bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Sexual Risk Behaviors Among Persons With HIV After Release From the Criminal Justice System
Authors: Biondi Breanne E , Frank Cynthia , Horn Brady P , Springer Sandra A 
Published: September 2019

AbstractBackgroundHIV prevalence is 3 times greater for those in the criminal justice system than the general population, with an assumed increase in sexual risk behaviors (SRBs) postrelease. HIV viral suppression impacts HIV transmission; however, studies of SRBs among persons with HIV leaving the criminal justice system are limited, and no studies have examined viral suppression in relation to SRBs in persons leaving the criminal justice system.MethodsData were examined from 2 double-blind placebo-controlled trials of extended-release naltrexone among persons with HIV and alcohol use or opioid use disorder. Participants self-reported sexual activity, including number of sexual partners, sex type, and condom use. HIV viral suppression was evaluated prerelease and at 6 months.ResultsThirty days before incarceration, 60% reported having sex compared with 41% and 46%, respectively, at months 1 and 6 postrelease. The number of sex partners and sexual intercourse events decreased from pre-incarceration to months 1 and 6 postrelease. Condom use increased but was not statistically significant. Of the 11 (9.7%) who reported having sex without a condom 1 month postrelease, only 2 did not have viral suppression (VS; HIV VL &lt;200 copies/mL), whereas the 7 (6.5%) who reported SRBs at 6 months all had VS.ConclusionsAfter release, SRBs decreased, and among those who reported SRBs, most were virally suppressed, and thus risk of transmitting HIV was low.
Feeding sows during the transition period—is a gestation diet, a simple transition diet, or a lactation diet the best choice?1
Authors: Pedersen Trine Friis , van Vliet Sophie , Bruun Thomas Sønderby , Theil Peter Kappel 
Published: September 2019

Abstract
Three experiments were carried out to study whether a gestation diet, a simple transition diet, or a lactation diet is the best choice in late gestation and when sows preferably should be transferred to a high crude protein (CP) lactation diet. In experiment 1, 35 sows were fed either a gestation diet (12.1% CP), a lactation diet (15.9% CP), or a 50/50 mix (simple transition diet; 14.0% CP) from 6 d before parturition until parturition, to study the impact on farrowing and colostrum performance. In experiment 2, 90 sows were studied from 6 d before parturition until weaning at day 24 and they were fed one of five strategies: a gestation diet until day 3 or day 10 of lactation (strategy 1 and 2) and then lactation diet; a simple transition diet until day 3 or day 10 (strategy 3 and 4) and then lactation diet; or a lactation diet throughout the study (strategy 5). In experiment 3, 124 sows were fed strategy 1 or 5. Sows were weighed and back fat (BF) scanned when entering the farrowing unit and at day 2, 10, 17, and 24. Piglets were weighed at birth and after 24 h, and colostrum production was studied (experiment 1). Litter weight at day 2, 10, 17, and 24 was recorded, milk and blood samples were collected weekly and sow fat and protein mobilization, and balances of energy, N, and Lys were calculated from day 3 to 10 of lactation (experiment 2). Total- and live born piglets, and frequencies of stillbirth and piglet diarrhea were recorded (experiment 3). Feeding sows a gestation diet, a simple transition diet, or a lactation diet showed no evidence of effects on colostrum production or farrowing process (experiments 1 and 3) or lactation performance (experiments 2 and 3). Compared to previous studies, sows had a poor milk yield. Plasma urea was elevated (P &lt; 0.001) indicating CP oversupply prior to parturition in sows fed the lactation diet as compared with the two other diets. According to calculated balances, all dietary strategies supplied insufficient amounts of N and Lys from day 3 to 10, indicating that the best choice is to feed sows with a high CP lactation diet from parturition and onwards. Primiparous sows had a higher plasma insulin concentration (P &lt; 0.01), lower colostrum yield (P &lt; 0.01), and higher frequency of piglet diarrhea (P &lt; 0.001) than multiparous sows. In conclusion, in our conditions (high CP in gestation diet; poor milk yield; restricted feeding in early lactation), sow performance was not compromised by the dietary strategies, but results indicate that primiparous and multiparous sows should be fed differently.
Dinoroseobacter shibaeouter membrane vesicles are enriched for the chromosome dimer resolution sitedif
Authors: Wang Hui , Beier Nicole , Bödeker Christian , Sztajer Helena , Henke Petra , Neumann-Schaal Meina , Mansky Johannes , Rohde Manfred , Overmann Jörg , Kucklick Martin , Engelmann Susanne , Tomasch Jürgen , Wagner-Döbler Irene 
Published: September 2019

