bluuebunny/crossref_metadata_2025_split huggingface dataset:
miqoGraph: Fitting admixture graphs using mixed-integer quadratic optimization
Authors: Yan Julia , Patterson Nick , Narasimhan Vagheesh 
Published: October 2019

AbstractAdmixture graphs represent the genetic relationship between a set of populations through splits, drift and admixture. In this paper we present the Julia package miqoGraph, which uses mixed-integer quadratic optimization to fit topology, drift lengths, and admixture proportions simultaneously. Inference of topology is particularly powerful, with integer optimization automating what is usually an arduous manual process.Availabilityhttps://github.com/juliayyan/PhylogeneticTrees.jlContactjyyan@mit.edu
Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces?
Authors: Guillerme Thomas , Puttick Mark N. , Marcy Ariel E. , Weisbecker Vera 
Published: October 2019

AbstractMultidimensional analysis of traits are now a common toolkit in ecology and evolution and are based on trait-spaces in which each dimension summarise the observed trait combination (a morphospace or an ecospace). Observations of interest will typically occupy a subset of this trait-space, and researchers will apply one or more metrics to quantify the way in which organisms “inhabit” that trait-space. In macroevolution and ecology these metrics are referred to as disparity or dissimilarity metrics and can be generalised as space occupancy metrics. Researchers use these metrics to investigate how space occupancy changes through time, in relation to other groups of organisms, and in response to global environmental changes, such as global warming events or mass extinctions. However, the mathematical and biological meaning of most space occupancy metrics is vague with the majority of widely-used metrics lacking formal description.Here we propose a broad classification of space occupancy metrics into three categories that capture changes in volume, density, or position. We analyse the behaviour of 25 metrics to study changes in trait-space volume, density and position on a series of simulated and empirical datasets.We find no one metric describes all of trait-space but that some metrics are better at capturing certain aspects compared to other approaches and that their performance depends on both the trait-space and the hypothesis analysed. However, our results confirm the three broad categories (volume, density and position) and allow to relate changes in any of these categories to biological phenomena.Since the choice of space occupancy metric should be specific to the data and question at had, we introduced moms, a user-friendly tool based on a graphical interface that allows users to both visualise and measure changes space occupancy for any metric in simulated or imported trait-spaces. Users are also provided with tools to transform their data in space (e.g. contraction, displacement, etc.). This tool is designed to help researchers choose the right space occupancy metrics, given the properties of their trait-space and their biological question.
Sequoia: An interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets
Authors: Koonchanok Ratanond , Daulatabad Swapna Vidhur , Mir Quoseena , Reda Khairi , Janga Sarath Chandra 
Published: October 2019

AbstractSequoia is a visualization tool that allows biologists to explore characteristics of signals generated by the Oxford Nanopore Technologies (ONT) in detail. From Fast5 files generated by ONT, the tool displays relative similarities between signals using the dynamic time warping and the t-SNE algorithms. Raw signals can be visualized through mouse actions while particular signals of interest can also be exported as a CSV file for further analysis. Sequoia consists of two major components: the command-line back-end that performs necessary computations using Python and the front-end that displays the visualization through a web interface. Two datasets are used to conduct a case study in order to illustrate the usability of the tool.
A fungal arrestin protein contributes to cell cycle progression and pathogenesis
Authors: Telzrow Calla L. , Nichols Connie B. , Castro-Lopez Natalia , Wormley Floyd L. , Alspaugh J. Andrew 
Published: October 2019

