bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
Authors: Duchêne David A , Tong K Jun , Foster Charles S P , Duchêne Sebastián , Lanfear Robert , Ho Simon Y W 
Published: December 2019

AbstractEvolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths, but form subsets that vary in their overall tree lengths. These models had substantially better statistical support than models that assume identical branch lengths across gene trees, or those in which genes form subsets with distinct branch-length patterns. We show using simulations and empirical data that the complexity of the branch-length model with the highest support depends on the length of the sequence alignment and on the numbers of taxa and loci in the data set. Our findings suggest that models in which branch lengths are proportionate between subsets have the highest statistical support under the conditions that are most commonly seen in practice. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.
Haemodialysis therapy and sustainable growth: a corporate experience in France
Authors: Bendine Georges , Autin Fabien , Fabre Bruno , Bardin Olivier , Rabasco François , Cabanel Jean-Marc , Chazot Charles 
Published: December 2019

AbstractIntroductionSustainable growth and environmental issues are currently a topic for all human activities, and dialysis represents a real challenge in this field because of high water and power consumption and the production of large amounts of care-related waste. In this article we describe data collection implemented in the NephroCare centres in France and the changes observed during a 13-year period regarding environmental parameters.MethodsMonthly data collection (eco-reporting) was implemented in NephroCare centres in France in 2005. It covers three topics designed as key performance indicators (KPIs): electricity and water consumption and care-related waste production expressed, respectively, as kilowatt-hour (kWh), litres (L) and kilograms per session. We report on the three action plans (2005–10, 2011–14 and 2015–18) and changes observed during this 13-year period.ResultsDuring the period, power and water consumption declined by 29.6% (from 23.1 to 16.26 kWh/session) and 52% (from 801 to 382 L/session), respectively. At the same time, the yearly number of dialysis sessions has increased from 169 335 to 399 336. The sources of savings came both from improvements in the dialysis technology (dialysis machines and water treatment systems) and from updating and remodelling of the dialysis unit equipment and buildings. The care-related waste decreased from 1.8 to 1.1 kg because of regular staff training and the retrofiltration system, allowing the voiding of the remaining saline solution after dialysis. These savings have been estimated as equivalent to 102 440 tons of carbon dioxide.DiscussionImplementation of KPIs and their regular monitoring by trained staff to evaluate water and power consumption and the reduction of care-related water production are essential to implement actions to reduce the impact of dialysis on the environment. These data show the importance of water treatment and dialysis technology to decrease water and power consumption and the production of care-related waste as well as upgrading or remodelling of buildings housing dialysis units. Other measures are discussed, including the reuse of rejected water by reverse osmosis, as well as behavioural changes that are needed to reach sustainable development of dialysis.ConclusionThe first step to reach ‘green’ dialysis is to collect precise information from defined KPIs. This is the only way to design action plans to reduce the impact of dialysis therapy on the environment. Beyond this, the nephrology community must be sensitized to this challenge to be proactive and to anticipate future regulations.
Characterization of Nicotine Salts in 23 Electronic Cigarette Refill Liquids
Authors: Harvanko Arit M , Havel Christopher M , Jacob Peyton , Benowitz Neal L 
Published: December 2019

Abstract

Introduction
Many electronic cigarette manufacturers have begun offering liquids containing “nicotine salts,” which are formed when an acid is mixed in a solution with free-base nicotine. Type of salt could play a significant role in the abuse liability of electronic cigarette liquids. As a first step to understanding nicotine salts, this study sought to identify the types of acids present in 23 commercially available electronic cigarette liquids.

Aims and Methods
Twenty-three electronic cigarette liquids advertised as containing nicotine salts were purchased for analysis. These liquids were tested for the presence of 11 different organic acids that were deemed likely to be used in a nicotine salt formulation. Liquids were analyzed using a combination of liquid chromatography–mass spectrometry and gas chromatography–mass spectrometry methods, then compared to authentic acid standards for identification.

Results
Six of the 11 possible acids were identified in the liquids, from most to least common: lactic, benzoic, levulinic, salicyclic, malic, and tartaric acid. Acid(s) could not be identified in one of the liquids. Though most liquids contained only one type, three of the liquids contained multiple acids.

Conclusions
These data demonstrate that several types of salts/acids are currently being used in electronic cigarette liquids. The type and concentration of salt(s) used in these liquids may differentially alter sensations in the throat and upper airway, and overall pharmacology of the aerosols by altering liquid pH and from flavor and sensory characteristics of the acids themselves.

