bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging markers associated with the development of post-stroke depression and apathy: Results of the Cognition and Affect after Stroke – a Prospective Evaluation of Risks study
Authors: Douven Elles , Staals Julie , Freeze Whitney M , Schievink Syenna HJ , Hellebrekers Danique MJ , Wolz Robin , Jansen Jacobus FA , van Oostenbrugge Robert J , Verhey Frans RJ , Aalten Pauline , Köhler Sebastian 
Published: October 2019

Introduction It has been suggested that the development of post-stroke apathy (PSA) and depression (PSD) may be more strongly associated with generalised brain pathology, rather than the stroke lesion itself. The present study aimed to investigate associations between imaging markers of lesion-related and generalised brain pathology and the development of PSA and PSD during a one-year follow-up. Patients and methods In a prospective cohort study, 188 stroke patients received 3-Tesla MRI at baseline (three months post-stroke) for evaluation of lesion-related, vascular, and degenerative brain pathology. Presence of lacunes, microbleeds, white matter hyperintensities, and enlarged perivascular spaces was summed to provide a measure of total cerebral small vessel disease (cSVD) burden (range 0–4). The Mini International Neuropsychiatric Interview and Apathy Evaluation Scale were administered at baseline and repeated at 6- and 12-month follow-up to define presence of PSD and PSA, respectively. Results Population-averaged logistic regression models showed that global brain atrophy and severe cSVD burden (score 3–4) were significantly associated with the odds of having PSA (ORGEE 5.33, 95% CI 1.99–14.25 and 3.04, 95% CI 1.20–7.69, respectively), independent of stroke lesion volume and co-morbid PSD. Medium cSVD burden (score 2) was significantly associated with the odds of having PSD (ORGEE 2.92, 95% CI 1.09–7.78), independent of stroke lesion volume, co-morbid PSA, and pre-stroke depression. No associations were found with lesion-related markers. Conclusions The results suggest that generalised degenerative and vascular brain pathology, rather than lesion-related pathology, is an important predictor for the development of PSA, and less strongly for PSD.
Bilateral Choroidal Neovascularization and Chorioretinal Anastomosis in Autosomal Recessive Bestrophinopathy
Authors: Zhang Youning , Danesh Jennifer , Green Kyle M. , Schmidt Ryan J. , Biegel Jaclyn , Gai Xiaowu , Lee Thomas C. , Kashani Amir H. , Nagiel Aaron 
Published: October 2019

Purpose: This case report discusses a case of bilateral chorioretinal anastomoses in autosomal recessive bestrophinopathy (ARB) unresponsive to antivascular endothelial growth factor therapy and its associated optical coherence tomography angiography (OCTA) findings. Methods: An observational case report is presented. Results: An 8-year-old girl initially presented at age 2 years with multifocal midperipheral yellow subretinal deposits with intraretinal and subretinal fluid. She was treated with intravitreal injections of bevacizumab in both eyes with minimal response. OCTA revealed the presence of choroidal neovascularization and chorioretinal anastomoses. Molecular diagnosis of ARB was achieved with the identification of compound heterozygous mutations in BEST1, including a silent exonic splicing mutation. Conclusions: Subretinal or intraretinal fluid in ARB may be exacerbated by the presence of chorioretinal anastomosis detected on OCTA. Silent exonic mutations that cause no amino acid change can be overlooked but are pathogenic in ARB.
Prognostic factors associated with long-term mortality in 1445 patients with nontuberculous mycobacterial pulmonary disease: a 15-year follow-up study
Authors: Jhun Byung Woo , Moon Seong Mi , Jeon Kyeongman , Kwon O Jung , Yoo Heejin , Carriere Keumhee C. , Huh Hee Jae , Lee Nam Yong , Shin Sung Jae , Daley Charles L. , Koh Won-Jung 
Published: October 2019

