bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pneumonia after Repair of Esophageal Atresia–Incidence and Main Risk Factors
Authors: Nurminen Paula , Koivusalo Antti , Hukkinen Maria , Pakarinen Mikko 
Published: November 2018

Introduction Esophageal atresia (EA) is associated with significant respiratory mortality. We aimed to assess incidence and predictive factors of EA associated pneumonia during the first 5 years of life.
Materials and Methods Institutional ethical consent was obtained. Hospital records of patients with EA from 2002 to 2017 were reviewed. Episodes of pneumonia that were diagnosed in university or regional hospitals were included. For instance, respiratory infections other than pneumonia, anastomotic complications, aortopexy, fundoplication, major EA associated diseases, types of EA, and EA anastomosis dilatations were tested as potential risk factors for pneumonia.
Results A total of 104 patients (56 males; type A 7, B 3, C 83, D 3, E 6, F 2) was included. Thirty-five (34%) patients had 94 episodes of pneumonia corresponding to median 2 (IQR [interquartile range]: 1–4) and 609 episodes per thousand patient years. Majority of pneumonias occurred before the age of 3 years. The cause of pneumonias could be identified as RS (respiratory syncytial) virus in 15(16%) and aspiration in seven (7.4%) episodes. In univariate analysis, pneumonia was predicted by occurrence and number of nonpneumonia respiratory infections, anastomotic reoperations, fundoplication, and number of EA anastomosis dilatations. In multivariate logistic regression analysis, significant risk factors for pneumonia were occurrence of nonpneumonia respiratory infections and number of anastomotic dilatations.
Conclusion Episodes of pneumonia occurred in one-third of patients with EA. After the final repair, the incidence of pneumonia was highest during the first 3 years of life. Patients with other acute respiratory infections and high number of dilatations were at the greatest risk.
A study of morbidity pattern among elderly population in urban India
Authors: Yadav Akhilesh , Prasad Jang , Shekher Chander , Vishvakarma Minakshi 
Published: November 2018

Abstract
Background: The people in urban area were suffering from different type of morbidities like chronic lung disease, depression, angina, diabetes, etc. Therefore, this study was designed to explore the age pattern of morbidities, level of substance use among elderly, and relationship between substances used and selected morbidities among elderly in urban India.
Material and Methods: The information on morbidity was obtained from Study on Global Ageing and Adult Health (SAGE) - 2007. The methods bivariate and multivariate were used for analyzing the data.
Results and Discussion: The hypertension, depression, diabetes and disease-related to oral health were highly prevalent in the age group of 50-59 years, while cataracts, asthma, and stroke were more frequent in 60-69 years. In urban India, around every second people in the age group of 50-59 years were smokers whereas people were more alcoholic in 60-69 years. In urban India, Assam was the state where the prevalence of smoking was highest while alcohol consumption was highest in the state of Rajasthan and lowest was in Assam. Moreover, among the elderly people; the third most powerful killer disease (diabetes) was highest in the age the group of 50-59 years. Age, tobacco consumption and improvements in wealth quintile were significant risk factors associated with the presence of morbidities like diabetes, hypertension, and stroke. Asthma and oral health were significant increases along with age.
Conclusion: Study confirm that, for reducing these non communicable diseases, there is need to improve old age policy to make proper intension towards the health facility especially among the elderly of middle and higher economic households.
Formal ontology for discourse analysis of a corpus of court interpreting
Authors: Pease Adam , Pease Jennifer Cheung , Cheung Andrew K. F. 
Published: November 2018

AbstractWe develop a new method of discourse analysis using speech act theory and formal ontology. The method constitutes an attempt to make discourse analysis more formal and repeatable. We apply the method to a corpus of bi-lingual, interpreted legal dialogue, focusing on the speech act of clarification and its component acts. While discourse analysis is primarily a qualitative tool, it can be applied quantitatively by counting certain types of discourse, such as clarification speech acts. Dialogues are still analysed, utterances are classified as speech acts and their semantic relationships are qualitatively assessed. Subjectivity of human analysis is minimised using a new method of discourse analysis that employs a formal ontology. The ontology is stated in higher-order logic making the annotation of the corpus more objective, formal and repeatable than prior research.
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
Authors: Czajkowski Matthew D , Vance Daniel P , Frese Steven A , Casaburi Giorgio 
Published: November 2018

Abstract

Summary
The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface.

