bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions
Authors: Solbakken Monica H. , Tørresen Ole K. , Nederbragt Alexander J. , Seppola Marit , Gregers Tone F. , Jakobsen Kjetill S. , Jentoft Sissel 
Published: April 2016

AbstractGenome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.
Impacts of Typhoon Soudelor (2015) on the water quality of Taipei, Taiwan
Authors: Fakour Hoda , Lo Shang-Lien , Lin Tsair-Fuh 
Published: April 2016

AbstractTyphoon Soudelor was one of the strongest storms in the world in 2015. The category 5 hurricane made landfall in Taiwan on August 8, causing extensive damage and severe impacts on the environment. This paper describes the changes of trihalomethane (THM) concentrations in tap and drinking fountain water in selected typhoon-affected areas in Taipei before and after the typhoon. Samples were taken from water transmission mains at various distances from the local water treatment plant. The results showed that organic matter increased between pre- and post-typhoon periods with a greater proportion of aromatic compounds. Although drinking fountains showed moderately less total trihalomethane (TTHM) levels than that of tap water, the intake of high turbidity water considerably diminished the efficiency of their purification systems after the typhoon. The percentage distribution of THM species increased throughout the distribution network, probably due to a longer contact time between chlorine and the organic matter in the pipelines. After 2 to 5 min of boiling, THM reduction was considerable in all cases with the greater extent in post-typhoon samples. It is evident that extreme weather conditions may have a severe impact on water quality, and thus more cautious strategies should be adopted in such cases.
An automated tuberculosis screening strategy combining X-ray-based computer-aided detection and clinical information
Authors: Melendez Jaime , Sánchez Clara I. , Philipsen Rick H. H. M. , Maduskar Pragnya , Dawson Rodney , Theron Grant , Dheda Keertan , van Ginneken Bram 
Published: April 2016

AbstractLack of human resources and radiological interpretation expertise impair tuberculosis (TB) screening programmes in TB-endemic countries. Computer-aided detection (CAD) constitutes a viable alternative for chest radiograph (CXR) reading. However, no automated techniques that exploit the additional clinical information typically available during screening exist. To address this issue and optimally exploit this information, a machine learning-based combination framework is introduced. We have evaluated this framework on a database containing 392 patient records from suspected TB subjects prospectively recruited in Cape Town, South Africa. Each record comprised a CAD score, automatically computed from a CXR and 12 clinical features. Comparisons with strategies relying on either CAD scores or clinical information alone were performed. Our results indicate that the combination framework outperforms the individual strategies in terms of the area under the receiving operating characteristic curve (0.84 versus 0.78 and 0.72), specificity at 95% sensitivity (49% versus 24% and 31%) and negative predictive value (98% versus 95% and 96%). Thus, it is believed that combining CAD and clinical information to estimate the risk of active disease is a promising tool for TB screening.
PATZ1 is a target of miR-29b that is induced by Ha-Ras oncogene in rat thyroid cells
Authors: Vitiello Michela , Valentino Teresa , De Menna Marta , Crescenzi Elvira , Francesca Paola , Rea Domenica , Arra Claudio , Fusco Alfredo , De Vita Gabriella , Cerchia Laura , Fedele Monica 
Published: April 2016

