bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barriers and Facilitators to Optimal Neuropathic Pain Management: SCI Consumer, Significant Other, and Health Care Provider Perspectives
Authors: Widerstrom-Noga Eva , Anderson Kim D , Perez Salome , Martinez-Arizala Alberto , Calle-Coule Lindsey , Fleming Loriann 
Published: February 2020

Abstract

Objective
Persistent neuropathic pain is a common and often severe consequence of spinal cord injury (SCI). There is a critical need to better understand how to overcome barriers and promote facilitators to optimal pain management. The present study was designed to identify, from the perspectives of persons living with SCI, their significant others, and SCI health care professionals, the barriers and facilitators to optimal pain management for intense neuropathic pain.

Design
Qualitative interviews.

Setting
University laboratory.

Subjects
People with SCI who had experienced intense neuropathic pain for a minimum of a year (N = 15), their significant others (N = 15), and SCI health care providers (N = 15).

Methods
Qualitative interviews were recorded, transcribed, and analyzed based on grounded theory using ATLAS.ti software.

Results
Inadequate access to care, information, or pain management expertise were frequently perceived barriers to optimal pain management across all three groups. Another major barrier was SCI stakeholders’ concerns regarding the risks of adverse effects and addiction to pain medication. Facilitators included having a better understanding of pain and available treatment options, effective patient–provider communication, resilience, and access to nonpharmacological treatment options.

Conclusions
Managing intense neuropathic pain poses significant challenges after SCI. SCI stakeholders felt that accessible treatment options were limited and primarily focused on pain medications with minimal benefit but with significant risks for addiction and adverse effects. Actionable facilitators to optimal pain management after SCI include education regarding neuropathic pain and treatment options for all stakeholders, better communication regarding neuropathic pain among stakeholders, and improved patient access to nonpharmacological treatment options.
The political economy of pension reforms in Europe under financial stress
Authors: Guardiancich Igor , Guidi Mattia 
Published: February 2020

AbstractDespite a substantially unchanged problem load in the last 20 years, EU Member States witnessed a recent surge in pension reforms. Since the Great Recession, external market and political pressures started outcompeting national politics in pension-related decisions. Employing European Commission data on major pension reforms during 2006–2015, we find that governments respond to higher risk premia charged by international financial actors. Macro-policy fundamentals, such as budget deficits, and micro-policy indicators, such as pension spending, instead, only signal the necessity to act. They trigger the reforms in the presence of EU conditionality, that is, in the presence of Excessive Deficit Procedures and Country-Specific Recommendations within the European Semester. These findings deepen our understanding of the Europeanization of social policy, contribute to the literature on the political economy of reforms and testify to the declining role of domestic factors in the politics of the welfare state.
Hybridization and hybrid zone stability between two lizards explained by population genetics and niche quantification
Authors: Cabaña Imanol , Chiaraviglio Margarita , Di Cola Valeria , Guisan Antoine , Broennimann Olivier , Gardenal Cristina N , Rivera Paula C 
Published: February 2020

AbstractUnderstanding the factors that affect hybridization is an important issue in the study of species evolution. In this work, we analyse the genetic structure of two lizard species, Salvator merianae and Salvator rufescens, at a microscale within a climatic niche analysis framework, to reveal the main factors that contribute to the stability of their hybrid zone. We assess the effect of climate in hybridization by quantifying and decomposing the niche overlap of both species. Using a mitochondrial and a nuclear marker, we find that hybridization is frequent and is not restricted to the sympatric region. The gene flow is mainly from S. rufescens to S. merianae, with introgression into the range of S. merianae. Also, S. merianae would have long been present in the area, while S. rufescens appears to be a recent colonizer. The climate contributes to the population structure of S. merianae, but not to that of S. rufescens. The niches occupied by S. rufescens in the hybrid zone and the non-hybrid zone are similar, while the niches of S. merianae are different. Our results do not fit previous models of hybrid zone stability, suggesting the need to develop new models that consider the evolutionary factors that can differentially affect parental species and hybrids.
Rethinking success, integrity, and culture in research (Part 2) — A multi-actor qualitative study on problems of science
Authors: Bonn Noémie Aubert , Pinxten Wim 
Published: February 2020