AbstractOuter membrane vesicles (OMVs) of Gram-negative bacteria have key roles in pathogenesis. However, little is known about their biogenesis and cargo in marine bacteria. InDinoroseobacter shibae,a marine member of theRhodobacteraceae, OMVs were produced throughout exponential growth, and DNA could be detected by fluorescence microscopy inside appr. 65% of vesicles. Single cell analysis using time-lapse microscopy showed that individual cells secreted multiple OMVs, preferentially at the septum during cell division. OMVs were enriched for saturated fatty acids, thus their secretion likely increases the fluidity of the membrane of the releasing cell locally. DNA was isolated from the vesicle lumen and sequenced; it was up to 40fold enriched for the region around the terminus of replication (ter). Within this region, the peak of coverage of vesicle DNA was located atdif,a conserved 28 bp palindromic sequence required for binding of the site specific tyrosine recombinases XerCD which are activated by the divisome protein FtsK immediately prior to septum formation. Some of the most abundant proteins of the vesicle proteome were predicted to be required for direct interaction with peptidoglycan during cell division. Single cell analysis, electron microscopy, proteome and DNA cargo show that constitutive OMV secretion inD. shibaeoccurs mainly prior to septum formation. The footprint of the FtsK/XerCD molecular machinery which resolves chromosome dimers suggests a novel highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of this type of vesicles.
Highly efficient and specific genome editing in human cells with paired CRISPR-Cas9 nickase ribonucleoproteins
Authors: Lamberth Jacob , Daley Laura , Natarajan Pachai , Khoruzhenko Stanislav , Becker Nurit , Taglicht Daniel , Davis Gregory D. , Ji Qingzhou 
Published: September 2019

ABSTRACTCRISPR technology has opened up many diverse genome editing possibilities in human somatic cells, but has been limited in the therapeutic realm by both potential off-target effects and low genome modification efficiencies. Recent advancements to combat these limitations include delivering Cas9 nucleases directly to cells as highly purified ribonucleoproteins (RNPs) instead of the conventional plasmid DNA and RNA-based approaches. Here, we extend RNP-based delivery in cell culture to a less characterized CRISPR format which implements paired Cas9 nickases. The use of paired nickase Cas9 RNP system, combined with a GMP-compliant non-viral delivery technology, enables editing in human cells with high specificity and high efficiency, a development that opens up the technology for further exploration into a more therapeutic role.
fCite: a fractional citation tool to quantify an individual’s scientific research output
Authors: Kozlowski Lukasz Pawel 
Published: September 2019

ABSTRACTHere, I present the fCite web service (fcite.org) a tool for the in-depth analysis of an individual’s scientific research output. While multiple existing tools (e.g., Google Scholar, iCite, Microsoft Academic) focus on the total number of citations and the H-index, I propose the analysis of the research output by considering multiple metrics to provide greater insight into a scientist’s multifaceted profile. The most distinguishing feature of fCite is its ability to calculate fractional scores for most of the metrics currently in use. Thanks to the division of citations (and RCR scores) by the number of authors, the tool provides a more detailed analysis of a scholar’s portfolio. fCite is based on PUBMED data (~18 million publications), and the statistics are calculated with respect to ORCID data (~600,000 user profiles).
Bird Song Learning is Mutually Beneficial for Tutee and Tutor
Authors: Beecher Michael D. , Akçay Çağlar , Campbell S. Elizabeth 
Published: September 2019

