bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-developing climate services for public health: stakeholder needs and perceptions for the prevention and control ofAedes-transmitted diseases in the Caribbean
Authors: Stewart-Ibarra Anna M. , Romero Moory , Hinds Avery Q. J. , Lowe Rachel , Mahon Roché , Van Meerbeeck Cedric J. , Rollock Leslie , Gittens-St. Hilaire Marquita , St. Ville Sylvester , Ryan Sadie J. , Trotman Adrian R. , Borbor-Cordova Mercy J. 
Published: March 2019

AbstractBackgroundSmall island developing states (SIDS) in the Caribbean region are challenged with managing the health outcomes of a changing climate. Health and climate sectors have partnered to co-develop climate services to improve the management of these diseases, for example, through the development of climate-driven early warning systems. The objective of this study was to identify health and climate stakeholder perceptions and needs in the Caribbean, with respect to the development of climate services for arboviruses (e.g. dengue, chikungunya, and Zika).MethodsStakeholders included public decision makers and practitioners from the climate and health sectors at the regional (Caribbean) level and from the countries of Dominica and Barbados. From April to June 2017, we conducted interviews (n=41), surveys (n=32), and national workshops with stakeholders. Survey responses were tabulated and audio recordings were transcribed and analyzed using qualitative coding to identify responses by research topic, country/region, and sector.ResultsHealth practitioners indicated that their jurisdiction is currently experiencing an increased risk of diseases transmitted byAe. aegyptidue to climate variability, and most anticipated that this risk will increase in the future. National health sectors reported financial limitations and a lack of technical expertise in geographic information systems (GIS), statistics, and modeling, which constrained their ability to implement climate services for arboviruses. National climate sectors were constrained by a lack of personnel. Stakeholders highlighted the need to strengthen partnerships with the private sector, academia, and civil society. They identified a gap in local research on climate-arbovirus linkages, which constrained the ability of the health sector to make informed decisions. Strategies to strengthen the climate-health partnership included a top-down approach by engaging senior leadership, multi-lateral collaboration agreements, national committees on climate and health, and shared spaces of dialogue. Mechanisms for mainstreaming climate services for health operations to control arboviruses included climate-health bulletins and an online GIS platform that would allow for regional data sharing and the generation of spatiotemporal epidemic forecasts.ConclusionsThese findings support the creation of interdisciplinary and intersectoral communities of practices and the co-design of climate services for the Caribbean public health sector. By fostering the effective use of climate information within health policy, research and practice, nations will have greater capacity to adapt to a changing climate.
Global Modulation in DNA Epigenetics during Pro-Inflammatory Macrophage Activation
Authors: Jain Nikhil , Shahal Tamar , Gabrieli Tslil , Gilat Noa , Torchinsky Dmitry , Michaeli Yael , Vogel Viola , Ebenstein Yuval 
Published: March 2019

AbstractDNA methylation patterns create distinct gene expression profiles. These patterns are maintained after cell division, thus enabling the differentiation and maintenance of multiple cell types from the same genome sequence. The advantage of this mechanism for transcriptional control is that chemical-encoding allows to rapidly establish new epigenetic patterns “on-demand” through enzymatic methylation and de-methylation of DNA. Here we show that this feature is associated with the fast response of macrophages during their pro-inflammatory activation. By using a combination of mass spectroscopy and single-molecule imaging to quantify global epigenetic changes in the genomes of primary macrophages, we followed three distinct DNA marks (methylated, hydroxymethylated and unmethylated), involved in establishing new DNA methylation patterns during pro-inflammatory activation. The observed epigenetic modulation together with gene expression data generated for the involved enzymatic machinery, may suggest that de-methylation upon LPS-activation starts with oxidation of methylated CpGs, followed by excision-repair of these oxidized bases and their replacement with unmodified cytosine.
Co-localization of pain and reduced intra-epidermal nerve fiber density in individuals with HIV-associated sensory neuropathy
Authors: Patel Imraan G , Kamerman Peter R 
Published: March 2019

