bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination
Authors: Boyer Benjamin , Danilowicz Claudia , Prentiss Mara , Prévost Chantal 
Published: July 2019

AbstractHomologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
Simultaneous precise editing of multiple genes in human cells
Authors: Riesenberg Stephan , Chintalapati Manjusha , Macak Dominik , Kanis Philipp , Maricic Tomislav , Pääbo Svante 
Published: July 2019

Abstract
When double-strand breaks are introduced in a genome by CRISPR they are repaired either by non-homologous end joining (NHEJ), which often results in insertions or deletions (indels), or by homology-directed repair (HDR), which allows precise nucleotide substitutions to be introduced if a donor oligonucleotide is provided. Because NHEJ is more efficient than HDR, the frequency with which precise genome editing can be achieved is so low that simultaneous editing of more than one gene has hitherto not been possible. Here, we introduced a mutation in the human PRKDC gene that eliminates the kinase activity of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This results in an increase in HDR irrespective of cell type and CRISPR enzyme used, sometimes allowing 87% of chromosomes in a population of cells to be precisely edited. It also allows for precise editing of up to four genes simultaneously (8 chromosomes) in the same cell. Transient inhibition of DNA-PKcs by the kinase inhibitor M3814 is similarly able to enhance precise genome editing.
The association of beta-blocker use with mortality in elderly patients with congestive heart failure and advanced chronic kidney disease
Authors: Molnar Amber O , Petrcich William , Weir Matthew A , Garg Amit X , Walsh Michael , Sood Manish M 
Published: July 2019

Abstract

Background
Whether the survival benefit of β-blockers in congestive heart failure (CHF) from randomized trials extends to patients with advanced chronic kidney disease (CKD) [estimated glomerular filtration rate (eGFR) &lt;30 mL/min/1.73 m2 but not receiving dialysis] is uncertain.

Methods
This was a retrospective cohort study using administrative datasets. Older adults from Ontario, Canada, with incident CHF (median age 79 years) from April 2002 to March 2014 were included. We matched new users of β-blockers to nonusers on age, sex, eGFR categories (&gt;60, 30–60, &lt;30), CHF diagnosis date and a high-dimensional propensity score. Using Cox proportional hazards models, we examined the association of β-blocker use versus nonuse with all-cause mortality.

Results
We matched 5862 incident β-blocker users (eGFR &gt;60, n = 3136; eGFR 30–60, n = 2368; eGFR &lt;30, n = 358). There were 2361 mortality events during follow-up. β-Blocker use was associated with reduced all-cause mortality [adjusted hazard ratio (HR) 0.58, 95% confidence interval (CI) 0.54–0.64]. This result was consistent across all eGFR categories (&gt;60: adjusted HR 0.55, 95% CI 0.49–0.62; 30–60: adjusted HR 0.63, 95% CI 0.55–0.71; &lt;30: adjusted HR 0.55, 95% CI 0.41–0.73; interaction term, P = 0.30). The results were consistent in an intention-to-treat analysis and with β-blocker use treated as a time-varying exposure.

Conclusions
β-Blocker use is associated with reduced all-cause mortality in elderly patients with CHF and CKD, including those with an eGFR &lt;30. Randomized trials that examine β-blockers in patients with CHF and advanced CKD are needed.
Sensor Modalities for Brain-Computer Interface Technology: A Comprehensive Literature Review
Authors: Martini Michael L , Oermann Eric Karl , Opie Nicholas L , Panov Fedor , Oxley Thomas , Yaeger Kurt 
Published: July 2019

Abstract
Brain-computer interface (BCI) technology is rapidly developing and changing the paradigm of neurorestoration by linking cortical activity with control of an external effector to provide patients with tangible improvements in their ability to interact with the environment. The sensor component of a BCI circuit dictates the resolution of brain pattern recognition and therefore plays an integral role in the technology. Several sensor modalities are currently in use for BCI applications and are broadly either electrode-based or functional neuroimaging-based. Sensors vary in their inherent spatial and temporal resolutions, as well as in practical aspects such as invasiveness, portability, and maintenance. Hybrid BCI systems with multimodal sensory inputs represent a promising development in the field allowing for complimentary function. Artificial intelligence and deep learning algorithms have been applied to BCI systems to achieve faster and more accurate classifications of sensory input and improve user performance in various tasks. Neurofeedback is an important advancement in the field that has been implemented in several types of BCI systems by showing users a real-time display of their recorded brain activity during a task to facilitate their control over their own cortical activity. In this way, neurofeedback has improved BCI classification and enhanced user control over BCI output. Taken together, BCI systems have progressed significantly in recent years in terms of accuracy, speed, and communication. Understanding the sensory components of a BCI is essential for neurosurgeons and clinicians as they help advance this technology in the clinical setting.
Is Excellence in the Cards?
Authors: McPoil Thomas G 
Published: July 2019

