bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anophelesbionomic, insecticide resistance and malaria transmission in southwest Burkina Faso: a pre-intervention study
Authors: Soma Dieudonné Diloma , Zogo Barnabas Muhugnon , Somé Anthony , Tchiekoi Bertin N’Cho , de Sales Hien Domonbabele François , Pooda Hermann Sié , Coulibaly Sanata , Gnambani Jacques Edounou , Ouari Ali , Mouline Karine , Dahounto Amal , Ouédraogo Georges Anicet , Fournet Florence , Koffi Alphonsine Amanan , Pennetier Cédric , Moiroux Nicolas , Dabiré Roch Kounbobr 
Published: May 2019

AbstractBackgroundThe present study presents results of entomological surveys conducted to address the malaria vectors bionomic, insecticide resistance and transmission prior to the implementation of new strategies complement long-lasting insecticidal nets (LLINs) in the framework of a randomized control trial in southwest Burkina Faso.MethodsWe conducted entomological surveys in 27 villages during the dry cold season (January 2017), dry hot season (March 2017) and rainy season (June 2017). We carried out hourly catches (from 17:00 to 09:00) inside and outside 4 houses in each village using the Human Landing Catch technique. Mosquitoes were identified using morphological taxonomic keys. Specimens belonging to theAnopheles gambiaecomplex andFunestusGroup were identified using molecular techniques as well as detection ofPlasmodium falciparuminfection and insecticide resistance target-site mutations.ResultsEightAnophelesspecies were detected in the area.Anopheles funestus s.swas the main vector during the dry cold season. It was replaced byAnopheles coluzziiduring the dry hot season whereasAn. coluzziiandAn. gambiae s.s.were the dominant species during the rainy season. Species composition of theAnophelespopulation varied significantly among surveys. All researched target site mutation of insecticide resistance (kdr-w, kdr-eandace-1) were detected in all members of theAn. gambiaecomplex of the area but at different frequencies. We observed early and late biting phenotypes in the main malaria vector species. Entomological inoculation rates were 0.087, 0.089 and 0.375 infected bites per human per night during dry cold season, dry hot season and rainy season, respectively.ConclusionThe intensity of malaria transmission was high despite the universal coverage with LLINs. We detected early and late biting phenotypes in the main malaria vector species as well as physiological insecticide resistance mechanisms. These vectors might mediate residual transmission. These data highlight the need to develop complementary tools in addition to LLINs in order to better control resistant malaria vectors and to monitor insecticide resistance.
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia
Authors: Fuller Gregory G. , Han Ting , Freeberg Mallory A. , Moresco James J. , Yates John R , Kim John K. 
Published: May 2019

AbstractIn hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. Formation of G bodies in yeast is correlated with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Tethering a G body component, the beta subunit of the yeast phosphofructokinase, Pfk2, to nonspecific endoribonucleases reveals that RNA nucleates G body formation and subsequent maintenance of G body structural integrity. Consistent with a phase separation mechanism of G body formation, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies can fuse in live cells and are largely insensitive to 1,6-hexanediol treatment, consistent with a hydrogel-like state in its composition. Taken together, our results elucidate the biophysical nature of G bodies and demonstrate that RNA nucleates phase separation of the glycolysis machinery in response to hypoxic stress.
Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes
Authors: Samir Khalil Ahmed Ibrahim , Khyriem Costerwell , Chattopadhyay Anupam , Sanyal Amartya 
Published: May 2019

AbstractMotivationDetection of copy number alterations (CNA) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales with distinct biological origin and function. Although several tools are available to identify CNAs using read depth (RD) of coverage, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. These tools are also affected by RD signal variations, pronounced in low-coverage data, which significantly inflate false detection of change points and inaccurate CNA calling.ResultsWe have developed CNAtra to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from whole-genome sequencing (WGS) data. CNAtra provides an analytical and visualization framework for CNV profiling using single sequencing sample. CNAtra first utilizes multimodal distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We utilized Savitzy-Golay filter and Modified Varri segmentation to capture the change points. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy number. Next, focal alterations were identified in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. We tested CNAtra calls using experimentally verified segmental aneuploidies and focal alterations which confirmed CNAtra’s ability to detect and distinguish the two alteration phenomena. We used realistic simulated data for benchmarking the performance of CNAtra against other detection tools where we artificially spiked-in CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall, andf-measure. CNAtra shows the highest sensitivity of 93% and 97% for detecting focal and large-scale alterations respectively. Visual inspection of CNAs showed that CNAtra is the most robust detection tool for low-coverage cancer data.Availability and implementationCNAtra is an open source software implemented in MATLAB, and is available athttps://github.com/AISKhalil/CNAtra
High-throughput microcircuit analysis of individual human brains through next-generation multineuron patch-clamp
Authors: Peng Yangfan , Mittermaier Franz X. , Planert Henrike , Schneider Ulf C. , Alle Henrik , Geiger Jörg R.P. 
Published: May 2019