AbstractIntroductionThere is poor correlation between decreases in intra-epidermal nerve fiber density (IENFD) and the presence of pain in HIV-associated sensory neuropathy (HIV-SN) and other painful distal symmetrical polyneuropathies.ObjectiveWe investigated whether in individuals with HIV-SN, having pain at the ankle skin biopsy site was associated with lower IENFD compared to when there was no pain at the ankle biopsy site.MethodsWe recruited 15 individuals with symptomatic HIV-SN. Nine had pain at the site where the ankle biopsy was taken, while six did not. Skin punch biopsies for IENFD quantification were taken from the ankle and the thigh. Contrasts between the two groups were made using the overlap of confidence interval (CI) method.ResultsIENFD was substantially lower in the group that had pain at the site of the ankle biopsy compared to the other group [6.6 (CI: 5.3 to 7.2) vs. 3.3 (CI: 10.0 to 15.0) fibers/mm]. However, there was no group differences at the thigh biopsy site [15.6 (CI: 15.0 to 15.9) vs 16.2 (CI: 14.5 to 17.8) fibers/mm]. When taking the ratio of ankle IENFD:thigh IENFD, the point estimate for the pain at the ankle group [0.43 (CI: 0.36 to 0.48)] was about half that of the other group [0.81 (CI: 0.68 to 0.87)].ConclusionThus, co-localization of pain to the ankle is associated with meaningful decreases in ankle IENFD.SummaryHaving pain at the ankle biopsy site is associated with lower intra-epidermal nerve fiber density compared to not having pain at the ankle biopsy site.
A tissue-like platform for studying engineered quiescent human T-cells’ interactions with dendritic cells
Authors: Abu-Shah Enas , Demetriou Philippos , Balint Stefan , Mayya Viveka , Kutuzov Mikhail A. , Dushek Omer , Dustin Michael L. 
Published: March 2019

AbstractResearch in the field of human immunology is restricted by the lack of a system that reconstitutes thein-situactivation dynamics of quiescent human antigen-specific T-cells interacting with dendritic cells. Here we report a tissue-like system that recapitulates the dynamics of engineered primary human immune cell. Our approach facilitates real-time single cell manipulations, tracking of interactions and functional responses complemented by population-based measurements of cytokines, activation status and proliferation. As a proof of concept, we recapitulate immunological phenomenon such as CD4 help to CD8 T-cells through enhanced maturation of DCs and effect of PD-1 checkpoint blockades. In addition, we characterise unique dynamics of T-cell/DC interactions as a function of antigen affinity.
Peaceful behaviour: a strategy employed by an obligate nest invader to avoid conflict with its host species
Authors: Hugo Helder , Cristaldo Paulo F. , DeSouza Og 
Published: March 2019

AbstractIn addition to its builders, termite nests are known to house a variety of secondary, opportunistic termite species, but little is known about the mechanisms governing the maintenance of such associations. In a single nest, host and intruder are likely to engage in intense conflict, due to their nestmate discrimination system. An intriguing question is how individuals cope with such a burden in the long term. Evasive behaviour has been previously suggested as a mechanism that reduces the frequency of encounters between non-nestmates. However, due to confinement imposed by the nests’ physical boundaries, it is likely that hosts and inquilines would eventually come across each other. Under these circumstances, it is plausible that inquilines would be required to behave accordingly to secure their housing. Here, we tested this hypothesis predicting that, once inevitably exposed to hosts, inquiline individuals would modulate their behaviour to circumvent conflict. While exploring the behavioural dynamics of the encounter between both cohabitants, we find evidence for an unusual lack of aggressiveness by inquilines towards hosts. Such a non-aggressive behaviour is characterised by evasive manoeuvres that include reversing direction, bypassing and a defensive mechanism using defecation to repel hosts. The behavioural adaptations we describe may play an intrinsic role in the stability of cohabitations between termite species: by reducing the costs of conflicts to both cohabitants, it may improve the chances for stable nest-sharing considerably.
A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data
Authors: Zhu Jiafan , Liu Xinhao , Ogilvie Huw A. , Nakhleh Luay K. 
Published: March 2019

AbstractReticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting (ILS). However, these methods can only handle a small number of loci from a handful of genomes.In this paper, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological data sets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with existing methods. The results are a significant and promising step towards accurate, large-scale phylogenetic network inference.We implemented the algorithms in the publicly available software package PhyloNet (https://bioinfocs.rice.edu/PhyloNet).Contactnakhleh@rice.edu
Membrane association of VAMP2 SNARE motif in cells and its regulation by different lipid phases of synaptic vesicle membrane
Authors: Wang Chuchu , Tu Jia , Zhang Shengnan , Cai Bin , Liu Zhenying , Hou Shouqiao , Liu Zhijun , Diao Jiajie , Zhu Zheng-Jiang , Liu Cong , Li Dan 
Published: March 2019

