bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions
Authors: Oki Shinya , Ohta Tazro , Shioi Go , Hatanaka Hideki , Ogasawara Osamu , Okuda Yoshihiro , Kawaji Hideya , Nakaki Ryo , Sese Jun , Meno Chikara 
Published: February 2018

ABSTRACTNoncoding regions of the human genome possess enhancer activity and harbor risk loci for heritable diseases. Whereas the binding profiles of multiple transcription factors (TFs) have been investigated, integrative analysis with the large body of public data available so as to provide an overview of the function of such noncoding regions has remained a challenge. Here we have fully integrated public ChIP-seq and DNase-seq data (n ~ 70,000), including those for 743 human transcription factors (TFs) with 97 million binding sites, and have devised a data-mining platform —designated ChIP-Atlas—to identify significant TF-genome, TF-gene, and TF-TF interactions. Using this platform, we found that TFs enriched at macrophage or T-cell enhancers also accumulated around risk loci for autoimmune diseases, whereas those enriched at hepatocyte or macrophage enhancers were preferentially detected at loci associated with HDL-cholesterol levels. Of note, we identified “hotspots” around such risk loci that accumulated multiple TFs and are therefore candidates for causal variants. Integrative analysis of public chromatin-profiling data is thus able to identify TFs and tissues associated with heritable disorders.
Chloroplasts of symbiotic microalgae remain active during bleaching induced by thermal stress in Collodaria (Radiolaria)
Authors: Villar Emilie , Dani Vincent , Bigeard Estelle , Linhart Tatiana , Mendez Sandin Miguel , Bachy Charles , Six Christophe , Lombard Fabien , Sabourault Cécile , Not Fabrice 
Published: February 2018

AbstractCollodaria (Radiolaria) are important contributors to planktonic communities and biogeochemical processes (e.g. the biologic pump) in oligotrophic oceans. Similarly to corals, Collodaria live in symbiosis with dinoflagellate algae, a relationship that is thought to explain partly their ecological success. In the context of global change, the robustness of the symbiotic interaction and potential subsequent bleaching events are worth consideration. In the present study, we compared the ultrastructure morphology, symbiont density, photosynthetic capacities and respiration rates of colonial Collodaria exposed to a range of temperatures corresponding to natural conditions (21°C), moderate (25°C) and high (28°C) thermal stress. We showed that symbiont density immediately decreased when temperature rises to 25°C and the collodaria holobiont metabolic activity increased. When temperature reached 28°C, the collodarian host arrived at a tolerance threshold with a respiration nearly stopped and largely damaged morphological structures. Over the course of the experiment the photosynthetic capacities of remaining symbionts were stable, chloroplasts being the last degraded organelles from the microalgae. These results contribute to a better characterization and understanding of temperature-induced bleaching processes in planktonic photosymbiosis.
Forget Pixels: Adaptive Particle Representation of Fluorescence Microscopy Images
Authors: Cheeseman Bevan L. , Günther Ulrik , Susik Mateusz , Gonciarz Krzysztof , Sbalzarini Ivo F. 
Published: February 2018

AbstractModern microscopy modalities create a data deluge with gigabytes of data generated each second, and terabytes per day. Storing and processing these data is a severe bottleneck, not fully alleviated by data compression. We argue that this is because images are processed as regular grids of pixels. To address the root of the problem, we here propose a content-adaptive representation of fluorescence microscopy images called the Adaptive Particle Representation (APR). The APR replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels. We present the ideas, concepts, and algorithms of the APR and validate them using noisy 3D image data. We show that the APR represents the content of an image while maintaining image quality. We then show that the adaptivity of the APR provides orders of magnitude benefits across a range of image processing tasks. Therefore, the APR provides a simple, extendable, and efficient content-aware representation of images that relaxes current data and processing bottlenecks.
Ultrastructure of salivary glands in Psammotettix alienus Dahlbom (Homoptera: Cicadellidae) infected with Taastrup virus
Authors: Lundsgaard Thorben 
Published: February 2018

SummaryTaastrup virus (TV) is a novel virus belonging to Mononegavirales and with filovirus-like morphology. In adult Psammotettix alienus infected with TV, the highest concentration of virus particles was found in salivary glands, consisting of a principal gland (type I-VI-cells) and an accessory gland. Examination of thin sections revealed enveloped particles, about 1300 nm long and 62 nm in diameter, located singly or in paracrystalline arrays in canaliculi of type III- and IV-cells. In gland cells with TV particles in canaliculi, granular masses up to 15 micrometer in diameter are present in the cytoplasm. These masses are believed to be viroplasms, the sites for viral replication. TV particles were observed at the connection between a canaliculus and the salivary duct system.
Competitive release in tumors
Authors: Ma Yongqian , West Jeffrey , Newton Paul K. 
Published: February 2018

