bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes
Authors: Knoch Tobias A. , Wachsmuth Malte , Kepper Nick , Lesnussa Michael , Abuseiris Anis , Imam A. M. Ali , Kolovos Petros , Zuin Jessica , Kockx Christel E. M. , Brouwer Rutger W. W. , van de Werken Harmen J. G. , van IJken Wilfred F. J. , Wendt Kerstin S. , Grosveld Frank G. 
Published: August 2016

AbstractThe dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function – the storage, expression, and replication of genetic information – is still one of the central issues in biology. Here, we describe the much debated 3D-architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D-architecture and the DNA sequence: The genome is compacted into a chromatin quasi-fibre with ∼5±1 nucleosomes/11nm, folded into stable ∼30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types/functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. This architecture, its dynamics, and accessibility balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow “architectural sequencing” at a genome mechanics level to understand the inseparable systems genomic properties.
Genome-scale rates of evolutionary change in bacteria
Authors: Duchêne Sebastian , Holt Kathryn E. , Weill François-Xavier , Hello Simon Le , Hawkey Jane , Edwards David J. , Fourment Mathieu , Holmes Edward C. 
Published: August 2016

ABSTRACTEstimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with“ancient DNA”data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6to 10−8nucleotide substitutions site-1year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
BinSanity: Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation
Authors: Graham Elaina , Heidelberg John , Tully Benjamin 
Published: August 2016

AbstractMetagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage alone, removing potential composition based biases in clustering contigs, but requires a minimum of two samples. To increase fidelity, a refinement script was developed that uses composition data (tetranucleotide frequency and %G+C content) to refine bins containing multiple source organisms. This separation of composition and coverage based signatures reduces clustering bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that this implementation of AP lead to a higher precision, recall, and Adjusted Rand Index over five commonly implemented methods. When tested on a previously published infant gut metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
Genome-wide analysis of lncRNAs and mRNAs expression during the differentiation of abdominal preadipocytes in chicken
Authors: Zhang Tao , Zhang Xiangqian , Han Kunpeng , Zhang Genxi , Wang Jinyu , Xie Kaizhou , Xue Qian 
Published: August 2016

AbstractlncRNAs regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in preadipocytes differentiation of chicken. Here, we identified lncRNAs in preadipocytes of different differentiation stages by RNA-sequencing using Jinghai Yellow chicken. A total of 1,300,074,528 clean reads and 27,023 lncRNAs were obtained from twenty samples. 3095 genes (1,336 lncRNAs and 1,759 mRNAs) were differentially expressed among different stages, of which the number of DEGs decreased with the differentiation, demonstrating that the early stage might be most important for chicken preadipocytes differentiation. Furthermore, 3,095 DEGs were clustered into 8 clusters with their expression patterns by K-means clustering. We identified six stage-specific modules related to A0, A2 and A6 stages using weighted co-expression network analysis. Many well-known/novel pathways associated with preadipocytes differentiation were found. We also identified highly connected genes in each module and visualized them by cytoscape. Many well-known genes related to preadipocytes differentiation were found such asIGFBP2andJUN. Yet, the majority of high connected genes were unknown in chicken preadipocytes. This study provides a valuable resource for chicken lncRNA study and contributes to batter understanding the biology of preadipocytes differentiation in chicken.
Frank-Starling law and Bowditch phenomenon may have the common theoretical grounds
Authors: Kamnev Yuri 
Published: August 2016

AbstractThe relationship between two different linear dimensions of the chamber (ventricle) and the two respective values of the force of contraction (which are applied to the imaginary piston in order to accelerate the initial venous inflow) is deduced as the ratio of forces which is equal to the ratio of squares of linear dimensions of the chamber; the equation is valid when the durations of both contractions (systoles) are identical. The relationship corresponds to Frank-Starling law (the right limb of parabola can be approximated to the direct proportionality of the law). When the durations of systoles are different the ratio of forces is equal to the inverse ratio of durations of systoles; the inverse proportionality permits to interpret the Bowditch phenomenon by means of the ascending asymptote of hyperbole. Stepwise shortening of systole is impossible due to extremely narrow range of variable (duration of systole), hence the shift of variable can be realized only as a leap; this leap is accompanied by the enormous rise of function (force of contraction) which can be accommodated to several contractions. Homoiometric regulation can be considered a safety device (presumably in the form of paroxysmal tachycardia with the shortened systole) in the case when heterometric regulation lacks to produce the adequate force of contraction in response to excessively distended chamber.
Changes in brain morphology and working memory capacity over childhood
Authors: Bathelt Joe , Gathercole Susan , Johnson Amy , Astle Duncan 
Published: August 2016