ABSTRACTBackgroundResearch misconduct and questionable research practices have been the subject of increasing attention in the past few years. But despite the rich body of research available, few empirical works provide the perspectives of non-researcher stakeholders.MethodsTo capture some of the forgotten voices, we conducted semi-structured interviews and focus groups with policy makers, funders, institution leaders, editors or publishers, research integrity office members, research integrity community members, laboratory technicians, researchers, research students, and former-researchers who changed career to inquire on the topics of success, integrity, and responsibilities in science. We used the Flemish biomedical landscape as a baseline to be able to grasp the views of interacting and complementary actors in a system setting.ResultsGiven the breadth of our results, we divided our findings in a two-paper series with the current paper focusing on the problems that affect the quality and integrity of science. We first discovered that perspectives on misconduct, including the core reasons for condemning misconduct, differed between individuals and actor groups. Beyond misconduct, interviewees also identified numerous problems which affect the integrity of research. Issues related to personalities and attitudes, lack of knowledge of good practices, and research climate were mentioned. Elements that were described as essential for success (in the associate paper) were often thought to accentuate the problems of research climates by disrupting research cultures and research environments. Even though everyone agreed that current research climates need to be addressed, no one felt responsible nor capable of initiating change. Instead, respondents revealed a circle of blame and mistrust between actor groups.ConclusionsOur findings resonate with recent debates, and extrapolate a few action points which might help advance the discussion. First, we must tackle how research is assessed. Second, approaches to promote better science should be revisited: not only should they directly address the impact of climates on research practices, but they should also redefine their objective to empower and support researchers rather than to capitalize on their compliance. Finally, inter-actor dialogues and shared decision making are crucial to building joint objectives for change.Trial registrationosf.io/33v3m
Estimating and Testing an Index of Bias Attributable to Composite Outcomes in Comparative Studies
Authors: Diaz-Quijano Fredi Alexander 
Published: February 2020

AbstractObjectiveTo develop an index to evaluate the bias attributable to composite outcomes (BACO) in comparative clinical studies.Study design and SettingI defined the BACO index as the ratio of the logarithm of the association measure (e.g., relative risk) of the composite outcome to that of its most relevant component endpoint (e.g., mortality). Methods to calculate the confidence intervals and test the null hypotheses (BACO index = 1) were described and applied in systematically selected clinical trials. Two other preselected trials were included as “positive controls” for being examples of primary composite outcomes disregarded due to inconsistency with the treatment effect on mortality.ResultsThe BACO index values different from one were classified according to whether the use of composite outcomes overestimated (BACO index >1), underestimated (BACO index between zero and <1), or inverted (BACO index <0) the association between exposure and prognosis. In three of 23 systematically selected trials and the two positive controls, the BACO indices were significantly lower than one (p <0.005).ConclusionBACO index can warn that the composite outcome association is stronger, weaker, or even opposite than that of its most critical component.What is new?BACO index is the ratio of the logarithm of the association measure (e.g., RR) of the composite outcome to the logarithm of the association measure of the component endpoint that represents the study target (e.g., mortality).In comparative studies, the BACO index can be used to evaluate the correspondence between the effect on a composite outcome and that on its most critical component.This index could help to preset rules to make decisions for interpretation of clinical studies.A significant BACO should lead to the caution that the association of the composite is stronger (BACO index >1), weaker (BACO index between zero and <1), or even opposite (BACO index <0) than that of its most critical component.
Transdiagnostic neurocognitive endophenotypes in major psychiatric illness
Authors: Holla Bharath , Dayal Pavithra , Das Aswathy , Bhattacharya Mahashweta , Manjula V , Ithal Dhruva , Balachander Srinivas , Mahadevan Jayant , Nadella Ravi Kumar , Sreeraj Vanteemar S , Benegal Vivek , Reddy Janardhan Y. C. , Mehta Urvakhsh Meherwan ,   ADBS Consortium, Viswanath Biju 
Published: February 2020

