9,23% utilizando o método 2 até 35,87% da precipitação com o emprego do método 3. Destaca-se, entretanto, que as diferenças nos valores, além de depender dos parâmetros e métodos utilizados podem estar associadas a uma série de fatores fisiográficos e climatológicos da bacia, sendo de suma importância sua avaliação na estimativa de recarga. http://dx.doi.org/10.18226/23185279.v6iss2p21
Methodological Approach for Developing a KMS: A Case Study
Authors: Griman Anna , Rojas Teresita , Pérez María 
Published: October 2018

This article describes the construction of a Knowledge Management System (KMS) by applying fundamental concepts and principles of Software Engineering, such as process, models, methodology, technology and architectures, among others. They are applied to the field of Knowledge Management as a means of improving the process of developing applications in this domain, in an endeavor to increase its effectiveness.
This paper’s main contribution is a methodological approach progressing from knowledge processes to a set of appropriate systems. The use of modeling techniques and technologies that may prove helpful to the Software Engineer are suggested as part of this approach, while the technological, social and organizational aspects to be considered are highlighted. This proposal was evaluated through the development of a Knowledge Management System for a Venezuelan organization – a research center.
The evaluation proved the effectiveness of the methodological aspects proposed. These may be of use as inputs for some Learning Software Organizations dedicated to the development of this type of system.
Selectivity of Very‐Long‐Chain Fatty Acid‐Inhibiting Herbicides in Rice as Influenced by Application Timing and Soil Texture
Authors: Godwin John , Norsworthy Jason K. , Scott Robert C. 
Published: October 2018

Core Ideas
Alternative herbicide sites of action are desperately needed in US rice.
Rice exhibited tolerance to the currently non‐labeled herbicides acetochlor and pethoxamid when applied at the one‐ to two‐leaf growth stage on a silt loam and clay soil.
Delaying application of very‐long‐chain fatty acid‐inhibiting herbicides until drill‐seeded rice has completely emerged enhanced crop tolerance.
Very‐long‐chain fatty acid (VLCFA)‐inhibiting herbicides include pyroxasulfone, S‐metolachlor, acetochlor, and pethoxamid. Currently, no VLCFA‐inhibiting herbicides are labeled for use in US rice production; however, if rice tolerance can be established they would provide an alternative herbicide site of action (SOA). In 2015 and 2016, pyroxasulfone (Zidua) at 0.14 lb a.i. ac−1, S‐metolachlor (Dual Magnum) at 0.95 lb a.i. ac−1, acetochlor (Warrant) at 0.95 lb a.i. ac−1, and pethoxamid at 0.75 lb a.i. ac−1 were applied delayed preemergence (DPRE) and to spiking and one‐ to two‐leaf rice on a Dewitt silt loam and a Sharkey clay soil. Trials were conducted at separate locations to determine the effect differing soil properties may have on the tolerance of rice to VLCFA‐inhibiting herbicides. Substantial rice injury was observed on the Dewitt silt loam soil following all pyroxasulfone and S‐metolachlor treatments, ranging from 20 to 100% injury 3 weeks after rice flooding. On the Dewitt silt loam, treatments containing acetochlor and pethoxamid applied to one‐ to two‐leaf rice resulted in minimal injury and the highest yields observed among VLCFA‐inhibiting herbicides. In general, rice injury ratings were less on the Sharkey clay soil. Pethoxamid and acetochlor applied to rice at any application timing resulted in ≤ 1% injury 2 weeks after treatment. Hence, contingent on a label, pethoxamid and acetochlor can be applied under similar conditions as early as DPRE on the Sharkey clay soil and not until the one‐ to two‐leaf rice stage on the Dewitt silt loam at the rates assessed.
Two Aphid Species, Phorodon cannabis and Rhopalosiphum rufiabdominale, Identified as Potential Pests on Industrial Hemp, Cannabis sativa L., in the US Midwest
Authors: Lagos‐Kutz Doris , Potter Bruce , DiFonzo Christina , Russell Howard , Hartman Glen L. 
Published: October 2018

Core Ideas
Two aphid species, Phorodon cannabis and Rhopalosiphum rufiabdominale, were identified as potential pests on industrial hemp, Cannabis sativa L., in the US Midwest.
Samples of aphids were obtained from field‐grown industrial hemp, hydroponic production, and suction traps in the US Midwest.
Morphological and molecular data were used to discriminate Phorodon cannabis from P. humuli.