bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of replication and repair in mitochondrial DNA deletion formation
Authors: Fontana Gabriele A , Gahlon Hailey L 
Published: September 2020

Abstract
Deletions in mitochondrial DNA (mtDNA) are associated with diverse human pathologies including cancer, aging and mitochondrial disorders. Large-scale deletions span kilobases in length and the loss of these associated genes contributes to crippled oxidative phosphorylation and overall decline in mitochondrial fitness. There is not a united view for how mtDNA deletions are generated and the molecular mechanisms underlying this process are poorly understood. This review discusses the role of replication and repair in mtDNA deletion formation as well as nucleic acid motifs such as repeats, secondary structures, and DNA damage associated with deletion formation in the mitochondrial genome. We propose that while erroneous replication and repair can separately contribute to deletion formation, crosstalk between these pathways is also involved in generating deletions.
ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures
Authors: Ye Tiantian , Ma Wenxiu 
Published: September 2020

Abstract
The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations. The ASHIC software is publicly available at https://github.com/wmalab/ASHIC.
High levels of gut-homing immunoglobulin A+ B lymphocytes support the pathogenic role of intestinal mucosal hyperresponsiveness in immunoglobulin A nephropathy patients
Authors: Sallustio Fabio , Curci Claudia , Chaoul Nada , Fontò Giulia , Lauriero Gabriella , Picerno Angela , Divella Chiara , Di Leo Vincenzo , De Angelis Maria , Ben Mkaddem Sanae , Macchia Luigi , Gallone Anna , Monteiro Renato C , Pesce Francesco , Gesualdo Loreto 
Published: September 2020

Abstract

Background
Immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulonephritis. The role of the microbiota and mucosal immunity in the pathogenesis of IgAN remains a key element. To date, the hypothetical relationship between commensal bacteria, elevated tumour necrosis factor (TNF) superfamily member 13 [also known as B-cell activating factor (BAFF)] levels, perturbed homoeostasis of intestinal-activated B cells and intestinal IgA class switch has not been clearly shown in IgAN patients.

Methods
We studied the intestinal–renal axis connections, analysing levels of BAFF, TNF ligand superfamily member 13 (APRIL) and intestinal-activated B cells in IgAN patients, healthy subjects (HSs) and patients with non-IgA glomerulonephritides.

Results
IgAN patients had increased serum levels of BAFF cytokine, correlating with higher amounts of five specific microbiota metabolites, and high APRIL cytokine serum levels. We also found that subjects with IgAN have a higher level of circulating gut-homing (CCR9+ β7 integrin+) regultory B cells, memory B cells and IgA+ memory B cells compared with HSs. Finally, we found that IgAN patients had high levels of both total plasmablasts (PBs) and intestinal-homing PBs. Interestingly, PBs significantly increased in IgAN but not in patients with other glomerulonephritides.

Conclusions
Our results demonstrate a significant difference in the amount of intestinal-activated B lymphocytes between IgAN patients and HSs, confirming the hypothesis of the pathogenic role of intestinal mucosal hyperresponsiveness in IgAN. The intestinal–renal axis plays a crucial role in IgAN and several factors may contribute to its complex pathogenesis and provide an important area of research for novel targeted therapies to modulate progression of the disease.
Long-lived tumor-associated macrophages in glioma
Authors: Georgieva Petya B , Mathivet Thomas , Alt Silvanus , Giese Wolfgang , Riva Matteo , Balcer Marly , Gerhardt Holger 
Published: September 2020

