bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection influences naive CD8+ TCR‐β repertoire sharing
Authors: Yiu Hao H. , Schoettle Louis N. , Garcia‐Neuer Marlene , Blattman Joseph N. , Johnson Philip L. F. 
Published: December 2020

SummaryWithin each individual, the adaptive immune system generates a repertoire of cells expressing receptors capable of recognizing diverse potential pathogens. The theoretical diversity of the T‐cell receptor (TCR) repertoire exceeds the actual size of the T‐cell population in an individual by several orders of magnitude – making the observation of identical TCRs in different individuals extremely improbable if all receptors were equally likely. Despite this disparity between the theoretical and the realized diversity of the repertoire, these ‘public’ receptor sequences have been identified in autoimmune, cancer and pathogen interaction contexts. Biased generation processes explain the presence of public TCRs in the naive repertoire, but do not adequately explain the different abundances of these public TCRs. We investigate and characterize the distribution of genomic TCR‐β sequences of naive CD8+ T cells from three genetically identical mice, comparing non‐productive (non‐functional sequences) and productive sequences. We find public TCR‐β sequences at higher abundances compared with unshared sequences in the productive, but not in the non‐productive, repertoire. We show that neutral processes such as recombination biases, codon degeneracy and generation probability do not fully account for these differences, and conclude that thymic or peripheral selection plays an important role in increasing the abundances of public TCR‐β sequences.
A Holocene history of monkey puzzle tree (pehuén) in northernmost Patagonia
Authors: Nanavati William , Whitlock Cathy , Outes Valeria , Villarosa Gustavo 
Published: December 2020

AbstractAimAlthough it is established that climate and fire have greatly influenced the long‐term ecosystem dynamics of Patagonia south of 40°S, the environmental history from northernmost Patagonia (37–40°S), where endemic and endangered monkey puzzle tree (Araucaria araucana) occurs, is poorly known. Here we ask: (a) What is the Holocene vegetation and fire history at the north‐eastern extent of A. araucana forest? (b) How have climate and humans influenced the past distribution of A. araucana?LocationNorthernmost Patagonia, Argentina and Chile (37–40°S).TaxaAraucaria araucana, Nothofagus, Poaceae.MethodsSedimentary pollen and charcoal from Laguna Portezuelo (37.9°S, 71.0°W; 1,730 m; 11,100 BP) were evaluated using statistical methods and compared with other palaeoecological, independent palaeoclimate, and historical records to assess how changes in climate and land use influenced local‐to‐regional environmental history.ResultsAn open forest‐steppe landscape persisted at L. Portezuelo throughout the Holocene with generally low‐to‐moderate fire activity. Increased Nothofagus pollen after ~6,590 BP suggests increases in shrubland and moisture in association with cooler conditions and greater seasonality and ENSO activity. Araucaria pollen appeared at L. Portezuelo at ~6,380 BP, but was low in abundance until ~370 BP, when it rose with charcoal levels. This increase in Araucaria and fire coincided with a regional influx of Mapuche American Indians. Nothofagus deforestation and Pinus silviculture marked Euro‐American settlement beginning in the 19–20th century.Main conclusions(a) Rapid postglacial warming and drying limited the distribution of Araucaria in the central valley of Chile. In the middle and late Holocene, decreased temperatures and greater seasonality and ENSO activity increased precipitation variability allowing Araucaria expansion at its north‐eastern limit. (b) Greater abundance of Araucaria and heightened fire activity at L. Portezuelo after 370 BP coincided with increased Mapuche‐Pehuenche American Indian land use, suggesting that Araucaria may have been managed in a human‐altered landscape.
ZCCHC14 regulates proliferation and invasion of non–small cell lung cancer through the MAPK‐P38 signalling pathway
Authors: Shi Xiuying , Han Xu , Cao Yu , Li Cheng , Cao Yaming 
Published: December 2020

