bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIMES: a tool for comparing species partition
Authors: Ducasse Jacques , Ung Visotheary , Lecointre Guillaume , Miralles Aurélien 
Published: December 2019

Abstract

Motivation
Species delimitation (SD) is on the verge of becoming a fully fledged research field in systematics, but the variety of available approaches tends to result in significant—sometimes striking—incongruences, when tested comparatively with a given taxonomic sampling.

Results
We present LIMES, an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. The program implements four different previously published indexes, and allows their automated calculation.

Availability and implementation
LIMES is freely downloadable at www.limes.cnrs.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Measurement Models in Social Work Research: A Data-Based Illustration of Four Confirmatory Factor Models and Their Conceptual Application
Authors: Cimino Andrea N , Killian Michael O , Von Ende Adam K , Segal Elizabeth A 
Published: December 2019

AbstractConfirmatory factor analysis (CFA) is a valuable tool for social work researchers to examine validity of measurements and other latent constructs. Best practice recommendations are to specify and evaluate the fit of multiple models, balancing plausibility, parsimony and quantitative indices. However, little attention has been given to the conceptual and theoretical implications of CFA model variations. This article offers a brief report on the state of CFA modelling published in social work research and presents a data-based illustration of four CFA models of a measure of empathy including a single-factor, correlated factors, higher order and bifactor models. We present results from each model and describe the models’ conceptual application with substantive explanation and theoretical application to the measurement of empathy. Syntax for all models in Mplus, R, Stata and EQS programmes are provided for reference. As familiarity with CFA and latent variable modelling methods grows, researchers must understand the theory-based implications of varying measurement models and test which model best represents their data and explain their conceptual application.
Temporal DNA methylation pattern and targeted therapy in colitis-associated cancer
Authors: Li Junshu , Su Xiaolan , Dai Lei , Chen Na , Fang Chao , Dong Zhexu , Fu Jiamei , Yu Yan , Wang Wenshuang , Zhang Hantao , Wang Huiling , Ji Yanhong , Liu Yi , Cheng Lin , Shi Gang , Zhang Shuang , Yang Yang , Deng Hongxin 
Published: December 2019

Abstract
DNA methylation plays a crucial role in the pathogenesis of various diseases, including colorectal cancer (CRC). However, the global and temporal DNA methylation pattern during initiation and progression of colitis-associated cancer (CAC) are still unknown, including the potential therapeutic strategy of targeting methylation for CAC. In the present study, the global DNA methylation pattern was determined at different time points during CAC using DNA methylation sequencing, followed by the Starburst plot integrating alterations and potential functional prediction analysis. After demonstrating the regulatory role of DNA methyltransferases (DNMTs) on the expression of hub-genes in CRC cells, DNMT inhibitors were administered to treat CAC mice. Our results indicated that 811 genes were hypermethylated at different time points during initiation and progression of CAC. Genes that were downregulated and hypermethylated during CAC, including hub-genes BAD and inositol polyphosphate phosphatase-like 1 (INPPL1), were involved in MAPK signaling pathways, kit receptor signaling pathways, apoptosis and EGF/EGFR signaling pathways. Upregulated DNMTs (DNMT1, DNMT3A and DNMT3B) mediated downregulation and hypermethylation of BAD and INPPL1 in CAC and CRC cells. Low doses of DNMT inhibitors (decitabine (DAC) and azacitidine (AZA)) exerted efficient antitumor effects in CAC, accompanied with upregulation of BAD and INPPL1 expression, and apoptosis induction. In summary, the present study demonstrates the temporal DNA methylation pattern during CAC and provides a novel therapeutic strategy for treating this disease.
Subclinical Vascular Disease in Children With Human Immunodeficiency Virus in Uganda Is Associated With Intestinal Barrier Dysfunction
Authors: Dirajlal-Fargo Sahera , Albar Zainab , Bowman Emily , Labbato Danielle , Sattar Abdus , Karungi Christine , Longenecker Chris T , Nazzinda Rashida , Funderburg Nicholas , Kityo Cissy , Musiime Victor , McComsey Grace A 
Published: December 2019

Abstract

Background
The risk of cardiovascular disease (CVD) and its mechanisms in children living with perinatally acquired HIV (PHIV) in sub-Saharan Africa has been understudied.

Methods
Mean common carotid artery intima-media thickness (IMT) and pulse-wave velocity (PWV) were evaluated in 101 PHIV and 96 HIV-negative (HIV−) children. PHIV were on ART, with HIV-1 RNA levels ≤400 copies/mL. We measured plasma and cellular markers of monocyte activation, T-cell activation, oxidized lipids, and gut integrity.

