bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic changes induced by Bacteroides fragilis toxin (BFT)
Authors: Allen Jawara , Hao Stephanie , Sears Cynthia L. , Timp Winston 
Published: April 2018

AbstractEnterotoxigenic Bacteroides fragilis (ETBF) is a gram negative, obligate anaerobe member of the gut microbial community in up to 40% of healthy individuals. This bacterium is found more frequently in people with colorectal cancer (CRC) and causes tumor formation in the distal colon of mice heterozygous for the adenomatous polyposis coli gene (Apc+/−); tumor formation is dependent on ETBF-secreted Bacteroides fragilis toxin (BFT). Though some of the immediate downstream effects of BFT on colon epithelial cells (CECs) are known, we still do not understand how this potent exotoxin causes changes in CECs that lead to tumor formation and growth. Because of the extensive data connecting alterations in the epigenome with tumor formation, initial experiments attempting to connect BFT-induced tumor formation with methylation in CECs have been performed, but the effect of BFT on other epigenetic processes, such as chromatin structure, remains unexplored. Here, the changes in chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) induced by treatment of HT29/C1 cells with BFT for 24 and 48 hours is examined. Our data show that several genes are differentially expressed after BFT treatment and these changes correlate with changes in chromatin accessibility. Also, sites of increased chromatin accessibility are associated with a lower frequency of common single nucleotide variants (SNVs) in CRC and with a higher frequency of common differentially methylated regions (DMRs) in CRC. These data provide insight into the mechanisms by which BFT induces tumor formation. Further understanding of how BFT impacts nuclear structure and function in vivo is needed.ImportanceColorectal cancer (CRC) is a major public health concern; there were approximately 135,430 new cases in 2017, and CRC is the second leading cause of cancer-related deaths for both men and women in the US (1). Many factors have been linked to CRC development, the most recent of which is the gut microbiome. Pre-clinical models support that enterotoxigenic Bacteroides fragilis (ETBF), among other bacteria, induce colon carcinogenesis. However, it remains unclear if the virulence determinants of any pro-carcinogenic colon bacterium induce DNA mutations or changes that initiate clonal CEC expansion. Using a reductionist model, we demonstrate that BFT rapidly alters chromatin structure and function consistent with capacity to contribute to CRC pathogenesis.
Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California
Authors: Retallack Hanna , Okihiro Mark S. , Britton Elliot , Van Sommeran Sean , DeRisi Joseph L. 
Published: April 2018

ABSTRACTDuring March to August of 2017, hundreds of leopard sharks (Triakis semifasciata) stranded and died on the shores of San Francisco Bay, California, USA. Similar mass stranding events occurred in 1967 and 2011, yet analysis of these epizootics was incomplete and no etiology was confirmed. Our investigation of the most recent epizootic revealed severe meningoencephalitis in stranded sharks, raising suspicion for infection. On this basis, we pursued a strategy for unbiased pathogen detection using metagenomic next-generation sequencing followed by orthogonal validation and further screening. We show that the ciliated protozoan pathogen, Miamiensis avidus, was present in the central nervous system of leopard (n=12) and other shark species (n=2) that stranded in San Francisco Bay, but absent in leopard sharks caught elsewhere. Whereas this protozoan has previously been implicated in devastating outbreaks in teleost marine fish, our findings represent the first report of a ciliated protozoan infection in wild elasmobranchs. This discovery highlights the benefits of adopting unbiased metagenomic sequencing in the study of wildlife health and disease.
Measuring single neuron visual receptive field sizes by fMRI
Authors: Keliris Georgios A. , Li Qinglin , Papanikolaou Amalia , Logothetis Nikos K. , Smirnakis Stelios M. 
Published: April 2018

AbstractThe non-invasive measurements of neuronal receptive field (RF) properties in-vivo allow a detailed understanding of brain organization as well as its plasticity by longitudinal following of potential changes. Visual RFs measured invasively by electrophysiology in animal models have traditionally provided a great extent of our current knowledge about the visual brain and its disorders. Voxel based estimates of population RF (pRF) by functional magnetic resonance imaging (fMRI) in humans revolutionized the field and have been used extensively in numerous studies. However, current methods cannot estimate single-neuron RF sizes as they reflect large populations of neurons with individual RF scatter. Here, we introduce a new approach to estimate RF size using spatial frequency selectivity to checkerboard patterns. This method allowed us to obtain non-invasive, single-unit, RF estimates in human V1 for the first time. These estimates were significantly smaller compared to prior pRF methods. Further, fMRI and electrophysiological experiments in non-human primates demonstrated an exceptional match validating the approach.
Spotting the path that leads nowhere: Modulation of human theta and alpha oscillations induced by trajectory changes during navigation
Authors: Javadi Amir-Homayoun , Patai Eva Zita , Margois Aaron , Tan Heng-Ru M. , Kumaran Darshan , Nardini Marko , Penny Will , Duzel Emrah , Dayan Peter , Spiers Hugo J. 
Published: April 2018

