bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronogram or phylogram for ancestral state estimation? Model‐fit statistics indicate the branch lengths underlying a binary character's evolution
Authors: Wilson Jeremy D. , Mongiardino Koch Nicolás , Ramírez Martín J. 
Published: April 2022

AbstractModern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (a) the effect of alternate branch lengths on ASE error and (b) whether phylogenetic signal statistics and/or model‐fit statistic can be used to select the branch lengths most correlated with a binary character.In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model‐fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model‐fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favourable for model optimization, and when shape differences between alternate phylogenies are greater.Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model‐fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model‐fit.
flexsdm: An r package for supporting a comprehensive and flexible species distribution modelling workflow
Authors: Velazco Santiago José Elías , Rose Miranda Brooke , de Andrade André Felipe Alves , Minoli Ignacio , Franklin Janet 
Published: April 2022

Abstract

Species distribution models (SDM) are widely used in diverse research areas because of their simple data requirements and application versatility. However, SDM outcomes are sensitive to data input and methodological choices. Such sensitivity and diverse applications mean that flexibility is necessary to create SDMs with tailored protocols for a given set of data and model use.

We introduce the r package flexsdm for supporting flexible species distribution modelling workflows. flexsdm functions and their arguments serve as building blocks to construct a specific modelling protocol for user's needs. The main flexsdm features are modelling flexibility, integration with other modelling tools, simplicity of the objects returned and function speed. As an illustration, we used flexsdm to define a complete workflow for California red fir Abies magnifica.

This package provides modelling flexibility by incorporating comprehensive tools structured in three steps: (a) The Pre‐modelling functions that prepare input, for example, sampling bias correction, sampling pseudo‐absences and background points, data partitioning, and reducing collinearity in predictors. (b) The Modelling functions allow fitting and evaluating different modelling approaches, including individual algorithms, tuned models, ensembles of small models and ensemble models. (c) The Post‐modelling functions include tools related to models' predictions, interpolation and overprediction correction.

Because flexsdm comprises a large part of the SDM process, from outlier detection to overprediction correction, flexsdm users can delineate partial or complete workflows based on the combination functions to meet specific modelling needs.
Sex differences in telomere length, lifespan, and embryonic dyskerin levels
Authors: Lansdorp Peter M. 
Published: April 2022

AbstractTelomerase levels in most human cells are insufficient to prevent loss of telomeric DNA with each replication cycle. The resulting “Hayflick” limit may have allowed lifespan to increase by suppressing the development of tumors early in life be it at the expense of compromised cellular responses late in life. At any given age, the average telomere length in leukocytes shows considerably variation between individuals with females having, on average, longer telomeres than males. Sex differences in average telomere length are already present at birth and correspond to reported differences in the average life expectancy between the sexes. Levels of telomerase RNA and dyskerin, encoded by DKC1, are known to limit telomerase activity in embryonic stem cells. X‐linked DKC1 is expressed from both alleles in female embryo cells and higher levels of dyskerin and telomerase could elongate telomeres prior to embryo implantation. The hypothesis that embryonic telomerase levels set the stage for the sex differences in telomere length and lifespan deserves further study.
Role of upregulation of the KATP channel subunit SUR1 in dopaminergic neuron degeneration in Parkinson’s disease
Authors: Liu Min , Liu Cui , Xiao Xue , Han Shuai‐Shuai , Bi Ming‐Xia , Jiao Qian , Chen Xi , Yan Chun‐Ling , Du Xi‐Xun , Jiang Hong 
Published: April 2022

