bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates
Authors: Muthukumarasamy Uthayakumar , Preusse Matthias , Kordes Adrian , Koska Michal , Schniederjans Monika , Khaledi Ariane , Häussler Susanne 
Published: March 2020

Abstract
Extensive use of next-generation sequencing has the potential to transform our knowledge on how genomic variation within bacterial species impacts phenotypic versatility. Because different environments have unique selection pressures, they drive divergent evolution. However, there is also parallel or convergent evolution of traits in independent bacterial isolates inhabiting similar environments. The application of tools to describe population-wide genomic diversity provides an opportunity to measure the predictability of genetic changes underlying adaptation. Here, we describe patterns of sequence variations in the core genome among 99 individual Pseudomonas aeruginosa clinical isolates and identified single-nucleotide polymorphisms that are the basis for branching of the phylogenetic tree. We also identified single-nucleotide polymorphisms that were acquired independently, in separate lineages, and not through inheritance from a common ancestor. Although our results demonstrate that the Pseudomonas aeruginosa core genome is highly conserved and in general, not subject to adaptive evolution, instances of parallel evolution will provide an opportunity to uncover genetic changes that underlie phenotypic diversity.
Do Welfare Regimes Moderate Cumulative Dis/advantages Over the Life Course? Cross-National Evidence from Longitudinal SHARE Data
Authors: Sieber Stefan , Cheval Boris , Orsholits Dan , van der Linden Bernadette W A , Guessous Idris , Gabriel Rainer , Kliegel Matthias , von Arx Martina , Kelly-Irving Michelle , Aartsen Marja J , Boisgontier Matthieu P , Courvoisier Delphine , Burton-Jeangros Claudine , Cullati Stéphane 
Published: March 2020

Abstract

Objectives
This study aimed to examine the cumulative disadvantage of different forms of childhood misfortune and adult-life socioeconomic conditions (SEC) with regard to trajectories and levels of self-rated health in old age and whether these associations differed between welfare regimes (Scandinavian, Bismarckian, Southern European, and Eastern European).

Method
The study included 24,004 respondents aged 50–96 from the longitudinal SHARE survey. Childhood misfortune included childhood SEC, adverse childhood experiences, and adverse childhood health experiences. Adult-life SEC consisted of education, main occupational position, and financial strain. We analyzed associations with poor self-rated health using confounder-adjusted mixed-effects logistic regression models for the complete sample and stratified by welfare regime.

Results
Disadvantaged respondents in terms of childhood misfortune and adult-life SEC had a higher risk of poor self-rated health at age 50. However, differences narrowed with aging between adverse-childhood-health-experiences categories (driven by Southern and Eastern European welfare regimes), categories of education (driven by Bismarckian welfare regime), and main occupational position (driven by Scandinavian welfare regime).

Discussion
Our research did not find evidence of cumulative disadvantage with aging in the studied life-course characteristics and age range. Instead, trajectories showed narrowing differences with differing patterns across welfare regimes.
Beyond Successful Aging 2.0: Inequalities, Ageism, and the Case for Normalizing Old Ages
Authors: Calasanti Toni , King Neal 
Published: March 2020

Abstract
This article reviews challenges to Rowe and Kahn’s Successful Aging (SA) framework, particularly those that focus on the ways social inequalities, including ageism, stratify age groups and affect possibilities for SA. We then assess the authors’ replies to these critiques. We find that SA 2.0 maintains a naturalization of outcomes of age relations, and retains both its focus on personal choice and its indifference to inequalities. We advocate a paradigm shift that recasts the problems of aging in three distinct ways: (i) avoids treating old age as a problem; (ii) avoids treating medical and other maladies as results of aging; and (iii) treats the problems of old age as results of age relations instead. By focusing on age relations, this paradigm goes beyond calls to examine inequalities over the life course, and seeks to normalize old ages, valuing both different modes of aging and old age itself.
Race Differences in Characteristics and Experiences of Black and White Caregivers of Older Americans
Authors: Fabius Chanee D , Wolff Jennifer L , Kasper Judith D 
Published: March 2020

Abstract

Background and Objectives
Racial disparities in health and socioeconomic characteristics of older adults have implications for the experiences of their family and unpaid caregivers, but knowledge to date has primarily drawn from convenience samples. Using a population-based sample, we examine associations between caregiver race and caregiving-related effects.

Research Design and Methods
Study participants include white (n = 992) and black (n = 556) respondents to the 2015 National Study of Caregiving who assisted community-dwelling older adults with disabilities who participated in the National Health and Aging Trends Study. Guided by Pearlin’s Stress Process Model, hierarchical logistic regression models were constructed to examine race differences in caregiving-related effects after adjusting for caregiving context, stressors, and resources.

