bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basic determinants of child growth in sub-Saharan Africa: cross-sectional survey analysis of positive deviants in poor households
Authors: Amugsi Dickson A. , Dimbuene Zacharie T. 
Published: September 2019

AbstractBackgroundChildhood malnutrition is a significant public health problem confronting countries across the globe. Nonetheless, recent evidence suggests a downward trend in undernutrition among children globally. Despite the progress made at the global level, sub-Saharan Africa did not experience significant improvement in the past decades. The objective of this study was to investigate the basic determinants associated with linear growth among children under 5 years living in poor households.MethodsThe study used nationally representative cross-sectional survey data from Ghana, Kenya, Democratic Republic of Congo (DRC), Nigeria and Mozambique. The participants are children aged 0–59 months (N=24,264) living in poor households. The DHS obtained information on children through face-to-face interviews with mothers. The height of the children was also measured and used to compute the height-for-age Z-scores (HAZ). In this study, HAZ is categorised into HAZ>-2 standard deviations (SD) (not stunted/better growth) and HAZ<-2 SD (stunted/poor growth).ResultsA unit change in maternal years of education was associated with increased odds of better growth among children living in poor households in DRC [adjusted odds ratio (aOR)= 1.03, 95% CI=1.01,1.07)], Ghana (aOR=1.06, 95% CI=1.01,1.11), Kenya (aOR=1.03, 95% CI= 1.01, 1.05) and Nigeria (aOR=1.08, 95%=1.06,1.10). Maternal antenatal attendance of at least four visits was associated positively with better child growth in DRC (aOR=1.32, 95% CI=1.05, 1.67) and Ghana (aOR=1.67, 95% CI=1.19, 2.33). In Ghana, Mozambique and DRC, breastfeeding was associated significantly with the likelihood of better linear growth when only socio-demographic correlates were included in the models but disappeared after the inclusion of child-level covariates. In Nigeria, normal maternal weight was associated with increased odds (aOR=1.24, 95% CI=1.08, 1.43) of positive growth among children living in poor households, so was overweight (aOR=1.51, 95% CI= 1.24, 1.83). In all the countries except Ghana, child biological factors such as sex and age were associated with reduced odds of better growth.ConclusionsThe socio-demographic factors included in this analysis have the potential to promote linear growth of children under 5 years living in poor households. Interventions aimed at fostering linear growth among children living in poverty should target at enhancing these factors.
Secrets of the hospital underbelly: patterns of abundance of antimicrobial resistance genes in hospital wastewater vary by specific antimicrobial and bacterial family
Authors: Perry Meghan R. , Lepper Hannah C. , McNally Luke , Wee Bryan A. , Munk Patrick , Warr Amanda , Moore Barbara , Kalima Pota , Philip Carol , de Roda Husman Ana Maria , Aarestrup Frank M. , Woolhouse Mark , van Bunnik Bram A.D. 
Published: September 2019

ABSTRACTBackgroundHospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater.MethodsSewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates.ResultsMicrobiota and ARG composition varied between collection points and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, P=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06 - 1.16, P<0.001). Furthermore, analysing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage (carbapenem rate ratio (RR) 1.91, 95% confidence intervals (CI) 1.01 – 3.72, P=0.07, and vancomycin RR 10.25, CI 2.32 – 49.10, P<0.01). Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance (odds ratio (OR) 1.62, CI 1.33 – 2.00, P<0.001, and OR 1.65, CI 1.21 – 2.30, P=0.006 respectively).ConclusionsWe found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.
Noise-Assisted MEMD-Based Phase-Connectivity Analysis to Personalize Closed-Loop DBS Therapy in Epilepsy Patients
Authors: Farahmand Sina , Sobayo Tiwalade , Mogul David J. 
Published: September 2019