AbstractThe regulatory transcriptional factor PATZ1 is constantly downregulated in human thyroid cancer where it acts as a tumour suppressor by targeting p53-dependent genes involved in Epithelial-Mesenchymal Transition and cell migration. The aim of the present work was to elucidate the upstream signalling mechanisms regulating PATZ1 expression in thyroid cancer cells. The bioinformatics search for microRNAs able to potentially target PATZ1 led to the identification of several miRNAs. Among them we focused on the miR-29b since it was found upregulated in rat thyroid differentiated cells transformed by the Ha-Ras oncogene towards a high proliferating and high migratory phenotype resembling that of anaplastic carcinomas. Functional assays confirmed PATZ1 as a target of miR-29b, and, consistently, an inverse correlation between miR-29b and PATZ1 protein levels was found upon induction of Ha-Ras oncogene expression in these cells. Interestingly, restoration of PATZ1 expression in rat thyroid cells stably expressing the Ha-Ras oncogene decreased cell proliferation and migration, indicating a key role of PATZ1 in Ras-driven thyroid transformation. Together, these results suggest a novel mechanism regulating PATZ1 expression based on the upregulation of miR-29b expression induced by Ras oncogene.
Phenylbutazone induces expression of MBNL1 and suppresses formation of MBNL1-CUG RNA foci in a mouse model of myotonic dystrophy
Authors: Chen Guiying , Masuda Akio , Konishi Hiroyuki , Ohkawara Bisei , Ito Mikako , Kinoshita Masanobu , Kiyama Hiroshi , Matsuura Tohru , Ohno Kinji 
Published: April 2016

AbstractMyotonic dystrophy type 1 (DM1) is caused by abnormal expansion of CTG repeats in the 3′ untranslated region of the DMPK gene. Expanded CTG repeats are transcribed into RNA and make an aggregate with a splicing regulator, MBNL1, in the nucleus, which is called the nuclear foci. The nuclear foci sequestrates and downregulates availability of MBNL1. Symptomatic treatments are available for DM1, but no rational therapy is available. In this study, we found that a nonsteroidal anti-inflammatory drug (NSAID), phenylbutazone (PBZ), upregulated the expression of MBNL1 in C2C12 myoblasts as well as in the HSALR mouse model for DM1. In the DM1 mice model, PBZ ameliorated aberrant splicing of Clcn1, Nfix and Rpn2. PBZ increased expression of skeletal muscle chloride channel, decreased abnormal central nuclei of muscle fibers and improved wheel-running activity in HSALR mice. We found that the effect of PBZ was conferred by two distinct mechanisms. First, PBZ suppressed methylation of an enhancer region in Mbnl1 intron 1 and enhanced transcription of Mbnl1 mRNA. Second, PBZ attenuated binding of MBNL1 to abnormally expanded CUG repeats in cellulo and in vitro. Our studies suggest that PBZ is a potent therapeutic agent for DM1 that upregulates availability of MBNL1.
Modeling of Nitrous Oxide Production from Nitritation Reactors Treating Real Anaerobic Digestion Liquor
Authors: Wang Qilin , Ni Bing-Jie , Lemaire Romain , Hao Xiaodi , Yuan Zhiguo 
Published: April 2016

AbstractIn this work, a mathematical model including both ammonium oxidizing bacteria (AOB) and heterotrophic bacteria (HB) is constructed to predict N2O production from the nitritation systems receiving the real anaerobic digestion liquor. This is for the first time that N2O production from such systems was modeled considering both AOB and HB. The model was calibrated and validated using experimental data from both lab- and pilot-scale nitritation reactors. The model predictions matched the dynamic N2O, ammonium, nitrite and chemical oxygen demand data well, supporting the capability of the model. Modeling results indicated that HB are the dominant contributor to N2O production in the above systems with the dissolved oxygen (DO) concentration of 0.5–1.0 mg O2/L, accounting for approximately 75% of N2O production. The modeling results also suggested that the contribution of HB to N2O production decreased with the increasing DO concentrations, from 75% at DO = 0.5 mg O2/L to 25% at DO = 7.0 mg O2/L, with a corresponding increase of the AOB contribution (from 25% to 75%). Similar to HB, the total N2O production rate also decreased dramatically from 0.65 to 0.25 mg N/L/h when DO concentration increased from 0.5 to 7.0 mg O2/L.
Fine‐pitch surface component mounting on screen‐printed fabric circuits
Authors: Lin X. , Seet B.‐C. , Joseph F. 
Published: April 2016