1AbstractDevelopmental improvements in working memory are important in the acquisition of new skills, like reading and maths. Current accounts of the brain systems supporting working memory rarely take development into account. However, understanding the development of these skills, and in turn where this development can go awry, will require more sophsiticated neuropsychological accounts that fully consider the role of development. The current study investigated how structural brain correlates of components of the working memory system change over developmental time. Verbal and visuospatial short-term and working memory were assessed in 153 children between 6 and 16 years and latent components of the working memory system were derived using principal component analysis. Further, fractional anisotropy and cortical thickness maps were derived from T1-weighted and diffusion-weighted MRI and processed using eigenanatomy decomposition, an advanced dimensionality reduction method for neuroimaging data. We were then able to explore how the structural brain correlates of working memory gradually shifted across childhood. Regression modelling indicated greater involvement of the corpus callosum and posterior temporal white matter in younger children for performance associated with the executive part of the working memory system, while thickness of the occipitotemporal cortex was more predictive in older children. These findings are consistent with an account in which increasing specialisation leads to shifts in the contribution of neural substrates over developmental time, from early reliance on a distributed system supported by long-range connections to later reliance on specialised local circuitry. Furthemore, our findings emphasise the importance of taking development into account when considering the neural systems that support complex cognitive skills, like working memory.
Statistical Association Mapping of Population-Structured Genetic Data
Authors: Najafi A. , Janghorbani S. , Motahari S. A. , Fatemizadeh E. 
Published: August 2016

AbstractAssociation mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the disease-causing sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease causal factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability distribution of the model parameters. We have implemented our proposed framework on a software package whose performance is extensively evaluated on a number of synthetic datasets, and compared to some of the well-known existing methods such as STRUCTURE. It has been shown that in extreme scenarios, up to 10 – 15% of improvement in the inference accuracy is achieved with a moderate increase in computational complexity.
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Authors: Huang Yi-Fei , Gulko Brad , Siepel Adam 
Published: August 2016

AbstractAcross many species, a large fraction of genetic variants that influence phenotypes of interest is located outside of protein-coding genes, yet existing methods for identifying such variants have poor predictive power. Here, we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences, and which therefore are likely to be phenotypically important. LINSIGHT combines a simple neural network for functional genomic data with a probabilistic model of molecular evolution. The method is fast and highly scalable, enabling it to exploit the “Big Data” available in modern genomics. We show that LINSIGHT outperforms the best available methods in identifying human noncoding variants associated with inherited diseases. In addition, we apply LINSIGHT to an atlas of human enhancers and show that the fitness consequences at enhancers depend on cell-type, tissue specificity, and constraints at associated promoters.
The large majority of intergenic sites in bacteria are selectively constrained, even when known regulatory elements are excluded
Authors: Thorpe Harry A. , Bayliss Sion , Hurst Laurence D. , Feil Edward J. 
Published: August 2016

AbstractThere are currently no broad estimates of the overall strength and direction of selection operating on intergenic variation in bacteria. Here we address this using large whole genome sequence datasets representing six diverse bacterial species; Escherichia coli, Staphylococcus aureus, Salmonella enterica, Streptococcus pneumoniae, Klebsiella pneumoniae, and Mycobacterium tuberculosis. Excluding M. tuberculosis, we find that a high proportion (62%-79%; mean 70%) of intergenic sites are selectively constrained, relative to synonymous sites. Non-coding RNAs tend to be under stronger selective constraint than promoters, which in turn are typically more constrained than rho-independent terminators. Even when these regulatory elements are excluded, the mean proportion of constrained intergenic sites only falls to 69%; thus our current understanding of the functionality of intergenic regions (IGRs) in bacteria is severely limited. Consistent with a role for positive as well as negative selection on intergenic sites, we present evidence for strong positive selection in Mycobacterium tuberculosis promoters, underlining the key role of regulatory changes as an adaptive mechanism in this highly monomorphic pathogen.
Transcriptomic Signatures for Ovulation in Vertebrates
Authors: Liu Dongteng , Brewer Michael S. , Chen Shixi , Hong Wanshu , Zhu Yong 
Published: August 2016

AbstractRecently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining Pgr regulated genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in pre-ovulatory follicular cells collected after the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 2,888 genes significantly differentially expressed between WT and Pgr-KO fish. Among those, 1,230 gene transcripts were significantly more expressed, while 1,658 genes were significantly less expressed in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans, that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, nuclear and cell division. Our results indicate that a large set of genes (>3,000) are differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs including growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in zebrafish model.
Making the case for gender sensitive climate policy – lessons from South Asia/IGP
Authors: Jafry Tahseen 
Published: August 2016