AbstractCompetitive release is a bedrock principle of coevolutionary ecology and population dynamics. It is also the main mechanism by which heterogeneous tumors develop chemotherapeutic resistance. Understanding, controlling, and exploiting this important mechanism represents one of the key challenges and potential opportunities of current medical oncology. The development of sophisticated mathematical and computational models of coevolution among clonal and sub-clonal cell populations in the tumor ecosystem can guide us in predicting and shaping various responses to perturbations in the fitness landscape which is altered by chemo-toxic agents. This in turn can help us design adaptive chemotherapeutic strategies to combat the release resistant cells.
Shugoshin protects centromere pairing and promotes segregation of non-exchange partner chromosomes in meiosis
Authors: de Almeida Luciana Previato , Evatt Jared M. , Chuong Hoa H. , Kurdzo Emily L. , Eyster Craig A. , Gladstone Mara N. , Gómez-H Laura , Llano Elena , Meyer Régis , Pendas Alberto M. , Pezza Roberto J. , Dawson Dean S. 
Published: February 2018

ABSTRACTFaithful chromosome segregation during meiosis I depends upon the formation of connections between homologous chromosomes. Crossovers between homologs connect the partners allowing them to attach to the meiotic spindle as a unit, such that they migrate away from one another at anaphase I. Homologous partners also become connected by pairing of their centromeres in meiotic prophase. This centromere pairing can promote proper segregation at anaphase I of partners that have failed to become joined by a crossover. Centromere pairing is mediated by synaptonemal complex (SC) proteins that persist at the centromere when the SC disassembles. Here, using mouse spermatocyte and yeast model systems, we tested the role of shugoshin in promoting meiotic centromere pairing by protecting centromeric synaptonemal components from disassembly. The results show that shugoshin protects centromeric SC in meiotic prophase and, in anaphase, promotes the proper segregation of partner chromosomes that are not linked by a crossover.SIGNIFICANCEMeiotic crossovers form a connection between homologous chromosomes that allows them to attach to the spindle as a single unit in meiosis I. In humans, failures in this process are a leading cause of aneuploidy. A recently described process, called centromere pairing, can also help connect meiotic chromosome partners in meiosis. Homologous chromosomes become tightly joined by a structure called the synaptonemal complex (SC) in meiotic prophase. After the SC disassembles, persisting SC proteins at the centromeres mediate their pairing. Here, studies in mouse spermatocytes and yeast are used to show that the shugoshin protein helps SC components persist at centromeres and helps centromere pairing promote the proper segregation of yeast chromosomes that fail to become tethered by crossovers.
GTFtools: a Python package for analyzing various modes of gene models
Authors: Li Hong-Dong 
Published: February 2018

AbstractSummaryGene-centric bioinformatics studies frequently involve calculation or extraction of various features of genes such as gene ID mapping, GC content calculation and different types of gene lengths, through manipulation of gene models that are often annotated in GTF format and available from ENSEMBL or GENCODE database. Such computation is essential for subsequent analysis such as intron retention detection where independent introns may need to be identified, converting RNA-seq read counts to FPKM where gene length is required, and obtaining flanking regions around transcription start sites. However, to our knowledge, a software package that is dedicated to analyzing various modes of gene models directly from GTF file is not publicly available. In this work, GTFtools (implemented in Python and not dependent on any non-python third-party software), a stand-alone command-line software that provides a set of functions to analyze various modes of gene models, is provided for facilitating routine bioinformatics studies where information about gene models needs to be calculated.AvailabilityGTFtools is freely available at www.genemine.org/gtftools.phpContacthongdong@csu.edu.cn.
Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration
Authors: Ba Hengxing , Wang Datao , Wu Weiyao , Sun Hongmei , Li Chunyi 
Published: February 2018

AbstractAntler regeneration, a stem cell-based epimorphic process, has potential as a valuable model for regenerative medicine. A pool of antler stem cells (ASCs) for antler development is located in the antlerogenic periosteum (AP). However, whether this ASC pool is homogenous or heterogeneous has not been fully evaluated. In this study, we produced a comprehensive transcriptome dataset at the single-cell level for the ASCs based on the 10x Genomics platform (scRNA-seq). A total of 4,565 ASCs were sequenced and classified into a large cell cluster, indicating that the ASCs resident in the AP are likely to be a homogeneous population. The scRNA-seq data revealed that tumor-related genes were highly expressed in these homogeneous ASCs: i.e. TIMP1, TMSB10, LGALS1, FTH1, VIM, LOC110126017 and S100A4. Results of screening for stem cell markers suggest that the ASCs may be considered as a special type of stem cell between embryonic (CD9) and adult (CD29, CD90, NPM1 and VIM) stem cells. Our results provide the first comprehensive transcriptome analysis at the single-cell level for the ASCs, and identified only one major cell type resident in the AP and some key stem cell genes, which may hold the key to why antlers, the unique mammalian organ, can fully regenerate once lost.
Photon yield enhancement of red fluorophores at cryogenic temperatures
Authors: Hulleman Christiaan N. , Li Weixing , Gregor Ingo , Rieger Bernd , Enderlein Jörg 
Published: February 2018