Limited data are available regarding the prognostic factors for patients with nontuberculous mycobacterial pulmonary disease (NTM-PD). We investigated the prognostic factors associated with long-term mortality in NTM-PD patients after adjusting for individual confounders, including aetiological organism and radiological form.A total of 1445 patients with treatment-naïve NTM-PD who were newly diagnosed between July 1997 and December 2013 were included. The aetiological organisms were as follows:Mycobacterium avium(n=655),M. intracellulare(n=487),M. abscessus(n=129) andM. massiliense(n=174). The factors associated with mortality in NTM-PD patients were analysed using a multivariable Cox model after adjusting for demographic, radiological and aetiological data.The overall 5-, 10- and 15-year cumulative mortality rates for the NTM-PD patients were 12.4%, 24.0% and 36.4%, respectively. On multivariable analysis, the following factors were significantly associated with mortality in NTM-PD patients: old age, male sex, low body mass index, chronic pulmonary aspergillosis, pulmonary or extrapulmonary malignancy, chronic heart or liver disease and erythrocyte sedimentation rate. The aetiological organism was also significantly associated with mortality:M. intracellularehad an adjusted hazard ratio (aHR) of 1.40, 95% CI 1.03–1.91;M. abscessushad an aHR of 2.19, 95% CI 1.36–3.51; andM. massiliensehad an aHR of 0.99, 95% CI 0.61–1.64, compared toM. avium. Mortality was also significantly associated with the radiological form of NTM-PD for the cavitary nodular bronchiectatic form (aHR 1.70, 95% CI 1.12–2.59) and the fibrocavitary form (aHR 2.12, 95% CI 1.57–3.08), compared to the non-cavitary nodular bronchiectatic form.Long-term mortality in patients with NTM-PD was significantly associated with the aetiological NTM organism, cavitary disease and certain demographic characteristics.
Diverse cardiopulmonary diseases are associated with distinct xenon magnetic resonance imaging signatures
Authors: Wang Ziyi , Bier Elianna A. , Swaminathan Aparna , Parikh Kishan , Nouls John , He Mu , Mammarappallil Joseph G. , Luo Sheng , Driehuys Bastiaan , Rajagopal Sudarshan 
Published: October 2019

BackgroundAs an increasing number of patients exhibit concomitant cardiac and pulmonary disease, limitations of standard diagnostic criteria are more frequently encountered. Here, we apply noninvasive129Xe magnetic resonance imaging (MRI) and spectroscopy to identify patterns of regional gas transfer impairment and haemodynamics that are uniquely associated with chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), left heart failure (LHF) and pulmonary arterial hypertension (PAH).MethodsHealthy volunteers (n=23) and patients with COPD (n=8), IPF (n=12), LHF (n=6) and PAH (n=10) underwent129Xe gas transfer imaging and dynamic spectroscopy. For each patient, three-dimensional maps were generated to depict ventilation, barrier uptake (129Xe dissolved in interstitial tissue) and red blood cell (RBC) transfer (129Xe dissolved in RBCs). Dynamic129Xe spectroscopy was used to quantify cardiogenic oscillations in the RBC signal amplitude and frequency shift.ResultsCompared with healthy volunteers, all patient groups exhibited decreased ventilation and RBC transfer (both p≤0.01). Patients with COPD demonstrated more ventilation and barrier defects compared with all other groups (both p≤0.02). In contrast, IPF patients demonstrated elevated barrier uptake compared with all other groups (p≤0.007), and increased RBC amplitude and shift oscillations compared with healthy volunteers (p=0.007 and p≤0.01, respectively). Patients with COPD and PAH both exhibited decreased RBC amplitude oscillations (p=0.02 and p=0.005, respectively) compared with healthy volunteers. LHF was distinguishable from PAH by enhanced RBC amplitude oscillations (p=0.01).ConclusionCOPD, IPF, LHF and PAH each exhibit unique129Xe MRI and dynamic spectroscopy signatures. These metrics may help with diagnostic challenges in cardiopulmonary disease and increase understanding of regional lung function and haemodynamics at the alveolar–capillary level.
Preliminary validation of the NTM Module: a patient-reported outcome measure for patients with pulmonary nontuberculous mycobacterial disease
Authors: Henkle Emily , Winthrop Kevin L. , Ranches Gregory P. , Plinke Wesley , Litvin Hana K. , Quittner Alexandra L. 
Published: October 2019