ABSTRACT
Thomas G. McPoil, PT, PhD, FAPTA, is Emeritus Professor of Physical Therapy at Regis University, Denver, Colorado, and Emeritus Regents’ Professor of Physical Therapy at Northern Arizona University. He has served as an Adjunct Honorary Professor in the School of Physiotherapy at the University of Queensland, Brisbane, Australia, and currently serves as a consultant to the Physical Therapy Orthotics Clinic at Denver Health Medical Center, Denver, Colorado. Dr. McPoil is known nationally and internationally for his scholarly contributions that have systematically examined foot and ankle function from both scientific and clinical perspectives. Dr. McPoil is an author or coauthor of 130 publications in peer-reviewed journals, coeditor of 2 books, and coauthor of 6 book chapters. His work reaches beyond the profession of physical therapy, as he served on the editorial boards of Foot and Ankle International, the Journal of Foot and Ankle Research, and Research in Sports Medicine and is currently on the editorial boards of the Journal of the American Podiatric Medical Association and The FOOT.
Dr McPoil received his PhD in kinesiology with a specialization in biomechanics from University of Illinois at Urbana–Champaign. He holds an MS in physical education with a specialization in athletic training from Louisiana State University and a BA in physical education from the California State University, Sacramento. During his career, he has held faculty appointments at the University of Illinois at Chicago, Northern Arizona University, and Regis University. Dr McPoil’s clinical practice has focused on the management of chronic orthopedic foot and ankle disorders for the past 38 years.
Dr McPoil is the founding president of the Foot and Ankle Special Interest Group of the Academy of Orthopaedic Physical Therapy. He has served as Vice President of the Academy of Orthopaedic Physical Therapy and as the Treasurer of the Journal of Orthopaedic and Sports Physical Therapy. He has received numerous teaching awards, including APTA’s Dorothy E. Baethke & Eleanor J. Carlin Award for Excellence in Academic Teaching and the Academy of Orthopaedic Physical Therapy’s James A. Gould Excellence in Teaching Orthopaedic Physical Therapy Award. He is a recipient of a Fulbright Senior Scholar Award, the William J. Stickel Award for Research in Podiatric Medicine, the Academy of Orthopaedic Physical Therapy’s Stanley Paris Distinguished Service Award and was elected a Catherine Worthingham Fellow of APTA in 2007.
Long-Term Impacts of Childhood Medicaid Expansions on Outcomes in Adulthood
Authors: Brown David W , Kowalski Amanda E , Lurie Ithai Z 
Published: July 2019

Abstract
We use administrative data from the Internal Revenue Service to examine long-term impacts of childhood Medicaid eligibility expansions on outcomes in adulthood at each age from 19 to 28. Greater Medicaid eligibility increases college enrolment and decreases fertility, especially through age 21. Starting at age 23, females have higher contemporaneous wage income, although male increases are imprecise. Together, both genders have lower mortality. These adults collect less from the earned income tax credit and pay more in taxes. Cumulatively from ages 19 to 28, at a 3% discount rate, the federal government recoups 58 cents of each dollar of its “investment” in childhood Medicaid.
The many faces of psoriatic arthritis: their genetic determinism
Authors: Winchester Robert , FitzGerald Oliver 
Published: July 2019