A novel method of bonding surface mount components to screen‐printed fabric circuits is proposed. The method is achieved by applying the same technique of screen‐printing conductive ink patterns of fabric circuit for printing a layer of low‐temperature solder paste onto uncured conductive ink pads, and placing the circuit with mounted components inside an oven for a one‐step curing process. A screen‐printing frame with 42 μm mesh opening is used for both conductive ink and solder paste layers. Thus, a 0.2 mm resolution for printed traces and spaces is achieved, which meets the demanding geometrical requirements of most integrated circuit chips with fine‐pitch and tiny footprints. Measurement results show the printed tracks after curing exhibit excellent conductivity while retaining good flexibility. Examination under the microscope shows the components are well‐bonded to their on‐fabric pads. The proposed method for surface component mounting and one‐step curing process for screen‐printed fabric circuits can potentially streamline and expedite the twin process of circuit fabrication and component mounting for future smart textile applications.
Factors affecting the abundance of age-0 Atlantic menhaden (Brevoortia tyrannus) in Chesapeake Bay
Authors: Houde Edward D. , Annis Eric R. , Harding Lawrence W. , Mallonee Michael E. , Wilberg Michael J. 
Published: April 2016

Abstract
The abundance of prerecruit, age-0 Atlantic menhaden (Brevoortia tyrannus), declined to low levels in Chesapeake Bay in the 1990s, after two decades of high abundances in the 1970s–1980s. Environmental factors and trophodynamics were hypothesized to control age-0 menhaden abundance. Data on age-0 menhaden abundance from seine and trawl surveys were analysed with respect to primary productivity, chlorophyll a (Chl a), and environmental variables. Abundance from 1989 to 2004 was strongly correlated with metrics of primary production and euphotic-layer Chl a, especially during spring months when larval menhaden transform into filter-feeding, phytoplanktivorous juveniles. Correlation, principal components, and multiple regression analyses were conducted that identified factors associated with age-0 menhaden abundance. Primary production, Chl a, and variables associated with freshwater flow, e.g. Secchi disk depth and zooplankton assemblages, were correlated with age-0 menhaden abundance. Lengths of age-0 menhaden were positively related to mean levels of annual primary production. However, lengths were negatively related to age-0 menhaden abundance, indicating that growth may be density-dependent. The identified relationships suggest that numbers of menhaden larvae ingressing to Chesapeake Bay and environmental factors that subsequently control primary productivity and food for juveniles within the Bay may control recruitment levels of Atlantic menhaden.
Prevalence of Dementia 7.5 Years after Coronary Artery Bypass Graft Surgery
Authors: Evered Lisbeth A. , Silbert Brendan S. , Scott David A. , Maruff Paul , Ames David 
Published: April 2016

AbstractAbstract
The prevalence of dementia at 7.5 yr after coronary artery bypass graft surgery is greatly increased compared to population prevalence. Impaired cognition before surgery or the presence of cardiovascular disease may contribute to the high prevalence.

Background
Although postoperative cognitive dysfunction (POCD) is well described after coronary artery bypass graft (CABG) surgery, a major concern has been that a progressive decline in cognition will ultimately lead to dementia. Since dementia interferes with the ability to carry out daily functions, the impact has far greater ramifications than cognitive decline defined purely by a decreased ability to perform on a battery of neurocognitive tests. The authors hypothesized that early cognitive impairment measured as baseline cognitive impairment is associated with an increased risk of long-term dementia.

Methods
The authors conducted a prospective longitudinal study on 326 patients aged 55 yr and older at the time of undergoing CABG surgery. Dementia was classified by expert opinion on review of performance on the Clinical Dementia Rating Scale and several other assessment tasks. Patients were also assessed for POCD at 3 and 12 months and at 7.5 yr using a battery of neuropsychologic tests and classified using the reliable change index. Associations were assessed using univariable analysis.

Results
At 7.5 yr after CABG surgery, the prevalence of dementia was 36 of 117 patients (30.8%; 95% CI, 23 to 40). POCD was detected in 62 of 189 patients (32.8%; 95% CI, 26 to 40). Due to incomplete assessments, the majority (113 patients), but not all, were assessed for both dementia and POCD. Fourteen of 32 (44%) patients with dementia were also classified as having POCD. Preexisting cognitive impairment and peripheral vascular disease were both associated with dementia 7.5 yr after CABG surgery. POCD at both 3 (odds ratio, 3.06; 95% CI, 1.39 to 9.30) and 12 months (odds ratio, 4.74; 95% CI, 1.63 to 13.77) was associated with an increased risk of mortality by 7.5 yr.

