bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods of engagement: On civic participation formats as composition devices in urban planning
Authors: Meilvang Marie Leth , Carlsen Hjalmar Bang , Blok Anders 
Published: April 2018

ABSTRACT
This article evaluates and develops the contribution of pragmatic sociology to the study of urban life and politics, by way of analysing recent shifts in the cultural-political forms of civic participation in formal urban planning. In doing so, it seeks to stage a critical test of the diagnosis of a ‘certified’, (neo-)liberal city that has recently emerged from work with Laurent Thévenot’s sociology of engagements and commonalities. Drawing on extensive empirical materials on the methods and formats of civic participation in contemporary Danish urban planning, we identify three dominant civic participation formats: the hearing, the dialogue meeting, and the workshop. These formats, we argue, work as composition devices that stabilise certain figures of the urban (quasi-)’citizen’, endowed with circumscribed possibilities for political engagement. Rather than a monolithic process of ‘certification’, we conclude, recent years have witnessed a partial and contested translation of the urban citizen into more manageable, liberal shapes.
Effect of substrates on Zinc Oxide thin films fabrication using sol-gel method
Authors: Kadir Rosmalini Ab , Mohd Taib Nurmalina , Wan Ahmad Wan Rosmaria , Aziz Anees Abdul , Zoolfakar Ahmad Sabirin 
Published: April 2018

Abstract
The properties of ZnO thin films were deposited on three different substrates via dip coating method was investigated. The films were prepared on glass, ITO and p-type silicon. Characterization of the film revealed that the properties of the dip coated ZnO thin films were influenced by the type of substrates. The grains on ITO and glass were ∼10 nm in size while the grains on wafer agglomerate together to form a denser film. Studies of the optical properties using UV-VIS-NIR of the fabricated films demonstrated that glass has the highest transmittance compared to ITO.
Inference of the human polyadenylation code
Authors: Leung Michael K K , Delong Andrew , Frey Brendan J 
Published: April 2018

Abstract

Motivation
Processing of transcripts at the 3′-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which site is cleaved, the process of alternative polyadenylation enables genes to produce transcript isoforms with different 3′-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the sequence determinants underlying this regulatory process, a computational model that can accurately predict polyadenylation patterns from genomic features is desirable.

Results
Previous works have focused on identifying candidate polyadenylation sites and classifying tissue-specific sites. By training on how multiple sites in genes are competitively selected for polyadenylation from 3′-end sequencing data, we developed a deep learning model that can predict the tissue-specific strength of a polyadenylation site in the 3′ untranslated region of the human genome given only its genomic sequence. We demonstrate the model’s broad utility on multiple tasks, without any application-specific training. The model can be used to predict which polyadenylation site is more likely to be selected in genes with multiple sites. It can be used to scan the 3′ untranslated region to find candidate polyadenylation sites. It can be used to classify the pathogenicity of variants near annotated polyadenylation sites in ClinVar. It can also be used to anticipate the effect of antisense oligonucleotide experiments to redirect polyadenylation. We provide analysis on how different features affect the model’s predictive performance and a method to identify sensitive regions of the genome at the single-based resolution that can affect polyadenylation regulation.

Supplementary information
Supplementary data are available at Bioinformatics online.
LipidPedia: a comprehensive lipid knowledgebase
Authors: Kuo Tien-Chueh , Tseng Yufeng Jane 
Published: April 2018

Abstract

Motivation
Lipids are divided into fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, sterols, prenol lipids and polyketides. Fatty acyls and glycerolipids are commonly used as energy storage, whereas glycerophospholipids, sphingolipids, sterols and saccharolipids are common used as components of cell membranes. Lipids in fatty acyls, glycerophospholipids, sphingolipids and sterols classes play important roles in signaling. Although more than 36 million lipids can be identified or computationally generated, no single lipid database provides comprehensive information on lipids. Furthermore, the complex systematic or common names of lipids make the discovery of related information challenging.

Results
Here, we present LipidPedia, a comprehensive lipid knowledgebase. The content of this database is derived from integrating annotation data with full-text mining of 3923 lipids and more than 400 000 annotations of associated diseases, pathways, functions and locations that are essential for interpreting lipid functions and mechanisms from over 1 400 000 scientific publications. Each lipid in LipidPedia also has its own entry containing a text summary curated from the most frequently cited diseases, pathways, genes, locations, functions, lipids and experimental models in the biomedical literature. LipidPedia aims to provide an overall synopsis of lipids to summarize lipid annotations and provide a detailed listing of references for understanding complex lipid functions and mechanisms.

