bluuebunny/crossref_metadata_2025_split huggingface dataset:
FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets
Authors: Moreno-Mayar J Víctor 
Published: October 2021

Abstract
Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyze their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualization of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.
Suppression of cdc13-2-associated senescence by pif1-m2 requires Ku-mediated telomerase recruitment
Authors: Fekete-Szücs Enikő , Rosas Bringas Fernando R , Stinus Sonia , Chang Michael 
Published: October 2021

Abstract
In Saccharomyces cerevisiae, recruitment of telomerase to telomeres requires an interaction between Cdc13, which binds single-stranded telomeric DNA, and the Est1 subunit of telomerase. A second pathway involving an interaction between the yKu complex and telomerase RNA (TLC1) contributes to telomerase recruitment but cannot sufficiently recruit telomerase on its own to prevent replicative senescence when the primary Cdc13-Est1 pathway is abolished—for example, in the cdc13-2 mutant. In this study, we find that mutation of PIF1, which encodes a helicase that inhibits telomerase, suppresses the replicative senescence of cdc13-2 by increasing reliance on the yKu-TLC1 pathway for telomerase recruitment. Our findings reveal new insight into telomerase-mediated telomere maintenance.
The Association of Prior Intensive Lifestyle Intervention and Diabetes Support and Education With Frailty Prevalence at Long-Term Follow-Up in the Action for Health in Diabetes Extension Study
Authors:   Look AHEAD Research Group, Espinoza Sara E , Hazuda Helen P , Maruthur Nisa M , Bray George A , Johnson Karen C , Synyer Xavier Pi , Newman Anne B , Wing Rena R , Yanovski Susan Z , Gaussoin Sarah A , Houston Denise K , Espinoza Sara E , Hazuda Helen P , Atkinson Karen , Bolin Paula , Bray George A , Clark Jeanne M , Coday Mace , Dutton Gareth , Egan Caitlin , Foreyt John P , Gaussoin Sarah A , Greenway Frank L , Gregg Edward W , Hill James O , Horton Edward S , Houston Denise K , Hubbard Van S , Jakicic John M , Jeffery Robert W , Johnson Karen C , Kahn Steven E , Knowler William C , Lewis Cora E , Maruthur Nisa M , Carey Barbara J Maschak , Middelbeek Roeland J W , Nathan David M , Newman Anne B , Pajewski Nicholas , Patricio Jennifer , Percy Carol , Peters Anne , Sunyer Xavier Pi , Pownall Henry , Redmon Bruce , Steinburg Helmut , Wadden Thomas A , Wing Rena R , Wyatt Holly , Yanovski Susan Z , Zhang Ping 
Published: October 2021

Abstract

Background
Frailty is common in older adults with obesity and diabetes. We compared prevalence of the frailty phenotype between intervention groups in long-term follow-up of Look Action for Health in Diabetes Study (AHEAD), a randomized trial comparing a multidomain intensive lifestyle intervention (ILI) that promoted weight loss and physical activity with a diabetes support and education (DSE) control group in adults with type 2 diabetes and overweight or obesity.

Method
Participants included 2 979 individuals randomized to ILI or DSE in 2001–2004 who completed frailty assessment in Look AHEAD—Extension Wave 1 (2016–2018) at an average age of 72.1 ± 6.2 years. Frailty was assessed using a modified frailty phenotype definition (excluding weight loss) defined as the presence of 3 or more of the following frailty characteristics: weakness, slow gait speed, low physical activity, and exhaustion. Frailty odds by intervention assignment (DSE vs ILI) were estimated using multivariable logistic regression, adjusting for sex, clinic site, and time since randomization.

Results
At median follow-up of 14.0 years (interquartile range: 13.8–14.1), frailty prevalence was 10.9% in ILI compared with 11.6% in DSE (odds ratio for frailty in ILI vs DSE = 0.94, 95% confidence interval: 0.75–1.18, p = .60). Frailty was more prevalent in participants who were older, female, non-White, of lower socioeconomic status, and at baseline had a higher body mass index and waist circumference, longer duration of diabetes, history of cardiovascular disease, and metabolic syndrome.

