bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Report: Medication Sharing Is Rare Among African HIV-1 Serodiscordant Couples Enrolled in an Efficacy Trial of Oral Pre-exposure Prophylaxis (PrEP) for HIV-1 Prevention
Authors: Thomson Kerry A. , Haberer Jessica E. , Marzinke Mark A. , Mujugira Andrew , Hendrix Craig W. , Celum Connie , Ndase Patrick , Ronald Allan , Bangsberg David R. , Baeten Jared M. ,   for the Partners PrEP Study Team
Published: March 2017

Abstract:
Sharing of pre-exposure prophylaxis (PrEP) medications is a concern for PrEP implementation. For HIV-1 serodiscordant couples, sharing may undermine the HIV-1 prevention benefit and also cause antiretroviral resistance if taken by HIV-1 infected partners. Within a PrEP efficacy trial among HIV-1 serodiscordant couples, we assessed the occurrence of PrEP sharing by self-report and plasma tenofovir concentrations in HIV-1 infected partners. PrEP sharing was self-reported at <0.01% of visits, and 0%–1.6% of randomly selected and 0% of purposively selected specimens from HIV-1 infected participants had detectable tenofovir concentrations (median: 66.5 ng/mL, range: 1.3–292 ng/mL). PrEP sharing within HIV-1 serodiscordant couples was extremely rare.
Safety of Tenofovir Disoproxil Fumarate–Based Antiretroviral Therapy Regimens in Pregnancy for HIV-Infected Women and Their Infants: A Systematic Review and Meta-Analysis
Authors: Nachega Jean B. , Uthman Olalekan A. , Mofenson Lynne M. , Anderson Jean R. , Kanters Steve , Renaud Francoise , Ford Nathan , Essajee Shaffiq , Doherty Meg C. , Mills Edward J. 
Published: March 2017

Background:
There are limited data on adverse effects of tenofovir disoproxil fumarate (TDF)-based antiretroviral therapy (ART) on pregnant women and their infants.

Methods:
We conducted a systematic review of studies published between January 1980 and January 2017 that compared adverse outcomes in HIV-infected women receiving TDF- vs. non–TDF-based ART during pregnancy. The risk ratio (RR) for associations was pooled using a fixed-effects model.

Results:
Seventeen studies met the study inclusion criteria. We found that the rate of preterm (<37 weeks gestation) delivery (RR = 0.90, 95% confidence interval [CI]: 0.81 to 0.99, I2 = 59%) and stillbirth (RR = 0.60, 95% CI: 0.43 to 0.84, I2 = 72.0%) were significantly lower in women exposed (vs. not) to TDF-based ART regimen. We found no increased risk in maternal severe (grade 3) or potentially life-threatening (grade 4) adverse events (RR = 0.62; 95% CI: 0.30 to 1.29), miscarriage (RR = 1.09; 95% CI: 0.80 to 1.48), very preterm (<34 weeks gestation) delivery (RR = 1.08, 95% CI: 0.72 to 1.62), small for gestational age (RR = 0.87, 95% CI: 0.67 to 1.13), low birth weight (RR = 0.91; 95% CI: 0.80 to 1.04), very low birth weight (RR = 3.18; 95% CI: 0.65 to 15.63), congenital anomalies (RR = 1.03; 95% CI: 0.83 to 1.28), infant adverse outcomes or infant mortality (age >14 days) (RR = 0.65; 95% CI: 0.23 to 1.85), but increased neonatal mortality (age <14 days) risk (RR = 5.64, 95% CI: 1.70 to 18.79) with TDR-based ART exposure. No differences were found for anthropomorphic parameters at birth; one study reported minor differences in z-scores for length and head circumference at age 1 year.

Conclusions:
TDF-based ART in pregnancy seems generally safe for women and their infants. However, data remain limited and further studies are needed, particularly to assess neonatal mortality and infant growth/bone effects.
Correlation of Bowel Wall Thickening Seen Using Computerized Tomography With Colonoscopies: A Preliminary Study
Authors: Isik Arda , Soyturk Mehmet , Süleyman Sakir , Firat Deniz , Peker Kemal , Yilmaz İsmayil , Celebi Fehmi 
Published: March 2017

Purpose:
Bowel wall thickening (BWT) is a common finding in abdominal computerized tomography imaging (CTi). The purpose of the present study was a prospective assessment and management of patients who have BWT in abdominal CTi.

Materials and Methods:
This study was conducted between January 2012 and July 2014 at Erzincan University Hospital, Turkey, with 64 patients who were admitted to the emergency and general surgery department. All of the patients had received colonoscopies due to BWT seen in abdominal CTi.

