bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of thoracic endovascular aortic repair in thoracic aortic aneurysm and penetrating aortic ulcer using the Conformable Gore TAG within and outside the instructions for use
Authors: Meisenbacher Katrin , Hagedorn Matthias , Grond-Ginsbach Caspar , Weber Dorothea , Böckler Dittmar , Bischoff Moritz S 
Published: November 2020

Objective To describe the outcome of thoracic endovascular aortic repair (TEVAR) in thoracic aortic aneurysm and penetrating aortic ulcer with respect to instructions for use status. Methods Between October 2009 and September 2017, a total of 532 patients underwent TEVAR; of which 195 have been treated using the Conformable GORE® TAG® thoracic endoprosthesis (CTAG). Fifty-six patients of this cohort underwent TEVAR for thoracic aortic aneurysm/penetrating aortic ulcer using the CTAG. Depending on the preoperative computed tomography angiography findings, patients were classified as inside or outside the device’s instructions for use. All inside instruction for use patients underwent postoperative reclassification regarding the instructions for use status. Study endpoints included TEVAR-related reintervention, exclusion of the pathology (endoleak type I/III), TEVAR-related mortality, and graft-related serious adverse events. The median duration of follow-up was 29.7 months (range: 0–109.4 months). Results Of the 56 patients, 17 were primarily classified as outside instruction for use, and in additional 13 patients, TEVAR was performed outside instruction for use, leading to 30 outside instruction for use patients (53.6%). Twenty-six patients (46.4%) were treated inside instruction for use. Reintervention-free survival was lower in outside instruction for use patients ( P = 0.016) with a hazard ratio of 9.74 (confidence interval 1.2–80.2; P = 0.034) for TEVAR-related reintervention. With respect to endoleak type I/III, relevant difference was detected between inside/outside instruction for use status ( P = 0.012). The serious adverse event rate was 30.4%, mainly in outside instruction for use patients ( P = 0.004). Logistic regression analysis indicated an association between graft-related serious adverse event/instructions for use status (odds ratio 6.11; confidence interval 1.6–30.06; P = 0.012). In-hospital death was seen more frequently in outside instruction for use patients ( P = 0.12) as was procedure-related death (log-rank test: P = 0.21). Conclusion TEVAR for thoracic aortic aneurysm/penetrating aortic ulcer is frequently performed outside instruction for use despite preoperative inside instruction for use eligibility, leading to important consequences for technical/clinical outcome. Instructions for use adherence in TEVAR should be of interest for further large-scale studies.
Revised intracerebral hemorrhage expansion definitions: Relationship with care limitations
Authors: Lun Ronda , Yogendrakumar Vignan , Walker Greg , Shamy Michel , Fahed Robert , Qureshi Adnan , Dowlatshahi Dar 
Published: November 2020

Background Hematoma expansion is an important therapeutic target in intracerebral hemorrhage. Recently proposed hematoma expansion definitions have not been validated, and no previous definition has accounted for withdrawal of care. Aims To externally validate revised definitions of hematoma expansion that incorporate intraventricular hemorrhage, and to test their validity in the context of withdrawal of care. Methods We analyzed data from the Antihypertensive Treatment of Acute Cerebral Hemorrhage II trial, comparing revised definitions of hematoma expansion incorporating intraventricular hemorrhage expansion to the conventional definition of “≥6 mL or ≥33%.” Primary outcome was modified Rankin Scale of 4–6 at 90 days. We calculated the incidence, sensitivity, specificity, positive and negative predictive values, and c-statistic for all definitions of hematoma expansion. Definitions were compared using nonparametric methods. Secondary analyses were performed after removing patients with withdrawal of care. Results Primary analysis included 948 patients. Using the conventional definition, the sensitivity was 37.1% and specificity was 83.2% for the primary outcome. Sensitivity improved with all three revised definitions (53.3%, 48.7%, and 45.3%, respectively), with minimal change to specificity (78.4%, 80.5%, and 81.0%, respectively). The greatest improvement was seen with the definition “≥6 mL or ≥33% or any intraventricular hemorrhage,” with increased c-statistic from 60.2% to 65.9% ( p < 0.001). Secondary analysis excluded 46 participants who experienced withdrawal of care. The revised definitions similarly outperformed the conventional definition in this population, with the greatest improvement in c-statistic using “≥6 mL or ≥33% or any intraventricular hemorrhage” (58.1% vs. 64.1%, p < 0.001). Conclusions Revised hematoma expansion definitions incorporating intraventricular hemorrhage expansion outperformed conventional definitions for predicting poor outcome, even after accounting for care limitations.
Revisiting the dogma of the Edinburgh position for safe immobilization
Authors: J. Jordan Daniel , Leow Jun M. , Stirling Paul H. C. , Lam Wee L. 
Published: November 2020