Implications
This study demonstrates that at least six different types of acids are being used to create the nicotine salts in electronic cigarette liquids, with the acids lactic, benzoic, and levulinic being the most frequently identified. Identification of these acids can serve as the foundation for future research to determine if type of nicotine salt alters pharmacological and toxicological effects of electronic cigarettes.
La gestion de la douleur et de l’anxiété chez les enfants lors de brèves interventions diagnostiques et thérapeutiques
Authors: Trottier Evelyne D , Doré-Bergeron Marie-Joëlle , Chauvin-Kimoff Laurel , Baerg Krista , Ali Samina 
Published: December 2019

RésuméLes interventions médicales courantes utilisées pour évaluer et traiter les patients peuvent causer une douleur et une anxiété marquées. Les cliniciens devraient adopter une approche de base pour limiter la douleur et l’anxiété chez les enfants, notamment à l’égard des interventions diagnostiques et thérapeutiques fréquentes. Le présent document de principes est axé sur les nourrissons, les enfants et les adolescents qui subissent des interventions médicales courantes mineures, mais douloureuses. Il n’aborde pas les soins prodigués à l’unité de soins intensifs néonatale. Les auteurs examinent des stratégies simples et fondées sur des données probantes pour gérer la douleur et l’anxiété et donnent des conseils pour en faire un volet essentiel de la pratique clinique. Les professionnels de la santé sont invités à utiliser des façons de procéder peu invasives et, lorsque les interventions douloureuses sont inévitables, à combiner des stratégies simples de réduction de la douleur et de l’anxiété pour améliorer l’expérience du patient, du parent et du professionnel de la santé. Les administrateurs de la santé sont encouragés à créer des politiques pour leurs établissements, à améliorer la formation et l’accès aux lignes directrices, à créer des environnements propices aux enfants et aux adolescents, à s’assurer de la disponibilité du personnel, de l’équipement et des agents pharmacologiques appropriés et à effectuer des contrôles de qualité pour garantir une gestion de la douleur optimale.
Global climate change and health in Canadian children
Authors: Buka Irena , Shea Katherine M 
Published: December 2019

Abstract
Climate change is a reality. Numerous expert authorities warn of the critical need to undertake and adapt environmental efforts to protect human health. Climate change is accelerating, and countries in high latitudes, such as Canada, are experiencing climate change more directly and, for some end points, more dramatically than mid- and low-latitude countries. Children are vulnerable to climate change health effects, and physicians and other health care providers need to be ready to identify, manage, and prevent climate change-related health hazards. This practice point highlights specific, climate change-related threats to the health of children and youth, and provides resources for health care providers. Climate challenges and their health impacts on children are described, based on key Canadian reports and scientifically referenced information. Enhanced awareness of the immediate and longer-term health effects of climate change on children allows physicians and other health care providers to counsel families and practice more effectively.
Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum
Authors: Li Zhen , Hua Xiuting , Zhong Weiming , Yuan Yuan , Wang Yongjun , Wang Zhengchao , Ming Ray , Zhang Jisen 
Published: December 2019

Abstract
WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs’ expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs’ expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.
Abatacept in rheumatoid arthritis and the risk of cancer: a world observational post-marketing study
Authors: de Germay Sibylle , Bagheri Haleh , Despas Fabien , Rousseau Vanessa , Montastruc François 
Published: December 2019

Abstract

Objectives
We aimed to investigate whether abatacept used in patients for RA was associated with an increased risk of reporting overall cancer and specific cancers, including breast, lung, lymphoma, melanoma and non-melanoma skin cancer when compared with other biologic DMARDs (bDMARDs).

Methods
We performed an observational study within VigiBase, the World Health Organization’s global database of individual case safety reports, from 2007 to 2017 to compare the cases of cancer reported in RA patients exposed to abatacept with those reported in RA patients exposed to other bDMARDs. We conducted disproportionality analyses allowing the estimation of reporting odds ratios (RORs) with 95% CIs of the exposure odds among spontaneous reporting of cancers to the exposure odds among other reported adverse effects.

Results
We identified 15 846 adverse effects reported in RA patients who received abatacept and 290 568 adverse effects reported in RA patients treated with other bDMARDs. Compared with other bDMARDs, the use of abatacept was not associated with an increased risk of reporting cancer overall [ROR 0.98 (95% CI 0.91, 1.05)]. Analyses by specific cancer sites showed a significantly increased ROR for melanoma [1.58 (95% CI 1.17, 2.08)], but not for other specific cancer sites.