AbstractIn this review, we propose a model of PsA as a complex genetically determined autoimmune-mediated disease having a heterogeneous variety of subphenotypes, with each subphenotype under the control of a different susceptibility-associated HLA allele. Since the specific HLA molecules encoded by each susceptibility allele dominantly select a T cell repertoire with the property of recognizing different peptides, we hypothesize each subphenotype reflects a distinct adaptive autoimmune response directed to different target molecules that is mediated by T cells within each selected repertoire. The interaction among the patients’ susceptibility alleles in the selection of their T cell repertoires determines a spectrum of overall clinical disease severity, varying from mild to severe. We further speculate that these different immune responses may result in activation of different immune effector pathways, which might therefore respond differently to various specific biologic agents.
Defining remission in rheumatoid arthritis: does it matter to the patient? A comparison of multi-dimensional remission criteria and patient reported outcomes
Authors: Gul Hanna L , Eugenio Gisella , Rabin Thibault , Burska Agata , Parmar Rekha , Wu Jianhua , Ponchel Frederique , Emery Paul 
Published: July 2019

Abstract

Objectives
In a cross-sectional study, we evaluated the prevalence of ‘multi-dimensional remission’ (MDR) and its component parameters, assessed using objective measures in a cohort of RA patients in treatment-induced DAS28-remission, and their relationship with patient-reported outcome measures. We sought to confirm the feasibility and face validity of the MDR construct, providing a platform for future longitudinal studies in which its clinical utility might be further established.

Methods
605 patients were selected from an inflammatory arthritis register using DAS28(CRP)<2.6. Demographic, clinical and patients reported outcomes (PRO) data were collected. Ultrasound power doppler synovitis (n = 364) and T-cell subsets (n = 297) were also measured. Remission using clinical parameters was defined as: tender and swollen joint count (TJC/SJC) and CRP all ⩽1; ultrasound remission: total power doppler = 0 and T cell remission: positive normalized naïve T-cell frequency. MDR was defined as the achievement of all three dimensions.

Results
Overall, only 53% (321/605) of the patients achieved clinical parameters, failures being mainly due to raised CRP (52%), TJC (28)>1 (37%) or SJC (28)>1 (16%). 211/364 (58%) of patients achieved ultrasound remission and 193/297 (65%) patients showed T-cell remission. Complete data were available for 231 patients. MDR was observed in only 35% and was associated with the best (lower) PRO scores (all P ⩽ 0.05 vs non-MDR) when compared with the other definitions of remission assessed. The MDR rate was similar in early and established RA patients on b-DMARDs; however, it was lower in established RA patients who received multiple cs-DMARDs (P = 0.011).

Conclusions
In this study, MDR, which may represent a state closer to normality, was found to occur in about a third of DAS28-remission patients and was associated with better patient-reported outcome measures. MDR could be a novel optimal treatment target, notably from a patient’s perspective. The relevance of these findings needs further assessment.
Conducting research in psoriatic arthritis: the emerging role of patient research partners
Authors: Goel Niti 
Published: July 2019

AbstractSince 2003, patients have become increasingly involved in research endeavours related to psoriatic arthritis (PsA), progressing into a patient research partner (PRP) role. This paper reviews the general considerations related to PRP involvement in research endeavours and more specifically, the evolution of PRP contributions related to PsA research. The addition of the perspective from individuals with lived experience of PsA can bring unique insights to the research process, and increase the likelihood that the results of research are meaningful and relevant to PsA patients. There are also potential issues to address when incorporating PRPs, such as the need for additional time and effort to identify, train, and collaborate with PRPs as members of a research team. Overall, while there are challenges to overcome, and the opportunities to include PRPs are sometimes overlooked, efforts to include PRPs in PsA research should offer significant benefits to patients, researchers, and trials.
Effect of Risperidone Monotherapy on Dynamic Functional Connectivity of Insular Subdivisions in Treatment-Naive, First-Episode Schizophrenia
Authors: Duan Xujun , Hu Maolin , Huang Xinyue , Su Chan , Zong Xiaofen , Dong Xia , He Changchun , Xiao Jinming , Li Haoru , Tang Jinsong , Chen Xiaogang , Chen Huafu 
Published: July 2019