SummaryVesicle associated membrane protein 2 (VAMP2) contains a conserved SNARE motif that forms helix bundles with the homologous motifs of syntaxin-1 and SNAP25 to assemble into a SNARE complex for the exocytosis of synaptic vesicles (SV). Prior to SNARE assembly, the structure of VAMP2 is unclear. Here, using in-cell NMR spectroscopy, we described the dynamic membrane association of VAMP2 SNARE motif in mammalian cells at atomic resolution, and further tracked the intracellular structural changes of VAMP2 upon the lipid environmental changes. The underlying mechanistic basis was then investigated by solution NMR combined with mass-spectrometry-based lipidomic profiling. We analyzed the lipid compositions of lipid-raft and non-raft phases of SV membrane and revealed that VAMP2 configures distinctive conformations in different phases of SV membrane. The phase of cholesterol-rich lipid rafts could largely weaken the association of SNARE motif with SV membrane and thus, facilitate vesicle docking; While in the non-raft phase, the SNARE motif tends to hibernate on SV membrane with minor activity. Our work provides a spatial regulation of different lipid membrane phases to the structure of core SNARE proteins, which deepens our knowledge on the modulation of SNARE machinery.
Genomic acquisitions in emerging populations ofXanthomonas vasicolapv.vasculoruminfecting corn in the U.S. and Argentina
Authors: Perez-Quintero Alvaro L , Ortiz-Castro Mary , Wu Guangxi , Lang Jillian M. , Liu Sanzhen , Chapman Toni A , Chang Christine , Ziegle Janet , Peng Zhao , White Frank F. , Plazas Maria Cristina , Leach Jan E. , Broders Kirk 
Published: March 2019

AbstractXanthomonas vasicolapv.vasculorum (Xvv)is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this bacteria have greatly increased in the past years in South America and in the U.S., where it is now present in most of the corn producing states. Phenotypic characterization showed that the emerging U.S. and South American Xvvpopulations may have increased virulence in corn compared to older strains. To understand the genetic mechanisms behind the increased virulence in this group, we used comparative genomics to identify gene acquisitions inXvvgenomes from the U.S. and Argentina. We sequenced 41 genomes ofXvvand the related sorghum-infectingX. vasicolapv.holcicola(Xvh).A comparison of all availableX. vasicolagenomes showed the phylogenetic relationships in the group and identified clusters of genes associated with the emergingXvvpopulations. The newly acquired gene clusters showed evidence of horizontal transfer toXvvand included candidate virulence factors. One cluster, in particular, corresponded to a prophage transferred fromXvhto allXvvfrom Argentina and the U.S. The prophage contains putative secreted proteins, which represent candidates for virulence determinants in these populations and await further molecular characterization.
NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains
Authors: Lhoumaud Priscillia , Badri Sana , Hernaez Javier Rodriguez , Sakellaropoulos Theodore , Sethia Gunjan , Kloetgen Andreas , Cornwell MacIntosh , Bhattacharyya Sourya , Ay Ferhat , Bonneau Richard , Tsirigos Aristotelis , Skok Jane A. 
Published: March 2019

AbstractCTCF and cohesin play a key role in organizing chromatin into TAD structures. Disruption of a single CTCF binding site is sufficient to change chromosomal interactions leading to alterations in chromatin modifications and gene regulation. However, the extent to which alterations in chromatin modifications can disrupt 3D chromosome organization leading to transcriptional changes is unknown. In multiple myeloma a 4;14 translocation induces overexpression of the histone methyltransferase, NSD2 resulting in expansion of H3K36me2 and shrinkage of antagonistic H3K27me3 domains. Using isogenic cell lines producing high and low levels of NSD2, we find oncogene activation is linked to alterations in H3K27ac and CTCF within H3K36me2 enriched chromatin. A linear regression model reveals that changes in both CTCF and/or H3K27ac significantly increase the probability that a gene sharing the same insulated domain will be differentially expressed. These results identify a bidirectional relationship between 2D chromatin and 3D genome organization in gene regulation.
Lower Extremity Long-Latency Reflexes Differentiate Walking Function After Stroke
Authors: Banks Caitlin L. , Little Virginia L. , Walker Eric R. , Patten Carolynn 
Published: March 2019