AbstractAccumulating evidence suggests that ATP‐sensitive potassium (KATP) channels play an important role in the selective degeneration of dopaminergic neurons in the substantia nigra (SN). Furthermore, the expression of the KATP channel subunit sulfonylurea receptor 1 (SUR1) is upregulated in the remaining nigral dopaminergic neurons in Parkinson's disease (PD). However, the mechanism underlying this selective upregulation of the SUR1 subunit and its subsequent roles in PD progression are largely unknown. In 3‐, 6‐, and 9‐month‐old A53T α‐synuclein transgenic (α‐SynA53T+/+) mice, only the SUR1 subunit and not SUR2B or Kir6.2 was upregulated, accompanied by neuronal damage. Moreover, the occurrence of burst firing in dopaminergic neurons was increased with the upregulation of the SUR1 subunit, whereas no changes in the firing rate were observed except in 9‐month‐old α‐SynA53T+/+ mice. After interference with SUR1 expression by injection of lentivirus into the SN, the progression of dopaminergic neuron degeneration was delayed. Further studies showed that elevated expression of the transcription factors FOXA1 and FOXA2 could cause the upregulation of the SUR1 subunit in α‐SynA53T+/+ mice. Our findings revealed the regulatory mechanism of the SUR1 subunit and the role of KATP channels in the progression of dopaminergic neuron degeneration, providing a new target for PD drug therapy.
Recent trends in prescription drug misuse in the United States by age, race/ethnicity, and sex
Authors: Schepis Ty S. , McCabe Sean E. , Ford Jason A. 
Published: April 2022

AbstractBackground and ObjectivesTo examine changes in United States past‐year opioid, stimulant, and benzodiazepine prescription drug misuse (PDM) and poly‐PDM by demographics.MethodsData were from the 2015–2019 National Survey on Drug Use and Health (N = 282,768), examining annualized PDM change by demographics.ResultsOpioid and poly‐PDM significantly declined among those under 35 years, White, and multiracial residents.Discussion and ConclusionsAge and race/ethnicity are important moderators of recent PDM trends, warranting investigation of mechanisms.Scientific SignificanceResults highlight ongoing PDM declines in younger groups but expand the literature by showing limited changes in adults 35 and older and non‐opioid PDM.
Risk factors for severe reactions in food allergy: Rapid evidence review with meta‐analysis
Authors: Turner Paul J. , Arasi Stefania , Ballmer‐Weber Barbara , Baseggio Conrado Alessia , Deschildre Antoine , Gerdts Jennifer , Halken Susanne , Muraro Antonella , Patel Nandinee , Van Ree Ronald , de Silva Debra , Worm Margitta , Zuberbier Torsten , Roberts Graham ,   the Global Allergy, Asthma European Network (GA2LEN) Food Allergy Guideline Group
Published: April 2022

AbstractThis rapid review summarizes the most up to date evidence about the risk factors for severe food‐induced allergic reactions. We searched three bibliographic databases for studies published between January 2010 and August 2021. We included 88 studies and synthesized the evidence narratively, undertaking meta‐analysis where appropriate. Significant uncertainties remain with respect to the prediction of severe reactions, both anaphylaxis and/or severe anaphylaxis refractory to treatment. Prior anaphylaxis, an asthma diagnosis, IgE sensitization or basophil activation tests are not good predictors. Some molecular allergology markers may be helpful. Hospital presentations for anaphylaxis are highest in young children, yet this age group appears at lower risk of severe outcomes. Risk of severe outcomes is greatest in adolescence and young adulthood, but the contribution of risk taking behaviour in contributing to severe outcomes is unclear. Evidence for an impact of cofactors on severity is lacking, although food‐dependent exercise‐induced anaphylaxis may be an exception. Some medications such as beta‐blockers or ACE inhibitors may increase severity, but appear less important than age as a factor in life‐threatening reactions. The relationship between dose of exposure and severity is unclear. Delays in symptom recognition and anaphylaxis treatment have been associated with more severe outcomes. An absence of prior anaphylaxis does not exclude its future risk.
Amplifying the Archive: Methodological Plurality and Geographies of the Black Atlantic
Authors: Watkins Case , Carney Judith A. 
Published: April 2022