Since the concept was first described 50 years ago in Edinburgh by J. I. P. James, the term ‘Edinburgh position’ has been synonymous with the position of safe immobilization for the hand. Widely employed for the management of injured hands, the position is associated with splinting the metacarpophalangeal joints at 90° and the proximal interphalangeal joints completely straight, namely, ‘the intrinsic-plus position’, to help reduce the long-term consequences of a stiff hand. Over the decades, the strict joint angles of the Edinburgh position have been debated due to changes in patterns of injury, treatment and rehabilitation. This article challenges the dogma that surrounds the use of the Edinburgh position in clinical practice. The history of the position was explored, and the results of a survey about current practice of hand immobilization from two study centres in Edinburgh is presented. Level of evidence: IV
Clinical experience with antifibrotics in fibrotic hypersensitivity pneumonitis: a 3-year real-life observational study
Authors: Tzilas Vasilios , Tzouvelekis Argyris , Bouros Evangelos , Karampitsakos Theodoros , Ntassiou Maria , Avdoula Eleni , Trachalaki Athena , Antoniou Katerina , Raghu Ganesh , Bouros Demosthenes 
Published: November 2020

BackgroundFibrotic hypersensitivity pneumonitis (f-HP) can exhibit a progressive course similar to idiopathic pulmonary fibrosis (IPF). The lack of diagnostic guidelines and randomised controlled trials in this population represent a significant unmet need.ObjectivesTo describe our clinical experience with antifibrotics in patients with f-HP.Material and methodsRetrospective study of 30 patients diagnosed with f-HP upon re-evaluation within a multidisciplinary team discussion of 295 consecutive patients (January 2012 to December 2017) who had been diagnosed initially with IPF at outside facilities and were referred to our centres.ResultsPirfenidone was initially administered to 14 (46.7%) patients and nintedanib to 16 (53.3%) patients. There were 26 (86.7%) males, with mean±sdage 70.2±8.4 years. The annual rate of decline in forced vital capacity (FVC) % predicted over the 3-year treatment period adjusted for baseline FVC % pred measurement was 4.2% (95% CI 1.9–6.6%, p=0.001) and 7.5% (95% CI 3.3–11.7%; p=0.001) in imputation analysis. The annual rate of decline in diffusing capacity of the lung for carbon monoxide (DLCO) % predicted throughout the 3-year treatment period adjusted for baselineDLCO% pred was 5.7% (95% CI 3.1–8.4%, p<0.001) and 5.8% (95% CI 3.4–8.1%, p<0.001) in imputation analysis. The nature of adverse events was related to the type of antifibrotic agent administered.ConclusionIn patients with f-HP receiving antifibrotics there is a statistically significant annual decline in FVC % pred andDLCO% pred over a period of 3 years. Prospective randomised trials exceeding 1 year are warranted to determine the long-term efficacy of antifibrotics.
Mortality prediction in chronic obstructive pulmonary disease comparing the GOLD 2015 and GOLD 2019 staging: a pooled analysis of individual patient data
Authors: García Castillo Elena , Alonso Pérez Tamara , Ancochea Julio , Pastor Sanz Maria Teresa , Almagro Pere , Martínez-Camblor Pablo , Miravitlles Marc , Rodríguez-Carballeira Mónica , Navarro Annie , Lamprecht Bernd , Ramírez-García Luna Ana S. , Kaiser Bernhard , Alfageme Inmaculada , Casanova Ciro , Esteban Cristóbal , Soler-Cataluña Juan J. , de-Torres Juan P. , Celli Bartolomé R. , Marín Jose M. , ter Riet Gerben , Sobradillo Patricia , Lange Peter , Garcia-Aymerich Judith , Anto Josep M. , Turner Alice M. , Han MeiLan K. , Langhammer Arnulf , Vikjord Sigrid Anna Aalberg , Sternberg Alice , Leivseth Linda , Bakke Per , Johannessen Ane , Oga Toru , Cosío Borja G. , Echazarreta Andrés , Roche Nicolás , Burgel Pierre-Régis , Sin Don D. , Puhan Milo A. , López-Campos Jose Luis , Carrasco Laura , Soriano Joan B. 
Published: November 2020