Availability and implementation
GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nestin Regulates Neurogenesis in Mice Through Notch Signaling From Astrocytes to Neural Stem Cells
Authors: Wilhelmsson Ulrika , Lebkuechner Isabell , Leke Renata , Marasek Pavel , Yang Xiaoguang , Antfolk Daniel , Chen Meng , Mohseni Paria , Lasič Eva , Bobnar Saša Trkov , Stenovec Matjaž , Zorec Robert , Nagy Andras , Sahlgren Cecilia , Pekna Marcela , Pekny Milos 
Published: November 2018

AbstractThe intermediate filament (nanofilament) protein nestin is a marker of neural stem cells, but its role in neurogenesis, including adult neurogenesis, remains unclear. Here, we investigated the role of nestin in neurogenesis in adult nestin-deficient (Nes–/–) mice. We found that the proliferation of Nes–/– neural stem cells was not altered, but neurogenesis in the hippocampal dentate gyrus of Nes–/– mice was increased. Surprisingly, the proneurogenic effect of nestin deficiency was mediated by its function in the astrocyte niche. Through its role in Notch signaling from astrocytes to neural stem cells, nestin negatively regulates neuronal differentiation and survival; however, its expression in neural stem cells is not required for normal neurogenesis. In behavioral studies, nestin deficiency in mice did not affect associative learning but was associated with impaired long-term memory.
Screening questions for the diagnosis of restless legs syndrome in hemodialysis
Authors: Collister David , Rodrigues Jennifer C , Mazzetti Andrea , Salisbury Kelsi , Morosin Laura , Rabbat Christian , Brimble K Scott , Walsh Michael 
Published: November 2018

Abstract

Background
Restless legs syndrome (RLS) is common in end-stage renal disease and is associated with reduced health-related quality of life. Simple and accurate screening instruments are needed since RLS is underdiagnosed and treatable. We examined the operating characteristics of screening questions and a disease-specific measurement tool for the diagnosis of RLS in hemodialysis.

Methods
We conducted a cohort study of prevalent adult hemodialysis patients in Hamilton, Canada. The diagnosis of RLS was made using the 2012 Revised International Restless Legs Syndrome Study Group (IRLSSG) criteria. All participants received three screening instruments: (i) a single screening question for RLS derived from a nondialysis population; (ii) a single question from the Edmonton Symptom Assessment System (ESAS); and (iii) the IRLSSG Rating Scale (IRLS). All instruments were compared with the reference standard using logistic regression from which receiver operating characteristics curves were generated. Cutoffs associated with maximum performance were identified.

Results
We recruited 50 participants with a mean (SD) age of 64 (12.4) years, of whom 52% were male and 92% were on three times weekly hemodialysis. Using the reference standard, 14 (28%) had a diagnosis of RLS. The single screening question for RLS had an area under the receiver operating curve (AUROC) of 0.72 with a sensitivity of 85.7% and specificity of 58.3%. An ESAS cutoff of ≥1 had the highest AUROC at 0.65 with a sensitivity of 79% and specificity of 56%. An IRLS cutoff of ≥20 had the highest AUROC at 0.75 with a sensitivity of 71% and specificity of 81%.

Conclusion
IRLS had better specificity than the single question or ESAS for the diagnosis of RLS.
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)
Authors: Luo Shiqi , Tang Min , Frandsen Paul B , Stewart Russell J , Zhou Xin 
Published: November 2018

Abstract

Background
Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (&gt;16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group.

Findings
We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled.