Results
Overall median (interquartile range, Q1–Q3) age was 13 (11–15) years and 52% were females. Groups were similar by age, sex, and BMI. Median ART duration was 10 (8–11) years. PHIV had higher waist–hip ratio, triglycerides, and insulin resistance (P ≤ .03). Median IMT was slightly thicker in PHIVs than HIV− children (1.05 vs 1.02 mm for mean IMT and 1.25 vs 1.21 mm for max IMT; P &lt; .05), while PWV did not differ between groups (P = .06). In univariate analyses, lower BMI and oxidized LDL, and higher waist–hip ratio, hsCRP, and zonulin correlated with thicker IMT in PHIV (P ≤ .05). After adjustment for age, BMI, sex, CD4 cell count, triglycerides, and separately adding sCD163, sCD14, and hsCRP, higher levels of intestinal permeability as measured by zonulin remained associated with IMT (β = 0.03 and 0.02, respectively; P ≤ .03).

Conclusions
Our study shows that African PHIV have evidence of CVD risk and structural vascular changes despite viral suppression. Intestinal intestinal barrier dysfunction may be involved in the pathogenesis of subclinical vascular disease in this population.
High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains
Authors: de Melo Beatriz Souza Toscano , Mendes-Marques Carina Lucena , Campos Túlio de Lima , Almeida Alzira Maria Paiva de , Leal Nilma Cintra , Xavier Danilo Elias 
Published: December 2019

ABSTRACT
Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA–DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.
Mortality and Obesity Among U.S. Older Adults: The Role of Polygenic Risk
Authors: Vinneau Justin M , Huibregtse Brooke M , Laidley Thomas M , Goode Joshua A , Boardman Jason D 
Published: December 2019

Abstract

Objectives
To examine the relationship between obesity and mortality as a function of polygenic risk for obesity among older U.S. adults.

Method
Using data from the 1994–2014 Health and Retirement Study in conjunction with genome-wide data, we evaluated the risk of mortality as a function of obesity classification, an individual’s polygenic risk score (PGS) for obesity, and their interaction, stratified by sex. We conducted our analyses using cox proportional hazard models.

Results
Among those with an average PGS for obesity (8,143 [68.8%]), obese I (hazard ratio [HR] = 0.79, p = .336) adults show no difference in their risk for mortality and obese II/III (HR = 3.17, p = .000) adults present higher risk of mortality relative to non-obese adults. The interaction of obesity classification and PGS suggests that obese II/III respondents with low PGS in the total sample (HR = 2.71, p = .006) and among women (HR = 3.02, p = .023) are at significantly higher risk of death when compared to obese II/III respondents with average or high PGS.

Discussion
We posit that these findings suggest that the pathway to obesity, in this case, more socio-behavioral rather than genetic, may influence subsequent risk of death in older adults. We suggest that practitioners and population researchers be mindful of these pathways as to better identify and understand mortality risk.
The political economy of universal health coverage: a systematic narrative review
Authors: Rizvi Syed Shahiq , Douglas Rundell , Williams Owain D , Hill Peter S 
Published: December 2019

Abstract
The uptake and implementation of universal health coverage (UHC) is primarily a political, rather than a technical, exercise, with contested ideas and diverse stakeholders capable of facilitation or resistance—even veto—of the policy uptake. This narrative systematic review, undertaken in 2018, sought to identify all peer-reviewed publications dealing with concepts relating to UHC through a political economy framing. Of the 627 papers originally identified, 55 papers were directly relevant, with an additional eight papers added manually on referral from colleagues. The thematic analysis adapted Fox and Reich’s framework of ideas and ideologies, interests and institutions to organize the analysis. The results identified a literature strong in its exploration of the ideologies and ideas that underpin UHC, but with an apparent bias in authorship towards more rights-based, left-leaning perspectives. Despite this, political economy analyses of country case studies suggested a more diverse political framing for UHC, with the interests and institutions engaged in implementation drawing on pragmatic and market-based mechanisms to achieve outcomes. Case studies offered limited detail on the role played by specific interests, though the influence of global development trends was evident, as was the role of donor organizations. Most country case studies, however, framed the development of UHC within a narrative of national ownership, with steps in implementation often critical political milestones. The development of institutions for UHC implementation was predicated largely on available infrastructure, with elements of that infrastructure—federal systems, user fees, pre-existing insurance schemes—needing to be accommodated in the incremental progress towards UHC. The need for technical competence to deliver ideological promises was underlined. The review concludes that, despite the disparate sources for the analyses, there is an emerging shared narrative in the growing literature around the political economy of UHC that offers an increasing awareness of the political dimensions to UHC uptake and implementation.
Environmental enrichment during the chronic phase after experimental stroke promotes functional recovery without synergistic effects of EphA4 targeted therapy
Authors: de Boer Antina , Storm Annet , Gomez-Soler Maricel , Smolders Silke , Rué Laura , Poppe Lindsay , B  Pasquale Elena , Robberecht Wim , Lemmens Robin 
Published: December 2019