AbstractSingle Molecule Localization Microscopy has become one of the most successful and widely applied methods of Super-resolution Fluorescence Microscopy. Its achievable resolution strongly depends on the number of detectable photons from a single molecule until photobleaching. By cooling a sample from room temperature down to liquid nitrogen temperatures, the photostability of dyes can be enhanced by more than 100 fold, which results in an improvement in localization precision greater than 10 times. Here, we investigate a variety of fluorescent dyes in the red spectral region, and we find an average photon yield between 3.5 · 106to 11 · 106photons before bleaching at liquid nitrogen temperatures, corresponding to a theoretical localization precision around 0.1 nm.
Culture-free generation of microbial genomes from human and marine microbiomes
Authors: Bishara Alex , Moss Eli L. , Kolmogorov Mikhail , Parada Alma , Weng Ziming , Sidow Arend , Dekas Anne E. , Batzoglou Serafim , Bhatt Ami S. 
Published: February 2018

AbstractOur understanding of natural microbial communities is shaped by the careful investigation of a relatively small number of isolated and cultured organisms, and by analysis of genomic sequences obtained by culture-free metagenomic sequencing approaches. Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire. Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture. Recent molecular techniques that partition long DNA fragments and then barcode short fragments derived from them produce “read clouds”, which are short-read sequences containing long-range information. Here, we present a novel application of a read cloud technique to microbiome samples, as well as Athena, a de novo assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to sequence human stool samples from two healthy individuals, and compare it to existing short read and synthetic long read metagenomic sequencing approaches. We find that read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts. These genome drafts are also highly contiguous (>200kb N50, <10 contigs), even for bacteria that have relatively low (20x) raw short read sequence coverage. We also apply this approach to a significantly more complex marine sediment sample and obtain 23 genome drafts with valuable 16S ribosomal RNA taxonomic marker sequences, nine of which are complete genome drafts. Read cloud metagenomic sequencing allows culture-free generation of high quality microbial genome drafts using only a single shotgun experiment.
An investigation on microstructural and mechanical properties of porous zirconia-alumina nanocomposite prepared by solid state sintering method
Authors: Yousefi Ebrahim , Adineh Morteza , Askari Mohammad Bagher 
Published: February 2018

PurposeThe purpose of this paper is to fabricate zirconia-nano alumina porous nanocomposites with different amount of alumina (0-30 Wt.%). Specimens were prepared by solid state sintering method at different temperature (1,400-1,700°C).Design/methodology/approachEffects of processing temperature and amount of alumina on microstructure, distribution of nanoparticles, flexural and compressive strengths, micro-hardness and densification were investigated.FindingsResults indicated that interpenetration of particles and their contacts increased by increasing sintering temperature. As a consequence of better particles contacts and microstructure coarsening, the porosity decreased. As alumina nanoparticles content increased, the amount of porosity decreased conversely and distribution of pores become more uniform. Simultaneous enhancement of temperature and alumina nanoparticles content caused an improvement of flexural and compressive strengths because of an improvement of sintering process resulted from porosity reduction. Increase in hardness and density were observed as porosity values diminished and alumina nanoparticles were distributed well at micro zirconia grain boundaries as a result of increasing the process temperature.Originality/valueThis article contains original research.
Credit constraints and the delay of homeownership by young households in Japan
Authors: Yukutake Norifumi , Moriizumi Yoko 
Published: February 2018

Purpose
Japan has been suffering from a decline in the rate of young adults homeownership for a long time. The reduction of the homeownership rate for young adults suggests a delay of tenure transition from renting to owning a home. Such delays further imply that there is insufficient wealth accumulation and a low level of welfare. This paper examines these influences of the credit rationing and the credit rationing impact on the reduction in the young adults’ homeownership rate.

Design/methodology/approach
Credit rationing impacts the timing of house purchases and the value of the houses at the same time. This paper estimates these impacts jointly using a simultaneous equation system (minimum distance estimation) and the micro data on Japan.

Findings
This paper divides the effect of credit rationing on the timing into direct and indirect effects. The former is the rationing effect on timing, keeping the other variables constant, while the latter is the effect via changes in house values. This paper finds that the indirect effect reduces the rationing effect on the timing by decreasing house values. Furthermore, the results show that credit rationing delays home acquisition by prospective young owners (direct effect) and necessarily lowers the quality of houses they purchase.