Conclusion
Compared with other bDMARDs, exposure to abatacept in RA patients was only significantly associated with an increased risk of reporting melanoma. This increased risk is consistent with the properties of abatacept (CTLA-4 agonist) since it has an opposite action than ipilimumab, an antibody that blocks CTLA-4 and is approved for the treatment of malignant melanoma.

Trial registration
ClinicalTrials.gov (http://clinicaltrials.gov), NCT03980639.
Comparison of methods to construct a genetic risk score for prediction of rheumatoid arthritis in the population-based Nord-Trøndelag Health Study, Norway
Authors: Rostami S , Hoff M , Brown M A , Hveem K , Videm V 
Published: December 2019

Abstract

Objectives
To evaluate selection methods among published single-nucleotide polymorphisms (SNPs) associated with RA to construct predictive genetic risk scores (GRSs) in a population-based setting.

Methods
The Nord-Trøndelag Health (HUNT) Study is a prospective cohort study among the whole adult population of northern Trøndelag, Norway. Participants in HUNT2 (1995–1997) and HUNT3 (2006–2008) were included (489 RA cases, 61 584 controls). The initial SNP selection from relevant genome-wide studies included 269 SNPs from 30 studies. Following different selection criteria, SNPs were weighted by published odds ratios. The sum of each person’s carriage of all weighted susceptibility variants was calculated for each GRS.

Results
The best-fitting risk score included 27 SNPs [weighted genetic risk score 27 (wGRS27)] and was identified using P-value selection criterion ≤5 × 10−8, the largest possible SNP selection without high linkage disequilibrium (r2 &lt; 0.8), and lasso regression to select for positive coefficients. In a logistic regression model adjusted for gender, age and ever smoking, wGRS27 was associated with RA [odds ratio 1.86 (95% CI 1.71, 2.04) for each s.d. increase, P &lt; 0.001]. The AUC was 0.76 (95% CI 0.74, 0.78). The positive and negative predictive values were 1.6% and 99.7%, respectively, and the positive predictive value was not improved in sensitivity analyses subselecting participants to illustrate settings with increased RA prevalences. Other schemes selected more SNPs but resulted in GRSs with lower predictive ability.

Conclusion
Constructing a wGRS based on a smaller selection of informative SNPs improved predictive ability. Even with a relatively high AUC, the low PPV illustrates that there was a large overlap in risk variants among RA patients and controls, precluding clinical usefulness.
ELECTRON EYE-LENS OPERATIONAL DOSE COEFFICIENTS
Authors: Dubeau J , Sun J 
Published: December 2019

Abstract
In 2012, the International Commission on Radiological Protection issued a recommendation for a reduced annual eye-lens dose limit in the face of mounting evidence of the risk of cataract induction. This led to worldwide research efforts in various areas including the dose simulation in realistic eye-models, the production of dosimeters and the elaboration of protection and operation fluence to eye-lens dose coefficients. In this last case, much efforts have been expanded with regards to photon operational coefficients for Hp (3) but much less for electron radiation. In this work, Hp (3) coefficients for electrons are presented following simulations using MCNP and compared to those that are available in the literature. It is found that, at energies of 1 MeV and less, Hp (3) coefficients depend strongly on the selected electron transport options and on the dose tally volume. The effect of these differences is demonstrated for two beta emitters.
An Ecological Systems Framework for Professional Resilience in Social Work Practice
Authors: Newell Jason M 
Published: December 2019

AbstractThe cumulative effects of chronic work-related stress pervasively and persistently affect the well-being of the human services workforce. As a preventive measure, the ongoing commitment to self-care strategies and resources is essential in maintaining a healthy and resilient professional quality of life. This article describes a holistic approach to cultivating professional resilience through the ongoing practice of self-care. A model for self-care using an ecological systems framework with activities across the biological, interpersonal, organizational, familial, peer-related, spiritual, and recreational aspects of the biopsychosocial self is proposed. Within this model, emphasis is placed on the role of compassion satisfaction and vicarious resilience as key components to fostering meaningful and rewarding careers for social workers.
The prevalence and risk factors for human Brucella species infection in a cross-sectional survey of a rural population in Punjab, India
Authors: Mangtani Punam , Berry Isha , Beauvais Wendy , Holt Hannah R , Kulashri Amit , Bharti Satinder , Sagar Vivek , Nguipdop-Djomo Patrick , Bedi Jasbir , Kaur Manmeet , Guitian Javier , McGiven John , Kaur Paviter , Singh Gill Jatinder P , Grover Gagandeep Singh , Kumar Rajesh 
Published: December 2019

Abstract

Background
Brucellosis is an important neglected zoonosis. Effective cattle vaccines are available but are infrequently used in India, where rural households commonly own one or two cattle as sources of protein and income. We assessed the prevalence of infection and risk factors in humans.