AbstractDeep brain stimulation (DBS) is a treatment that has been explored for controlling seizures in patients with intractable epilepsy. Many clinical and pre-clinical studies using DBS therapy determine stimulation parameters through trial and error. The same stimulation parameters are often applied to the whole cohort, which consequently produces mixed results of responders and non-responders. In this paper, an adaptive non-linear analytical methodology is proposed to extract stimulation frequency and location(s) from endogenous brain dynamics of epilepsy patients, using phase-synchrony and phase-connectivity analysis, as seizures evolve. The proposed analytical method was applied to seizures recorded using depth electrodes implanted in hippocampus and amygdala in three patients. A reduction in phase-synchrony was observed in all patients around seizure onset. However, phase-synchrony started to gradually increase from mid-ictal and achieved its maximum level at seizure termination. This result suggests that hyper-synchronization of the epileptic network may be a crucial mechanism by which the brain naturally terminates seizure. Stimulation frequency and locations that matched the network phase-synchrony at seizure termination were extracted using phase-connectivity analysis. One patient with temporal lobe epilepsy (TLE) had a stimulation frequency ∼15 Hz with the stimulation locations confined to the hippocampus. The other two patients with extra-temporal lobe epilepsy (ETE) had stimulation frequency ∼90 Hz with at least one stimulation location outside of hippocampus. These results suggest that DBS parameters should vary based on the patient’s underlying pathology. The proposed methodology provides an algorithm for tuning DBS parameters for individual patients in an effort to increase the clinical efficacy of the therapy.
kinfitr: Reproducible PET Pharmacokinetic Modelling in R
Authors: Matheson Granville J. 
Published: September 2019

ABSTRACTQuantification of Positron Emission Tomography (PET) data is performed using pharmacokinetic models. There exist many models for describing this data, each of which may describe the data better or worse depending on the specific application, and there are both theoretical, practical and empirical reasons to select any one model over another. As such, effective PET modelling requires a high degree of flexibility, while effective communication of all steps taken through scientific publications is not always feasible. Reproducible research practices address these concerns, in that researchers share analysis code, and data if possible, such that all steps are recorded, allowing an independent researcher to reproduce the results and assess their veracity. In this article, I presentkinfitr: a software package for performing kinetic modelling using the open-source R language, in a reproducible manner. The R community has a strong culture of reproducible research, and the language consists of numerous tools which allow both effective and easy sharing and communication of analysis code. The package is written in such a way as to allow the analyst the freedom to use and rapidly exchange between approaches, and to assess goodness of fit, with 14 different kinetic models currently implemented using a consistent syntax, as well as tools for working with the data. By providing open-source tools for kinetic modelling, including documentation and examples, it is hoped that this will extend access to methodology for research groups lacking software engineering expertise, as well as simplify and thereby encourage transparent and reproducible reporting.
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
Authors: Chen Yuhao , Brook Thomas C. , Soe Cho Zin , O’Neill Ian , Alcon-Giner Cristina , Leelastwattanagul Onnicha , Phillips Sarah , Caim Shabhonam , Clarke Paul , Hall Lindsay J. , Hoyles Lesley 
Published: September 2019

ABSTRACTKlebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis, nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella as previous studies have focussed on recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for isolates. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. ‘healthy’) encoded multiple β-lactamases, which may prove problematic when defining treatment regimens for NEC or sepsis, and suggest ‘healthy’ preterm infants contribute to the resistome. No difference was observed between isolates recovered from ‘healthy’ and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Using a curated dataset of Klebsiella oxytoca, K. grimontii and K. michiganensis whole-genome sequences, metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut, and highlight the importance of refined analyses with curated sequence databases when studying closely related species present in metagenomic data.
Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage
Authors: Janissen Richard , Eslami-Mossallam Behrouz , Artsimovitch Irina , Depken Martin , Dekker Nynke H. 
Published: September 2019

ABSTRACTPausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examined the E. coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identified, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We further identified two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlie elongation-rate switching, and RNA cleavage deficiency that underpins different long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.
Trypsin treatment unlocks barrier for zoonotic coronaviruses infection
Authors: Menachery Vineet D. , Dinnon Kenneth H. , Yount Boyd L. , McAnarney Eileen T. , Gralinski Lisa E. , Hale Andrew , Graham Rachel L. , Scobey Trevor , Anthony Simon J. , Wang Lingshu , Graham Barney , Randell Scott H. , Lipkin W. Ian , Baric Ralph S. 
Published: September 2019