Originality/value
In the previous papers, the endogeneity among the variables related to the housing purchase was not addressed. To separate the endogeneity of the timing from the house value, this paper applies the simultaneous equation model. Furthermore, this paper exhibits that there are direct and indirect effects of credit rationing on the timing of housing purchase made by young households. None of the previous papers recognize these two effects.
Attitude of Muslim minority in Spain towards Islamic finance
Authors: Kaakeh Abdulkader , Hassan M. Kabir , van Hemmen Almazor Stefan F. 
Published: February 2018

PurposeThis paper aims to use a theoretical model based on the theory of reasoned actions to investigate the effects of attitude, religious motivation, awareness and service and pricing on the intention to use Islamic banking among the Muslim minority in Spain. It also aims to determine the profile of a potential Islamic banking customer among this minority.Design/methodology/approachThe research focuses on a survey of Muslims living in Barcelona, Spain, who know of the existence of Islamic finance but do not have access to it. The research uses factor analysis and logit regression to analyse the data.FindingsThe results show that attitude, religious motivation and awareness are important factors affecting the intention to use Islamic banking. The study also shows that the potential Islamic banking customer in Spain is a Muslim (Spanish, Moroccan or Pakistani), male, and did not reach university degree in his education.Research limitations/implicationsThe sample has 154 participants living in Barcelona, with the rest of Spain being ignored, although results should apply to all Muslims in Spain. Also, this study does not consider attitude as a moderator.Practical implicationsThe research shows the potential for Islamic banks in the Spanish market and the possibility of raising awareness about Islamic banking.Social implicationsIslamic banking in Spain could help the Muslim minority to participate effectively in financial activities, thus leveraging their capacity to integrate into the community. The study also highlights the importance of empowering the women in this minority and could help society by encouraging off-banking money to flow into the financial sector.Originality/valueThe research is the first empirical attempt to test the factors affecting the intention among Muslims in Spain to deal with Islamic banking. The study also highlights the importance of Islamic finance for Muslim minorities as a method to support their religious identity.
Objective environmental conditions and perceived environmental uncertainty
Authors: Weiss Martin , Wittmann Christina 
Published: February 2018

PurposeIt appears as if a gap exists between objective environmental conditions and the respective managerial perception of those conditions. This situation poses severe problems for executives deriving effective strategies and initiating successful organizational change. Therefore, the purpose of this paper is to develop and provide a deeper understanding of the factors that lead to such a gap.Design/methodology/approachOn the basis of the literature from psychology and strategic management, this paper develops a conceptual framework of the cognitive model with the perception process and potentially moderating factors. Furthermore, more precise mechanisms and relationships within the perception of environmental conditions are proposed.FindingsThe perception process consists of three stages, attention, encoding and storage/retrieval, which all may explain variations in how individuals interpret the environment. Moreover, dispositional factors (such as cognitive styles, cognitive structures, intelligence and motivation) as well as situational factors (such as emotion and stress) further cause variations between and within individuals, which ultimately leads to a gap between objective and perceived environmental conditions.Originality/valueThis study not only highlights the existence and the severe consequence of a misperception of environmental conditions, but also offers a variety of factors that could lead to this undesirable effect. Furthermore, while previous research has typically focused on single factors that might influence the perception process, this study assumes a holistic view on the cognitive model and provides more detailed and specific mechanisms on a perceptual gap.
Living in the clouds: conceptual reconstructions of harbour structures
Authors: Shotton Elizabeth Anne 
Published: February 2018

Purpose
The harbours of Ireland, under threat from deterioration and rising sea levels, are being documented using terrestrial LiDAR augmented by archival research to develop comprehensive histories and timeline models for public dissemination. While methods to extract legible three-dimensional models from scan data have been developed and such operational formats for heritage management are imperative, the need for this format in interpretive visualisations should be reconsidered. The paper aims to discuss these issues.

Design/methodology/approach
Interpretive visualisations are forms of history making, where factual evidence is drawn together with conjecture to illustrate a plausible account of events, and differentiation between fact and conjecture is the key to their intellectual transparency. A procedure for superimposing conjectural reconstructions, generated using Rhinoceros and CloudCompare, on original scan data in Cyclone and visualised on a web-based viewer is discussed.

Findings
Embellishing scan data with conjectural elements to visualise the evolution of harbours is advantageous for both research and public dissemination. The accuracy and density of the scans enables the interrogation of the harbour form and the irregular details, the latter in danger of generalisation if translated into parametric or mesh format. Equally, the ethereal quality of the point cloud conveys a sense of tentativeness, consistent with a provisional hypothesis. Finally, coding conjectural elements allows users to intuit the difference between fact and historical narrative.

Originality/value
While various web-based point clouds viewers are used to disseminate research, the novelty here is the potential to develop didactic representations using point clouds that successfully capture a provisional thesis regarding each harbour’s evolution in an intellectually transparent manner to enable further inquiry.