ABSTRACTArrestins, a structurally specialized and functionally diverse group of proteins, are central regulators of adaptive cellular responses in eukaryotes. Previous studies on fungal arrestins have demonstrated their capacity to modulate diverse cellular processes through their adaptor functions, facilitating the localization and function of other proteins. However, the mechanisms by which arrestin-regulated processes are involved in fungal virulence remain unexplored. We have identified a small family of four arrestins - Ali1, Ali2, Ali3, and Ali4 - in the human fungal pathogenCryptococcus neoformans. Using complementary microscopy, proteomic, and reverse genetic techniques, we have defined a role for Ali1 as a novel contributor to cytokinesis, a fundamental cell cycle-associated process. We observed that Ali1 strongly interacts with proteins involved in lipid synthesis, and thatali1Δ mutant phenotypes are rescued by supplementation with lipid precursors that are used to build cellular membranes. From these data, we hypothesize that Ali1 contributes to cytokinesis by serving as an adaptor protein, facilitating the localization of enzymes that modify the plasma membrane during cell division, specifically the fatty acid synthases, Fas1 and Fas2. Finally, we assessed the contributions of theC. neoformansarrestin family to virulence, to better understand the mechanisms by which arrestin-regulated adaptive cellular responses influence fungal infection. We observed that theC. neoformansarrestin family contributes to virulence, and that the individual arrestin proteins likely fulfill distinct functions that are important for disease progression.IMPORTANCETo survive in unpredictable conditions, all organisms must adapt to stressors by regulating adaptive cellular responses. Arrestin proteins are conserved regulators of adaptive cellular responses in eukaryotes. Studies that have been limited to mammals and model fungi have demonstrated that disruption of arrestin-regulated pathways is detrimental for viability. The human fungal pathogenCryptococcus neoformanscauses more than 180,000 infection-related deaths annually, especially among immunocompromised patients. In addition to being genetically-tractable,C. neoformanshas a small arrestin family of four members, lending itself to a comprehensive characterization of its arrestin family. This study serves as a functional analysis of arrestins in a pathogen, particularly in the context of fungal fitness and virulence. We investigate the functions of one arrestin protein, Ali1, and define its novel contributions to cytokinesis. We additionally explore the virulence contributions of theC. neoformansarrestin family and find that they contribute to disease establishment and progression.
Ultra-high field imaging reveals increased whole brain connectivity underpins cognitive strategies that attenuate pain
Authors: Schulz Enrico , Stankewitz Anne , Winkler Anderson M , Irving Stephanie , Witkovsky Viktor , Tracey Irene 
Published: October 2019

ABSTRACTWe investigate how the attenuation of pain with cognitive interventions affects the strength of cortical connections by pursuing a whole brain approach. While receiving tonic cold pain, 20 healthy participants were asked to utilise three different pain attenuation strategies. During a 7T fMRI recording, participants were asked to rate their pain after each single trial. We related the trial-by-trial variability of the attenuation performance to the trial-by-trial functional connectivity of the cortical data.Across all conditions, we found that a higher performance of pain attenuation was predominantly associated with higher functional connectivity. Of note, we observed an association between low pain and high connectivity for regions that belong to the core areas of pain processing, i.e. the insular and cingulate cortices. For one of the cognitive strategies (safe place), the performance of pain attenuation was explained by diffusion tensor imaging metrics of increased white matter integrity.Impact StatementIn a single trial analysis, the more effective attempts to attenuate pain in three different conditions are associated with general higher functional connectivity across the entire brain.
The Effects of Leukocyte- and Platelet-Rich Plasma (L-Prp) and Pure Platelet-Rich Plasma (P-Prp) an a Rat Endometriosis Model
Authors: Anğın Ali Doğukan , Gün İsmet , Sakin Önder , Çıkman Muzaffer Seyhan , Pirioğlu Zehra Meltem , Kale Ahmet , Başak Kayhan , Kaygın Pınar , Oğuztüzün Serpil 
Published: October 2019