AbstractTraditionally, the emergence of coronaviruses (CoVs) has been attributed to a gain in receptor binding in a new host. Our previous work with SARS-like viruses argued that bats already harbor CoVs with the ability to infect humans without adaptation. These results suggested that additional barriers limit the emergence of zoonotic CoV. In this work, we describe overcoming host restriction of two MERS-like bat CoVs using exogenous protease treatment. We found that the spike protein of PDF2180-CoV, a MERS-like virus found in a Ugandan bat, could mediate infection of Vero and human cells in the presence of exogenous trypsin. We subsequently show that the bat virus spike can mediate infection of human gut cells, but is unable to infect human lung cells. Using receptor-blocking antibodies, we show that infection with the PDF2180 spike does not require MERS-CoV receptor DPP4 and antibodies developed against the MERS spike receptor-binding domain and S2 portion are ineffective in neutralizing the PDF2180 chimera. Finally, we found that addition of exogenous trypsin also rescues replication of HKU5-CoV, a second MERS-like group 2c CoV. Together, these results indicate that proteolytic cleavage of the spike, not receptor binding, is the primary infection barrier for these two group 2c CoVs. Coupled with receptor binding, proteolytic activation offers a new parameter to evaluate emergence potential of CoVs and offer a means to recover previously unrecoverable zoonotic CoV strains.ImportanceOverall, our studies demonstrate that proteolytic cleavage is the primary barrier to infection for a subset of zoonotic coronaviruses. Moving forward, the results argue that both receptor binding and proteolytic cleavage of the spike are critical factors that must be considered for evaluating the emergence potential and risk posed by zoonotic coronaviruses. In addition, the findings also offer a novel means to recover previously uncultivable zoonotic coronavirus strains and argue that other tissues, including the digestive tract, could be a site for future coronavirus emergence events in humans.
Phylogenetic, sequence and structural analysis of Insulin superfamily proteins reveals an indelible link between evolution and structure-function relationship
Authors: S. Shrilakshmi , Kundapura Shankar V. , Dey Debayan , Kulal Ananda , Ramagopal Udupi A. 
Published: September 2019

AbstractThe insulin superfamily proteins (ISPs), in particular, insulin, IGFs and relaxins are key modulators of animal physiology. They are known to have evolved from the same ancestral gene and have diverged into proteins with varied sequences and distinct functions, but maintain a similar structural architecture stabilized by highly conserved disulphide bridges. A recent surge of sequence data and the structures of these proteins prompted a need for a comprehensive analysis which connects the evolution of these sequences in the light of available functional and structural information and their interaction with cognate receptors. This study reveals a) unusually high sequence conservation of IGFs (>90%), which has never been reported before. In fact, it was interesting to observe that the functional domains (excluding signal peptide) of human, horse, pig and Ord’s kangaroo rat are 100% identical. (b) an updated definition of the signature motif of the relaxin family (c) a non-canonical C-peptide cleavage site in a few killifish insulin sequences and so on. We also provide a structure-based rationale for such conservation by introducing a concept called binding partners imposed evolutionary constraints. Furthermore, the high conservation of IGFs appears to represent a classic case of resistance to sequence diversity exerted by physiologically important interactions with multiple partners. Furthermore, we propose a probable mechanism for C-peptide cleavage in killifish insulin sequences.
Insertions ofP{lacW}andP{EP}artificial transposons on the chromosomal divisions ofDrosophila melanogasterare not randomly distributed
Authors: Marian Bologa Alexandru , Cristian Ghita Iulian , Cristian Ratiu Attila , Al. Alexandru Ecovoiu 
Published: September 2019