AbstractFirst published in 2001, Judith Carney’s Black Rice drew on a complex methodology to argue that enslaved Africans, despite the brutal oppression of bondage, made fundamental intellectual and cultural contributions to agricultural landscapes and economies in the Americas. This thesis sparked a spirited debate in the Anglophone academy, especially among historians, some of whom took issue with the book’s inclusive geographical methodology. That discussion provides a point of departure to show how plural geographical methods work to amplify the archive, historical and otherwise, and enhance our knowledge with more complex and inclusive narratives. After summarising the debate touched off by Black Rice, we update its thesis with inter‐ and multi‐disciplinary research findings over the past two decades. We then survey theoretical and methodological developments in subsequent geographies of the Black Atlantic, before exploring new pathways and connections made possible when we amplify the archive beyond colonial and other written texts.
Safety of sequential biological therapy in inflammatory bowel disease: results from a tertiary referral centre
Authors: Moens Annick , Sadat Seyed Tabib Nasim , Ballet Vera , Sabino João , Vermeire Séverine , Ferrante Marc 
Published: April 2022

SummaryBackgroundBiologicals represent the cornerstone of treatment for moderate‐to‐severe inflammatory bowel diseases (IBD). Many patients cycle between biologicals when encountering loss of response or adverse events. Aim: To assess the occurrence of serious infections and malignancies with exposure to several (classes of) biologicals.MethodsWe performed a retrospective cohort study in a tertiary referral centre including consecutive IBD patients exposed to adalimumab, infliximab, ustekinumab or vedolizumab between 1996 and 2019. All serious infections and malignancies, as well as potential confounders, were accounted for.ResultsIn total, 1575 patients were included with a median (interquartile range) follow‐up of 10 (6–16) years and a duration of biological therapy of 71 (39–112) months. Incidence rates of serious infections were 3.4 per 100 patients' years (PY) in the post‐biological setting. Serious infections after biological exposure were associated with systemic steroids in monotherapy (hazard ratio 2.96 [95% confidence interval 1.78–4.93], p < 0.0001), combination therapy of systemic steroids and a biological (2.44 [1.37–4.34], p = 0.002), female gender (1.25 [1.04–1.51], p = 0.02), and prior serious infections in the pre‐biological setting (1.42 [1.03–1.96], p = 0.03). Malignancy rates were 1.06 per 100PY in the post‐biological setting and increased with older age at biological initiation (1.04 [1.02–1.05], p < 0.0001). The risk for serious infections or malignancies was independent of type and number of biologicals to which the patient was exposed.ConclusionThis study shows that the sequential use of biological therapy in IBD does not seem to convey an overall higher risk of serious infections or malignancies, but that underlying more refractory disease seems to increase this risk.
The Validated Investigator Global Assessment for Atopic Dermatitis (vIGA-AD™): a clinical outcome measure for the severity of atopic dermatitis
Authors: Simpson Eric L. , Bissonnette Robert , Paller Amy S. , King Brett , Silverberg Jonathan I. , Reich Kristian , Thyssen Jacob P. , Doll Helen , Sun Luna , DeLozier Amy M. , Nunes Fabio P. , Eichenfield Lawrence F. 
Published: April 2022

Abstract

Background
The validated Investigator Global Assessment for Atopic Dermatitis (vIGA-AD™) is a standardized severity assessment for use in clinical trials and registries for atopic dermatitis (AD).

Objectives
To investigate the reliability, validity, responsiveness and within-patient meaningful change of the vIGA-AD.

Methods
Data were analysed from adult patients with moderate-to-severe AD in the BREEZE-AD1 (N = 624 patients; NCT03334396), BREEZE-AD2 (N = 615; NCT03334422) and BREEZE-AD5 (N = 440; NCT03435081) phase III baricitinib clinical studies.