Availability and implementation
LipidPedia is available at http://lipidpedia.cmdm.tw.

Supplementary information
Supplementary data are available at Bioinformatics online.
Whole-genome resequencing reveals signatures of selection and timing of duck domestication
Authors: Zhang Zebin , Jia Yaxiong , Almeida Pedro , Mank Judith E , van Tuinen Marcel , Wang Qiong , Jiang Zhihua , Chen Yu , Zhan Kai , Hou Shuisheng , Zhou Zhengkui , Li Huifang , Yang Fangxi , He Yong , Ning Zhonghua , Yang Ning , Qu Lujiang 
Published: April 2018

Abstract

Background
The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.

Results
Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus.

Conclusions
Our results advance the understanding of animal domestication and selection for complex phenotypic traits.
Field of genes: using Apache Kafka as a bioinformatic data repository
Authors: Lawlor Brendan , Lynch Richard , Mac Aogáin Micheál , Walsh Paul 
Published: April 2018

Abstract

Background
Bioinformatic research is increasingly dependent on large-scale datasets, accessed either from private or public repositories. An example of a public repository is National Center for Biotechnology Information's (NCBI's) Reference Sequence (RefSeq). These repositories must decide in what form to make their data available. Unstructured data can be put to almost any use but are limited in how access to them can be scaled. Highly structured data offer improved performance for specific algorithms but limit the wider usefulness of the data. We present an alternative: lightly structured data stored in Apache Kafka in a way that is amenable to parallel access and streamed processing, including subsequent transformations into more highly structured representations. We contend that this approach could provide a flexible and powerful nexus of bioinformatic data, bridging the gap between low structure on one hand, and high performance and scale on the other. To demonstrate this, we present a proof-of-concept version of NCBI's RefSeq database using this technology. We measure the performance and scalability characteristics of this alternative with respect to flat files.

Results
The proof of concept scales almost linearly as more compute nodes are added, outperforming the standard approach using files.

Conclusions
Apache Kafka merits consideration as a fast and more scalable but general-purpose way to store and retrieve bioinformatic data, for public, centralized reference datasets such as RefSeq and for private clinical and experimental data.
The draft genome sequence of forest musk deer (Moschus berezovskii)
Authors: Fan Zhenxin , Li Wujiao , Jin Jiazheng , Cui Kai , Yan Chaochao , Peng Changjun , Jian Zuoyi , Bu Ping , Price Megan , Zhang Xiuyue , Shen Yongmei , Li Jing , Qi Wenhua , Yue Bisong 
Published: April 2018

Abstract

Background
The forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally and is currently hunted for its musk (i.e., global perfume industry). Considerable hunting pressure and habitat loss have caused significant population declines. Consequently, the Chinese government commenced captive breeding programs for musk harvesting in the 1950s. However, the prevalence of fatal diseases is considerably restricting population increases. Disease severity and extent are exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential that knowledge of captive and wild forest musk deer populations' immune system and genome be gained in order to improve their physical and genetic health. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses.

Findings
A total of 407 Gb raw reads from whole-genome sequencing were generated using the Illumina HiSeq 4000 platform. The final genome assembly is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length of 2.85 Mb. We identified 24,352 genes and found that 42.05% of the genome is composed of repetitive elements. We also detected 1,236 olfactory receptor genes. The genome-wide phylogenetic tree indicated that the forest musk deer was within the order Artiodactyla, and it appeared as the sister clade of four members of Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage.

Conclusions
We provide the first genome sequence and gene annotation for the forest musk deer. The availability of these resources will be very useful for the conservation and captive breeding of this endangered and economically important species and for reconstructing the evolutionary history of the order Artiodactyla.
Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm
Authors: Zhou Yang , Connor Erin E , Bickhart Derek M , Li Congjun , Baldwin Ransom L , Schroeder Steven G , Rosen Benjamin D , Yang Liguo , Van Tassell Curtis P , Liu George E 
Published: April 2018

Abstract

Background
Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown.

Results
Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements.