Conclusions
We report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.
A unique nanoparticulate TLR9 agonist enables a HA split vaccine to confer FcγR-mediated protection against heterologous lethal influenza virus infection
Authors: Yamamoto Takuya , Masuta Yuji , Momota Masatoshi , Kanekiyo Masaru , Kanuma Tomohiro , Takahama Shoukichi , Moriishi Eiko , Yasutomi Yasuhiro , Saito Takashi , Graham Barney S , Takahashi Yoshimasa , Ishii Ken J 
Published: November 2018

Abstract
The development of a universal influenza vaccine that can provide a robust and long-lasting protection against a broader range of influenza virus strains is a global public health priority. One approach to improve vaccine efficacy is to use an adjuvant to boost immune responses to the target antigens; nevertheless, the role of adjuvants in the context of influenza vaccines is not fully understood. We have previously developed the K3-schizophyllan (SPG) adjuvant, which is composed of nanoparticulated oligodeoxynucleotides K3, a TLR9 agonist, with SPG, a non-agonistic β-glucan ligand of Dectin-1. In this study, K3-SPG given with conventional influenza hemagglutinin (HA) split vaccine (K3-SPG HA) conferred protection against antigenically mismatched heterologous virus challenge. While K3-SPG HA elicited robust cross-reactive HA-specific IgG2c and CD8 T-cell responses, CD8 T-cell depletion had no impact on this cross-protection. In contrast, K3-SPG HA was not able to confer protection against heterologous virus challenge in FcRγ-deficient mice. Our results indicated that FcγR-mediated antibody responses induced by the HA antigen and K3-SPG adjuvant were important for potent protection against antigenically mismatched influenza virus infection. Thus, we demonstrated that the K3-SPG-adjuvanted vaccine strategy broadens protective immunity against influenza and provides a basis for the development of next-generation influenza vaccines.
Suzaku detection of enigmatic geocoronal solar wind charge exchange event associated with coronal mass ejection
Authors: Ishi Daiki , Ishikawa Kumi , Numazawa Masaki , Miyoshi Yoshizumi , Terada Naoki , Mitsuda Kazuhisa , Ohashi Takaya , Ezoe Yuichiro 
Published: November 2018

Abstract
Suzaku detected an enhancement of the soft X-ray background associated with solar eruptions on 2013 April 14–15. The solar eruptions were accompanied by an M6.5 solar flare and a coronal mass ejection with magnetic flux ropes. The enhanced soft X-ray background showed a slight variation over half a day and then a clear one in a few hours. The former spectrum was composed of oxygen emission lines, while the later one was characterized by a series of emission lines from highly ionized carbon to silicon. The soft X-ray enhancement originated from geocoronal solar wind charge exchange. However, there appeared to be no significant time correlation with the solar wind proton flux measured by the ACE and WIND satellites. From other solar wind signatures, we considered that an interplanetary shock associated with the coronal mass ejection and a turbulent sheath immediately behind the shock compressed the ambient solar wind ions and then resulted in the soft X-ray enhancement. Furthermore, the enriched emission lines were presumed to be due to an unusual set of ion abundances and ionization states within the coronal mass ejection. We found a better time correlation with the solar wind alpha flux rather than the solar wind proton flux. Our results suggest that the solar wind proton flux is not always a good indicator of geocoronal solar wind charge exchange, especially associated with coronal mass ejections. Instead, the solar wind alpha flux should be investigated when such a soft X-ray enhancement is detected in astronomical observations.
Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data
Authors: Harris Robert S. , Cechova Monika , Makova Kateryna D. 
Published: November 2018

ABSTRACTSummaryTandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response.Availability and implementationNCRF is implemented in C, supported by several python scripts. Source code, under the MIT open source license, and simulation data are available at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder, and also in bioconda.
Refinement of metabolite detection in cystic fibrosis sputum reveals heme negatively correlates with lung function
Authors: Glasser Nathaniel R. , Hunter Ryan C. , Liou Theodore G. , Newman Dianne K. ,   Mountain West CF Consortium Investigators
Published: November 2018