Results
Across studies, test–retest reliability for stable patients showed moderate-to-good agreement [range of Kappa values for Patient Global Impression of Severity–Atopic Dermatitis (PGI-S-AD), 0·516–0·639; for Eczema Area and Severity Index (EASI), 0·658–0·778]. Moderate-to-large correlations between vIGA-AD and EASI or body surface area (range at baseline, 0·497–0·736; Week 16, 0·716–0·893) supported convergent validity. Known-groups validity was demonstrated vs. EASI and PGI-S-AD (vIGA-AD for severe vs. moderate EASI categories at baseline, P &lt; 0·001). Responsiveness was demonstrated vs. EASI (P &lt; 0·001 for much improved vs. improved and improved vs. stable). Anchor- and distribution-based methods supported a vIGA-AD change of –1·0 as clinically meaningful. These findings are limited to populations defined by the studies’ inclusion and exclusion criteria.

Conclusions
The vIGA-AD demonstrated sufficient reliability, validity, responsiveness and interpretation standards for use in clinical trials.
What is already known about this topic? A description of the development of the validated Investigator Global Assessment for Atopic Dermatitis (vIGA-AD™) has been published previously.
What does this study add? The current study validates the vIGA-AD by demonstrating appropriate test–retest reliability, convergent validity, known-groups validity and responsiveness across three baricitinib clinical studies.In addition, a 1-point change was identified as a clinically meaningful patient-perceived change minimal clinically important difference in the vIGA-AD.
What are the clinical implications of the work? The vIGA-AD is a measure for investigator assessment of atopic dermatitis suitable for use in clinical research.
IL‐27 improves adoptive CD8+ T cells’ antitumor activity via enhancing cell survival and memory T cell differentiation
Authors: Ding Miao , Fei Yi , Zhu Jianmin , Ma Ji , Zhu Guoqing , Zhen Ni , Zhu Jiabei , Mao Siwei , Sun Fenyong , Wang Feng , Pan Qiuhui 
Published: April 2022

AbstractIL‐27 is an anti‐inflammatory cytokine that triggers enhanced antitumor immunity, particularly cytotoxic T lymphocyte responses. In the present study, we sought to develop IL‐27 into a therapeutic adjutant for adoptive T cell therapy using our well‐established models. We have found that IL‐27 directly improved the survival status and cytotoxicity of adoptive OT‐1 CD8+ T cells in vitro and in vivo. Meanwhile, IL‐27 treatment programs memory T cell differentiation in CD8+ T cells, characterized by upregulation of genes associated with T cell memory differentiation (T‐bet, Eomes, Blimp1, and Ly6C). Additionally, we engineered the adoptive OT‐1 CD8+ T cells to deliver IL‐27. In mice, the established tumors treated with OT‐1 CD8+ T‐IL‐27 were completely rejected, which demonstrated that IL‐27 delivered via tumor antigen–specific T cells enhances adoptive T cells’ cancer immunity. To our knowledge, this is the first application of CD8+ T cells as a vehicle to deliver IL‐27 to treat tumors. Thus, this study demonstrates IL‐27 is a feasible approach for enhancing CD8+ T cells’ antitumor immunity and can be used as a therapeutic adjutant for T cell adoptive transfer to treat cancer.
Integration of qualitative and quantitative methods for land‐use‐change modeling in a deforestation frontier
Authors: Siegel Katherine , Farah Perez Aldo , Kinnebrew Eva , Mills‐Novoa Megan , Ochoa José , Shoffner Elizabeth 
Published: April 2022