AbstractWe aimed to characterize potential transdiagnostic neurocognitive endophenotypes in a large cohort of multiplex families affected with two or more individuals having a major psychiatric illness(MPI) i.e., schizophrenia(SCZ), bipolar disorder(BPAD), substance use disorders(SUD) and obsessive-compulsive disorder(OCD). We recruited 640 individuals that included 256 affected individuals with MPI, 227 of their unaffected first-degree relatives(FDR) and 157 population healthy-controls(PHC). Neurocognitive battery included assessments of executive function, working memory, social cognition, verbal learning and recall. Linear mixed effects models were applied to the neurocognitive components to examine their transdiagnostic and endophenotype status after accounting for demographic and family variables. We also examined the relationship of cognitive domains with diagnosis-specific Family History Density score(FHD).The deficits in cognitive flexibility, working memory and social cognition were transdiagnostic; processing speed was impaired in SCZ and BPAD groups while verbal learning and recall in SCZ, BPAD and SUD groups. These deficits with the exception of social cognition, worsened with age and parental education had protective effect. The unaffected FDRs had deficits in all the domains except processing speed in comparison to PHC; social cognition deficits were comparable to affected individuals. The diagnosis-specific FHD analysis showed that deficits in cognitive flexibility, working memory and social cognition were endophenotypes across disorders.Evaluation of neurocognitive functions across multiple affected individuals in a large multiplex family-based cross-disorder cohort, has the potential to elucidate transdiagnostic as well as endophenotype vulnerabilities to psychiatric illness. This study adds to the emerging conceptualization of psychiatric illness as a combination of both diagnosis-specific and transdiagnostic markers.
Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19)
Authors: Li Ruiyun , Pei Sen , Chen Bin , Song Yimeng , Zhang Tao , Yang Wan , Shaman Jeffrey 
Published: February 2020

AbstractBackgroundEstimation of the fraction and contagiousness of undocumented novel coronavirus (COVID-19) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Many mild infections are typically not reported and, depending on their contagiousness, may support stealth transmission and the spread of documented infection.MethodsHere we use observations of reported infection and spread within China in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with the emerging coronavirus, including the fraction of undocumented infections and their contagiousness.ResultsWe estimate 86% of all infections were undocumented (95% CI: [82%-90%]) prior to the Wuhan travel shutdown (January 23, 2020). Per person, these undocumented infections were 52% as contagious as documented infections ([44%-69%]) and were the source of infection for two-thirds of documented cases. Our estimate of the reproductive number (2.23; [1.77-3.00]) aligns with earlier findings; however, after travel restrictions and control measures were imposed this number falls considerably.ConclusionsA majority of COVID-19 infections were undocumented prior to implementation of control measures on January 23, and these undocumented infections substantially contributed to virus transmission. These findings explain the rapid geographic spread of COVID-19 and indicate containment of this virus will be particularly challenging. Our findings also indicate that heightened awareness of the outbreak, increased use of personal protective measures, and travel restriction have been associated with reductions of the overall force of infection; however, it is unclear whether this reduction will be sufficient to stem the virus spread.
A model simulation study on effects of intervention measures in Wuhan COVID-19 epidemic
Authors: Zhou Guopeng , Chi Chunhua 
Published: February 2020

AbstractBackgroundIn the beginning of January 2020, new unknown virus pneumonia cases started to emerge in local hospitals in Wuhan, China. This virus epidemic quickly became a public health emergency of international concern by the WHO. Enormous amount of medical supplies as well as healthcare personals from other provinces were mobilized to support Wuhan. This current work tent to help people understanding how infectious disease spread and the purpose and consequences of various efforts based on simulation model.Methoda simulation model was created using known parameters. R0 set to 3 and mean incubation time to be 7.5days. the epidemic was divided to 3 periods. Simulation would run 50 times to mimic different patient0 status. Personal activity index was used to mimic different level of control measures. 141427709 simulated patients were created. Cumulation number of patients at the end of period 1 (day50) is 2868.7±1739.0. Total infected patients could be 913396.5 ± 559099.9 by the end of period 2 (day70) in free transmission state. And at day90, total patients number is 913396.5 ± 559099.9.ConclusionCOVID-19 is a novel severe respiratory disease. This will put great burden on the shoulder of healthcare workers as well as on medical hardware and supplements. Current strict control measures help to contain disease from spreading. An early detecting, reporting and fast reacting system needs to be setup to prevent future unknown infectious disease.
Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary, CTCF-mediated chromatin looping and a long-range intergenic enhancer
Authors: Cheng Jessica , Clayton Joshua S. , Acemel Rafael D. , Zheng Ye , Taylor Rhonda L. , Keleş Sündüz , Franke Martin , Boackle Susan A. , Harley John B. , Quail Elizabeth , Gómez-Skarmeta José L. , Ulgiati Daniela 
Published: February 2020