Conclusions
Prior randomization to ILI compared with DSE was not associated with a lower prevalence of frailty after a median follow-up of 14.0 years in adults with diabetes and overweight or obesity.
Network approaches for formalizing conceptual models in ecosystem-based management
Authors: Reum Jonathan C P , Kelble Christopher R , Harvey Chris J , Wildermuth Robert P , Trifonova Neda , Lucey Sean M , McDonald P Sean , Townsend Howard 
Published: October 2021

AbstractQualitative Network Models (QNMs), Fuzzy Cognitive Maps (FCMs), and Bayesian Belief Networks (BBNs) have been proposed as methods to formalize conceptual models of social–ecological systems and project system responses to management interventions or environmental change. To explore how these different methods might influence conclusions about system dynamics, we assembled conceptual models representing three different coastal systems, adapted them to the network approaches, and evaluated outcomes under scenarios representing increased fishing effort and environmental warming. The sign of projected change was the same across the three network models for 31–60% of system variables on average. Pairwise agreement between network models was higher, ranging from 33 to 92%; average levels of similarity were comparable between network pairs. Agreement measures based on both the sign and strength of change were substantially worse for all model comparisons. These general patterns were similar across systems and scenarios. Different outcomes between models led to different inferences regarding trade-offs under the scenarios. We recommend deployment of all three methods, when feasible, to better characterize structural uncertainty and leverage insights gained under one framework to inform the others. Improvements in precision will require model refinement through data integration and model validation.
Livestock and Risk Group 4 Pathogens: Researching Zoonotic Threats to Public Health and Agriculture in Maximum Containment
Authors: Lewis Charles E , Pickering Bradley 
Published: October 2021

Abstract
Maximum-containment laboratories are a unique and essential component of the bioeconomy of the United States. These facilities play a critical role in the national infrastructure, supporting research on a select set of especially dangerous pathogens, as well as novel, emerging diseases. Understanding the ecology, biology, and pathology at the human-animal interface of zoonotic spillover events is fundamental to efficient control and elimination of disease. The use of animals as human surrogate models or as target-host models in research is an integral part of unraveling the interrelated components involved in these dynamic systems. These models can prove vitally important in determining both viral- and host-factors associated with virus transmission, providing invaluable information that can be developed into better risk mitigation strategies. In this article, we focus on the use of livestock in maximum-containment, biosafety level-4 agriculture (BSL-4Ag) research involving zoonotic, risk group 4 pathogens and we provide an overview of historical associated research and contributions. Livestock are most commonly used as target-host models in high-consequence, maximum-containment research and are routinely used to establish data to assist in risk assessments. This article highlights the importance of animal use, insights gained, and how this type of research is essential for protecting animal health, food security, and the agriculture economy, as well as human public health in the face of emerging zoonotic pathogens. The utilization of animal models in high-consequence pathogen research and continued expansion to include available species of agricultural importance is essential to deciphering the ecology of emerging and re-emerging infectious diseases, as well as for emergency response and mitigation preparedness.
Potential for Machine Learning in Burn Care
Authors: Robb Lydia 
Published: October 2021

Abstract
Burn-related injuries are a leading cause of morbidity across the globe. Accurate assessment and treatment have been demonstrated to reduce the morbidity and mortality. This essay explores the forms of artificial intelligence to be implemented the field of burns management to optimize the care we deliver in the National Health Service (NHS) in the United Kingdom. Machine learning methods that predict or classify are explored. This includes linear and logistic regression, artificial neural networks, deep learning, and decision tree analysis. Utilizing machine learning in burns care holds potential from prevention, burns assessment, predicting mortality, and critical care monitoring to healing time. Establishing a regional or national Machine Learning group would be the first step toward the development of these essential technologies. The implementation of machine learning technologies will require buy-in from the NHS health boards, with significant implications with cost of investment, implementation, employment of machine learning teams, and provision of training to medical professionals.
ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data
Authors: Inoue Jun 
Published: October 2021

AbstractComparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: 1) Analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and 2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole-genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.
Making Sense of a Complex Notion: Debates on State Religious Neutrality in Canada — A View from Quebec
Authors: Bosset Pierre 
Published: October 2021

Abstract
Under Canadian constitutional law, state neutrality acts as an implicit organizing principle for the relations between the state and religions. Neutrality, however, is a polysemic word: conceptions of neutrality vary. Competing versions of neutrality feature in the decisions of Canadian courts. This is starkly evident in decisions that originate from Quebec, where judges have harboured divergent views of neutrality on matters such as the reciting of prayers in town hall meetings or the teaching of religious diversity in schools. This article analyses how the Canadian Supreme Court has manoeuvred through competing conceptions of state religious neutrality. Initially divided, the Court seems to have eventually opted for a type of neutrality that allows the state to recognize the existence of religions in laws and policies, but that also prevents it from indoctrination and from arbitrating between competing viewpoints within religions. This view of neutrality, I argue, is consistent with the principle of multiculturalism and with the Court’s characterization of a ‘free and democratic society’, as this notion is understood in Canada.
Intergovernmental Influence, Managerial Turnover, and City Energy Policy Adoption
Authors: Huang Chien-Shih , Berry Frances 
Published: October 2021