AbstractZCCHC14 is a CCHC‐type zinc finger protein which is expressed in tissues in human and mouse. The function of ZCCHC14 in tumours remains unclear. In this research, we explored the expression, function and related molecular mechanisms of ZCCHC14 in human non–small cell lung cancer (NSCLC). Immunochemistry staining showed that ZCCHC14 was low‐expressed or absent in NSCLC tissues. In NSCLC patients, the low expression of ZCCHC14 in tumour tissues was significantly correlated with TNM stage, differentiation degree and adverse clinical outcome (P < .05). The proliferation and invasion ability of cancer cells transfected with ZCCHC14 CRISPR/Ca9 KO plasmids was significantly enhanced (P < .05). Immunoblotting analysis indicated that the expression of p‐P38, cyclinD1 and MMP7 were significantly up‐regulated after disabling ZCCHC14 (P < .05). We used MAPK‐P38 pathway inhibitor doramapimod (BIRB 796) to inhibit P38 signalling pathway activity and determined that the agent significantly disrupted the function of ZCCHC14 and hindered the proliferation and invasion of the tumour. The finding revealed that ZCCHC14 can regulate proliferation and invasion of NSCLC through the P38 pathway. ZCCHC14 plays a crucial regulatory role in the development of NSCLC and may become a zinc finger target for clinical treatment.
Does shelter influence the metabolic traits of a teleost fish?
Authors: Chrétien Emmanuelle , Cooke Steven J. , Boisclair Daniel 
Published: December 2020

AbstractAvailability of shelter is an important component of habitat selection for animals as it can influence survival (protection against harsh physical conditions and predation) and growth (energy acquisition and expenditure). Few studies address the effect of shelter on metabolic expenditures associated with non‐mechanical tasks (excluding station holding or movement). The main goal of this study was to investigate the influence of shelter use on metabolic traits of smallmouth bass (Micropterus dolomieu) from two populations (Kiamika River and Lake Long). Respirometry experiments on smallmouth bass were conducted to measure standard metabolic rate (SMR), resting metabolic rate (RMR), aerobic scope (AS), recovery time (RT) and excess post‐exercise oxygen consumption (EPOC) in the presence or absence of shelter. The presence of shelter did not affect most metabolic traits, except for RMR, which was reduced in the presence of shelter for Lake Long fish. The results of this study also show that larger fish had lower SMR in the presence of shelter than when it was absent. When accounting for social hierarchy, there were no differences in most metabolic traits in dominant or subordinate fish in the presence or absence of shelter, except for RT, which was significantly lower in the presence of shelter for dominant fish. These results do not support the existence of an unequivocal relationship between individual metabolic traits and the presence of shelter. If physiological motives may influence the use of shelter, sheltering in itself might not have important consequences on energy expenditures required for non‐mechanical tasks.
Exploring the ontogenetic development of the inner ear in Aardvarks
Authors: Berlioz Emilie , Cornette Raphaël , Lenoir Nicolas , Santin Mathieu D. , Lehmann Thomas 
Published: December 2020

AbstractThe aardvark is the last living Tubulidentata, an order of afrotherian mammals. Afrotheria is supported strongly by molecular analyses, yet sparingly by morphological characters. Moreover, the biology of the aardvark remains incompletely known. The inner ear, and its ontogeny in particular, has not been studied in details yet, though it bears key ecomorphological characters and phylogenetical signal. The aim of this study is to decipher and discuss the ontogenetic development of the different areas of the inner ear of Orycteropus afer. We focused in particular on their relative size and morphological rates of development. Specimens were scanned with 3D imaging techniques. 3D and 2D geometric morphometrics coupled with qualitative descriptions of the petrosal ossification allowed us to evidence several stages through development. Based on our sample, the cochlea is the first structure of the inner ear to reach adult size, but it is the last one to acquire its adult morphology close to parturition. In contrast, after a delayed growth spurt, the semicircular canals reach their mature morphology before the cochlea, concomitantly with the increase of petrosal ossification. The ontogeny of the aardvark inner ear shows similarities with that of other species, but the apex of the cochlea presents some autapomorphies.This work constitutes a first step in the study of the ontogeny of this sensorial organ in Afrotheria.
Surgical repair for luxation of the superficial digital flexor tendon using a temporary restraining pin
Authors: Jury A. 
Published: December 2020