ABSTRACTThe Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression ofCR2and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within theCR1gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2andCD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.SIGNIFICANCEThe complement system is a complex network of protein effectors and regulators that play a key role in immunity. Several regulators of complement response are clustered within Regulators of Complement Activation (RCA) gene family. Its members are all functionally, structurally, and genetically related. However, the functional relevance of this close gene organisation is unknown. We show that the clustering of the RCA members is due to shared long-range regulatory elements and physical chromatin looping. We also reveal that the RCA genes are divided into two adjacent chromatin domains and a domain boundary falls within the body of an expressed gene (CR1). Overall, our findings in the RCA cluster offer insights into their evolution, biology and roles in disease.
Coral reef restoration efforts in Latin American countries and territories
Authors: Bayraktarov Elisa , Banaszak Anastazia T. , Montoya Maya Phanor , Kleypas Joanie , Arias-González Jesús E. , Blanco Macarena , Calle Triviño Johanna , Charuvi Nufar , Cortés Useche Camilo , Galván Victor , García Salgado Miguel A. , Gnecco Mariana , Guendulain García Sergio D. , Hernández Delgado Edwin A. , Marín Moraga José A. , Maya María Fernanda , Mendoza Quiroz Sandra , Cervantes Samantha Mercado , Morikawa Megan , Nava Gabriela , Pizarro Valeria , Sellares-Blasco Rita I. , Suleimán Ramos Samuel E. , Villalobos Cubero Tatiana , Villalpando María , Frías-Torres Sarah 
Published: February 2020

AbstractCoral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, bleaching and diseases. In areas where natural recovery is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions. The symposium highlighted that solutions and discoveries from long-term and ongoing coral reef restoration projects in Spanish-speaking countries in the Caribbean and Eastern Tropical Pacific were not well known internationally. Therefore, a meeting of scientists and practitioners working in these locations was held to compile the data on the extent of coral reef restoration efforts, advances and challenges. Here, we present unpublished data from 12 coral reef restoration case studies from five Latin American countries, describe their motivations and techniques used, and provide estimates on total annual project cost per unit area of reef intervened, spatial extent as well as project duration. We found that most projects used direct transplantation, the coral gardening method, micro-fragmentation or larval propagation, and aimed to optimize or scale-up restoration approaches (51%) or provide alternative, sustainable livelihood opportunities (15%) followed by promoting coral reef conservation stewardship and re-establishing a self-sustaining, functioning reef ecosystem (both 13%). Reasons for restoring coral reefs were mainly biotic and experimental (both 42%), followed by idealistic and pragmatic motivations (both 8%). The median annual total cost from all projects was $93,000 USD (range: $10,000 USD - $331,802 USD) (2018 dollars) and intervened a median spatial area of 1 ha (range: 0.06 ha - 8.39 ha). The median project duration was 3 years; however, projects have lasted up to 17 years. Project feasibility was high with a median of 0.7 (range: 0.5 - 0.8). This study closes the knowledge gap between academia and practitioners and overcomes the language barrier by providing the first comprehensive compilation of data from ongoing coral reef restoration efforts in Latin America.
APA-Scan: Detection and Visualization of 3’-UTR Alternative Polyadenylation with RNA-seq and 3’-end-seq Data
Authors: Fahmi Naima Ahmed , Ahmed Khandakar Tanvir , Chang Jae-Woong , Nassereddeen Heba , Fan Deliang , Yong Jeongsik , Zhang Wei 
Published: February 2020

AbstractBackgroundThe eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3’-untranslated region (3’-UTR) of mRNA produces transcripts with shorter or longer 3’-UTR. Often, 3’-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3’-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3’-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3’-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3’-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations.MethodsAPA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3’-UTR transcripts in the RNA-seq data. APA-Scan works in three major steps: (i) calculate the read coverage of the 3’-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3’-UTR annotation and read coverage on the 3’-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user’s manual are freely available athttps://github.com/compbiolabucf/APA-Scan.ResultAPA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3’-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3’-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3’ -UTR APA events and improve genome annotation.ConclusionAPA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3’-UTR APA events. The pipeline integrates both RNA-seq and 3’-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.