Results
Relative to white caregivers, blacks more often provided in excess of 40 hr of care per week (54.3% vs 38.6%) and more often cared for an older adult with dementia (27.1% vs 20.7%) who was living below the federal poverty line (31.7% vs 11.9%) or was Medicaid-eligible (42.2% vs 11.8%). Black caregivers more often used supportive services (32.9% vs 24.8%). In fully adjusted regression models, black caregivers were more likely to report gains and less likely to report emotional difficulty than whites. Service utilization did not attenuate caregiving-related emotional difficulty or participation restrictions, regardless of race.

Discussion and Implications
Findings highlight caregiving disparities and counterintuitive differences in experiences and indicate the importance of identifying supports such as paid family leave and faith and community-based programming to better support community-dwelling low-income older adults and their family and unpaid caregivers.
Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly
Authors: Meng Fanming , Liu Zhuoying , Han Han , Finkelbergs Dmitrijs , Jiang Yangshuai , Zhu Mingfei , Wang Yang , Sun Zongyi , Chen Chao , Guo Yadong , Cai Jifeng 
Published: March 2020

Abstract

Background
Blowflies (Diptera: Calliphoridae) are the most commonly found entomological evidence in forensic investigations. Distinguished from other blowflies, Aldrichina grahami has some unique biological characteristics and is a species of forensic importance. Its development rate, pattern, and life cycle can provide valuable information for the estimation of the minimum postmortem interval.

Findings
Herein we provide a chromosome-level genome assembly of A. grahami that was generated by Pacific BioSciences sequencing platform and chromosome conformation capture (Hi-C) technology. A total of 50.15 Gb clean reads of the A. grahami genome were generated. FALCON and Wtdbg were used to construct the genome of A. grahami, resulting in an assembly of 600 Mb and 1,604 contigs with an N50 size of 1.93 Mb. We predicted 12,823 protein-coding genes, 99.8% of which was functionally annotated on the basis of the de novo genome (SRA: PRJNA513084) and transcriptome (SRA: SRX5207346) of A. grahami. According to the co-analysis with 11 other insect species, clustering and phylogenetic reconstruction of gene families were performed. Using Hi-C sequencing, a chromosome-level assembly of 6 chromosomes was generated with scaffold N50 of 104.7 Mb. Of these scaffolds, 96.4% were anchored to the total A. grahami genome contig bases.

Conclusions
The present study provides a robust genome reference for A. grahami that supplements vital genetic information for nonhuman forensic genomics and facilitates the future research of A. grahami and other necrophagous blowfly species used in forensic medicine.
De novo assembly of the cattle reference genome with single-molecule sequencing
Authors: Rosen Benjamin D , Bickhart Derek M , Schnabel Robert D , Koren Sergey , Elsik Christine G , Tseng Elizabeth , Rowan Troy N , Low Wai Y , Zimin Aleksey , Couldrey Christine , Hall Richard , Li Wenli , Rhie Arang , Ghurye Jay , McKay Stephanie D , Thibaud-Nissen Françoise , Hoffman Jinna , Murdoch Brenda M , Snelling Warren M , McDaneld Tara G , Hammond John A , Schwartz John C , Nandolo Wilson , Hagen Darren E , Dreischer Christian , Schultheiss Sebastian J , Schroeder Steven G , Phillippy Adam M , Cole John B , Van Tassell Curtis P , Liu George , Smith Timothy P L , Medrano Juan F 
Published: March 2020

Abstract

Background
Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.

Results
We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is &gt;250× more continuous than the original assembly, with contig N50 &gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.

Conclusions
We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.
Stress modulation of the seismic gap between the 2008 Ms 8.0 Wenchuan earthquake and the 2013 Ms 7.0 Lushan earthquake and implications for seismic hazard
Authors: Guo Rumeng , Zheng Yong , Xu Jianqiao 
Published: March 2020

SUMMARYBetween 2008 and 2013, the Ms 8.0 Wenchuan earthquake and the Ms 7.0 Lushan earthquake occurred successively in the Longmenshan fault zone. Their aftershocks delineated a prominent seismic gap approximately 50 km long, hereafter referred to as the WLSG. The possibility of an event of Ms 7.0 or above occurring in the WLSG is a matter of great concern. In this study, we estimated the change of Coulomb failure stress (ΔCFS) along the WLSG caused by historical earthquakes in the last 300 yr. Our results revealed that 20 major earthquakes cast a stress shadow on the WLSG before 2008 (−148.7 to −7.0 kPa), hindering the rupture of the Wenchuan earthquake and the Lushan earthquake. The Wenchuan earthquake had an important influence on the stress redistribution of the WLSG, resulting in significant stress increase (14.7 to 337.5 kPa). As of 2018, although the negative ΔCFS caused by historical earthquakes (especially the Dayi earthquake) pushed the southern end of the WLSG away from failure, the positive peak ΔCFS of 323.0 kPa greatly encouraged the rupture of the northern WLSG. The small afterslip and weak microseismicity indicate that the WLSG is a stress barrier with high seismic potential, which can explain the mechanism of rupture termination of the Wenchuan earthquake and the Lushan earthquake.
What steps can researchers take to increase research uptake by policymakers? A case study in China
Authors: Wu Shishi , Khan Mishal , Legido-Quigley Helena 
Published: March 2020