AbstractOur aim was to investigate the effect of platelet-rich plasma (PRP) derivatives, which can be produced from the patient’s own blood and have minimal side effects, on endometriosis. To the best of our knowledge, this is the first study in the literature that studies the relationship between PRP and endometriosis. Endometriosis foci were created in the first operation. In the second operation (30th day) groups were formed. Group 1 (n= 8) was administered saline, group 2 (n= 7) leukocyte- and platelet-rich plasma (L-PRP), and group 3 (n= 8) pure platelet-rich plasma (P-PRP). Group 4 (n= 10) was used to obtain PRP. In the last operation (60th day), the endometriotic foci were measured, and then excised. There was no statistically significant difference between the pre and post volumes of the endometriotic foci, between their volume differences and volume difference rates (p > .05). However, it was observed that existing implant volumes in all groups decreased statistically significantly within their own groups by the end of the experiment compared to the previous volumes (p < .05). When the implants were assessed through histopathological scoring in terms of edema, vascular congestion, inflammatory cell infiltration, hemorrhage, epithelial line, and hemosiderin accumulation and immunohistochemical staining in terms of VEGF, there was no significant difference in the comparison between the groups. Although L-PRP and P-PRP generated more reduction in the endometriosis foci, they did not create any statistical differences.
The protein translation machinery is expressed for maximal efficiency inEscherichia coli
Authors: Hu Xiao-Pan , Dourado Hugo , Lercher Martin J. 
Published: October 2019

AbstractProtein synthesis is the most expensive process in fast-growing bacteria1,2. The economic aspects of protein synthesis at the cellular level have been investigated by estimating ribosome activity3–5and the expression of ribosomes3,6, tRNA7–9, mRNA2, and elongation factors10,11. The observed growth-rate dependencies form the basis of powerful phenomenological bacterial growth laws5,12–16; however, a quantitative theory allowing us to understand these phenomena on the basis of fundamental biophysical and biochemical principles is currently lacking. Here, we show that the observed growth-rate dependence of the concentrations of ribosomes, tRNAs, mRNA, and elongation factors inEscherichia colican be predicted accurately by minimizing cellular costs in a detailed mathematical model of protein translation; the mechanistic model is only constrained by the physicochemical properties of the molecules and requires no parameter fitting. We approximate the costs of molecule species through their masses, justified by the observation that cellular dry mass per volume is roughly constant across growth rates17and hence represents a limited resource. Our results also account quantitatively for observed RNA/protein ratios and ribosome activities inE. coliacross diverse growth conditions, including antibiotic stresses. Our prediction of active and free ribosome abundance facilitates an estimate of the deactivated ribosome reserve14,18,19, which reaches almost 50% at the lowest growth rates. We conclude that the growth rate dependent composition ofE coli’s protein synthesis machinery is a consequence of natural selection for minimal total cost under physicochemical constraints, a paradigm that might generally be applied to the analysis of resource allocation in complex biological systems.
How flexible is tool use in Eurasian jays (Garrulus glandarius)?
Authors: Amodio Piero , Boeckle Markus , Jelbert Sarah A. , Ostoijc Ljerka , Clayton Nicola S. 
Published: October 2019

AbstractEurasian jays (Garrulus glandarius) do not habitually use tools, yet they can be trained to solve object-dropping tasks, i.e. to insert a tool into an apparatus to release a food reward. Previous research suggests the these jays can learn a preference toward functional tools – objects allowing to obtain a food reward placed inside an apparatus – according to their density (Cheke et al., 2011). However, it is not yet known whether they can also select functional tools (tool selectivity) according to other physical properties such as size and shape, and use different kinds of tools to solve a similar task. Here we conducted three object-dropping experiments aimed at exploring these abilities in Eurasian jays. In Experiment 1, jays tended to select large stones as tools irrespective of the diameter of the apparatus. However, jays progressively developed a preference for the small tool, which was functional with both the wide and the narrow apparatuses. In Experiment 2, only vertically-oriented long stones could fit into the narrow apparatus, whereas both long and round stones were functional with the wide apparatus. Jays showed a preference for the long stone and, with the narrow apparatus, tended to achieve the correct manipulation after one or more unsuccessful attempts. In Experiment 3, jays were able to use sticks and adopt a novel technique on the same object-dropping apparatus, thus providing the first evidence that Eurasian jays can use sticks as tools. Taken together, these results indicate that Eurasian jays may have limited tool selectivity abilities but nonetheless can use different kinds of tools to solve similar tasks.
Accounting and the business of sport: past, present and future
Authors: Andon Paul , Free Clinton 
Published: October 2019

Purpose
The purpose of this paper is to examine prominent issues and knowledge contributions from research exploring the nexus between accounting and the business of sport, overview the other papers presented in this AAAJ Special Issue and draw from this work to scope out future impactful research opportunities in this area.