AbstractUrban sustainability policy provides opportunities for expanding global efforts for climate change mitigation. Yet local governments may not commit to make such policy efforts. It is well recognized that internal and external factors in state and local governments can be potential drivers. Less recognized is that green energy policy adoption can also be impacted by competitive federalism, under which state laws might influence the likelihood of local adoption. Drawing on prior studies on inter-governmental interactions and managerial turnover, we hypothesize the effect of intergovernmental influence, managerial turnover, and their interactions on city adoption of energy efficiency and renewable energy programs. Results of the multilevel regression model indicate that state influence via regulatory or financial tools can encourage city sustainable energy consumption and production, while managerial turnover can inhibit these conditions, but the negative impacts of managerial turnover can be reversed when the successors are recruited externally. Our tests support the existence of both local government free-riding and city mobilization to enact more green policies with externally hired city managers, thereby helping us to distinguish the impact of competitive federalism in local energy policy.
Suicide reporting of LGBTQI+ population in India: An analysis of online media reports of the past decade
Authors: Kar Sujita Kumar , Menon Vikas , Mukherjee Srijeeta , Bascarane Sharmi , Sharma Ginni , Pattnaik Jigyansa Ipsita , Ransing Ramdas , Padhy Susanta Kumar , Agarwal Vivek 
Published: October 2021

AbstractBackgroundImbalanced portrayal of suicide by the media can have adverse public health consequences. We aimed to evaluate the psychosocial context, as well as the quality of media reporting, of suicide among lesbian, gay, bisexual, transgender people, queer and intersex (LGBTQI+) population.MethodsA cross-sectional study was conducted to evaluate online news reports discussing the suicide of LGBTQI+ persons published between January 2011 and January 2021. Psychosocial factors associated with suicide were extracted from the reports. Quality of suicide reporting was checked against international as well as locally relevant reporting guidelines.ResultsA total of 135 suicide reports from five newspapers were analyzed. Multiple psychosocial stressors were reported in 54.5% of the suicides. Social stigma was the most common factor associated with LGBTQI+ suicide. Several breaches of reporting were noted in relation to mentioning the identity (55.6%) and method of suicide (54.3%) in the title of report and inclusion of the deceased’s photograph (20.4%). Potentially helpful reporting characteristics, such as including educational information (2.2%), mentioning warning signs (12.6%) and suicide support service details (3.7%), were rarely practiced. Local language news articles displayed more frequent and serious violations compared to English news reports.ConclusionIndian media reporting of suicide among LGBTQI+ persons is poorly adherent to reporting guidelines.
Placebo response in psoriatic arthritis clinical trials: a systematic review and meta-analysis
Authors: Erre Gian Luca , Mavridis Dimitris , Woodman Richard John , Mangoni Arduino Aleksander 
Published: October 2021

Abstract

Objective
To determine the placebo response rate in PsA randomized clinical trials (RCTs), its contributing factors and impact on the effect size of active treatments.

Methods
We searched multiple databases, from inception to 20 December 2020, for placebo-controlled RCTs in PsA. We used a random-effects meta-analysis to pool the response rates for the ACR20 criteria in the placebo arm, determined the risk difference for treatment vs placebo, and used meta-regression to determine the factors associated with placebo response rates. The risk of bias was assessed in duplicate. The study protocol was registered with PROSPERO: CRD42021226000.

Results
We included 42 RCTs (5050 patients receiving placebo) published between 2000 and 2020. The risk of bias was low in 28 trials, high in four, and with some concerns in 10. The pooled placebo response rate was 20.3% (95% CI: 18.6%, 22.1%; predicted intervals, 11.7–29.0%), with significant between-trial heterogeneity (I2 = 56.8%, P &lt; 0.005). The pooled risk difference for treatment vs placebo was 27% (95% CI: 24%, 31%). In the multivariable meta-regression, there was a 15% (95% CI: 2.9%, 29.8%) increase in the odds of achieving the placebo response for each 5-year increment in publication year (P = 0.016). In addition, the active treatment risk difference decreased for every 5-year increment in publication year (β = −0.053, 95% CI: −0.099, −0.007; P = 0.024) but was not associated with the placebo response.