Objectives(1) To report the clinical features of luxation of the superficial digital flexor tendon in dogs and (2) to report the outcome and complications of a novel surgical technique where postoperative immobilisation was not used.Materials and MethodsMedical records from one Swedish veterinary hospital were retrospectively reviewed for cases of superficial digital flexor tendon treated by the author, between July 2007 and August 2019, where a temporary restraining pin was used as part of the surgical repair.ResultsTwenty‐three procedures were performed in 19 dogs. Fourteen of the dogs were Shetland Sheepdogs with five other breeds represented. Lateral luxation occurred in all but one case. Minor complications occurred in eight cases (35%). Major complications requiring unplanned surgery occurred in three cases (13%). All cases ultimately returned to their pre‐injury level of activity.Clinical SignificanceThe use of a temporary restraining pin is useful in the surgical repair of superficial digital flexor tendon luxation. All cases were successfully treated without using post‐operative immobilisation of the tarsal joint. Plain radiography is unreliable in the identification of morphological defects of the calcaneus.
Exosome‐derived differentiation antagonizing non‐protein coding RNA with risk of hepatitis C virus‐related hepatocellular carcinoma recurrence
Authors: Wang Shu‐Chi , Li Chia‐Yang , Chang Wen‐Tsan , Cheng Wei‐Chung , Yen Chia‐Hung , Tu Wen‐Yu , Lin Zu‐Yau , Lin Ching‐Chih , Yeh Ming‐Lun , Huang Chung‐Feng , Huang Jee‐Fu , Dai Chia‐Yen , Chuang Wan‐Long , Chen Yao‐Li , Yu Ming‐Lung 
Published: December 2020

AbstractBackground & AimsDifferentiation antagonizing non‐protein coding RNA is associated with various types of neoplasms. Hepatitis C virus‐related hepatocellular carcinoma has a high risk of recurrence. Here we determined the role of differentiation antagonizing non‐protein coding RNA in hepatitis C virus‐related hepatocarcinogenesis and identified potential therapeutic targets and non‐invasive prognostic markers for long‐term outcome of hepatitis C virus‐related hepatocellular carcinoma after surgical resection.MethodsDifferentiation antagonizing non‐protein coding RNAs relevant to hepatitis C virus‐related hepatocellular carcinoma were identified through comparative RNA‐sequencing of tumour and adjacent non‐tumour (ANT) tissues in a screening set, and were validated using real‐time polymerase chain reaction. Target long non‐coding RNAs (lncRNAs) in tissues and serum exosomes were used to predict the recurrence of hepatitis C virus‐related hepatocellular carcinoma after curative surgical resection in a large application cohort from 2005 to 2012.ResultsWe confirmed that differentiation antagonizing non‐protein coding RNA was upregulated following hepatitis C virus infection and identified as the lncRNA most relevant to hepatitis C virus‐related hepatocellular carcinoma in tumour tissues as compared to that in ANT tissues. In 183 hepatitis C virus‐related hepatocellular carcinoma patients followed for 10 years after curative HCC resection, the expression level of circulating exosomal differentiation antagonizing non‐protein coding RNA was positively associated with HCC recurrence and was the most predictive factor associated with HCC recurrence and mortality (hazard ratio/95% confidence intervals: 7.0/4.3‐11.6 and 2.7/1.5‐5.1 respectively).ConclusionsDifferentiation antagonizing non‐protein coding RNA is highly relevant to disease progression of hepatitis C virus‐related hepatocellular carcinoma. Our finding indicated that circulating exosomal differentiation antagonizing non‐protein coding RNA might serve as a non‐invasive prognostic biomarker for hepatitis C virus‐related hepatocellular carcinoma.
Patient and family involvement in escalating concerns about clinical deterioration in acute adult wards: A qualitative systematic review
Authors: McKinney Aidín , Fitzsimons Donna , Blackwood Bronagh , McGaughey Jennifer 
Published: December 2020

AbstractBackgroundDespite international standards for recognition and response to deterioration, warning signs are not always identified by staff on acute hospital wards. Patient and family‐initiated escalation of care schemes have shown some benefit in assisting early recognition, but are not widely used in many clinical practice areas.ObjectivesTo explore (a) patients' and relatives' experiences of acute deterioration and (b) patients', relatives' and healthcare professionals' perceptions of the barriers or facilitators to patient and family‐initiated escalation of care in acute adult hospital wards.MethodsWe conducted a qualitative review using Cochrane methodology. Two reviewers independently screened studies, extracted data, and appraised the quality using a qualitative critical appraisal tool. Findings were analysed using thematic synthesis and confidence in findings was assessed using GRADE‐CERQual.Search strategyMEDLINE, CINAHL, EMBASE, PsychINFO databases and grey literature from 2005 to August 2019.Inclusion criteriaAny research design that had a qualitative element and focused on adult patients' and relatives' experiences of deterioration and perceptions of escalating care.ResultsWe included five studies representing 120 participants and assessed the certainty of evidence as moderate using GRADE‐CERQual. Findings indicated that a number of patients/relatives have the ability to detect acute deterioration, however, various factors act as both barriers and facilitators to being heard. These include personal factors, perceptions of role, quality of relationships with healthcare staff, and organisational factors. Theoretical understanding suggests that patient and relative involvement in escalation is dependent on both inherent capabilities and the factors that influence empowerment.ConclusionThis review highlights that patient and family escalation of care interventions need to be designed with the aim of improving patient/relative—clinician collaboration and the sharing of responsibility.Relevance to practiceThese factors need to be addressed to promote more active partnerships when designing and implementing patient and family‐initiated escalation of care interventions.
The fate of melanocyte: Mechanisms of cell death in vitiligo
Authors: Wu Xiuyi , Yang Yiwen , Xiang Leihong , Zhang Chengfeng 
Published: December 2020