Abstract
Worldwide, stroke is the main cause of long-term adult disability. After the initial insult, most patients undergo a subacute period with intense plasticity and rapid functional improvements. This period is followed by a chronic phase where recovery reaches a plateau that is only partially modifiable by rehabilitation. After experimental stroke, various subacute rehabilitation paradigms improve recovery. However, in order to reach the best possible outcome, a combination of plasticity-promoting strategies and rehabilitation might be necessary. EphA4 is a negative axonal guidance regulator during development. After experimental stroke, reduced EphA4 levels improve functional outcome with similar beneficial effects upon the inhibition of EphA4 downstream targets. In this study, we assessed the effectiveness of a basic enriched environment in the chronic phase after photothrombotic stroke in mice as well as the therapeutic potential of EphA4 targeted therapy followed by rehabilitation. Our findings show that environmental enrichment in the chronic phase improves functional outcome up to 2 months post-stroke. Although EphA4 levels increase after experimental stroke, subacute EphA4 inhibition followed by environmental enrichment does not further increase recovery. In conclusion, we show that environmental enrichment during the chronic phase of stroke improves functional outcome in mice with no synergistic effects of the used EphA4 targeted therapy.
On the Discretized Sum-Product Problem
Authors: Guth Larry , Katz Nets Hawk , Zahl Joshua 
Published: December 2019

Abstract
We give a new proof of the discretized ring theorem for sets of real numbers. As a special case, we show that if $A\subset \mathbb {R}$ is a $(\delta ,1/2)_1$-set in the sense of Katz and Tao, then either $A+A$ or $A.A$ must have measure at least $|A|^{1-\frac {1}{68}}$.
De Novo Genotypic Heterogeneity in the UL56 Region in Cytomegalovirus-Infected Tissues: Implications for Primary Letermovir Resistance
Authors: Jo Horim , Kwon Da Eun , Han Sang Hoon , Min Seo Yeon , Hong Yeon-Mi , Lim Beom Jin , Lee Kyoung Hwa , Jo Jeong-Hyeon 
Published: December 2019

AbstractBackgroundLetermovir, an inhibitor of unique long (UL)56-encoded cytomegalovirus (CMV)-terminase, shows prophylactic effects with low-grade adverse events in hematopoietic stem cell transplant recipients. Despite few case reports on acquired letermovir resistance, the frequency of de novo amino acid (A.A.) changes encoded by UL56 in CMV-infected tissues is unclear.MethodsWe analyzed CMV UL56 sequences between the conserved region IV and variable region I in 175 formalin-fixed, paraffin-embedded tissues obtained from 147 patients showing positive CMV immunochemical staining between November 2012 and October 2016. Nucleotides 552–1330 of the open reading frame of UL56 were amplified with 5 primers and sequenced by a dideoxy fluorescence-based cycle.ResultsSix (3.4%) tissues from 4 (2.7%) patients harbored A.A. substitutions. There were no known potent resistant mutations. However, we found C325Y in 2 tissues from 1 patient, along with other mutations. Four novel A.A. changes, which have not been observed in previous in vitro experiments, were identified (T244I, S301T, G312V, and M434I). Most (9 of 11, 81.8%) of the A.A. changes occurred between the codons 301 and 325 present between the conserved regions V and VI.ConclusionsThe treatment difficulties associated with letermovir resistance in a clinical setting need to be verified before its widespread use.
The Interleukin (IL) 17R/IL-22R Signaling Axis Is Dispensable for Vulvovaginal Candidiasis Regardless of Estrogen Status
Authors: Peters Brian M , Coleman Bianca M , Willems Hubertine M E , Barker Katherine S , Aggor Felix E Y , Cipolla Ellyse , Verma Akash H , Bishu Srinivas , Huppler Anna H , Bruno Vincent M , Gaffen Sarah L 
Published: December 2019