AbstractEmpirical analysis of the connections between research and health policymaking is scarce in middle-income countries. In this study, we focused on a national multidrug-resistant tuberculosis (TB) healthcare provider training programme in China as a case study to examine the role that research plays in influencing health policy. We specifically focused on the factors that influence research uptake within the complex Chinese policymaking process. Qualitative data were collected from 34 participants working at multilateral organizations, funding agencies, academia, government agencies and hospitals through 14 in-depth interviews and 2 focus group discussions with 10 participants each. Themes were derived inductively from data and grouped based on the ‘Research and Policy in Developing countries’ framework developed by the Overseas Development Institute. We further classified how actors derive their power to influence policy decisions following the six sources of power identified by Sriram et al. We found that research uptake by policymakers in China is influenced by perceived importance of the health issues addressed in the research, relevance of the research to policymakers’ information needs and government’s priorities, the research quality and the composition of the research team. Our analysis identified that international donors are influential in the TB policy process through their financial power. Furthermore, the dual roles of two government agencies as both evidence providers and actors who have the power to influence policy decisions through their technical expertise make them natural intermediaries in the TB policy process. We concluded that resolving the conflict of interests between researchers and policymakers, as suggested in the ‘two-communities theory’, is not enough to improve evidence use by policymakers. Strategies such as framing research to accommodate the fast-changing policy environment and making alliances with key policy actors can be effective to improve the communication of research findings into the policy process, particularly in countries undergoing rapid economic and political development.
Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content
Authors: Woldegebriel Rosa , Kvist Jouni , Andersson Noora , Õunap Katrin , Reinson Karit , Wojcik Monica H , Bijlsma Emilia K , Hoffer Mariëtte J V , Ryan Monique M , Stark Zornitza , Walsh Maie , Cuppen Inge , van den Boogaard Marie-Jose´ H , Bharucha-Goebel Diana , Donkervoort Sandra , Winchester Sara , Zori Roberto , Bönnemann Carsten G , Maroofian Reza , O’Connor Emer , Houlden Henry , Zhao Fang , Carpén Olli , White Matthew , Sreedharan Jemeen , Stewart Murray , Ylikallio Emil , Tyynismaa Henna 
Published: March 2020

AbstractDefects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
The Impact of Social and Behavioral Factors on Reproducibility in Terrestrial Vertebrate Models
Authors: Whittaker Alexandra L , Hickman Debra L 
Published: March 2020

AbstractThe use of animal models remains critical in preclinical and translational research. The reliability of the animal models and aspects of their validity is likely key to effective translation of findings to medicine. However, despite considerable uniformity in animal models brought about by control of genetics, there remain a number of social as well as innate and acquired behavioral characteristics of laboratory animals that may impact on research outcomes. These include the effects of strain and genetics, age and development, sex, personality and affective states, and social factors largely brought about by housing and husbandry. In addition, aspects of the testing environment may also influence research findings. A number of considerations resulting from the animals’ innate and acquired behavioral characteristics as well as their social structures are described. Suggestions for minimizing the impact of these factors on research are provided.
Ending the HIV Epidemic Among Persons Who Inject Drugs: A Cost-Effectiveness Analysis in Six US Cities
Authors: Krebs Emanuel , Zang Xiao , Enns Benjamin , Min Jeong E , Behrends Czarina N , Del Rio Carlos , Dombrowski Julia C , Feaster Daniel J , Gebo Kelly A , Marshall Brandon D L , Mehta Shruti H , Metsch Lisa R , Pandya Ankur , Schackman Bruce R , Strathdee Steffanie A , Nosyk Bohdan ,   Localized HIV Modeling Study Group, Behrends Czarina N , Del Rio Carlos , Dombrowski Julia C , Feaster Daniel J , Gebo Kelly A , Marshall Brandon D L , Mehta Shruti H , Metsch Lisa R , Nosyk Bohdan , Pandya Ankur , Schackman Bruce R , Strathdee Steffanie A , Golden Matthew , Kirk Gregory , Montaner Julio , Shoptaw Steven , Behrends Czarina N , Del Rio Carlos , Dombrowski Julia C , Feaster Daniel J , Gebo Kelly A , Marshall Brandon D L , Mehta Shruti H , Metsch Lisa R , Nosyk Bohdan , Pandya Ankur , Schackman Bruce R , Strathdee Steffanie A , Golden Matthew , Kirk Gregory , Montaner Julio , Shoptaw Steven 
Published: March 2020

Abstract

Background
Persons who inject drugs (PWID) are at a disproportionately high risk of HIV infection. We aimed to determine the highest-valued combination implementation strategies to reduce the burden of HIV among PWID in 6 US cities.