AbstractBackgroundThe tumor microenvironment plays a major tumor-supportive role in glioma. In particular, tumor-associated macrophages (TAMs), which can make up to one-third of the tumor mass, actively support tumor growth, invasion, and angiogenesis. Predominantly alternatively activated (M2-polarized) TAMs are found in late-stage glioma in both human and mouse tumors, as well as in relapse samples from patients. However, whether tumor-educated M2 TAMs can actively contribute to the emergence and growth of relapse is currently debated.MethodsTo investigate whether tumor-educated stromal cells remaining in the brain after surgical removal of the primary tumor can be long-lived and retain their tumor-supporting function, we developed a transplantation mouse model and performed lineage-tracing.ResultsWe discovered that macrophages can survive transplantation and stay present in the tumor much longer than previously suggested, while sustaining an M2-polarized protumorigenic phenotype. Transplanted tumors showed a more aggressive growth and faster polarization of the TAMs toward an M2 phenotype compared with primary tumors, a process dependent on the presence of few cotransplanted macrophages.ConclusionsOverall, we propose a new way for tumor-educated TAMs to contribute to glioma aggressiveness by long survival and stable protumorigenic features. These properties could have a relapse-supporting effect.
Evenness is important in assessing progress towards sustainable development goals
Authors: Liu Yali , Du Jianqing , Wang Yanfen , Cui Xiaoyong , Dong Jichang , Hao Yanbin , Xue Kai , Duan Hongbo , Xia Anquan , Hu Yi , Dong Zhi , Wu Bingfang , Zhao Xinquan , Fu Bojie 
Published: September 2020

ABSTRACT
Sustainable development goals (SDGs) emphasize a holistic achievement instead of cherry-picking a few. However, no assessment has quantitatively considered the evenness among all 17 goals. Here, we propose a systematic method, which first integrates both the evenness and the overall status of all goals, to distinguish the ideal development pathways from the uneven ones and then revisit the development trajectory in China from 2000 to 2015. Our results suggest that, despite the remarkable progress, a bottleneck has occurred in China since 2013 due to the stagnant developments in some SDGs. However, many far-reaching policies in China have been targeting these deficiencies since then, providing a perspective on how a country approaches sustainable development by promoting evenness among all SDGs. Our results also indicate that regions with the slowest progress are the developed provinces, owing to the persistent uneven status of all goals. Our study demonstrates the importance of adopting evenness in assessing and guiding sustainable development.
Prognostic Role of Bacterial and Fungal Infections in Patients With Liver Cirrhosis With and Without Acute-on-Chronic Liver Failure: A Prospective 2-Center Study
Authors: Bartoletti Michele , Baldassarre Maurizio , Domenicali Marco , Lewis Russell E , Giannella Maddalena , Antognoli Agnese , Rinaldi Matteo , Zaccherini Giacomo , Verucchi Gabriella , Marconi Lorenzo , Tamè Mariarosa , Berardi Sonia , Napoli Lucia , Siniscalchi Antonio , Fabbri Angela , Biselli Maurizio , Tufoni Manuel , Pavarin Raimondo M , Trevisani Franco , Viale Pierluigi , Bernardi Mauro , Caraceni Paolo 
Published: September 2020

Abstract

Background
Bacterial and fungal infections (BFIs) are frequent in patients with cirrhosis and often trigger acute-on-chronic liver failure (ACLF). This prospective observational study aims to describe the interactions between BFI and ACLF in terms of mortality and related risk factors.

Methods
We performed a 2-center prospective observational study enrolling hospitalized patients with cirrhosis admitted for acute decompensation. Data were recorded at admission and during hospitalization. Survival was recorded up to 1 year.

Results
Among the 516 patients enrolled, 108 (21%) were infected at admission, while an additional 61 patients (12%) developed an infection during hospital stay. In the absence of ACLF, the 1-year mortality rate of patients with BFI did not differ from that of patients without BFI (33% vs 31%; P = .553). In contrast, those with ACLF triggered or complicated by BFI had a significantly higher mortality rate than those who remained free from BFI (75% vs 54%; P = .011). Competing risk analysis showed that the negative impact of ACLF-related BFI on long-term prognosis was independent from Model for End-stage Liver Disease (MELD) incorporating serum sodium concentration score, comorbidity, and basal C-reactive protein level. Finally, multivariable logistic regression showed that higher MELD score (P &lt; .001), QuickSOFA score ≥2 points (P = .007), and secondary bloodstream (P = .022) and multidrug-resistant pathogen isolation (P = .030) were independently associated with ACLF in patients with BFI.