AbstractHerein we describe the distribution of P{lacW} and P{EP} artificial transposons in the genome of Drosophila melanogaster. A total number of 5,560 P{lacW} and 3,786 P{EP} insertions available on FlyBase were extracted from this database and ordered according to the chromosomal regions they hit. Comparative bioinformatics analysis revealed that the insertion’s patterns are similar for P{lacW} and P{EP}. The two patterns are significantly correlated for chromosomes X, 2L, 2R and 3L, but not for 3R.Fourier analysis revealed a periodic behaviour in the distribution of insertions, which approximates insertional hotspots. Our results raise questions concerning if and how the local chromosomal landscape affects the insertion patterns of different but related transposons.
Miocene and Pliocene speciation ofRussulasubsectionRoseinaein temperate forests of eastern North America
Authors: Looney Brian P. , Adamčík Slavomír , Matheny P. Brandon 
Published: September 2019

AbstractNumerous lineages of mushroom-forming fungi have been subject to bursts of diversification throughout their evolutionary history, events that can impact our ability to infer well-resolved phylogenies. However, groups that have undergone quick genetic change may have the highest adaptive potential. As the second largest genus of mushroom-forming fungi,Russulaprovides an excellent model for studying hyper-diversification and processes in evolution that drives it. This study focuses on the morphologically defined group –RussulasubsectionRoseinae. Species hypotheses based on morphological differentiation and multi-locus phylogenetic analyses are tested in theRoseinaeusing different applications of the multi-species coalescent model. Based on this combined approach, we recognize fourteen species inRoseinaeincluding the Albida and wholly novel Magnarosea clades. Reconstruction of biogeographic and host association history suggest that parapatric speciation in refugia during glacial cycles of the Pleistocene drove diversification within theRoseinae, which is found to have a Laurasian distribution with an evolutionary origin in the Appalachian Mountains of eastern North America. Finally, we detect jump dispersal at a continental scale that has driven diversification since the most recent glacial cycles.
Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene
Authors: Qiao Wenjing , Puentes Jácome Luz A. , Tang Xianjin , Lomheim Line , Yang Minqing Ivy , Gaspard Sarra , Avanzi Ingrid Regina , Wu Jichun , Ye Shujun , Edwards Elizabeth A. 
Published: September 2019

AbstractIntensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient γ-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3µM/day to ∼12µM/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from β (0.77±0.15), α (0.55±0.09), γ (0.13±0.02) to δ (0.06±0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance ofPelobacterandDehalobacter, especially in the α-HCH and δ-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.
Mate-finding dispersal reduces local mate limitation and sex bias in dispersal
Authors: Mishra Abhishek , Tung Sudipta , Sruti V.R. Shree , Srivathsa Sahana V. , Dey Sutirth 
Published: September 2019

AbstractSex-biased dispersal (SBD) often skews the local sex ratio in a population. This can result in a shortage of mates for individuals of the less-dispersive sex. Such mate limitation can lead to Allee effects in populations that are small or undergoing range expansion, consequently affecting their survival, growth, stability and invasion speed.Theory predicts that mate shortage can lead to either an increase or a decrease in the dispersal of the less-dispersive sex. However, neither of these predictions have been empirically validated.To investigate how SBD-induced mate limitation affects dispersal of the less-dispersive sex, we used Drosophila melanogaster populations with varying dispersal propensities. To rule out any mate-independent density effects, we examined the behavioral plasticity of dispersal in presence of mates as well as same-sex individuals with differential dispersal capabilities.In the presence of high-dispersive mates, the dispersal of both male and female individuals was significantly increased. However, the magnitude of this increase was much larger in males than in females, indicating that the former show greater mate-finding dispersal. Moreover, the dispersal of either sex did not change when dispersing alongside high- or low-dispersive individuals of the same sex. This suggested that the observed plasticity in dispersal was indeed due to mate-finding dispersal, and not mate-independent density effects.Strong mate-finding dispersal can diminish the magnitude of sex bias in dispersal. This can modulate the evolutionary processes that shape range expansions and invasions, depending on the population size. In small populations, mate-finding dispersal can ameliorate Allee effects. However, in large populations, it can dilute the effects of spatial sorting.