Methods
Using a dynamic HIV transmission model calibrated for Atlanta, Baltimore, Los Angeles, Miami, New York City, and Seattle, we assessed the value of implementing combinations of evidence-based interventions at optimistic (drawn from best available evidence) or ideal (90% coverage) scale-up. We estimated reduction in HIV incidence among PWID, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios (ICERs) for each city (10-year implementation; 20-year horizon; 2018 $ US).

Results
Combinations that maximized health benefits contained between 6 (Atlanta and Seattle) and 12 (Miami) interventions with ICER values ranging from $94 069/QALY in Los Angeles to $146 256/QALY in Miami. These strategies reduced HIV incidence by 8.1% (credible interval [CI], 2.8%–13.2%) in Seattle and 54.4% (CI, 37.6%–73.9%) in Miami. Incidence reduction reached 16.1%–75.5% at ideal scale.

Conclusions
Evidence-based interventions targeted to PWID can deliver considerable value; however, ending the HIV epidemic among PWID will require innovative implementation strategies and supporting programs to reduce social and structural barriers to care.
Preservation of fertility in patients with hematological malignancies
Authors: Ashizawa Masahiro , Kanda Yoshinobu 
Published: March 2020

Abstract
Oncofertility is the medical field that bridges oncology and reproduction that seeks to give healthcare providers and patients the opportunity to optimize residual fertility. The treatment for hematological malignancies carries gonadal toxicity, so that the preservation of fertility should be considered in all patients in childhood, adolescence and young adulthood. Most patients who receive only chemotherapy remain fertile, whereas those who receive regimens consisting of high-dose alkylating agents or total body irradiation can develop permanent infertility. In postpubertal patients, there are established methods for preserving fertility, such as the cryopreservation of sperm, oocytes and embryos. Although ideally performed before the initiation of gonadotoxic treatment, these procedures for fertility preservation can be performed any time prior to the loss of gonadal function. In contrast, a standard option is not available in prepubertal patients, and the preservation of fertility must be sought through experimental methods. Future advances in reproductive medicine may overcome this limitation. Gonadal tissue cryopreservation might be performed in the hope that sperm or mature oocytes could later be extracted from cryopreserved tissue. Healthcare providers, including hematologists, reproductive endocrinologists, nurses, clinical psychotherapists and embryologists, need to optimize the patient’s fertility through shared decision-making while always remaining aware of the rapidly progressing developments in reproductive medicine.
The Irrelevance of Harm for a Theory of Disease
Authors: Muckler Dane , Taylor James Stacey 
Published: March 2020

Abstract
Normativism holds that there is a close conceptual link between disease and disvalue. We challenge normativism by advancing an argument against a popular normativist theory, Jerome Wakefield’s harmful dysfunction account. Wakefield maintains that medical disorders are breakdowns (dysfunctions) in evolved mechanisms that cause significant harm to the organism. We argue that Wakefield’s account is not a promising way to distinguish between disease and health because being harmful is neither necessary nor sufficient for a dysfunction to be a disorder. Counterexamples to the harmful dysfunction account are considered, such as mild infections, perceptual deficits, and beneficial illnesses. Then we consider two ways of amending the harmful dysfunction account to address these cases and argue that the proposed amendments raise even more serious problems for this account. These problems apply generally to any normativist theory and raise doubts about the entire normative approach to the philosophy of health and disease.
Spatial ecology of copperhead snakes (Agkistrodon contortrix) in response to urban park trails
Authors: Carrasco-Harris Malle F , Bowman Dale , Reichling Steve , Cole Judith A 
Published: March 2020

Abstract
Urban forests and parks are important for recreation and may serve as a natural corridor for commuters. The consequences of human-mediated disturbance in natural areas are documented for avian and mammalian species. Less is known about the consequences of human disturbance on reptile species, specifically snakes, residing in natural refuges within the urban matrix. Thus, we examined the spatial activity of copperheads (Agkistrodon contortrix) in regard to pedestrian trails within an urban forest. We used radio telemetry to track snakes during the active season and estimated distances moved in between relocations, distances to the nearest trail and home range size for individuals. We found sex and season, but not distance to the nearest trail, affected the distance snakes moved. In addition, we observed a weak, positive relationship between home range size and average distance to the trail. Sex, season and body condition did not explain snake distance to the trail, but individual patterns were variable for snakes compared to random locations generated from snake relocations. Our study indicates copperheads may be tolerant of low-level human disturbances found in an urban forest. Further work should be done to quantify levels of disturbance, such as trail use, and compare the behavior of reptiles across urban park types and locations.