AbstractComparing neuronal microcircuits across different brain regions, species and individuals can reveal common and divergent principles of network computation. Simultaneous patch-clamp recordings from multiple neurons offer the highest temporal and subthreshold resolution to analyse local synaptic connectivity. However, its establishment is technically complex and the experimental performance is limited by high failure rates, long experimental times and small sample sizes. We introduce an in-vitro multipatch setup with an automated pipette pressure and cleaning system facilitating recordings of up to 10 neurons simultaneously and sequential patching of additional neurons. We present hardware and software solutions that increase the usability, speed and data throughput of multipatch experiments which allowed probing of 150 synaptic connections between 17 neurons in one human cortical slice and screening of over 600 connections in tissue from a single patient. This method will facilitate the systematic analysis of microcircuits and allow unprecedented comparisons at the level of individuals.
Analysis tools to quantify dissemination of pathology in zebrafish larvae
Authors: Stirling David R. , Suleyman Oniz , Gil Eliza , Elks Philip M. , Torraca Vincenzo , Noursadeghi Mahdad , Tomlinson Gillian S. 
Published: May 2019

ABSTRACTWe used the zebrafish larval Mycobacterium marinum infection model of tuberculosis to develop image analysis software called QuantiFish, to enable rapid, objective quantitation of bacterial load and dissemination. Our analysis tools provide novel outcome measures of infection; the proportional distribution of bacteria between sites and their spatial distribution throughout the host. We anticipate the broader application of these parameters to other zebrafish models of infection and metastatic cancer.
Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection
Authors: Chato Connor , Kalish Marcia L. , Poon Art F. Y. 
Published: May 2019

AbstractGenetic clustering is a popular method for characterizing variation in transmission rates for rapidly-evolving viruses, and could potentially be used to detect outbreaks in ‘near real time’. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analyzed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B pol sequences from Seattle (n = 1, 653) and Middle Tennessee, USA (n = 2, 779), and northern Alberta, Canada (n = 809). Under varying TN93 thresholds, we fit two models to the distributions of new cases relative to clusters of known cases: (1) a null model that assumes cluster growth is strictly proportional to cluster size, i.e., no variation in transmission rates among individuals; and (2) a weighted model that incorporates individual-level covariates, such as recency of diagnosis. The optimal threshold maximizes the difference in information loss between models, where covariates are used most effectively. Optimal TN93 thresholds varied substantially between data sets, e.g., 0.0104 in Alberta and 0.016 in Seattle and Tennessee, such that the optimum for one population will potentially mis-direct prevention efforts in another. The range of thresholds where the weighted model conferred greater predictive accuracy tended to be narrow (±0.005 units), but the optimal threshold for a given population also tended to be stable over time. We also extended our method to demonstrate that variation in recency of HIV diagnosis among clusters was significantly more predictive of new cases than sample collection dates (ΔAIC> 50). These results demonstrate that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications. Our framework not only provides an objective procedure to optimize a clustering method, but can also be used for variable selection in forecasting new cases.
Risk Factors Associated to Types of Gallstone Diagnosed at Ibn-Sina Specialized Teaching Hospital, Khartoum, Sudan
Authors: Shaddad Mahasin Ibrahim , Fadl Azza Abdulrahman , Jervase Ayat , Garelnabi Nur Ibrahim Ali , Hakem Suzan Al , Hussein Tariq Mohamed , Ahmed Mohamed H , Almobark Ahmed Omer 
Published: May 2019