AbstractDevelopment and implementation of effective protected area management to reduce deforestation depend in part on identifying factors contributing to forest loss and areas at risk of conversion, but standard land‐use‐change modeling may not fully capture contextual factors that are not easily quantified. To better understand deforestation and agricultural expansion in Amazonian protected areas, we combined quantitative land‐use‐change modeling with qualitative discourse analysis in a case study of Brazil's Jamanxim National Forest. We modeled land‐use change from 2008 to 2018 and projected deforestation through 2028. We used variables identified in a review of studies that modeled land‐use change in the Amazon (e.g., variables related to agricultural suitability and economic accessibility) and from a critical discourse analysis that examined documents produced by different actors (e.g., government agencies and conservation nonprofit organizations) at various spatial scales. As measured by analysis of variance, McFadden's adjusted pseudo R2, and quantity and allocation disagreement, we found that including variables in the model identified as important to deforestation dynamics through the qualitative discourse analysis (e.g., the proportion of unallocated public land, distance to proposed infrastructure developments, and density of recent fires) alongside more traditional variables (e.g., elevation, distance to roads, and protection status) improved the predictive ability of these models. Models that included discourse analysis variables and traditional variables explained up to 19.3% more of the observed variation in deforestation probability than a model that included only traditional variables and 4.1% more variation than a model with only discourse analysis variables. Our approach of integrating qualitative and quantitative methods in land‐use‐change modeling provides a framework for future interdisciplinary work in land‐use change.
Local abundances of terrestrial mammal and bird species around indigenous villages in Suriname
Authors: Van Kuijk Marijke , De Jager Monique , Van Oosterhout Martin , De Laender Leen , Parahoe Minu 
Published: April 2022

AbstractHunting is an important threat to tropical wildlife, yet many people are dependent on forest fauna for protein provisioning. We analyzed abundances of terrestrial mammal and bird species around four indigenous villages in the south of Suriname, using camera trap data and the Royle–Nichols abundance model. We hypothesized that hunting pressure increases with decreasing distance to a village and with increasing village size (expressed as cropland area). We detected 24 animal species in all villages combined, including several rare species. For 11 of the 24 species, we were able to examine if and how distance to a village and village size related to local abundances and found a positive effect of distance to village on local abundances in five species, and a negative effect of village size in one species. Because villages, and thus hunting, affect local abundances of terrestrial bird and mammal species in our study, we recommend monitoring forest fauna in areas where people are highly dependent on animals for food provisioning.
A comparison of pediatric liver transplant anesthesia practices with new organ procurement and transplant network pediatric policy requirements: A report from the society for the advancement of transplant anesthesia and the society for pediatric anesthesia
Authors: Moguilevitch Marina , Polaner David M. , Mann Glenn , Mauner Aaron , Beagley Britni , Hendrickse Adrian , Stoll William D , DeMarchi Lorenzo , Damian Daniela , Sridhar Srikanth , Costandi Andrew , Tran Lieu , Jorge Lydia M , Mandell M. Susan 
Published: April 2022

AbstractIntroductionOrgan Procurement and Transplant Network (OPTN) pediatric policies on knowledge and skill requirements for key personnel failed to address the Director of Anesthesia for Pediatric Liver Transplantation. A Joint Committee representing the Society for the Advancement of Transplant Anesthesia and Society for Pediatric Anesthesia (SPA) surveyed all pediatric anesthesia liver transplant practices to determine if practices were aligned with policies and what changes would be needed for compliance.MethodsA survey of the Director or equivalent at each program collected data about specialized knowledge and skill sets. Questions focused on (1) skill and knowledge of the Director and team, (2) requirements for appointment, (3) experience in pediatrics, and (4) characteristics of the program including the availability of pediatric resources.ResultsResponse rate was 73% (n = 63). Most responding programs had a Director (67%) with certification, selection committee, and continuing education credits outlined in existing policies. Team members met similar requirements. Alternate pathways for acquiring knowledge and skill sets were identified between programs.ConclusionsPediatric liver transplant anesthesiologists use knowledge and skill pathways that align with the new pediatric policies. We suggest that collaborative work with oversight agencies is needed to resolve high case volume requirements originally designed for adult programs.SummaryMost pediatric liver transplant anesthesiologists in the US have specialized knowledge and skills for expert care consistent with current oversight policies. Differences in pathways to acquire knowledge and skill sets were still aligned with the new policies for pediatric transplant surgeons and bylaws for the Director of Transplant Anesthesia. We conclude that minimal changes in case volume requirements to the existing Pediatric Transplant Anesthesiology Directorship criteria that authenticates the pediatric anesthesia Director's position would improve the safety of care without limiting access to transplantation.