AbstractLoss of melanocytes (MCs) is the most notable feature of vitiligo. Hence, it is critical to clarify the mechanisms of MC destruction in vitiligo. Apoptosis is most widely studied cell death pathways in vitiligo. In addition, the other two forms of cell death, conventional necrosis and autophagy seem to be involved in the death of vitiligo MCs under certain situations. Moreover, new types of regulated cell death including necroptosis, pyroptosis, and ferroptosis may also participate in the pathogenesis of vitiligo. Anoikis is likely to be connected with the death of detached MCs, which is provoked specifically by loss of anchorage. Primary phagocytosis, later called phagoptosis can execute death of viable cells, probably partly responsible for the loss of MCs in vitiligo. In this review, we aim to summarize the latest insights into various forms of MC death in vitiligo and discuss the corresponding mechanisms.
The Feasibility of Collecting Longitudinal Cardiovascular and Fitness Outcomes From a Neighborhood Park-Based Fitness Program in Ethnically Diverse Older Adults: A Proof-of-Concept Study
Authors: Kling Hannah E. , D’Agostino Emily M. , Booth Ja’mese , Hansen Eric , Hawver Emily , Mathew M. Sunil , Messiah Sarah E. 
Published: December 2020

This proof-of-concept study examined feasibility of assessing longitudinal changes in body mass index, strength, mobility, and cardiovascular health outcomes in older, racial/ethnic minority adults participating in a park-based physical activity program. Study feasibility was based on follow-through data collection procedures and ability to manage and implement data collection, enrollment, and repeated measures data collection in older adults (≥50 years; n = 380; 45% Hispanic, 41% non-Hispanic Black) over a 28-month period. Mixed models were developed to estimate the effects of program participation over time on participant cardiovascular and fitness outcomes and across poverty and age subgroups. Model estimates adjusted for individual-level sociodemographics showed improvements across each 4 month time point in arm strength (0.55 arm curl; 95% confidence interval [0.33, 0.77]) and systolic (−0.68 mmHg; 95% confidence interval [−1.22, −0.13]) and diastolic (−0.47 mmHg; 95% confidence interval [−0.79, −0.16]) blood pressure. An Age × Poverty interaction found greater improvements in systolic and diastolic blood pressure among younger participants living in low poverty (vs. older in higher poverty). Study of the longitudinal association between fitness class participation and health outcomes was feasible in park-based settings.
Safety of 3‐Month Dual Antiplatelet Therapy After Implantation of Ultrathin Sirolimus‐Eluting Stents With Biodegradable Polymer (Orsiro): Results From the SMART‐CHOICE Trial
Authors: Yun Kyeong Ho , Lee Seung‐Yul , Cho Byung Ryul , Jang Woo Jin , Song Young Bin , Oh Ju‐Hyeon , Chun Woo Jung , Park Yong Hwan , Im Eul‐Soon , Jeong Jin‐Ok , Oh Seok Kyu , Cho Deok‐Kyu , Lee Jong‐Young , Koh Young‐Youp , Bae Jang‐Whan , Choi Jae Woong , Lee Wang Soo , Yoon Hyuck Jun , Lee Seung Uk , Cho Jang Hyun , Choi Woong Gil , Rha Seung‐Woon , Lee Joo Myung , Park Taek Kyu , Yang Jeong Hoon , Choi Jin‐Ho , Choi Seung‐Hyuck , Lee Sang Hoon , Gwon Hyeon‐Cheol , Hahn Joo‐Yong , Kim Dong‐Bin , Cho Sang Cheol , Hwang Sun‐Ho , Jeon Dong Woon , Ryu Jae Kean , Kim Moo‐Hyun , Chae In‐Ho , Kim Sang‐Hyun , Kim Hack‐Lyoung , Jin Dong Kyu , Suh Il Woo , Park Jong Seon , Shin Eun‐Seok , Kim Shin‐Jae , Cheong Sang‐Sig , Ho Kyeong , Lee Sung Yun , Lee Jong‐Young , Chae Jei Keon , Yang Yong Mo , Jeong Jin‐Ok , Bae Jang‐Whan , Choi Joon‐Hyouk 
Published: December 2020

Background
This study sought to investigate the safety of 3‐month dual antiplatelet therapy (DAPT) in patients receiving ultrathin sirolimus‐eluting stents with biodegradable polymer (Orsiro).