IntroductionNontuberculous mycobacteria (NTM) cause chronic, debilitating pulmonary disease. Patient-reported outcomes provide measures of symptoms, functioning and treatment response. Here we describe the preliminary validation of the recently developed NTM Module.MethodsThe study population included Northwest NTM Biobank patients in whomMycobacterium aviumcomplex (MAC) was isolated and who had ever met the 2007 American Thoracic Society/Infectious Diseases Society of America pulmonary disease criteria. The NTM Module was administered at enrolment and 12 months; a subset also completed the Quality of Life Questionnaire–Bronchiectasis (QOL-B). The NTM Module generates four domain scores (0–100; higher scores indicate better functioning) reflecting NTM-specific symptoms (NTM Symptoms, Body Image, Digestive Symptoms and Eating Problems). We described patient characteristics and mean scores, and evaluated psychometric properties, including response to treatment at 12 months, for each domain.ResultsOverall, 203 patients with pulmonary MAC disease were included. Average enrolment scores ranged from 76 (NTM Symptoms) to 84 (Eating Problems). Ceiling effects were observed for Body Image (26% of participants) and Eating Problems (52%). Internal consistency (Cronbach's alpha) ranged from 0.67 (Digestive Symptoms) to 0.89 (Eating Problems). The intraclass correlation for test–retest reproducibility (n=27) ranged from 0.72 (Body Image) to 0.94 (Eating Problems). Patients starting treatment (n=35) had statistically significant increases in scores for NTM Symptoms (+5, p=0.04), Digestive Symptoms (+7, p=0.002), Body Image (+7, p=0.03) and QOL-B Respiratory Symptoms (n=25, +10, p=0.006). NTM Symptoms scores increased by 15 points (p=0.002) in the 16 patients with scores ≤80 at enrolment.ConclusionThe NTM Module generally performs well as a valid patient-reported outcome for pulmonary MAC disease and was responsive to MAC treatment.
Acute wheeze-specific gene module shows correlation with vitamin D and asthma medication
Authors: Katayama Shintaro , Stenberg Hammar Katarina , Krjutškov Kaarel , Einarsdottir Elisabet , Hedlin Gunilla , Kere Juha , Söderhäll Cilla 
Published: October 2019

BackgroundAirway obstruction and wheezing in preschool children with recurrent viral infections are a major clinical problem, and are recognised as a risk factor for the development of chronic asthma. We aimed to analyse whether gene expression profiling provides evidence for pathways that delineate distinct groups of children with wheeze, and in combination with clinical information could contribute to diagnosis and prognosis of disease development.MethodsWe analysed leukocyte transcriptomes from preschool children (6 months–3 years) at acute wheeze (n=107), and at a revisit 2–3 months later, comparing them to age-matched healthy controls (n=66). RNA-sequencing applying GlobinLock was used. The cases were followed clinically until age 7 years. Differential expression tests, weighted correlation network analysis and logistic regression were applied and correlations to 76 clinical traits evaluated.FindingsSignificant enrichment of genes involved in the innate immune responses was observed in children with wheeze. We identified a unique acute wheeze-specific gene-module, which was associated with vitamin D levels (p<0.005) in infancy, and asthma medication and FEV1%/FVC (forced expiratory volume in 1 s/forced vital capacity) ratio several years later, at age 7 years (p<0.005). A model that predicts leukotriene receptor antagonist medication at 7 years of age with high accuracy was developed (area under the curve 0.815, 95% CI 0.668–0.962).InterpretationGene expression profiles in blood from preschool wheezers predict asthma symptoms at school age, and therefore serve as biomarkers. The acute wheeze-specific gene module suggests that molecular phenotyping in combination with clinical information already at an early episode of wheeze may help to distinguish children who will outgrow their wheeze from those who will develop chronic asthma.
The Core-Shell Heterostructure CNT@Li2FeSiO4@C as a Highly Stable Cathode Material for Lithium-Ion Batteries
Authors: Peng Tao , Guo Wei , Zhang Yingge , Wang Yangbo , Zhu Kejia , Guo Yan , Wang Yinghui , Lu Yang , Yan Hailong 
Published: October 2019