AbstractSong learning is generally assumed to be beneficial for a young songbird, but merely incidental, without costs or benefits, for the older song ‘tutors’. In the present study we contrast two mutually exclusive hypotheses about the tutor/tutee relationship: (1) that it is cooperative, or at least mutually tolerant, with tutor and tutee mutually benefiting from their relationship,vs.(2) that it is competitive, with tutor and tutee competing over territory, so that one or the other suffers negative fitness consequences of their relationship. In a field study of three consecutive cohorts of song sparrows (Melospiza melodia) we determined the older bird (primary tutor) from whom the young bird (tutee) learned most of his songs, and how long tutee and primary tutor survived subsequently. We found that the more songs a tutee learns from his primary tutor, the longer their mutual survival on their respective territories. This study provides the first evidence of a mutual benefit of bird song learning and teaching in nature.
Exaiptasia diaphanafrom the Great Barrier Reef: a valuable resource for coral symbiosis research
Authors: Dungan Ashley M. , Hartman Leon , Tortorelli Giada , Belderok Roy , Lamb Annika M. , Pisan Lynn , McFadden Geoffrey I. , Blackall Linda L. , van Oppen Madeleine J. H. 
Published: September 2019

AbstractThe sea anemone,Exaiptasia diaphana, commonly known asExaiptasia pallidaorAiptasia pallida, has become increasingly popular as a model for cnidarian-microbiome symbiosis studies due to its relatively rapid growth, ability to reproduce sexually and asexually, and symbiosis with diverse prokaryotes and the same microalgal symbionts (family Symbiodiniaceae) as its coral relatives. ClonalE. diaphanastrains from Hawaii, the Atlantic Ocean, and Red Sea are now established for use in research. Here, we introduce Great Barrier Reef (GBR)-sourcedE. diaphanastrains as additions to the model repertoire. Sequencing of the 18S rRNA gene confirmed the anemones to beE. diaphanawhile genome-wide single nucleotide polymorphism analysis revealed four distinct genotypes. Based onExaiptasia-specific inter-simple sequence repeat (ISSR)-derived sequence characterized amplified region (SCAR) marker and gene loci data, these fourE. diaphanagenotypes are distributed across several divergent phylogenetic clades with no clear phylogeographical pattern. The GBRE. diaphanagenotypes comprised three females and one male, which all hostBreviolum minutumas their homologous Symbiodiniaceae endosymbiont. When acclimating to an increase in light levels from 12 to 28 μmol photons m-2s-1, the genotypes exhibited significant variation in maximum quantum yield of Symbiodiniaceae photosystem II and Symbiodiniaceae cell density. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes makes these animals representative of globalE. diaphanadiversity and thus excellent model organisms. The addition of these GBR strains to the worldwideE. diaphanacollection will contribute to cnidarian symbiosis research, particularly in relation to the climate resilience of coral reefs.
B cells rapidly target antigen and surface-derived MHCII into peripheral degradative compartments
Authors: Hernández-Pérez S , Vainio M , Kuokkanen E , Sustar V , Petrov P , Fórsten S , Paavola V , Rajala J , Awoniyi LO , Sarapulov AV , Vihinen H , Jokitalo E , Bruckbauer A , Mattila PK 
Published: September 2019

AbstractIn order to mount high-affinity antibody responses, B cells internalise specific antigens and process them into peptides loaded onto MHCII for presentation to Thcells. While the biochemical principles of antigen processing and MHCII loading have been well dissected, how the endosomal vesicle system is wired to enable these specific functions remains much less studied. Here, we performed a systematic microscopy-based analysis of antigen trafficking in B cells to reveal its route to the MHCII peptide-loading compartment (MIIC). Surprisingly, we detected fast targeting of internalised antigen into peripheral acidic compartments that possessed the hallmarks of MIIC and also showed degradative capacity. In these vesicles, internalised antigen converged rapidly with membrane-derived MHCII and partially overlapped with Cathepsin-S and H2-M, both required for peptide loading. These early compartments appeared heterogenous and atypical as they contained a mixture of both early and late markers, indicating specialized endosomal route. Together, our data suggests that, in addition to previously-reported perinuclear late endosomal MIICs, antigen processing and peptide loading could start already in these specialized early peripheral acidic vesicles (eMIIC) to support fast peptide-MHCII presentation.
Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease
Authors: Wegrzyn Agnieszka B. , Herzog Katharina , Gerding Albert , Kwiatkowski Marcel , Wolters Justina C. , Dolga Amalia M. , van Lint Alida E. M. , Wanders Ronald J. A. , Waterham Hans R. , Bakker Barbara M. 
Published: September 2019