Design/methodology/approach
A review and examination of the prior literature and the other papers published in this AAAJ Special Issue.

Findings
The paper identifies and summarises three key research themes in the extant literature: financial regulation and assurance; commercialisation and professionalism; and accountability and control. Then it draws from work within these research themes to set out four broad areas for future impactful research.

Research limitations/implications
The value of this paper rests with collating and synthesising several important research issues on the nexus between accounting (broadly defined) and the business of sport, and in prompting future extensions of this work through setting out areas for further innovative accounting research on sport.

Practical implications
The research examined in this paper and the future research avenues proposed are highly relevant to administrators and regulators in sport. They also offer important insights into matters of accounting, accountability, valuation and control more generally.

Originality/value
This paper adds to vibrant existing streams of research in the area by bringing together authors from different areas of accounting research for this AAAJ Special Issue. In scoping out an agenda for impactful research at the intersection of accounting and sport, this paper also draws attention to underexplored issues pertaining to the rise of integrity and accountability concerns in sport, strategic choices in financial regulation, valuation issues and practices and the rise of technology in sport.
Health education for deaf Romanian children: parents’ opinions
Authors: Ionescu Laura , Ursache Lacramioara , Nicolae Adelina , Conea Adriana , Potora Cristian , Stan Ovidiu , Lotrean Lucia Maria 
Published: October 2019

Purpose
The purpose of this paper is to focus on parents of children with hearing disabilities from Romania and has three objectives. First, it assesses their characteristics regarding use of communication technology. Second, it investigates their opinions regarding the importance of school-based education for healthy lifestyle promotion among their children. Third, it evaluates the availability for their involvement in educational activities using face-to-face approach and communication technology dedicated to helping parents to promote healthy lifestyle among their children, as well as factors which influence this availability.

Design/methodology/approach
The study was performed in October–November 2015 in two schools deserving children with hearing disabilities from North-West part of Romania. Anonymous questionnaire were filled in by 182 parents.

Findings
The majority of parents recognize the importance of school-based health education and more than 77 per cent totally agree that it should include issues regarding healthy nutrition, promotion of physical activity and smoking prevention. In total, 80.2 per cent of the parents declared that they are interested to participate in educational activities organized periodically at school and 66.5 per cent declared their interest in educational activities developed through communication technology in order to help them to stimulate the adoption of healthy lifestyle among their children. The availability was influenced by residence, educational level, understanding the importance of parents’ involvement, characteristics regarding the use of communication technology.

Originality/value
This represents the first study from Romania investigating the opinions and availability for their involvement with regard to school health education among parents of children with hearing deficiencies. The results have several implications for health education among children with hearing deficiencies and their parents.
Factors affecting the spatial pattern of nitrate contamination in Texas aquifers
Authors: Lotfata Aynaz , Ambinakudige Shrinidhi 
Published: October 2019

Purpose
The elevated level of nitrate in groundwater is a serious problem in Texas aquifers. To control and manage groundwater quality, the characterization of groundwater contamination and identification of the factors affecting the nitrate concentration of groundwater are significant. The purpose of this paper is to determine factors which have significant impacts on the elevated groundwater nitrate concentrations of the Southern High-Plains and the Edwards-Trinity aquifers.

Design/methodology/approach
The characterization of groundwater nitrate contamination was undertaken by analyzing the hydrochemical data of groundwater within a statistical framework. The multivariate statistical analysis (ordinary least square) and geographically weighted regression (GWR) models were used to study the relationship between groundwater nitrate contamination and land use of the study areas.