PurposeThe purpose of this paper is to provide an overview of gender and social inequality in the agricultural sector of South Asia with a focus on wheat as a major staple crop, which underpins the breadbasket of the Indo-Gangetic Plains (IGP). It provides new insights, as examined through a climate justice lens, into the status of women and socially excluded groups in the region and, based on this, calls for re-thinking both politically and practically on how to shape future initiatives to be more gender and socially inclusive, thereby supporting the rights of the neediest.Design/methodology/approachAn overview of research and evidence is conducted on how gender and social inequality is currently being addressed in the agricultural sector through an analysis of peer reviewed and grey literature. This is followed by a synthesis which is presented as directions and recommendations for future initiatives developed through a climate justice lens.FindingsGender and social inequality issues are rife across the IGP. This may be for many reasons including poor targeting, little capacity, lack of strategic positioning in programme and project design – all of which have enormous implications for the poorest and most marginalised communities and, especially, women. The need to conduct more gender-inclusive and socially inclusive research to enhance gender equity and equal opportunities for women and men is highlighted. The need to include a human rights-based approach to safeguarding the rights of the most vulnerable affected by climate change is indicated through the gender analysis; the finding provides some guiding principles in moving towards the new 2015 climate agreement and Post 2015 Development Goals.Originality/valueThe results provide a foundation which stimulates thinking around climate justice, and the contribution this approach can make to better inform future agricultural initiatives/policies to be more gender-inclusive and socially inclusive.
A gender justice approach to eliminating Sudan’s Savannah belt’s vulnerability to climate change
Authors: Ahmed Mey Eltayeb 
Published: August 2016

Purpose
Arguing that a gendered invisibility surrounding climate justice contributes to the overall vulnerability and burden placed upon the ability of women from disadvantaged communities, the purpose of this paper is to demonstrate the importance of developing a participative gender framework for climate justice with the potential to address the policy and programme vulnerability gap within climate change and conflict in Sudan’s Savannah Belt.

Design/methodology/approach
In utilising gender responsive discourse analysis, along with setting out the history of gender engagement within social forestry, this paper examines both the method of Sudan’s reducing emissions from deforestation and forest degradation (REDD+) development and its content.

Findings
The paper’s findings demonstrate that the REDD+ programme in Sudan provides ample evidence of the importance of integrating climate justice and gender approaches to policy, programming and projects through ensuring women and local community participation at all levels and interaction within policy and programme development, along with its implementation.

Research limitations/implications
The paper is theoretical in nature but did draw upon case studies and consultations, and the author was involved in some of the research.

Originality/value
The paper provides a positive and arguably original example of social forestry within the Savannah Belt and its utilisation as a best practice that has fed into Sudan’s REDD+ Proposal/Policy Document so as to potentially drive and streamline similar such initiatives across Sudan.
The role of rights, risks and responsibilities in the climate justice debate
Authors: Shaw Christopher 
Published: August 2016

Purpose
This paper aims to use the results of a synthesis of six social science fellowships to explore how alternative framings of the climate justice debate can support fairer climate policies.

Design/methodology/approach
The original fellowships drew on sociology, economics, geography, psychology and international relations. Cross-cutting themes of rights, risks and responsibilities were identified following a series of workshops. Results of these workshops were discussed in a number of policy fora. Analysis of the feedback from that fora is used to propose the case for a rights, risks and responsibilities approach to building a more accessible climate justice debate.

Findings
Existing climate policy unjustly displaces a) responsibility for emission reductions, b) risks from climate impacts and c) loss of rights. Foundational questions of acceptable risk have been ignored and a just climate policy requires procedurally just ways of revisiting this first-order question.

Research limitations/implications
The contribution a rights, risks and responsibilities framework can bring to a process of educating for climate stewardship is at this stage theoretical. It is only through trialling a rights, risks and responsibilities approach to climate justice debates with the relevant stakeholders that its true potential can be assessed.

Practical implications
Policy actors expressed strong resistance to the idea of overhauling current decision-making processes and policy frameworks. However, moving forward from this point with a more nuanced and tactical understanding of the dialectical relationship between rights, risks and responsibilities has the potential to improve those processes.

Social implications
Educating for climate stewardship will be more effective if it adopts an approach which seeks a co-production of knowledge. Beginning with the foundational question of what counts as an acceptable level of climate risk offers an inclusive entry point into the debate.

Originality/value
Reveals limits to public engagement with climate policy generated by a ‘justice’ framing.