Results:
Twenty-three (36%) female and 41 (64%) male patients were included in the study. The mean age was 56.2 years (range, 14 to 84 y). The positive predictive value of CTi for BWT was 87.5%. The positive predictive value of a CTi diagnosis of the disease according to a radiologist’s report was 78.1%. Common pathologies detected by colonoscopy included neoplasia and inflammatory bowel disease.

Conclusions:
Diagnosis of BWT by abdominal CTi reveals pathologies in many cases. Colonoscopies will be helpful in the differential diagnosis.
Transmission dynamics: critical questions and challenges
Authors: Antonovics Janis 
Published: March 2017

This article overviews the dynamics of disease transmission in one-host–one-parasite systems. Transmission is the result of interacting host and pathogen processes, encapsulated with the environment in a ‘transmission triangle’. Multiple transmission modes and their epidemiological consequences are often not understood because the direct measurement of transmission is difficult. However, its different components can be analysed using nonlinear transmission functions, contact matrices and networks. A particular challenge is to develop such functions for spatially extended systems. This is illustrated for vector transmission where a ‘perception kernel’ approach is developed that incorporates vector behaviour in response to host spacing. A major challenge is understanding the relative merits of the large number of approaches to quantifying transmission. The evolution of transmission mode itself has been a rather neglected topic, but is important in the context of understanding disease emergence and genetic variation in pathogens. Disease impacts many biological processes such as community stability, the evolution of sex and speciation, yet the importance of different transmission modes in these processes is not understood. Broader approaches and ideas to disease transmission are important in the public health realm for combating newly emerging infections.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Growth rate, transmission mode and virulence in human pathogens
Authors: Leggett Helen C. , Cornwallis Charlie K. , Buckling Angus , West Stuart A. 
Published: March 2017

The harm that pathogens cause to hosts during infection, termed virulence, varies across species from negligible to a high likelihood of rapid death. Classic theory for the evolution of virulence is based on a trade-off between pathogen growth, transmission and host survival, which predicts that higher within-host growth causes increased transmission and higher virulence. However, using data from 61 human pathogens, we found the opposite correlation to the expected positive correlation between pathogen growth rate and virulence. We found that (i) slower growing pathogens are significantly more virulent than faster growing pathogens, (ii) inhaled pathogens and pathogens that infect via skin wounds are significantly more virulent than pathogens that are ingested, but (iii) there is no correlation between symptoms of infection that aid transmission (such as diarrhoea and coughing) and virulence. Overall, our results emphasize how virulence can be influenced by mechanistic life-history details, especially transmission mode, that determine how parasites infect and exploit their hosts.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Uncertain links in host–parasite networks: lessons for parasite transmission in a multi-host system
Authors: Walker Josephine G. , Plein Michaela , Morgan Eric R. , Vesk Peter A. 
Published: March 2017

For many parasites, the full set of hosts that are susceptible to infection is not known, and this could lead to a bias in estimates of transmission. We used counts of individual adult parasites from historical parasitology studies in southern Africa to map a bipartite network of the nematode parasites of herbivore hosts that occur in Botswana. Bipartite networks are used in community ecology to represent interactions across trophic levels. We used a Bayesian hierarchical model to predict the full set of host–parasite interactions from existing data on parasitic gastrointestinal nematodes of wild and domestic ungulates given assumptions about the distribution of parasite counts within hosts, while accounting for the relative uncertainty of less sampled species. We used network metrics to assess the difference between the observed and predicted networks, and to explore the connections between hosts via their shared parasites using a host–host unipartite network projected from the bipartite network. The model predicts a large number of missing links and identifies red hartebeest, giraffe and steenbok as the hosts that have the most uncertainty in parasite diversity. Further, the unipartite network reveals clusters of herbivores that have a high degree of parasite sharing, and these clusters correspond closely with phylogenetic distance rather than with the wild/domestic boundary. These results provide a basis for predicting the risk of cross-species transmission of nematode parasites in areas where livestock and wildlife share grazing land.
This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics
Authors: Beattie Kylie A. , Hill Adam P. , Bardenet Rémi , Cui Yi , Vandenberg Jamie I. , Gavaghan David J. , de Boer Teun P. , Mirams Gary R. 
Published: March 2017