Findings
Results show groundwater nitrate contamination is typically due to an overapplication of N fertilizers to cotton in the Southern High-Plains aquifer and to grassland in the Edwards-Trinity aquifer. Adjusted R2 (0.45) explains variations of nitrate concentration by well-depth, cotton production, shrubland and grassland in the Edwards-Trinity aquifer. The results of an analysis of variations in N concentration with well depth for all 192 wells indicate that nitrate concentrations in water from wells in the Southern High-Plains and Edwards-Trinity aquifers tend to decrease with increasing well-depth.

Originality/value
In this study, the GWR model was built to identify nitrate concentration within a geographic framework to ensure sustainable use of groundwater, which is important for local management purposes. The analysis should include local spatial variations of elements such as hydrologic characteristics and the land use activities if groundwater nitrate contamination causes adverse effects on human and ecosystem health.
Use of the SF‐12 questionnaire to assess physical and mental health status in patients with psoriasis
Authors: Sampogna Francesca , Mastroeni Simona , Pallotta Sabatino , Fusari Roberta , Uras Claudia , Napolitano Monica , Abeni Damiano 
Published: October 2019

AbstractHealth‐related quality of life (HRQoL) in psoriasis patients is generally measured using disease‐ or dermatology‐specific questionnaires. Our objective was to use the generic 12‐item Short Form Health Survey (SF‐12) instrument to measure the physical and mental impact of psoriasis and to compare scores with those already published for different diseases. An observational study was conducted among mild‐to‐severe psoriasis outpatients. Health status was assessed by the SF‐12, which includes a physical (PCS) and a mental (MCS) scale. The 12‐item General Health Questionnaire (GHQ‐12) was used to assess the possible presence of depression or anxiety, and the Skindex‐17 to measure dermatology‐specific HRQoL. Statistical analyses were performed to estimate the association between physical and mental health status and demographic and clinical characteristics. The study population included 1592 patients. Psoriasis PCS scores were similar to the general population and to non‐severe diseases such as allergies, dermatitis, or back pain, while MCS mean scores were very similar to that of depression, and lower than those of all the other chronic conditions. Poor physical health was associated with female sex, older age, lower educational level, joint involvement, ≥2 comorbidities, moderate to very severe clinical status, GHQ‐12 score ≥4, and moderate to severe Skindex‐17 psychosocial scores. Poor mental health was associated with younger age (<30 years), GHQ ≥ 4, and severe Skindex‐17 psychosocial scores. In conclusion, a general health measure, such as the SF‐12, appears to be able to capture, in psoriasis patients, the burden of the disease both from a physical and a mental point of view.
Effects of climate change on pup growth and survival in a cooperative mammal, the meerkat
Authors: Van de Ven Tanja M. F. N. , Fuller Andrea , Clutton‐Brock Tim H. 
Published: October 2019

Abstract

Breeding systems in which group members help to raise the offspring of co‐members are associated with arid, unpredictable environments. Cooperative rearing may mitigate the effects of adverse environmental conditions on pup growth and survival. However, few studies have explored the relationship between environmental variation and breeding success, and the role of helpers.

Here, we show that reductions in the growth and survival of meerkat (Suricata suricatta) pups have been associated with increases in daily maximum air temperatures (Tmax) in the southern Kalahari over the last 20 years.

On days when Tmax was high, meerkat pups gained less body mass than on cooler days. Reductions in the diurnal body mass gain (ΔMb) of pups on hotter days were not a consequence of reductions in the frequency with which pups were fed by adults as feeding rate increased with Tmax, suggesting that the reductions in ΔMb by pups on hot days reflected a decrease in water content of the food items or an increased water and energy cost of thermoregulation.

Reductions in pup ΔMb on hot days were smaller in larger groups, in which helper‐to‐pup ratios were relatively high.

As increases in air temperature are predicted with climate change, further reductions in meerkat pup growth and survival seem inevitable.

A free Plain Language Summary can be found within the Supporting Information of this article.