ABSTRACTRefsum disease is an inborn error of metabolism that is characterised by a defect in peroxisomal α-oxidation of the branched-chain fatty acid phytanic acid. The disorder presents with late-onset progressive retinitis pigmentosa and polyneuropathy and can be diagnosed biochemically by elevated levels of phytanic acid in plasma and tissues of patients. To date, no cure exists for Refsum disease, but phytanic acid levels in patients can be reduced by plasmapheresis and a strict diet.In this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction. We used transcriptomics (available via GEO database with identifier GSE138379), metabolomics, and proteomics data (available via ProteomeXchange with identifier PXD015518), which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.Our model correctly represents the metabolism of phytanic acid and displays fibroblast-specific metabolic functions. Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 53 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism. Ultimately, these insights in metabolic changes may provide leads for pathophysiology and therapy.
BrainNET: Inference of brain network topology using Machine Learning
Authors: Murugesan Gowtham Krishnan , Ganesh Chandan , Nalawade Sahil , Davenport Elizabeth M , Wagner Ben , Hwa Kim Won , Maldjian Joseph A. 
Published: September 2019

AbstractObjectiveTo develop a new fMRI network inference method, BrainNET, that utilizes an efficient machine learning algorithm to quantify contributions of various regions of interests (ROIs) in the brain to a specific ROI.MethodsBrainNET is based on Extremely Randomized Trees (ERT) to estimate network topology from fMRI data and modified to generate an adjacency matrix representing brain network topology, without reliance on arbitrary thresholds. Open source simulated fMRI data of fifty subjects in twenty-eight different simulations under various confounding conditions with known ground truth was used to validate the method. Performance was compared with correlation and partial correlation (PC). The real-world performance was then evaluated in a publicly available Attention-deficit/hyperactivity disorder (ADHD) dataset including 134 Typically Developing Children (mean age: 12.03, males: 83), 75 ADHD Inattentive (mean age: 11.46, males: 56) and 93 ADHD Combined (mean age: 11.86, males: 77) subjects. Network topologies in ADHD were inferred using BrainNET, correlation, and PC. Graph metrics were extracted to determine differences between the ADHD groups.ResultsBrainNET demonstrated excellent performance across all simulations and varying confounders in identifying true presence of connections. In the ADHD dataset, BrainNET was able to identify significant changes (p< 0.05) in graph metrics between groups. No significant changes in graph metrics between ADHD groups was identified using correlation and PC.
Do Walking Muscle Synergies Influence Propensity of Severe Slipping?
Authors: Nazifi Mohammad Moein , Beschorner Kurt , Hur Pilwon 
Published: September 2019

AbstractSlipping is frequently responsible for falling injuries. Preventing slips, and more importantly severe slips, is of importance in fall prevention. Our previous study characterized mild slipping and severe slipping by the analysis of muscle synergies. Significant discrepancies in motor control of slipping have been observed between mild and severe slippers. We are further interested in whether differences exist in baseline motor control patterns between persons who experience mild and severe slips when exposed to a slippery contaminant. This study investigated walking with a muscle synergy approach to detect if walking muscle synergies differ between groups experiencing different slip severities. Twenty healthy young adults (8 mild slippers and 12 severe slippers) participated in this study and their muscle synergies of walking were extracted. Muscle synergy analysis showed that mild slippers had a higher contribution of hamstring and quadriceps during walking while severe slippers had increased contribution of tibialis group. This study provides novel information that may contribute to identifying diagnostic techniques for identifying persons or populations with a high risk of fall based on their walking patterns.
Secondary Motor Cortex Transforms Spatial Information into Planned Action During Navigation
Authors: Olson Jacob M. , Li Jamie , Montgomery Sarah E. , Nitz Douglas A. 
Published: September 2019