AbstractUnderstanding the roles of ion currents is crucial to predict the action of pharmaceuticals and mutations in different scenarios, and thereby to guide clinical interventions in the heart, brain and other electrophysiological systems. Our ability to predict how ion currents contribute to cellular electrophysiology is in turn critically dependent on our characterisation of ion channel kinetics — the voltage-dependent rates of transition between open, closed and inactivated channel states. We present a new method for rapidly exploring and characterising ion channel kinetics, applying it to the hERG potassium channel as an example, with the aim of generating a quantitatively predictive representation of the ion current. We fit a mathematical model to currents evoked by a novel 8 second sinusoidal voltage clamp in CHO cells over-expressing hERG1a. The model is then used to predict over 5 minutes of recordings in the same cell in response to further protocols: a series of traditional square step voltage clamps, and also a novel voltage clamp comprised of a collection of physiologically-relevant action potentials. We demonstrate that we can make predictive cell-specific models that outperform the use of averaged data from a number of different cells, and thereby examine which changes in gating are responsible for cell-cell variability in current kinetics. Our technique allows rapid collection of consistent and high quality data, from single cells, and produces more predictive mathematical ion channel models than traditional approaches.Table of Contents CategoryTechniques for Physiology1Key PointsIon current kinetics are commonly represented by current-voltage relationships, time-constant voltage relationships, and subsequently mathematical models fitted to these. These experiments take substantial time which means they are rarely performed in the same cell.Rather than traditional square-wave voltage clamps, we fit a model to the current evoked by a novel sum-of-sinusoids voltage clamp that is only 8 seconds long.Short protocols that can be performed multiple times within a single cell will offer many new opportunities to measure how ion current kinetics are affected by changing conditions.The new model predicts the current under traditional square-wave protocols well, with better predictions of underlying currents than literature models. The current under a novel physiologically-relevant series of action potential clamps is predicted extremely well.The short sinusoidal protocols allow a model to be fully fitted to individual cells, allowing us to examine cell-cell variability in current kinetics for the first time.
Visualizing Long-Term Single-Molecule Dynamics in vivo by Stochastic Protein Labeling
Authors: Liu Hui , Dong Peng , Ioannou Maria S. , Li Li , Shea Jamien , Pasolli H. Amalia , Grimm Jonathan , Rivlin Pat , Lavis Luke D. , Koyama Minoru , Liu Zhe 
Published: March 2017

ABSTRACTOur ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic titration range of >10,000 fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by 2 orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact zebrafish. We found axon initial segment utilizes a ‘waterfall’ mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially-restricted sub-nuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics in vivo.
Pyroxasulfone resistance inLolium rigidumconferred by enhanced metabolic capacity
Authors: Busi R , Porri A , Gaines TA , Powles SB 
Published: March 2017

Author ContributionsRB and AP designed and performed the experiments. RB, AP, TG, SP wrote the manuscript.One sentence summaryThis study provides novel insight into herbicide resistance conferred by GST-based detoxification to allow proactive intervention to minimize weed resistance evolution.AbstractThe evolution of herbicide-resistant weed populations in response to synthetic herbicide selective pressure is threatening safe weed control practices achieved by these molecules. In Australia multiple-resistant populations of annual ryegrass (Lolium rigidum) are effectively controlled by soil-applied herbicides which provide adequate weed control.In this study we define the mechanistic basis of the experimentally-evolved resistance to the soil-applied herbicide pyroxasulfone in aL. rigidumpopulation. TLC and HPLC-MS provide biochemical confirmation that pyroxasulfone resistance is metabolism-based with identification and quantification of pyroxasulfone metabolites formedviaa glutathione conjugation pathway in pyroxasulfone-resistantL. rigidumplants. The observed over-expression of two putative resistance-endowingGSTgenes is consistent with pyroxasulfone-resistance in parental plants (P6) and positively correlated to pyroxasulfone resistance in F1pair-cross progenies. Thus, a major detoxification mechanism involves glutathione conjugation to pyroxasulfone andGSTover-expression in pyroxasulfone-resistantL. rigidumplants. The definition of the genetic basis of metabolic resistance in weeds can be a first crucial step towards chemical means to reverse resistance and improve long-term weed resistance management.
Pediatric Sarcoma Data Forms a Unique Cluster Measured via the Earth Mover’s Distance
Authors: Chen Yongxin , Dela Cruz Filemon , Sandhu Romeil , Kung Andrew , Mundi Prabhjot , Deasy Joseph , Tannenbaum Allen 
Published: March 2017

AbstractIn this note, we combined pediatric sarcoma data from Columbia University with adult sarcoma data collected from TCGA, in order to see if one can automatically discern a unique pediatric cluster in the combined data set. Using a novel clustering pipeline based on optimal transport theory, this turned out to be the case. The overall methodology may find uses for the classification of data from other biological networking problems.
Automated assembly of a reference taxonomy for phylogenetic data synthesis
Authors: Rees Jonathan A. , Cranston Karen 
Published: March 2017

AbstractTaxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive supertrees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.
Deletion of the short N-terminal extension in OCP reveals the main site for the FRP binding
Authors: Sluchanko Nikolai N. , Slonimskiy Yury B. , Moldenhauer Marcus , Friedrich Thomas , Maksimov Eugene G. 
Published: March 2017