Methods and Results

The SMART‐CHOICE (Smart Angioplasty Research Team: Comparison Between P2Y12 Antagonist Monotherapy vs Dual Anti‐ platelet Therapy in Patients Undergoing Implantation of Coronary Drug‐Eluting Stents) randomized trial compared 3‐month DAPT followed by P2Y12 inhibitor monotherapy with 12‐month DAPT in 2993 patients undergoing percutaneous coronary intervention. The present analysis was a prespecified subgroup analysis for patients receiving Orsiro stents. As a post hoc analysis, comparisons between Orsiro and everolimus‐eluting stents were also done among patients receiving 3‐month DAPT. Of 972 patients receiving Orsiro stents, 481 patients were randomly assigned to 3‐month DAPT and 491 to 12‐month DAPT. At 12 months, the target vessel failure, defined as a composite of cardiac death, target vessel–related myocardial infarction, or target vessel revascularization, occurred in 8 patients (1.7%) in the 3‐month DAPT group and in 14 patients (2.9%) in the 12‐month DAPT group (hazard ratio [HR], 0.58; 95% CI, 0.24–1.39;
P
=0.22). In whole population who were randomly assigned to receive 3‐month DAPT (n=1495), there was no significant difference in the target vessel failure between the Orsiro group and the everolimus‐eluting stent group (n=1014) (1.7% versus 1.8%; HR, 0.96; 95% CI, 0.41–2.22;
P
=0.92).

Conclusions
In patients receiving Orsiro stents, clinical outcomes at 1 year were similar between the 3‐month DAPT followed by P2Y12 inhibitor monotherapy and 12‐month DAPT strategies. With 3‐month DAPT, there was no significant difference in target vessel failure between Orsiro and everolimus‐eluting stents.

Registration

URL:
https://www.clinicaltrials.gov
; Unique identifier: NCT02079194.
Introduction
Authors: Akhtar Rajnaara C. , Al-Sharmani Mulki , Moors Annelies 
Published: December 2020

Abstract
Muslim marriages are far from homogeneous, and the inherent variability of norms and practices is often missing in the framing of such marriages in Western societies. Marriage and family laws in Muslim-majority contexts are sights of contention, debate, and development. These debates often centre around family as a site of state governance driven by overlapping national and international agendas; gender equality and calls for marriage law reform; and tensions between Islamic jurisprudence, state laws, and lived realities. This introductory article sets the scene for this special issue focussing on the plurality of norms and practices in Muslim marriages within Muslim-majority jurisdictions.
A comprehensive evaluation of long read error correction methods
Authors: Zhang Haowen , Jain Chirag , Aluru Srinivas 
Published: December 2020

AbstractBackgroundThird-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstream analysis. This difficulty has motivated the development of many long read error correction tools, which tackle this problem through sampling redundancy and/or leveraging accurate short reads of the same biological samples. Existing studies to asses these tools use simulated data sets, and are not sufficiently comprehensive in the range of software covered or diversity of evaluation measures used.ResultsIn this paper, we present a categorization and review of long read error correction methods, and provide a comprehensive evaluation of the corresponding long read error correction tools. Leveraging recent real sequencing data, we establish benchmark data sets and set up evaluation criteria for a comparative assessment which includes quality of error correction as well as run-time and memory usage. We study how trimming and long read sequencing depth affect error correction in terms of length distribution and genome coverage post-correction, and the impact of error correction performance on an important application of long reads, genome assembly. We provide guidelines for practitioners for choosing among the available error correction tools and identify directions for future research.ConclusionsDespite the high error rate of long reads, the state-of-the-art correction tools can achieve high correction quality. When short reads are available, the best hybrid methods outperform non-hybrid methods in terms of correction quality and computing resource usage. When choosing tools for use, practitioners are suggested to be careful with a few correction tools that discard reads, and check the effect of error correction tools on downstream analysis. Our evaluation code is available as open-source athttps://github.com/haowenz/LRECE.