Conclusions
This large prospective study indicated that the adverse impact of BFI on long-term survival in decompensated cirrhosis is not universal but is limited to those patients who also develop ACLF. Both disease severity and microbiological factors predispose infected decompensated patients to ACLF.
The Stressful Characteristics of Pain That Drive You NUTS: A Qualitative Exploration of a Stress Model to Understand the Chronic Pain Experience
Authors: Pagé M Gabrielle , Dassieu Lise , Develay Elise , Roy Mathieu , Vachon-Presseau Etienne , Lupien Sonia , Rainville, PhD Pierre 
Published: September 2020

Abstract

Objective
Despite decades of research on the identification of specific characteristics of situations that trigger a physiological stress response (novelty, unpredictability, threat to the ego, and sense of low control [NUTS]), no integrative research has examined the validity of this framework applied to pain experiences. This study aimed to 1) explore the stressful characteristics of pain among individuals living with chronic pain and 2) examine whether the NUTS framework comprehensively captures the stressful nature of pain.

Subjects
Participants were 41 adult participants living with chronic pain.

Methods
Interviews in six focus groups were conducted in French using a semistructured interview guide. Participants first discussed how pain is stressful. Then, they were introduced to the NUTS framework and commented on the extent to which it captured their experience. The verbatim transcriptions of interviews were reviewed using reflexive thematic analysis. Analyses were conducted in French; quotes and themes were translated into English by a professional translator.

Results
The pain-NUTS framework adequately captured participants’ experiences. Multiple aspects of pain (pain intensity fluctuations, pain flare-up duration, pain quality and location, functional limitations, diagnosis and treatment) were associated with one or more stress-inducing characteristics. In addition, a second layer of meaning emerged in the context of chronic pain that provided contextual information regarding when, how, and why pain became more or less stressful.

Conclusions
The NUTS characteristics seem to offer a comprehensive framework to understand how pain and its context of chronicity can be a source of stress. This study provides preliminary support for the pain-NUTS framework to allow the formal integration of pain and stress research.
Prior sleep problems and adverse post-traumatic neuropsychiatric sequelae of motor vehicle collision in the AURORA study
Authors: Neylan Thomas C , Kessler Ronald C , Ressler Kerry J , Clifford Gari , Beaudoin Francesca L , An Xinming , Stevens Jennifer S , Zeng Donglin , Linnstaedt Sarah D , Germine Laura T , Sheikh Sophia , Storrow Alan B , Punches Brittany E , Mohiuddin Kamran , Gentile Nina T , McGrath Meghan E , van Rooij Sanne J H , Haran John P , Peak David A , Domeier Robert M , Pearson Claire , Sanchez Leon D , Rathlev Niels K , Peacock William F , Bruce Steven E , Joormann Jutta , Barch Deanna M , Pizzagalli Diego A , Sheridan John F , Harte Steven E , Elliott James M , Hwang Irving , Petukhova Maria V , Sampson Nancy A , Koenen Karestan C , McLean Samuel A 
Published: September 2020

Abstract

Study Objectives
Many patients in Emergency Departments (EDs) after motor vehicle collisions (MVCs) develop post-traumatic stress disorder (PTSD) or major depressive episode (MDE). This report from the AURORA study focuses on associations of pre-MVC sleep problems with these outcomes 8 weeks after MVC mediated through peritraumatic distress and dissociation and 2-week outcomes.

Methods
A total of 666 AURORA patients completed self-report assessments in the ED and at 2 and 8 weeks after MVC. Peritraumatic distress, peritraumatic dissociation, and pre-MVC sleep characteristics (insomnia, nightmares, daytime sleepiness, and sleep duration in the 30 days before the MVC, trait sleep stress reactivity) were assessed retrospectively in the ED. The survey assessed acute stress disorder (ASD) and MDE at 2 weeks and at 8 weeks assessed PTSD and MDE (past 30 days). Control variables included demographics, MVC characteristics, and retrospective reports about PTSD and MDE in the 30 days before the MVC.

Results
Prevalence estimates were 41.0% for 2-week ASD, 42.0% for 8-week PTSD, 30.5% for 2-week MDE, and 27.2% for 8-week MDE. Pre-MVC nightmares and sleep stress reactivity predicted 8-week PTSD (mediated through 2-week ASD) and MDE (mediated through the transition between 2-week and 8-week MDE). Pre-MVC insomnia predicted 8-week PTSD (mediated through 2-week ASD). Estimates of population attributable risk suggest that blocking effects of sleep disturbance might reduce prevalence of 8-week PTSD and MDE by as much as one-third.