AbstractIntroductionGallstone disease (Cholelithiasis) affects 10 to 15% of the population of developed countries. Our study aimed to determine the risk factors associated to different types of gallstone in patients diagnosed in Khartoum State Ibnsina Gastroenterology Center.MethodsA facility-based prospective cross-sectional study was implemented on a convenient sample of 47 participants diagnosed with gallstone through ultrasonography in Ibnsina Gastroenterology center and who underwent surgical interventions for gallstone removal. A standardized interviewer-administrated research tool comprising three parts was used to collect data related to the characteristics of the participants, their medical presentation and examination as well as information on types of gallstone, surgical interventions and outcomes. The data were computerized through Epi-info7and analyzed through SPSS 23. Descriptive statistics were firstly performed and association was tested through Chi square tests and ANOVA. A multinomial regression analysis established the relationship between types of gallstone and their associated risk factors. All statistical tests were considered as significant whenp< 0.05.ResultsThe risk factors statistically associated to gallstone types were family history (p= 0.011) and duration of living in the residence area (p= 0.043) in pigment-cholesterol gallstone model vs mixed-cholesterol gallstone model. Other four risk factors contributing to the pathogenesis of gallstone were parity (OR = 1.623 [95% CI: 0.795-3.315]) vs (OR = 1.426, [95% CI: 0.729- 2.790]), waist circumference (OR= 1.014 [95% CI: 0.948-1.085]) vs (OR = 1.001 [95% CI: 0.942- 1.065]), chronic disease (OR = 0.698, [95% CI: 0.028 - 17.445]) vs (OR = 0.354, [95% CI: 0.021- 6.087]) and serum triglyceride (OR = 0.985, [95% CI: 0.950- 1.022]) vs (OR= 0.980, [95% CI: 0.949- 1.012]).ConclusionOur finding indicated six risk factors related to types of gallstone. Further multicenter research in Sudan on risk factors is needed to calibrate and validate our model.
Varied effects of algal symbionts on transcription factor NF-κB in a sea anemone and a coral: possible roles in symbiosis and thermotolerance
Authors: Mansfield Katelyn M. , Cleves Phillip A. , Van Vlack Emily , Kriefall Nicola G. , Benson Brooke E. , Camacho Dimitrios J. , Hemond Olivia , Pedroza Monique , Siggers Trevor , Pringle John R. , Davies Sarah W. , Gilmore Thomas D. 
Published: May 2019

AbstractMany cnidarians, including the reef-building corals, undergo symbiotic mutualisms with photosynthetic dinoflagellate algae of the family Symbiodiniaceae. These partnerships are sensitive to temperature extremes, which cause symbiont loss and increased coral mortality. Previous studies have implicated host immunity and specifically immunity transcription factor NF-κB as having a role in the maintenance of the cnidarian-algal symbiosis. Here we have further investigated a possible role for NF-κB in establishment and loss of symbiosis in various strains of the anemone Exaiptasia (Aiptasia) and in the coral Pocillopora damicornis. Our results show that NF-κB expression is reduced in Aiptasia larvae and adults that host certain algae strains. Treatment of Aiptasia larvae with a known symbiosis-promoting cytokine, transforming growth factor β, also led to decreased NF-κB expression. We also show that aposymbiotic Aiptasia (with high NF-κB expression) have increased survival following infection with the pathogenic bacterium Serratia marcescens as compared to symbiotic Aiptasia (low NF-κB expression). Furthermore, a P. damicornis coral colony hosting Durusdinium spp. (formerly clade D) symbionts had higher basal NF-κB expression and decreased heat-induced bleaching as compared to two individuals hosting Cladocopium spp. (formerly clade C) symbionts. Lastly, genome-wide gene expression profiling and genomic promoter analysis identified putative NF-κB target genes that may be involved in thermal bleaching, symbiont maintenance, and/or immune protection in P. damicornis. Our results provide further support for the hypothesis that modulation of NF-κB and immunity plays a role in some, but perhaps not all, cnidarian-Symbiodiniaceae partnerships as well as in resistance to pathogens and bleaching.
COSS: A fast and user-friendly tool for spectral library searching
Authors: Shiferaw Genet Abay , Vandermarliere Elien , Hulstaert Niels , Gabriels Ralf , Martens Lennart , Volders Pieter-Jan 
Published: May 2019

ABSTRACTSpectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tool. Our comparison showed that COSS more reliably identifies spectra and is faster than other spectral library searching tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.
Distributed Biomanufacturing of Liquefied Petroleum Gas
Authors: Hoeven Robin , Hughes John M. X. , Amer Mohamed , Wojcik Emilia Z. , Tait Shirley , Faulkner Matthew , Yunus Ian Sofian , Hardman Samantha J. O. , Johannissen Linus O. , Chen Guo-Qiang , Smith Michael H. , Jones Patrik R. , Toogood Helen S. , Scrutton Nigel S. 
Published: May 2019