Conclusion
Despite increasing over time, the placebo response for ACR20 in PsA RCTs was not associated with the active treatment effect size.
Fathers’ involvement in early childcare is associated with amygdala resting-state connectivity
Authors: Horstman Lisa I , Riem Madelon M E , Alyousefi-van Dijk Kim , Lotz Anna M , Bakermans-Kranenburg Marian J 
Published: October 2021

Abstract
Becoming a parent requires new skills and frequent task switching during daily childcare. Little is known about the paternal brain during the transition to fatherhood. The present study examined intrinsic neuronal network connectivity in a group of first-time expectant and new fathers (total N = 131) using amygdala seed-based resting-state functional connectivity analysis. Furthermore, we examined the association between paternal involvement (i.e. hours spent in childcare and real-time push notifications on smartphone) and connectivity within the parental brain network in new fathers. There were no significant differences in functional connectivity between expectant and new fathers. However, results show that in new fathers, time spent in childcare was positively related to amygdala connectivity with the supramarginal gyrus, postcentral gyrus and the superior parietal lobule—all regions within the cognition/mentalizing network that have been associated with empathy and social cognition. Our results suggest that fathers’ time investment in childcare is related to connectivity networks in the parental brain.
Impacts for whom? Assessing inequalities in NSF-funded broader impacts using the Inclusion-Immediacy Criterion
Authors: Woodson Thomas , Boutilier Sophia 
Published: October 2021

Abstract
Broader impacts (BI) policies generate debate on the purpose of science, measuring the impact of research, and is an important topic for the science policy community. However, BI policies often fail to determine if R&D funding helps marginalized communities. This paper introduces a new framework, the Inclusion-Immediacy Criterion, that assesses who benefits from research impacts as divided into three groups: (1) advantaged groups; (2) the general population; and (3) marginalized groups. The study analyzes National Science Foundation (NSF) project outcome reports and finds that advantaged groups are the most likely to benefit from NSF-funded research. The study also shows that certain areas of NSF research, such as Social, Behavioral, and Economic Sciences, more efficiently generate impacts for marginalized groups compared to other directorates. This paper further argues that persistent inequalities in BIs limit the potential of R&D to increase prosperity and well-being, two of NSF’s mandated goals.
A new cytometry-based method reveals an accumulation of Nrf2 in dendritic cells exposed to two respiratory sensitizers
Authors: Audry Adrien , Mathiot Julianne , Muller Samuel , Coiscaud Amélie , Langonné Isabelle , Battais Fabrice , Leininger Brigitte , Sponne Isabelle 
Published: October 2021

Abstract
The mechanisms underlying chemical respiratory sensitization are incompletely understood. One of the major cell types involved in this pathology are dendritic cells. In this study, the mechanisms of the NRF2–Keap1 pathway were studied using a bone marrow-derived dendritic cell model exposed to two respiratory sensitizers: ammonium hexachloroplatinate (HCP) and ammonium tetrachloroplatinate (ATCP). Expression levels for two Nrf2-regulated genes, hmox1 and srxn1, were analyzed by real time-quantitative polymerase chain reaction. A flow cytometry-based method was also developed to measure intracellular Nrf2 accumulation in dendritic cells following exposure. Exposure to HCP and ATCP increased both hmox1 and srxn1 gene expression, and was associated with accumulation of Nrf2 protein in cells. Overall, these results show that the respiratory sensitizers, in addition to skin sensitizers, can also induced markers associated with NRF2–Keap1 pathway activation in dendritic cells. This study contributes to a better understanding of the adverse outcome of respiratory sensitization.
Prevention and Detection of Fungicide Resistance Development in Rhizoctonia zeae from Soybean and Corn in Nebraska
Authors: Gambhir Nikita , Kodati Srikanth , Huff Matthew , Silva Flávio , Ajayi-Oyetunde Olutoyosi , Staton Margaret , Bradley Carl , Adesemoye Anthony O. , Everhart Sydney E. 
Published: October 2021

The goal of this research was to advance the foundational knowledge required to quantify and mitigate fungicide resistance in Rhizoctonia zeae, the seedling disease pathogen of soybean and corn. In vitro sensitivity to azoxystrobin, fludioxonil, sedaxane, and/or prothioconazole was determined for 91 R. zeae isolates obtained mostly from soybean and corn fields in Nebraska. Isolates were sensitive to fludioxonil, sedaxane, and prothioconazole (EC50 < 3 µg/ml) and had a positively skewed EC50 distribution. Isolates were not sensitive to azoxystrobin in vitro (EC50 > 100 µg/ml) or in planta. Application of azoxystrobin did not significantly decrease disease severity or improve total dry weight of the soybean plants (P > 0.05). The risk of resistance development in R. zeae was estimated by characterizing its population structure. Eighty-one R. zeae isolates were genotyped using six microsatellite markers. Results showed that the population has a mixed mode of reproduction and is structured according to geographic region, suggesting limited dispersal. These population characteristics suggest that R. zeae has an intermediate risk of resistance development. Overall, this research established the current status of fungicide sensitivity in R. zeae in Nebraska and estimated its risk of resistance development, which can inform fungicide resistance management for R. zeae.