Methods
We conducted a cross-sectional sero-survey in randomly selected individuals in 60 villages in Punjab. Infection prevalence was assessed by positive Rose Bengal testing or immunoglobulin G enzyme-linked immunosorbent assay. Risk factors were adjusted for potential confounding using multivariable analyses.

Results
Of the 1927 subjects who were approached, 93% agreed to participate. Age-standardised prevalence for Brucella infection was 2.24% (95% confidence interval [CI] 1.61 to 3.11). More than 60% of households kept cattle and 10% assisted with calving or abortions. Nearly all individuals consumed boiled cow/buffalo milk from their own or neighbours' cattle and 3.3% consumed goat’s milk. There was a 2.18 times increased odds (95% CI 0.96 to 4.95) of infection with calving/abortions and a 4.26 times increased odds (95% CI 1.33 to 13.6) with goat’s milk but not bovine milk consumption.

Conclusions
An association with calving/abortions and goat’s milk consumption was seen. Brucella vaccination of household livestock would reduce the risk to humans in such settings. Additional measures include biosecurity training around calving/abortions, education to boil all milk and for healthcare workers to test for brucellosis.
The Role of Historical Christian Missions in the Location of World Bank Aid in Africa
Authors: Alpino Matteo , Hammersmark Eivind Moe 
Published: December 2019

Abstract
This article documents a positive and sizable correlation between the location of historical Christian missions and the allocation of present-day World Bank aid at the grid-cell level in Africa. The correlation is robust to an extensive set of geographical and historical control variables that predict settlement of missions. The study finds no correlation with aid effectiveness, as measured by project ratings and survey-based development indicators. Mission areas display a different political aid cycle than other areas, whereby new projects are less likely to arrive in years with new presidents. Hence, political connections between mission areas and central governments could be one likely explanation for the correlation between missions and aid.
Mitophagy contributes to endothelial adaptation to simulated microgravity
Authors: Locatelli Laura , Cazzaniga Alessandra , De Palma Clara , Castiglioni Sara , Maier Jeanette A. M. 
Published: December 2019

AbstractExposure to real or simulated microgravity is sensed as a stress by mammalian cells, which activate a complex adaptive response. In human primary endothelial cells, we have recently shown the sequential intervention of various stress proteins which are crucial to prevent apoptosis and maintain cell function. We here demonstrate that mitophagy contributes to endothelial adaptation to gravitational unloading. After 4 and 10 d of exposure to simulated microgravity in the rotating wall vessel, the amount of BCL2 interacting protein 3, a marker of mitophagy, is increased and, in parallel, mitochondrial content, oxygen consumption, and maximal respiratory capacity are reduced, suggesting the acquisition of a thrifty phenotype to meet the novel metabolic challenges generated by gravitational unloading. Moreover, we suggest that microgravity induced‐disorganization of the actin cytoskeleton triggers mitophagy, thus creating a connection between cytoskeletal dynamics and mitochondrial content upon gravitational unloading.
DDIT4 gene expression is switched on by a new HDAC4 function in ataxia telangiectasia
Authors: Ricci Anastasia , Galluzzi Luca , Magnani Mauro , Menotta Michele 
Published: December 2019

AbstractAtaxia telangiectasia (AT) is a rare, severe, and ineluctably progressive multisystemic neurodegenerative disease. Histone deacetylase 4 (HDAC4) nuclear accumulation has been related to neurodegeneration in AT. Since treatment with glucocorticoid analogues has been shown to improve the neurological symptoms that characterize this syndrome, the effects of dexamethasone on HDAC4 were investigated. In this paper, we describe a novel nonepigenetic function of HDAC4 induced by dexamethasone, through which it can directly modulate HIF‐1a activity and promote the upregulation of the DDIT4 gene and protein expression. This new HDAC4 transcription regulation mechanism leads to a positive effect on autophagic flux, an AT‐compromised biological pathway. This signaling was specifically induced by dexamethasone only in AT cell lines and can contribute in explaining the positive effects of dexamethasone observed in AT‐treated patients.