Conclusions
Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
Are We Delivering Optimal Pulmonary Rehabilitation? The Importance of Quality Indicators in Evaluating Clinical Practice
Authors: Camp Pat G , Cheung Walden 
Published: April 2018

Abstract
Pulmonary rehabilitation (PR) is a complex intervention that has been shown to improve exercise capacity and quality of life, reduce dyspnea, and decrease the risk of exacerbations and hospitalization. Although the evidence for PR is strong, the translation of this evidence into clinical practice remains a challenge, and important gaps in care exist. To date, most research in PR has focused on questions related to treatment efficacy. Less attention has been paid to confirming whether the strong evidence base of PR has been effectively translated to this complex clinical setting. Policy makers and other stakeholders in PR are calling for the establishment of core standards and quality indicators in PR to evaluate existing programs and improve patient care. However, what are quality indicators, and how are they used? This Perspective explores quality assurance in the context of PR and introduces the concepts and uses of quality indicators that can be used to evaluate and improve the quality of care.
The ERBB network facilitates KRAS-driven lung tumorigenesis
Authors: Kruspig Björn , Monteverde Tiziana , Neidler Sarah , Hock Andreas , Kerr Emma , Nixon Colin , Clark William , Hedley Ann , Dick Craig , Vousden Karen , Martins Carla , Murphy Daniel J. 
Published: April 2018

AbstractKRAS is the most frequently mutated driver oncogene in human adenocarcinoma of the lung. There are presently no clinically proven strategies for treatment of KRAS-driven lung cancer. Activating mutations in KRAS are thought to confer independence from upstream signaling, however recent data suggest that this independence may not be absolute. Here we show that initiation and progression of KRAS-driven lung tumors requires input from ERBB family RTKs: Multiple ERBB RTKs are expressed and active from the earliest stages of KRAS driven lung tumor development, and treatment with a multi-ERBB inhibitor suppresses formation of KRasG12D-driven lung tumors. We present evidence that ERBB activity amplifies signaling through the core RAS pathway, supporting proliferation of KRAS mutant tumor cells in culture and progression to invasive disease in vivo. Importantly, brief pharmacological inhibition of the ERBB network significantly enhances the therapeutic benefit of MEK inhibition in an autochthonous tumor setting. Our data suggest that lung cancer patients with KRAS-driven disease may benefit from inclusion of multi-ERBB inhibitors in rationally designed treatment strategies.One Sentence SummaryG12 Mutant KRAS requires tonic ERBB network activity for initiation and maintenance of lung cancer
Snapshot: clustering and visualizing epigenetic history during cell differentiation
Authors: Xiang Guanjue , Giardine Belinda , An Lin , Sun Chen , Keller Cheryl A. , Heuston Elisabeth , Bodine David , Hardison Ross C , Zhang Yu 
Published: April 2018

AbstractEpigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation. Here, we present a new method, called Snapshot, that uses epigenetic data to generate a hierarchical visualization for DNA regions with epigenetic features segregating along any given cell differentiation hierarchy of interest. Different hierarchies of cell types may be used to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from the VISION project, an international project for ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis.Availability and implementation: https://github.com/guanjue/snapshot
Analgesia linked to Nav1.7 loss of function requires μ and δ opioid receptors
Authors: Pereira Vanessa , Millet Queensta , Aramburu Jose , Lopez-Rodriguez Cristina , Ruff Claire Gaveriaux , Wood John N 
Published: April 2018

AbstractFunctional deletion of the SCN9A gene encoding sodium channel Nav1.7 makes humans and mice pain-free (1,2). Opioid signaling contributes to this analgesic state (3). Here we show that the pharmacological block or deletion of both μ and δ opioid receptors is required to abolish Nav1.7 null opioid-related analgesia.κ-opioid receptor antagonists were without effect. Enkephalins encoded by the Penk gene are upregulated in Nav1.7 nulls (3). Deleting Nfat5, a transcription factor with binding motifs upstream of Penk (4), induces the same level of enkephalin mRNA expression as found in Nav1.7 nulls, but without consequent analgesia. These data confirm that a combination of events linked to SCN9A gene loss is required for analgesia. Higher levels of endogenous enkephalins (3), potentiated opioid receptors (5), diminished electrical excitability (6,7) and loss of neurotransmitter release (2,1) together contribute to the analgesic phenotype found in Nav1.7 null mouse and human mutants. These observations help explain the failure of Nav1.7 channel blockers alone to produce analgesia and suggest new routes for analgesic drug development.
Strategies for quantitative RNA-seq analyses among closely related species
Authors: Parekh Swati , Vieth Beate , Ziegenhain Christoph , Enard Wolfgang , Hellmann Ines 
Published: April 2018