AbstractThe photoactive Orange Carotenoid Protein (OCP) plays a central role in cyanobacterial photoprotection. Photoconversion entails significant structural rearrangements in OCP required for its binding to the phycobilisome to induce excitation energy dissipation, whereas the fluorescence recovery protein (FRP) is required for OCP detachment and restoration of phycobilisome fluorescence. Although key to understanding the whole reversible mechanism of photoprotection, the FRP binding site on OCP has been representing challenge since the discovery of FRP in 2010 and is currently unknown. OCP comprises two structural domains organized into a compact basic orange form due to specific protein-chromophore and inter-domain protein-protein interactions and interacts with FRP tightly only when photoactivated. As an important stabilizing element in the orange OCP, the short αA-helix within the N-terminal extension (NTE) binds to OCP’s C-terminal domain (CTD), but unfolds upon photoactivation and interferes with phycobilisome binding. By using an alloy of biochemical and biophysical techniques, here we demonstrate that the NTE shares specific structural and functional similarities with FRP and discover the main site of OCP-FRP interactions in the OCP-CTD.
Interaction between maleic acid andN-R-furfurylamines: crystal structure of 2-methyl-N-[(5-phenylfuran-2-yl)methyl]propan-2-aminium (2Z)-3-carboxyacrylate andN-[(5-iodofuran-2-yl)methyl]-2-methylpropan-2-aminium (2Z)-3-carboxyprop-2-enoate
Authors: Kvyatkovskaya Elisaveta A. , Zaytsev Vladimir P. , Zubkov Fedor I. , Dorovatovskii Pavel V. , Zubavichus Yan V. , Khrustalev Victor N. 
Published: March 2017

The title molecular salts, C15H20NO+·C4H3O4−, (I), and C9H15INO+·C4H3O4−, (II), have very similar molecular geometries for both cation and anion. The anions of both (I) and (II) are practically planar (r.m.s. deviations = 0.062 and 0.072 Å, respectively) and adopt a rare symmetrical geometry with the hydroxy H atom approximately equidistant from the two O atoms. In their crystals, the cations and anions in both (I) and (II) form tight ionic pairsviastrong N—H...O hydrogen bonds, with a roughly perpendicular disposition of the anion to the furan ring of the cation. This ion-pair conformation appears to correlate with the lack of reactivity of these salts in [4 + 2] cycloaddition reactions. In the extended structures of (I) and (II), the ion pairs form hydrogen-bonded chains propagating along [010] and [001], respectively,viaN—H...O hydrogen bonds.
Improving the accuracy of time-harmonic FE simulations in induction heating applications
Authors: McMeekin Kevin , Sirois Frédéric , Tousignant Maxime , Bocher Philippe 
Published: March 2017

Purpose
Surface heat treatment by induction heating (10-100 kHz) requires precise prediction and control of the depth of the induced phase transformation. This paper aims at identifying common issues with the measurement and modeling of magnetic properties used in induction heating simulations, and it proposes ways to improve the situation.

Design/methodology/approach
In particular, it is demonstrated how intrinsic magnetic properties (i.e. the B-H curve) of a sample can change during the magnetic characterization process itself, due to involuntary annealing of the sample. Then, for a B-H curve that is supposed perfectly known, a comparison is performed between multiple models, each one representing the magnetic properties of steel in time-harmonic (TH) finite element method simulations. Finally, a new model called “power-equivalent model” is proposed. This model provides the best possible accuracy for a known nonlinear and hysteretic B-H curve used in TH simulations.

Findings
By carefully following the guidelines identified in this paper, reduction of errors in the range of 5-10 per cent can be achieved, both at the experimental and modeling levels. The new “power-equivalent model” proposed is also expected to be more generic than existing models.

Originality/value
This paper highlights common pitfalls in the measurement and modeling of magnetic properties, and suggests ways to improve the situation.
Improved Litz wire manufacture process using resonant power converter-based induction heating
Authors: Naval Alejandro , Sarnago Hector , Lope Ignacio , Lucia Oscar , Burdio José M. 
Published: March 2017

Purpose
Litz wire manufacturing using mechanical procedures presents several limitations regarding reliability and repeatability, especially when a small strand diameter is used. This paper aims to propose a power supply design for Litz wire manufacturing using a high-frequency high-performance resonant converter.

Design/methodology/approach
This paper proposes the design of a resonant power supply for induction heating specially designed to tackle with the challenge of heating Litz wires quickly.

Findings
The proposed converter enables the removal of the isolating coating from the Litz wire through induction heating, improving significantly the manufacturing process.

Originality/value
The proposed converter improves significantly the manufacturing process of Litz wire through induction heating, with economic and reliability benefits.