AbstractLiquefied Petroleum Gas (LPG) is a major domestic and transport fuel. Its combustion lessens NOx, greenhouse gas and particulates emissions compared to other fuels. Propane – the major constituent of LPG – is a clean, high value ‘drop-in’ fuel that can help governments develop integrated fuels and energy policies with low carbon burden, providing solutions to the multi-faceted challenges of future energy supply. We show that bio-LPG (bio-propane and bio-butane) can be produced by microbial conversion of waste volatile fatty acids that can be derived from anaerobic digestion, industrial waste, or CO2via photosynthesis. Bio-LPG production was achieved photo-catalytically, using biomass propagated from bioengineered bacteria includingE. coli, Halomonas(in non-sterile seawater), andSynechocystis(photosynthetic). These fuel generation routes could be implemented rapidly in advanced and developing nations of the world to meet energy needs, global carbon reduction targets and clean air directives.
De novo phased assembly of the Vitis riparia grape genome
Authors: Girollet Nabil , Rubio Bernadette , Bert Pierre-François 
Published: May 2019

AbstractGrapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
TDP-43 α-helical structure tunes liquid-liquid phase separation and function
Authors: Conicella Alexander E. , Dignon Gregory L. , Zerze Gül H. , Schmidt Hermann Broder , D’Ordine Alexandra M. , Kim Young C. , Rohatgi Rajat , Ayala Yuna M. , Mittal Jeetain , Fawzi Nicolas L. 
Published: May 2019

AbstractLiquid-liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. Present in several MLOs, TDP-43 undergoes LLPS and is linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some disease variants of TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes in a dimeric TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix-helix interaction, which are removed in part by variants including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a mini-gene assay. Therefore, TDP-43 helical region serves as a short but uniquely tunable module that shows promise as for controlling assembly and function in cellular and synthetic biology applications of LLPS.
Interdependence of intra- and inter-domain motions in the PSD-95 PDZ12 tandem
Authors: Kovács Bertalan , Zajácz-Epresi Nóra , Gáspári Zoltán 
Published: May 2019

AbstractPSD-95 is the most abundant scaffold protein in the postsynaptic density of neurons. Its two N-terminal PDZ domains form an autonomous structural unit and their interdomain orientation and dynamics was shown to be dependent on binding to various partner proteins. To understand the mechanistic details of the effect of ligand binding on interdomain structure and dynamics, we generated conformational ensembles using experimentally determined NOE interatomic distances and S2order parameters, available from the literature. In our approach no explicit restraints between the two domains were used and their fast dynamics was also treated independently. We found that intradomain structural changes induced by ligand binding have a profound effect on the interfaces where interdomain contacts can be formed, modulating the probability of the occurrence of specific domain-domain orientations. Our results suggest that the β2-β3 loop in the PDZ domains is a key regulatory region that, through interacting with the upstream residues of the C-terminal peptide ligand, influences both intradomain motions and supramodular rearrangement.
Visual pathways in the brain of the jumping spiderMarpissa muscosa
Authors: Steinhoff Philip O.M. , Uhl Gabriele , Harzsch Steffen , Sombke Andy 
Published: May 2019

AbstractSome animals have evolved task differentiation among their eyes. A particular example is spiders, where most species have eight eyes, of which two (the principal eyes) are used for object discrimination, whereas the other three pairs (secondary eyes) detect movement. In the spider speciesCupiennius saleithese two eye types correspond to two visual pathways in the brain. Each eye is associated with its own first and second order visual neuropil. The second order neuropils of the principal eyes are connected to the arcuate body, whereas the second order neuropils of the secondary eyes are linked to the mushroom body. However, eye size and visual fields are considerably different in jumping spiders. We explored the principal- and secondary eye visual pathways of the jumping spiderMarpissa muscosa. We found that the connectivity of the principal eye pathway is the same as inC. salei, while there are differences in the secondary eye pathways. InM. muscosa,all secondary eyes are connected to their own first order visual neuropils. The first order visual neuropils of the anterior lateral and posterior lateral eyes are further connected with two second order visual neuropils, whereas the posterior median eyes lack second order visual neuropils and their axons project only to the arcuate body. This suggests that the posterior median eyes probably do not serve movement detection inM. muscosa.Furthermore, the second order visual neuropil (L2) inMarpissa muscosapotentially integrates information from the secondary eyes and might thus enable faster movement decisions.