In 2019, The Global Initiative for Chronic Obstructive Lung Disease (GOLD) modified the grading system for patients with COPD, creating 16 subgroups (1A–4D). As part of the COPD Cohorts Collaborative International Assessment (3CIA) initiative, we aim to compare the mortality prediction of the 2015 and 2019 COPD GOLD staging systems.We studied 17 139 COPD patients from the 3CIA study, selecting those with complete data. Patients were classified by the 2015 and 2019 GOLD ABCD systems, and we compared the predictive ability for 5-year mortality of both classifications.In total, 17 139 patients with COPD were enrolled in 22 cohorts from 11 countries between 2003 and 2017; 8823 of them had complete data and were analysed. Mean±sdage was 63.9±9.8 years and 62.9% were male. GOLD 2019 classified the patients in milder degrees of COPD. For both classifications, group D had higher mortality. 5-year mortality did not differ between groups B and C in GOLD 2015; in GOLD 2019, mortality was greater for group B than C. Patients classified as group A and B had better sensitivity and positive predictive value with the GOLD 2019 classification than GOLD 2015. GOLD 2015 had better sensitivity for group C and D than GOLD 2019. The area under the curve values for 5-year mortality were only 0.67 (95% CI 0.66–0.68) for GOLD 2015 and 0.65 (95% CI 0.63–0.66) for GOLD 2019.The new GOLD 2019 classification does not predict mortality better than the previous GOLD 2015 system.
The effect of bronchial thermoplasty on airway volume measured 12 months post-procedure
Authors: Langton David , Banks Ceri , Noble Peter B. , Plummer Virginia , Thien Francis , Donovan Graham M. 
Published: November 2020

Bronchial thermoplasty induces atrophy of the airway smooth muscle layer, but the mechanism whereby this improves patient health is unclear. In this study, we use computed tomography (CT) to evaluate the effects of bronchial thermoplasty on airway volume 12 months post-procedure.10 consecutive patients with severe asthma were evaluated at baseline by the Asthma Control Questionnaire (ACQ), and high-resolution CT at total lung capacity (TLC) and functional residual capacity (FRC). The CT protocol was repeated 4 weeks after the left lung had been treated by bronchial thermoplasty, but prior to right lung treatment, and then again 12 months after both lungs were treated. The CT data were also used to model the implications of including the right middle lobe (RML) in the treatment field.The mean patient age was 62.7±7.7 years and forced expiratory volume in 1 s (FEV1) 42.9±11.5% predicted. 12 months post-bronchial-thermoplasty, the ACQ improved, from 3.4±1.0 to 1.5±0.9 (p=0.001), as did the frequency of oral steroid-requiring exacerbations (p=0.008).The total airway volume increased 12 months after bronchial thermoplasty in both the TLC (p=0.03) and the FRC scans (p=0.02). No change in airway volume was observed in the untreated central airways. In the bronchial thermoplasty-treated distal airways, increases in airway volume of 38.4±31.8% at TLC (p=0.03) and 30.0±24.8% at FRC (p=0.01) were observed. The change in distal airway volume was correlated with the improvement in ACQ (r=−0.71, p=0.02). Modelling outputs demonstrated that treating the RML conferred no additional benefit.Bronchial thermoplasty induces long-term increases in airway volume, which correlate with symptomatic improvement.
Emergency department visits and hospitalisations for asthma, COPD and respiratory tract infections: what is the role of respiratory viruses, and return to school in September, January and March?
Authors: Satia Imran , Adatia Adil , Yaqoob Sarah , Greene Justina M. , O'Byrne Paul M. , Killian Kieran J. , Johnston Neil 
Published: November 2020

BackgroundAsthma exacerbations increase in September coinciding with children returning to school. The aim of this study was to investigate whether this occurs 1) for COPD and respiratory tract infections (RTIs); 2) after school resumes in January and March; and 3) identify which viruses may be responsible.MethodsEmergency department (ED) visits and admissions for asthma, COPD and RTIs and the prevalence of viruses in Ontario, Canada were analysed daily between 2003 and 2013. ED visits and admissions were provided by the Canadian Institute for Health Information. Viral prevalence was obtained from the Centre for Immunisation and Respiratory Infectious Diseases.ResultsED visits and admissions rates demonstrated a biphasic pattern. Lowest rates occurred in July and August and the highest rates in September for asthma, and after December for COPD and RTI. The increase in rates for 30 days before and after school return in September was greatest for children with asthma <15 years (2.4–2.6×). Event rates fell after school return in January for all three conditions ranging from 10–25%, and no change followed March break for asthma and COPD. Human rhinovirus was prevalent in summer with a modest relationship to asthma rates in September. The prevalence of respiratory syncytial virus, influenza A and coronavirus was associated with sustained event rates for COPD and RTIs.ConclusionsAsthma, COPD and RTIs increase in September but do not occur after return to school in January and March. Human rhinovirus is associated with ED visits and admissions only in September.
A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly
Authors: Dias Guilherme Rezende , Dupim Eduardo Guimarães , Vanderlinde Thyago , Mello Beatriz , Carvalho Antonio Bernardo 
Published: November 2020

AbstractBackgroundThe Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.ResultsMost of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).ConclusionsSteganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.
A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease
Authors: Sethi Siddharth , Vorontsov Ilya E. , Kulakovskiy Ivan V. , Greenaway Simon , Williams John , Makeev Vsevolod J. , Brown Steve D. M. , Simon Michelle M. , Mallon Ann-Marie 
Published: November 2020

Abstract

Background
Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematically annotating multiple mouse tissues with super- and typical-enhancers, we have explored their relationship with gene function and phenotype.