AbstractThe neural mechanisms of walking impairment after stroke are not well characterized. There is a need for a neurophysiologic marker that can unambiguously differentiate functional status and potential for walking recovery. The long-latency reflex (LLR) is a supraspinally-mediated response that integrates sensorimotor information during movement. It is hypothesized that lower extremity LLRs contribute to regulation of motor output during walking in healthy individuals. The goal of the present study was to assess the relationship between lower extremity LLRs, measures of supraspinal drive, and walking function. Thirteen individuals with chronic post-stroke hemiparesis and thirteen healthy controls performed both isometric and dynamic plantarflexion. Transcranial magnetic stimulation (TMS) assessed supraspinal drive to the tibialis anterior. LLR activity was assessed during dynamic voluntary plantarflexion and individuals post-stroke were classified as either LLR present (LLR+) or absent (LLR-). All healthy controls and nine individuals post-stroke exhibited LLRs, while four did not. LLR+ individuals revealed higher clinical scores, walking speeds, and greater ankle plantarflexor power during walking compared to LLR- individuals. LLR- individuals exhibited exaggerated responses to TMS during dynamic plantarflexion relative to healthy controls. This LLR- subset revealed dysfunctional modulation of stretch responses and antagonist supraspinal drive relative to healthy controls and the higher functioning LLR+ individuals post-stroke. These abnormal responses allow for unambiguous differentiation between individuals post-stroke and are associated with multiple measures of motor function. These findings provide an opportunity to distinguish among the heterogeneity of lower extremity motor impairments present following stroke by associating them with responses at the nervous system level.
Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north-western PacificAcropora digitifera
Authors: Selmoni Oliver , Rochat Estelle , Lecellier Gael , Berteaux-Lecellier Veronique , Joost Stéphane 
Published: March 2019

AbstractCoral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance of anomalous heat waves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating the set-up of preservation frameworks to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system.Here, we study the relationships between frequencies of genetic markers with that of environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against thermal stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale.The combination between the results of these analyses portrayed the adaptive potential of this population: we were able to identify reefs carrying potential adaptive genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable, and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system, and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reef in warming oceans.
Proteomics analysis of extracellular matrix remodeling during zebrafish heart regeneration
Authors: Garcia-Puig Anna , Mosquera Jose Luis , Jiménez-Delgado Senda , García-Pastor Cristina , Jorba Ignasi , Navajas Daniel , Canals Francesc , Raya Angel 
Published: March 2019

AbstractAdult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days post-amputation) time-point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.
On the move: Redox –dependent protein relocation
Authors: Foyer Christine H. , Baker Alison , Wright Megan , Sparkes Imogen A. , Mhamdi Amna , Schippers Jos H.M. , Van Breusegem Frank 
Published: March 2019

ABSTRACTCompartmentation of proteins and processes is a defining feature of eukaryotic cells. The growth and development of organisms is critically dependent on the accurate sorting of proteins within cells. The mechanisms by which cytosol-synthesized proteins are delivered to the membranes and membrane compartments have been extensively characterised. However, the protein complement of any given compartment is not precisely fixed and some proteins can move between compartments in response to metabolic or environmental triggers. The mechanisms and processes that mediate such relocation events are largely uncharacterized. Many proteins can in addition perform multiple functions, catalyzing alternative reactions or performing structural, non-enzymatic functions. These alternative functions can be equally important functions in each cellular compartment. Such proteins are generally not dual targeted proteins in the classic sense of having targeting sequences that directde novosynthesised proteins to specific cellular locations. Accumulating evidence suggests that redox post-translational modifications (PTMs) can control the compartmentation of many such proteins, including antioxidant and/or redox associated enzymes.
Childhood intelligence attenuates the association between biological ageing and health outcomes in later
Authors: Stevenson Anna J. , McCartney Daniel L. , Hillary Robert F. , Redmond Paul , Taylor Adele M. , Zhang Qian , McRae Allan F. , Spires-Jones Tara L. , McIntosh Andrew M. , Deary Ian J. , Marioni Riccardo E. 
Published: March 2019

AbstractThe identification of biomarkers that discriminate individual ageing trajectories is a principal target in ageing research. Some of the most promising predictors of biological ageing have been developed using DNA methylation. One recent candidate, which tracks age-related phenotypes in addition to chronological age, is ‘DNAm PhenoAge’. Here, we performed a phenome-wide association analysis of this biomarker in a cohort of older adults to assess its relationship with a comprehensive set of both historical and contemporaneously-measured phenotypes. Higher than expected DNAm PhenoAge compared to chronological age, known as epigenetic age acceleration, was found to associate with a number of blood, cognitive, physical fitness and lifestyle variables, and with mortality. Notably, DNAm PhenoAge, assessed at age 70, was associated with cognitive ability at age 11, and with educational attainment. Adjusting for age 11 cognitive ability attenuated the majority of the cross-sectional later-life associations between DNAm PhenoAge and health outcomes. These results highlight the importance of early-life factors on healthy ageing.