AbstractThe capacity to take efficient detours and exploit novel shortcuts during navigation is thought to be supported by a cognitive map of the environment. Despite advances in understanding the neural basis of the cognitive map, little is known about the neural dynamics associated with detours and shortcuts. Here, we recorded magnetoencephalography from humans as they navigated a virtual desert island riven by shifting lava flows. The task probed their ability to take efficient detours and shortcuts to remembered goals. We report modulation in event-related fields and theta power as participants identified real shortcuts and differentiated these from false shortcuts that led along suboptimal paths. Additionally, we found that a decrease in alpha power preceded ‘back-tracking’ where participants spontaneously turned back along a previous path. These findings help advance our understanding of the fine-grained temporal dynamics of human brain activity during navigation and support the development of models of brain networks that support navigation.
Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies
Authors: Zheng Ye , Ay Ferhat , Keleş Sündüz 
Published: April 2018

AbstractAbstract Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological signal from repetitive regions of genomes. We developed and validated mHi-C, a multi-read mapping strategy to probabilistically allocate Hi-C multi-reads. mHi-C exhibited superior performance over utilizing only uni-reads and heuristic approaches aimed at rescuing multi-reads on benchmarks. Speciffically, mHi-C increased the sequencing depth by an average of 20% resulting in higher reproducibility of contact matrices and detected interactions across biological replicates. The impact of the multi-reads on the detection of signifficant interactions is influenced marginally by the relative contribution of multi-reads to the sequencing depth compared to uni-reads, cis-to-trans ratio of contacts, and the broad data quality as reflected by the proportion of mappable reads of datasets. Computational experiments highlighted that in Hi-C studies with short read lengths, mHi-C rescued multi-reads can emulate the effect of longer reads,. mHi-c also revealed biologically supported bona fide promoter-enhancer interactions and topologically associating domains involving repetitive genomic regions, thereby unlocking a previously masked portion of the genome for conformation capture studies.
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
Authors: Cornet Luc , Meunier Loïc , Van Vlierberghe Mick , Léonard Raphaël R. , Durieu Benoit , Lara Yannick , Misztak Agnieszka , Sirjacobs Damien , Javaux Emmanuelle J. , Philippe Hervé , Wilmotte Annick , Baurain Denis 
Published: April 2018

AbstractBACKGROUNDPublicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes.RESULTSAs reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods).CONCLUSIONSOur results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
Long non-coding RNAs in wild wheat progenitors
Authors: Pieri Alice , Enrico Pè Mario , Bertolini Edoardo 
Published: April 2018

AbstractTriticum urartuandAegilops tauschiiare the diploid progenitors of the hexaploidTriticum aestivum(AuAuBBDD), donors of the Auand D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515T. urartuand 20,908Ae. tauschii bona-fidelncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority ofT. urartuandAe. tauschiilncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and theircisregulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.
A kinetic model for fluorescence microscopy experiments in disordered media that contains binding sites and obstacles
Authors: Shkilev V.P. 
Published: April 2018

AbstractA model is proposed that describes the diffusion of molecules in a disordered medium with binding sites (traps) and obstacles (barriers). The equations of the model are obtained using the subordination method. As the parent process, random walks on a disordered lattice are taken, described by the random barriers model. As the leading process, the renewal process that corresponds to the multiple-trapping model is taken. Theoretical expressions are derived for the curves obtained in experiments using fluorescence microscopy (FRAP, FCS and SPT). Generalizations of the model are proposed, allowing to take into account correlations in the mutual arrangement of traps and barriers. The model can be used to find parameters characterizing the diffusion and binding properties of biomolecules in living cells.
Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding
Authors: Franklin Meghan Whitney , Slusky Joanna S.G. 
Published: April 2018

I.AbstractAs a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4-6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the sidechain and backbone two to four residues away plays an important role. These bonds preferentially use an Asp, Asn, Ser or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.
ACDtool: a web-server extending the original Audic-Claverie statistical test to the comparison of large data sets of counts
Authors: Claverie Jean-Michel , Thi Ngan TA 
Published: April 2018

AbstractMotivationMore than 20 years ago, our laboratory published an original statistical test (referred to as the Audic-Claverie (AC) test in the literature) to identify differentially expressed genes from the pairwise comparison of counts of cognate RNA-seq reads (then called “expressed sequence tags”) determined in different conditions. Despite its antiquity and the publications of more sophisticated software packages, this original article continued to gather more than 200 citations per year, indicating the persistent usefulness of the simple AC test for the community. This prompted us to propose a fully revamped version of the AC test with a user interface adapted to the diverse and much larger datasets produced by contemporary omics techniques.ResultsWe implemented ACDtool as an interactive, freely accessible web service proposing 3 types of analyses: 1) the pairwise comparison of individual counts, 2) pairwise comparisons of arbitrary large lists of counts, 3) the all-at-once pairwise comparisons of multiple datasets. Statistical computations are implemented using standard R functions and mathematically reformulated as to accommodate all practical ranges of count values. ACDtool can thus analyze datasets from transcriptomic, proteomic, metagenomics, barcoding, ChlP'seq, population genetics, etc, using the same mathematical approach. ACDtool is particularly well suited for comparisons of large datasets without replicates.AvailabilityACDtool is at URL: www.igs.cnrs-mrs.fr/acdtool/ContactJean-Michel.Claverie@univ-amu.frSupplementary informationnone.
Impact of Brownian moment and thermophoresis on magnetohydrodynamic flow of magnetic nanofluid past an elongated sheet in the presence of thermal diffusion
Authors: Sulochana C. , Ashwinkumar G.P. 
Published: April 2018

Purpose
The purpose of this paper is to report the impact of thermophoresis and Brownian moment on MHD two-dimensional forced convection flow of nanofluid past a permeable stretching sheet in the presence of thermal diffusion.