AbstractThe reasonable design of nanostructure is the key to solving the inherent defects and realizing a high performance of Li2FeSiO4cathode materials. In this work, a novel heterostructure CNT@Li2FeSiO4@C has been designed and synthesized and used as a cathode material for lithium-ion battery. It is revealed that the product has a uniform core-shell structure, and the thickness of the Li2FeSiO4layer and the outer carbon layer is about 19 nm and 2 nm, respectively. The rational design effectively accelerates the diffusion of lithium ions, improves the electric conductivity, and relieves the volume change during the charging/discharging process. With the advantages of its specific structure, CNT@Li2FeSiO4@C has successfully overcome the inherent shortcomings of Li2FeSiO4and shown good reversible capacity and cycle properties.
Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models
Authors: Wilbrandt Jeanne , Misof Bernhard , Panfilio Kristen A. , Niehuis Oliver 
Published: October 2019

AbstractBackgroundThe location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative.ResultsOur results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities.ConclusionsIn our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.
RETRACTED ARTICLE: Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis
Authors: Ma Qiang , Wang Nuohan , Hao Pengbo , Sun Huiru , Wang Congcong , Ma Liang , Wang Hantao , Zhang Xianlong , Wei Hengling , Yu Shuxun 
Published: October 2019

Abstract
Background
Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.).

Results
In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers.

Conclusion
We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.
Dynamic Electronic Tracking and Escalation to reduce Critical care Transfers (DETECT): the protocol for a stepped wedge mixed method study to explore the clinical effectiveness, clinical utility and cost-effectiveness of an electronic physiological surveillance system for use in children
Authors: Sefton Gerri , Carter Bernie , Lane Steven , Peak Matthew , Mateus Ceu , Preston Jen , Mehta Fulya , Hollingsworth Bruce , Killen Roger , Carrol Enitan D. 
Published: October 2019

Abstract

Background
Active monitoring of hospitalised adults, using handheld electronic physiological surveillance systems, is associated with reduced in-patient mortality in the UK. Potential also exists to improve the recognition and response to deterioration in hospitalised children. However, the clinical effectiveness, the clinical utility, and the cost-effectiveness of this technology to reduce paediatric critical deterioration, have not been evaluated in an NHS environment.

Method
This is a non-randomised stepped-wedge prospective mixed methods study. Participants will be in-patients under the age of 18 years, at a tertiary children’s hospital. Day-case, neonatal surgery and Paediatric Intensive Care Unit (PICU) patients will be excluded.
The intervention is the implementation of Careflow Vitals and Connect (System C) to document vital signs and sepsis screening. The underpinning age-specific Paediatric Early Warning Score (PEWS) risk model calculates PEWS and provides associated clinical decision support. Real-time data of deterioration risk are immediately visible to the entire clinical team to optimise situation awareness, the chronology of the escalation and response are captured with automated reporting of the organisational safety profile.
Baseline data will be collected prospectively for 1 year preceding the intervention. Following a 3 month implementation period, 1 year of post-intervention data will be collected.
The primary outcome is unplanned transfers to critical care (HDU and/or PICU). The secondary outcomes are critical deterioration events (CDE), the timeliness of critical care transfer, the critical care interventions required, critical care length of stay and outcome.
The clinical effectiveness will be measured by prevalence of CDE per 1000 hospital admissions and per 1000 non-PICU bed days.
Observation, field notes, e-surveys and focused interviews will be used to establish the clinical utility of the technology to healthcare professionals and the acceptability to in-patient families. The cost-effectiveness will be analysed using Health Related Group costs per day for the critical care and hospital stay for up to 90 days post CDE.

Discussion
If the technology is effective at reducing CDE in hospitalised children it could be deployed widely, to reduce morbidity and mortality, and associated costs.

Trial registration
Current Controlled Trials ISRCTN61279068, date of registration 03.06.19, retrospectively registered.