SummaryPseudomonas aeruginosalung infections are a leading cause of morbidity and mortality in cystic fibrosis (CF) patients (1, 2). Our laboratory has studied a class of small molecules produced byP. aeruginosaknown as phenazines, including pyocyanin and its biogenic precursor phenazine-1-carboxylic acid (PCA). As phenazines are known virulence factors (3), we and others have explored the possibility of using phenazine concentrations as a marker for disease progression (4–6). Previously, we reported that sputum concentrations of pyocyanin and PCA negatively correlate with lung function in cystic fibrosis patients (6). Our study used high performance liquid chromatography (HPLC) to quantify phenazines by UV–vis absorbance after extraction from lung sputum. Since our initial study, methods for metabolite analysis have advanced considerably, aided in large part by usage of mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS). Because a more recent study employing LC-MS/MS revealed a surprising decoupling ofP. aeruginosametabolites in sputum and the detection ofP. aeruginosathrough culturing or microbiome profiles (4), we decided to check whether we could reproduce our previous findings by analyzing sputum samples from a different patient cohort with a new LC-MS instrument in our laboratory. Our new samples were provided by the Mountain West CF Consortium Sputum Biomarker study (7). In the course of performing our new analyses, comparison of our old HPLC data to our new LC-MS data led us to realize that the peak previously assigned to PCA instead originates from heme, and the peak assigned to pyocyanin originates from an as-yet unknown compound. This correction only affects the measurements of phenazines in sputum, and we are confident in the phenazine measurements from isolated cultures and the 16S rRNA gene sequencing data from that study (6). Here we outline the basis for our correction and present additional data showing that heme concentration negatively correlates with lung function in cystic fibrosis patients.
High-resolution mass spectrometry-based non-targeted metabolomic discovery of disease and glucocorticoid biomarkers in an animal model of muscular dystrophy
Authors: Thangarajh Mathula , Boca Simina M. , Zhang Aiping , Gill Kirandeep , Ressom Habtom , Li Zhenzhi , Hoffman Eric P. , Nagaraju Kanneboyina , Hathout Yetrib 
Published: November 2018

AbstractUrine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we used the mdx mice—a murine model of DMD—to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle. We used high-resolution mass spectrometry to discover metabolic biomarkers of both disease and glucocorticoid treatment. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a peak with m/z=357 and creatine, which were also discovered in a previous human study looking at serum. Novel observations included biliverdin and hypusine. These four peaks were also significantly higher in mdx mice compared to wild-type, as well as significantly associated with time after the baseline. Creatine and biliverdin were also associated with treatment after the baseline, but the association with creatine may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD and/or prednisolone treatment.
Campylobacter jejunitransmission and colonisation in broiler chickens is inhibited by Faecal Microbiota Transplantation
Authors: Gilroy Rachel , Chaloner Gemma , Wedley Amy , Lacharme-Lora Lizeth , Jopson Sue , Wigley Paul 
Published: November 2018

ABSTRACTBACKGROUNDCampylobacter jejuni,the most frequent cause of foodborne bacterial infection, is found on around 70% of retail chicken. As such there is a need for effective controls in chicken production. Microbial-based controls such as probiotics are attractive to the poultry industry, but of limited efficacy. Furthermore, as commercially-produced chickens have no maternal contact, their pioneer microbiome is likely to come from the hatchery environment. Early delivery of microbials that lead to a more ‘natural avian’ microbiome may, therefore, improve bird health and reduce susceptibility toC.jejunicolonisation.A faecal microbiota transplant (FMT) was used to transfer a mature cecal microbiome to newly-hatched broiler chicks and its effects onC.jejunichallenge assessed. We used both a seeder-bird infection model that mimics natural bird-to-bird infection alongside a direct-challenge model. We used a 16S rRNA gene sequencing-based approach to characterize the transplant material itself alongside changes to the chicken microbiome following FMT.RESULTSFMT changes the composition of the chicken intestinal microbiome. We observed little change in species richness following FMT compared to untreated samples, but there is an increase in phylogenetic diversity within those species. The most significant difference in the ceca is an increase inLactobacilli,although not a major component of the transplant material, suggesting the FMT results in a change in the intestinal milieu as much as a direct change to the microbiome.Upon direct challenge, FMT resulted in lower initial intestinal colonisation withC.jejuni.More significantly, in a seeder-bird challenge of infection transmission, FMT reduced transmission and intestinal colonisation until common UK retail age of slaughter. In a repeat experiment, transmission was completely blocked following FMT treatment. Delayed FMT administration at 7 days of-age had limited effect on colonisation and transmission.CONCLUSIONSWe show that transfer of a whole mature microbiome to newly-hatched chicks reduces transmission and colonisation ofC.jejuni.This indicates that modification of the broiler chick microbiome can reduce intestinal colonisation ofC.jejunito levels projected to lead to lower the human infection rate. We believe these findings offer a way to identify key taxa or consortia that are effective in reducingC.jejunicolonisation and improving broiler gut health.