AbstractCandida albicans, a ubiquitous commensal fungus that colonizes human mucosal tissues and skin, can become pathogenic, clinically manifesting most commonly as oropharyngeal candidiasis and vulvovaginal candidiasis (VVC). Studies in mice and humans convincingly show that T-helper 17 (Th17)/interleukin 17 (IL-17)–driven immunity is essential to control oral and dermal candidiasis. However, the role of the IL-17 pathway during VVC remains controversial, with conflicting reports from human data and mouse models. Like others, we observed induction of a strong IL-17–related gene signature in the vagina during estrogen-dependent murine VVC. As estrogen increases susceptibility to vaginal colonization and resulting immunopathology, we asked whether estrogen use in the standard VVC model masks a role for the Th17/IL-17 axis. We demonstrate that mice lacking IL-17RA, Act1, or interleukin 22 showed no evidence for altered VVC susceptibility or immunopathology, regardless of estrogen administration. Hence, these data support the emerging consensus that Th17/IL-17 axis signaling is dispensable for the immunopathogenesis of VVC.
Quality healthcare in extreme adversity: Developing a framework for action
Authors: Leatherman Sheila , Tawfik Linda , Jaff Dilshad , Jaworski Grace , Neilson Matthew , Letaief Mondher , Syed Shamsuzzoha Babar 
Published: December 2019

AbstractQuality issue: Improving quality of care has become a global health priority to improve health outcomes and strengthen health systems, particularly in the context of achieving universal health coverage. Initial assessment: The delivery of quality essential health services in settings of extreme adversity, such as fragile, conflict-affected, vulnerable or disaster contexts, has been identified as a high priority globally to address the massive level of need. Choice of solution: This paper provides an action framework to systematically address the quality of health services for state and non-state actors working in such settings. The framework is designed to be practical, comprehensible and simple in adoption and implementation. It describes challenges, a set of medical needs and population priorities, a menu of quality-related interventions, and a hierarchy of health system levels defining the roles and responsibilities of key actors. Conclusion: Optimizing the use of limited resources in delivering the best quality possible in ‘the hardest of the hard settings’ is imperative.
Use and impact of an online community for hospital patients
Authors: Haldar Shefali , Mishra Sonali R , Kim Yoojung , Hartzler Andrea , Pollack Ari H , Pratt Wanda 
Published: December 2019

AbstractObjectiveAlthough patient-peer support technologies have demonstrated effectiveness in a variety of health contexts—including diabetes, weight loss, and cancer—less is known about how hospitalized patients can benefit from this support. We investigated the nature of peer support in the hospital and the impact this support had on patients’ hospital stays.Materials and MethodsWe created a technology, resembling an online health community, in which patients could exchange advice about their hospitalization. We deployed it at 1 pediatric hospital and 1 adult hospital. With 30 participants, we conducted bedside interviews, observed how they used the technology during their hospitalization, and completed follow-up phone interviews.ResultsParticipants shared advice about several topics, including adjusting to the hospital and building relationships with providers. Contrary to concerns that such a system would primarily serve as a place for patients to “complain,” sentiment analysis showed that 23 of 36 (64%) of the shared advice reflected positive sentiment. Patients also reported positive impacts to their quality, safety, and hospital experience due to the inpatient peer support community.DiscussionParticipants benefited from peer support that transcended diagnoses and individual health conditions. The shared experience of being in the hospital was sufficient to yield valuable and practical peer support. Participants who did not contribute their own advice still experienced benefits from reading their peers’ advice.ConclusionsOur study demonstrated the positive nature of peer advice exchanged, and the benefits of this advice on patients’ hospital stays. Inpatient peer support technologies could be an additional resource for patients to engage in their care.
Home Is Where the Heart Is: Identity, Return and the Toleka Bicycle Taxi Union in Congo’s Equateur
Authors: Carayannis Tatiana , Pangburn Aaron 
Published: December 2019

Abstract
Since the end of the 2006 post-war transition, the Democratic Republic of Congo (DRC) and the international community have struggled to design, finance and implement a host of national and regional disarmament, demobilization and reintegration (DDR) programmes. The weak capacity of implementing institutions, widespread corruption, funding gaps, Western-driven processes and a misdiagnosis of local needs have all been raised as core reasons behind failures. Little is known about how processes of ex-combatant return shape and reshape public authority, where former combatants return to, how they negotiate and experience ‘return’ and how viable ways of life are successfully constituted post return. While many ex-combatants in the DRC continue to be re-recruited into militia groups, one group that has reintegrated successfully is the Toleka—a several-thousand-strong group of ex-combatants who returned (or remained) in the provincial capital of Mbandaka (Equateur province). The Toleka formed a bicycle-taxi organization and unionized its membership, providing protections and collective-bargaining authority to the group, while providing a public good. It also helped to reshape identities, produce a sense of civilian solidarity and provide a bridging function from life in the military. This article looks at how this organization was formed, how the former fighters identified and capitalized on a local need and the conditions that allowed them to successfully unionize and protect their rights as they re-entered civilian life. Based on extensive fieldwork and interviews, this article seeks to understand a case of ‘successful’ return in a region with few such successes.