AbstractWith the growing appreciation for the role of regulatory differences in evolution, researchers need to reliably quantify expression levels within and among species. However, for non-model organisms genome assemblies and annotations are often not available or have inferior quality, biasing the inference of expression changes to an unknown extent. Here, we explore the possibility to map RNA-seq reads from diverged species to one high quality reference genome. As test case, we used a small primate phylogeny ranging from Human to Marmoset spanning 12% nucleotide divergence. To distinguish the effect of sequence divergence and genome quality, we used in silico evolved genomes and existing genomes to simulate RNA-seq reads. These were then mapped to the genome of origin (self-mapping) as well as to one common reference (cross-mapping) to infer the quantification biases. We find that the bias due to cross-mapping is small for the closely related great apes (≤ 4% divergence), and preferable to self-mapping given current genome qualities. For closely related species, cross-mapping provides easy access, high power and a well controlled false discovery rate for both; the analysis of intra-species expression differences as well as the detection of relative differences between species. If divergence increases, so that a substantial fraction of reads exceeds the limits of the mapper used, we find that gene-specific corrections and effect-size cutoffs can limit the bias before self-mapping becomes unavoidable. In summary, for the first time we systematically quantify biases in cross-species RNA-seq studies, providing guidance to best practices for these important evolutionary studies.
RGS14 restricts plasticity in hippocampal CA2 by limiting postsynaptic calcium signaling
Authors: Evans Paul R. , Parra-Bueno Paula , Smirnov Michael S. , Lustberg Daniel J. , Dudek Serena M. , Hepler John R. , Yasuda Ryohei 
Published: April 2018

AbstractPyramidal neurons in hippocampal area CA2 are distinct from neighboring CA1 in that they resist synaptic long-term potentiation (LTP) at CA3 Schaffer Collateral synapses. Regulator of G Protein Signaling 14 (RGS14) is a complex scaffolding protein enriched in CA2 dendritic spines that naturally blocks CA2 synaptic plasticity and hippocampus-dependent learning, but the cellular mechanisms by which RGS14 gates LTP are largely unexplored. A previous study has attributed the lack of plasticity to higher rates of calcium (Ca2+) buffering and extrusion in CA2 spines. Additionally, a recent proteomics study revealed that RGS14 interacts with two key Ca2+-activated proteins in CA2 neurons: calcium/calmodulin, and CaMKII. Here, we investigate whether RGS14 regulates Ca2+ signaling in its host CA2 neurons. We find the nascent LTP of CA2 synapses due to genetic knockout (KO) of RGS14 in mice requires Ca2+-dependent postsynaptic signaling through NMDA receptors, CaMK, and PKA, revealing similar mechanisms to those in CA1. We report RGS14 negatively regulates the long-term structural plasticity of dendritic spines of CA2 neurons. We further show that wild-type (WT) CA2 neurons display significantly attenuated spine Ca2+ transients during structural plasticity induction compared with the Ca2+ transients from CA2 spines of RGS14 KO mice and CA1 controls. Finally, we demonstrate that acute overexpression of RGS14 is sufficient to block spine plasticity, and elevating extracellular Ca2+ levels restores plasticity to RGS14-expressing neurons. Together, these results demonstrate for the first time that RGS14 regulates plasticity in hippocampal area CA2 by restricting Ca2+ elevations in CA2 spines and downstream signaling pathways.Significance StatementRecent studies of hippocampal area CA2 have provided strong evidence in support of a clear role for this apparently plasticity-resistant subregion of the hippocampus in social, spatial, and temporal aspects of memory. Regulator of G Protein Signaling 14 (RGS14) is a critical factor that inhibits synaptic plasticity in CA2, but the molecular mechanisms by which RGS14 limits LTP remained unknown. Here we provide new evidence that RGS14 restricts spine calcium (Ca2+) in CA2 neurons and that key downstream Ca2+-activated signaling pathways are required for CA2 plasticity in mice lacking RGS14. These results define a previously unrecognized role for RGS14 as a natural inhibitor of postsynaptic Ca2+ signaling in hippocampal area CA2.