AbstractFluid navigation requires constant updating of planned movements to adapt to evolving obstacles and goals. A neural substrate for navigation demands spatial and environmental information and the ability to effect actions through efferents. Secondary motor cortex is a prime candidate for this role given its interconnectivity with association cortices that encode spatial relationships and its projection to primary motor cortex. Here we report that secondary motor cortex neurons robustly encode both planned and current left/right turning actions across multiple turn locations in a multi-route navigational task. Comparisons within a common statistical framework reveal that secondary motor cortex neurons differentiate contextual factors including environmental position, route, action sequence, orientation, and choice availability. Despite significant modulation by context, action planning and execution are the dominant output signals of secondary motor cortex neurons. These results identify secondary motor cortex as a structure integrating environmental context toward the updating of planned movements.
Analysing plasma membrane asymmetry of lipid organisation by fluorescence lifetime and correlation spectroscopy
Authors: Gupta Anjali , Korte Thomas , Herrmann Andreas , Wohland Thorsten 
Published: September 2019

ABSTRACTA fundamental feature of a eukaryotic cell membrane is the asymmetric arrangement of lipids in the two leaflets. A cell invests significant energy to maintain this asymmetry and utilizes it to regulate important biological processes such as apoptosis and vesiculation. Here, we employ fluorescence lifetime imaging microscopy (FLIM) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS) to differentiate the dynamics and organization of the exofacial and cytoplasmic leaflet of live mammalian cells. We characterize the biophysical properties of fluorescent analogues of phosphatidylcholine (PC), sphingomyelin (SM) and phosphatidylserine (PS) in two mammalian cell membranes. Due to their specific transverse membrane distribution, these probes allow leaflet specific investigation of the plasma membrane. We compare the results with regard to the different temporal and spatial resolution of the methods. Fluorescence lifetimes of fluorescent lipid analogues were found to be in a characteristic range for the liquid ordered phase in the outer leaflet and liquid disordered phase in the inner leaflet. The observation of a more fluid inner leaflet is supported by free diffusion in the inner leaflet with high average diffusion coefficients. The liquid ordered phase in the outer leaflet is accompanied by slower diffusion and diffusion with intermittent transient trapping. Our results show that the combination of FLIM and ITIR-FCS with specific fluorescent lipid analogues provides a powerful tool to investigate lateral and trans-bilayer characteristics of plasma membrane in live cells.Abstract Figure
The signal and the noise - characteristics of antisense RNA in complex microbial communities
Authors: Michaelsen Thomas Yssing , Brandt Jakob , Singleton Caitlin , Kirkegaard Rasmus Hansen , Segata Nicola , Albertsen Mads 
Published: September 2019

AbstractHigh-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With the onset of metatranscriptomics, it is now possible to interrogate the transcriptome of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic datasets contain a rich suite of additional information which is just beginning to be explored. In this minireview we discuss the different computational strategies for handling antisense expression in metatranscriptomic samples and highlight their potentially detrimental effects on downstream analysis and interpretation. We also surveyed the antisense transcriptome of multiple genomes and metagenome-assembled genomes (MAGs) from five different datasets and found high variability in the level of antisense transcription for individual species which were consistent across samples. Importantly, we tested the hypothesis that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from a compounded effect of both random, biological and technical factors. Antisense transcription can provide a rich set of information, from technical details about data quality to novel insight into the biology of complex microbial communities.Key pointsSeveral fundamentally different approaches are used to handle antisense RNAPrevalence of antisense RNA is highly variable between communities, genomes, and genes.Antisense RNA is likely an opaque mixture of technical, biological and random effects