Results
Though super-enhancers drive high total- and tissue-specific expression of their associated genes, we find that typical-enhancers also contribute heavily to the tissue-specific expression landscape on account of their large numbers in the genome. Unexpectedly, we demonstrate that both enhancer types are preferentially associated with relevant ‘tissue-type’ phenotypes and exhibit no difference in phenotype effect size or pleiotropy. Modelling regulatory data alongside molecular data, we built a predictive model to infer gene-phenotype associations and use this model to predict potentially novel disease-associated genes.

Conclusion
Overall our findings reveal that differing enhancer architectures have a similar impact on mammalian phenotypes whilst harbouring differing cellular and expression effects. Together, our results systematically characterise enhancers with predicted phenotypic traits endorsing the role for both types of enhancers in human disease and disorders.
Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches
Authors: Zhang Chuan-Bo , Ren Chao-Hui , Wang Yan-Li , Wang Qi-Qi , Wang Yun-Sheng , Weng Qing-Bei 
Published: November 2020

Abstract

Background
The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approaches.

Results
A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices, Ophiocordyceps, Sebacinia and Archaeorhizomyces were predominant genera with the abundance of 95.86, 1.14, 0.85%, respectively. A total of 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, unclassified Ascomycota and unclassified fungi were predominant genera with an average abundance of 53.32, 8.69, 8.12, 8.12, 7.21, 4.6, 3.08 and 3.05%, respectively. The fungal communities in external mycelial cortices were significantly distinct from soil microhabitat. Meanwhile, seven types of culture media were used to isolate culturable fungi at 16 °C, resulted in 77 fungal strains identified by rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora and Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera.

Conclusions
The significantly differences and overlap in fungal community structure between two approaches highlight that the integration of high-throughput sequencing and culture-dependent approaches would generate more information. Our result reveal a comprehensive understanding of fungal community structure of natural O. sinensis, provide new insight into O. sinensis associated fungi, and support that microbiota of natural O. sinensis is an untapped source for novel bioactive metabolites discovery.
The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota
Authors: Feye Kristina M. , Swaggerty Christina L. , Kogut Michael H. , Ricke Steven C. , Piva Andrea , Grilli Ester 
Published: November 2020

Abstract

Background
Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of organic acids and botanicals (AviPlus®P) has previously shown to reduce Salmonella and Campylobacter in chickens; however, changes to the microbiota of the jejunum and ileum have not been evaluated. Microbiota diversity is linked to, but not correlated with, the efficacy of natural products; therefore, understanding the effects on the microbiota is necessary for evaluating their potential as an antibiotic alternative.

Results
Ileal and jejunal segments from control and supplement-fed chickens (300 and 500 g/metric ton [MT]) were subjected to alpha diversity analysis including Shannon’s diversity and Pielou’s Evenness. In both analytics, the diversity in the ileum was significantly decreased compared to the jejunum irrespective of treatment. Similarly, beta diversity metrics including Bray-Curtis dissimilarity index and Weighted Unifrac Distance Matrix, were significant (Q < 0.05) for both tissue and treatments comparisons. Alpha and beta diversity analytics indicated compartmentalization effects between the ileum and jejunum. Additionally, analysis of communities in the microbiota (ANCOM) analysis showed Lactobacilliaceae predominated the total operational taxonomic units (OTU), with a stepwise increase from 53% in the no treatment control (NTC) to 56% in the 300 g/MT and 67% in the 500 g/MT group. Staphylococcaceae were 2% in NTC and 2 and 0% in 300 and 500 g/MT groups. Enterobacteriaceae decreased in the 500 g/MT (31%) and increased in the 300 g/MT (37%) compared to the NTC (35%). Aerococcaceae was 0% for both doses and 7% in NTC. Ruminococcaceae were 0% in NTC and 2 and 1% in the 300 and 500 g/MT. These changes in the microbial consortia were statistically (Q < 0.05) associated with treatment groups in the jejunum that were not observed in the ileum. Least discriminant analysis effect size (LEfSE) indicated different changes directly corresponding to treatment. Enterobacteriaceae demonstrated a stepwise decrease (from NTC onward) while Clostridiaceae, were significantly increased in the 500 g/MT compared to NTC and 300 g/MT (P < 0.05).

Conclusion
The bioactive site for the microencapsulated blend of organic acids and botanicals was the jejunum, and dietary inclusion enhanced the GIT microbiota and may be a viable antibiotic alternative for the poultry industry.