Conclusions
Targeting disturbed sleep in the immediate aftermath of MVC might be one effective way of reducing MVC-related PTSD and MDE.
Documentation of Hepatitis B Immunity in Nursing Students
Authors: Elting Julie Kientz 
Published: September 2020

Abstract
Because of the risk of occupational exposure, preparation for nursing student clinical placement includes documentation of the hepatitis B immunization series. Requiring a hepatitis B antibody titer is less common. Immunity from the hepatitis B vaccine decreases over time, particularly for those immunized as infants. A record review of one nursing program that required both immunization and an antibody titer found 86 percent of students immunized as infants had low antibody levels, requiring reimmunization following 2013 Centers for Disease Control and Prevention guidelines. Nursing education programs that do not require antibody titers should reevaluate their policies to protect their students.
Critical Thinking With Diverse Students: The Effects of a Concurrent RN-BSN Program and Nursing Residency
Authors: Wright Joyce 
Published: September 2020

Abstract
Critical thinking is an analytical attribute for nurses to make accurate clinical decisions. This study examined critical thinking progression though a concurrent RN-BSN program and nursing residency for a diverse cohort of associate degree graduates. A pretest/posttest design revealed improvement in scores; however, no statistical significance was established. There was a statistically significant (p = .015) reduction in scores for a bilingual subset group in the subcategories of Prioritization of Care and Ethical Dilemmas. Future research is warranted to assess critical thinking progression and critical thinking test construction with diverse students.
Changes in Neuroanesthesia Practice During the Early Stages of the COVID-19 Pandemic: Experiences From a Single Center in China
Authors: Jian Minyu , Liang Fa , Liu Haiyang , Zeng Hengyu , Peng Yuming , Han Ruquan 
Published: September 2020

Background:
Coronavirus disease 2019 (COVID-19), caused by a novel coronavirus, is highly contagious. Global medical systems have been heavily impacted by the COVID-19 pandemic. Although the majority of patients with intracranial disease require time-sensitive surgery, how to conduct neurosurgery and prevent and control nosocomial infection during a pandemic is challenging.

Materials and Methods:
We retrospectively reviewed the clinical data of patients undergoing neurosurgical and neurointerventional procedures at Beijing Tiantan Hospital, China during the early stages of the COVID-19 pandemic between January 21 and July 31, 2020. A 3-level system of COVID-19 risk was established based on medical conditions, epidemiologic, and symptom inquiry and the results of triage. A transitional unit was established for patients in whom COVID-19 had not been ruled out on admission to hospital.

Results:
A total of 4025 patients underwent neurosurgery during the study period, including 768 emergent and 3257 nonemergent procedures. Of these patients, 3722 were low-risk for COVID-19, 303 were moderate-risk, and none were high-risk. In addition, 1419 patients underwent neurointerventional procedures, including 114 emergent and 1305 nonemergent interventions, of which 1339 were low-risk patients, 80 were moderate-risk and none were high-risk. A total of 895 patients (neurosurgical and neurointerventional) were admitted to the transitional unit. Forty-five patients were diagnosed with COVID-19 and transferred to the COVID-19 designated hospital. There were no cases of COVID-19 nosocomial infections among surgical patients or health care workers.

Conclusion:
On the basis of our single-center experience, developing a full screening protocol for COVID-19, establishing a risk level, and using a transitional unit for those with unknown COVID-19 status are effective measures to provide a safe environment for patients and health care workers.
Arthroscopic Superior Capsular Reconstruction With Achilles Tendon Allograft: A Good Option for Irreparable Supraspinatus Tendon Tears
Authors: Xará-Leite Francisco , Barros Luís H. , Claro Rui 
Published: September 2020

Introduction:
Irreparable rotator cuff tears in the elderly population are still a challenge for the orthopedic surgeon, with no consensus regarding ideal treatment strategies and their respective indications. Superior capsule reconstruction has shown good results in the treatment of this condition, however ideal graft origin is yet to be established.

Methods and Results:
The authors describe our team’s technique for superior capsule reconstruction, which uses an Achilles tendon allograft, and has shown good short-term functional and radiologic results.