Design/methodology/approach
The flow governing PDEs are reduced to ODEs by utilizing pertinent transmutations and then resolved by employing a fourth-order Runge-Kutta-based shooting technique. The energy and diffusion equations are incorporated with Brownian motion, thermophoresis and Soret parameters. The velocity, thermal and concentration attributes along with skin friction factor, local Nusselt and Sherwood number are discussed under the influence of sundry pertinent parameters and presented with the assistance of graphical and tabular values.

Findings
The results infer that Sherwood number is accelerated by Soret parameter but it controls the thermal transport rate. And also, Brownian and thermophoresis play a vital role in enhancing heat conduction process.

Originality/value
Considering the industrial applications of flow of magnetic nanofluid over a stretching surface, this paper presents the solution of the flow problem considering thermophoresis, Brownian motion, magnetic field and thermal diffusion effects. In addition, the aim and objectives of this paper fills a gap in the industry.
On the development of a predictive functional trait approach for studying terrestrial arthropods
Authors: Brousseau Pierre‐Marc , Gravel Dominique , Handa Ira Tanya 
Published: April 2018

Abstract

The characterization of ecological communities with functional traits allows to consider simultaneously the ability of a species to survive and reproduce in an environment, its interactions with other species and its effects on the ecosystem.

Functional traits have been studied mainly by plant ecologists, but are increasingly common in the study of other taxa including arthropods. Arthropods represent a group for which a functional trait approach could be highly profitable because of their high diversity, abundance, ubiquity and role in many important ecological processes.

This review synthesizes two decades of functional trait research on terrestrial arthropods. We show that while the approach has gained popularity, particularly in the last decade, the absence of clearly postulated hypotheses is a recurrent problem limiting generalization. Furthermore, studied traits are often poorly related to studied functions. To address these problems, we propose a step‐by‐step protocol to postulate clear hypotheses prior to trait selection and emphasize the need for a common set of more generalizable traits in future studies.

Extending the functional trait approach to arthropods opens the door to improving our understanding of interspecific interactions and potential links between response and effect traits. We present the concept of trait‐matching with several examples of arthropod traits known to be effective predictors of consumer–resource interactions.

The development of a successful functional trait approach for terrestrial arthropods will necessitate an understanding of relevant traits, standardized measurement protocols and open access databases to share this information. Such progress will provide ecologists with a new set of tools to answer broad questions in several fields including the study of community assembly, ecological networks and multitrophic functionality.
Scaling Up Community Action for Tackling Climate Change
Authors: Shaw Deirdre , Cumbers Andrew , McMaster Robert , Crossan John 
Published: April 2018

AbstractTackling climate change requires a set of deeply intertwined geographical responsibilities whereby actors at and across different geographical scales are intimately connected. Creating effective strategies requires far more than an invocation for individual behavioural change in thinking globally and acting locally, but attention to the multi‐scalar conflicts, tensions and also opportunities to develop the most appropriate collective responses. In this paper, we use the example of community gardening initiatives in a large UK city to critically interrogate the problems facing groups at the local neighbourhood level in pursuing sustainability agendas. We focus on the organizational imperative to create a multi‐scalar food policy partnership at the city level as a way of confronting dominant global neoliberal urban competitiveness agendas. Our results emphasize the critical importance of scalar politics in enabling effective climate change strategies.
Reimagining the Scales, Dimensions and Fields of Socio‐ecological Sustainability
Authors: O'Reilly Dermot , Allen Stephen , Reedy Patrick 
Published: April 2018

AbstractThis paper critiques the two‐dimensional (hierarchical–spatial) focus on scales evident in management and organizational studies, and the capitalist ecological modernization (CEM) paradigm that dominates current corporate and governmental approaches to sustainability. Our contribution is to propose a more complex and nuanced understanding of scale, which incorporates social, political, temporal and material dimensions. We propose a heuristic framework from Harvey, in order to evaluate different paradigms of socio‐ecological organizing: specifically, the dominant paradigm of CEM against a social ecology (SE) alternative. We explore the divergent conceptions of, and relative importance placed upon, concepts of scale, grain, level and field in these two contrasting paradigms. Our analysis highlights the limitations and contradictions of the CEM expression of scale, namely its predominant focus on measurement and expansion through ‘economies of scale’. By offering an alternative conception of the links between scales, grains, levels and social fields, we show how this enriches the conceptualization of potential forms of socio‐ecological organizing and opens up the potential for alternative modes of organizing socio‐ecological sustainability.