AbstractObjectiveThe insula consists of functionally diverse subdivisions, and each division plays different roles in schizophrenia neuropathology. The current study aimed to investigate the abnormal patterns of dynamic functional connectivity (dFC) of insular subdivisions in schizophrenia and the effect of antipsychotics on these connections.MethodsLongitudinal study of the dFC of insular subdivisions was conducted in 42 treatment-naive first-episode patients with schizophrenia at baseline and after 8 weeks of risperidone treatment based on resting-state functional magnetic resonance image (fMRI).ResultsAt baseline, patients showed decreased dFC variance (less variable) between the insular subdivisions and the precuneus, supplementary motor area and temporal cortex, as well as increased dFC variance (more variable) between the insular subdivisions and parietal cortex, compared with healthy controls. After treatment, the dFC variance of the abnormal connections were normalized, which was accompanied by a significant improvement in positive symptoms.ConclusionsOur findings highlighted the abnormal patterns of fluctuating connectivity of insular subdivision circuits in schizophrenia and suggested that these abnormalities may be modified after antipsychotic treatment.
Social Norms about Father Involvement and Women’s Fertility
Authors: Lappegård Trude , Kornstad Tom 
Published: July 2019

AbstractWe argue that father involvement at the societal level influences women’s fertility decisions. If father involvement becomes a social norm, it provides expectations about shared parenthood and father involvement in care for young children, making it easier to realize childbearing plans. We test our theoretical assumption using administrative register data from Norway covering 25 years of exposure to a social policy aiming at fathers becoming more involved in childcare and an equal division of labor within the family. Hazard model regression analyses including macro indicators of father involvement reveal that father engagement – in the sense that fathers are visible in the community being on parental leave – is positively associated with women becoming mothers and one-child mothers’ transition to second birth, but the effect is strongest for the second birth. Simulation experiments show that in a scenario where no fathers take parental leave, only 63 percent of all women have a second child, while in the scenario where almost all fathers take leave, as many as 74 percent of all women will do so. In many low fertility countries, women often stop at one child. Our results suggest that in such societies that are concerned about low fertility, policies that encourage father involvement could be a valuable investment.
Fighting for Their Neighborhood: Urban Policy and Anti-State Riots in France
Authors: Moutselos Michalis 
Published: July 2019

AbstractWhy does anti-state, violent rioting take place in advanced democracies? The paper investigates the role of the urban environment in shaping grievances expressed and mobilization/counter-mobilization processes observed during a riotous episode. In particular, I look at large social-housing estates as a propitious urban setting for the eruption and sustenance of anti-state violence. I identify three mechanisms (stigma amplification and inversion, failure of state intervention in the form of everyday administration and emergency policing, and advantages for network activation and resource mobilization among potential rioters) that complement standard explanations of rioting based on socioeconomic and ethno-cultural grievances. I test the theoretical model using a controlled case study of two neighboring suburbs in the North of Paris, with similar socioeconomic, demographic, and political characteristics but different violent outcomes in the 2005 nation-wide wave of French riots. The paper traces the source of local variation to the exogenous presence of large, concentrated social-housing estates in one, but not the other. The analysis here treats anti-state rioting as a form of urban protest and looks at state-society divisions rooted in urban geography and policy that have been overlooked in conventional scholarship on minority mobilization in Europe.
Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction
Authors: Matsui Motomu , Iwasaki Wataru 
Published: July 2019

Abstract
A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.
GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments
Authors: Crotty Stephen M , Minh Bui Quang , Bean Nigel G , Holland Barbara R , Tuke Jonathan , Jermiin Lars S , Haeseler Arndt Von 
Published: July 2019

AbstractMolecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce the General Heterogeneous evolution On a Single Topology (GHOST) model of sequence evolution, implemented under a maximum-likelihood framework in the phylogenetic program IQ-TREE (http://www.iqtree.org). Simulations show that using the GHOST model, IQ-TREE can accurately recover the tree topology, branch lengths, and substitution model parameters from heterotachously evolved sequences. We investigate the performance of the GHOST model on empirical data by sampling phylogenomic alignments of varying lengths from a plastome alignment. We then carry out inference under the GHOST model on a phylogenomic data set composed of 248 genes from 16 taxa, where we find the GHOST model concurs with the currently accepted view, placing turtles as a sister lineage of archosaurs, in contrast to results obtained using traditional variable rates-across-sites models. Finally, we apply the model to a data set composed of a sodium channel gene of 11 fish taxa, finding that the GHOST model is able to elucidate a subtle component of the historical signal, linked to the previously established convergent evolution of the electric organ in two geographically distinct lineages of electric fish. We compare inference under the GHOST model to partitioning by codon position and show that, owing to the minimization of model constraints, the GHOST model offers unique biological insights when applied to empirical data.