Discussion:
Achilles tendon allograft is a valuable alternative to other sources, providing an easy-to-prepare graft with a low-risk profile and avoiding donor-site morbidity.
Using Anterior Segment Optical Coherence Tomography (ASOCT) Parameters to Determine Pupillary Block Versus Plateau Iris Configuration
Authors: Crowell Eric L. , Chuang Alice Z. , Bell Nicholas P. , Blieden Lauren S. , Feldman Robert M. 
Published: September 2020

Précis:
The potential parameters for differentiating pupillary block (PB) from plateau iris configuration (PIC) on anterior segment optical coherence tomography (ASOCT) are lens/pupil size parameters and angles. Further study is needed to determine a landmark peripheral to the centroid of the iris.

Purpose:
Investigate anterior segment parameters to distinguish between 2 mechanisms of angle closure, PB and PIC, using swept-source Fourier domain ASOCT.

Patients and Methods:
Retrospective ASOCT images from narrow angle eyes were reviewed. PIC was defined either by ultrasound biomicroscopy and/or clinically when an iridoplasty was performed. Images were read by a masked reader using Anterior Chamber Analysis and Interpretation software to identify scleral spur landmarks and calculate anterior chamber, peripheral angle, iris size, iris shape, and lens/pupil size parameters. ASOCT parameters were summarized and compared using the 2-sample t test. Thresholds and area under receiver operating characteristic curve were calculated using logistic regression analysis.

Results:
One hundred eyes (66 PB and 34 PIC) of 100 participants were reviewed. Of all ASOCT parameters, iris length in each quadrant, pupil arc, lens/pupil parameters (pupil arc, lens vault, and pupil diameter), all pupillary margin-center point-scleral spur landmark (PM-C-SSL) parameters, and all except superior central iris vault parameters were significantly different between PB and PIC. On threshold evaluation, lens/pupil parameters had the greatest area under receiver operating characteristic curve values (0.77 to 0.80), followed by PM-C-SSL angles (0.71 to 0.75).

Conclusions:
We propose that the pupil size parameters and PM-C-SSL angle are the most reliable novel ASOCT parameters to distinguish between PB and PIC eyes. These parameters do not rely on the visibility of the posterior iris surface, which is difficult to identify with ASOCT, but may be ambient lighting dependent.
Reduction of High School Ice Hockey Injuries With Implementation of New Checking/Boarding Rules
Authors: Nadkarni Lauren , Haskins Amy , Holt Christina , Dexter William 
Published: September 2020

Objective:
Evaluate whether rule changes by the National Federation of State High School Associations (NFHS) were associated with reduced injury rates in US high school ice hockey players.

Design:
We compared injury rates for the 3 seasons before the rule changes (2011-2012, 2012-2013, and 2013-2014) with the 2 subsequent seasons (2014-2015 and 2015-2016) using data from the High School Reporting Information Online (RIO) database.

Setting:
Convenience sample of US high schools.

Participants:
High school ice hockey athletes.

Interventions:
The sports injury surveillance system that supplied the data for this study was funded in part by the Centers for Disease Control and Prevention (grant Nos. R49/CE000674-01, R49/CE001172-01, and R49/CE002106-01) as well as research funding contributions of the NFHS, National Operating Committee on Standards for Athletic Equipment (NOCSAE), DonJoy Orthotics, and EyeBlack. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention or any other funding agency. In the 2014 to 2015 ice hockey season, the NFHS increased the penalty for boarding (illegally causing opponent to be thrown violently into the boards) and for checking from behind.

Main Outcome Measures:
Injury rates and mechanism of injury.

Results:
There was a statistically significant 40% reduction in rates of injury attributed to being checked in the 2 seasons after the rule changes (5.0 injuries per 10 000 athlete exposures) compared with the 3 previous seasons (8.3) (rate ratio = 0.60, P = 0.002). There were no significant differences in overall injury rates (P = 0.12) or injury rates due to checking (P = 0.27), contact with the boards (P = 0.31), or contact with another player (P = 0.55).

Conclusions:
Among US high school ice hockey athletes, implementation of stricter penalties for boarding and checking from behind was associated with a significant decrease in injury rate due to being checked. Rates of injury due to other mechanisms were not significantly altered, suggesting the rule changes achieved their targeted effect.