Conclusions
The prevalence of dementia at 7.5 yr after CABG surgery is greatly increased compared to population prevalence. Impaired cognition before surgery or the presence of cardiovascular disease may contribute to the high prevalence.
Nociceptin/orphanin FQ receptor expression in clinical pain disorders and functional effects in cultured neurons
Authors: Anand Praveen , Yiangou Yiangos , Anand Uma , Mukerji Gaurav , Sinisi Marco , Fox Michael , McQuillan Anthony , Quick Tom , Korchev Yuri E. , Hein Peter 
Published: April 2016

Abstract
The nociceptin/orphanin FQ peptide receptor (NOP), activated by its endogenous peptide ligand nociceptin/orphanin FQ (N/OFQ), exerts several effects including modulation of pain signalling. We have examined, for the first time, the tissue distribution of the NOP receptor in clinical visceral and somatic pain disorders by immunohistochemistry and assessed functional effects of NOP and μ-opioid receptor activation in cultured human and rat dorsal root ganglion (DRG) neurons. Quantification of NOP-positive nerve fibres within the bladder suburothelium revealed a remarkable several-fold increase in detrusor overactivity (P < 0.0001) and painful bladder syndrome patient specimens (P = 0.0014) compared with controls. In postmortem control human DRG, 75% to 80% of small/medium neurons (≤50 μm diameter) in the lumbar (somatic) and sacral (visceral) DRG were positive for NOP, and fewer large neurons; avulsion-injured cervical human DRG neurons showed similar numbers. NOP immunoreactivity was significantly decreased in injured peripheral nerves (P = 0.0004), and also in painful neuromas (P = 0.025). Calcium-imaging studies in cultured rat DRG neurons demonstrated dose-dependent inhibition of capsaicin responses in the presence of N/OFQ, with an IC50 of 8.6 pM. In cultured human DRG neurons, 32% inhibition of capsaicin responses was observed in the presence of 1 pM N/OFQ (P < 0.001). The maximum inhibition of capsaicin responses was greater with N/OFQ than μ-opioid receptor agonist DAMGO. Our findings highlight the potential of NOP agonists, particularly in urinary bladder overactivity and pain syndromes. The regulation of NOP expression in visceral and somatic sensory neurons by target-derived neurotrophic factors deserves further study, and the efficacy of NOP selective agonists in clinical trials.
Group 3 innate lymphoid cells in tissue damage and graft-versus-host disease pathogenesis
Authors: Karrich Julien J. , Cupedo Tom 
Published: April 2016

Purpose of review
Innate lymphoid cells (ILC) have emerged as modulators of conditioning-induced tissue damage and development of graft-versus-host disease (GVHD) in the context of allogeneic hematopoietic stem cell transplantation (HSCT). This review highlights experimental and clinical evidence for a role of ILC in GVHD pathogenesis.

Recent findings
ILC are well known for their role in epithelial homeostasis and innate immunity. In addition, recent studies identified ILC as architects of intestinal responses to tissue damage after experimental radio and chemotherapy. Group 3 ILC, and their signature cytokine IL-22, can enhance intestinal stem cell regeneration and protect the stem cell niche from damage during experimental HSCT. Moreover, in leukemia patients undergoing HSCT conditioning, appearance of activated group 3 ILC prior to transplant is correlated to reduced incidence of acute GVHD.

Summary
ILC have a profound impact on the recovery from tissue damage and severity of GVHD in experimental models. Together with the available data from leukemia patients, this argues for in-depth analysis of the mechanisms of ILC function and the translation of experimental findings to clinical application. Ultimately, control of ILC activation, or of the cytokines they produce, could be employed to reduce GVHD lesion in patients receiving allogeneic HSCT.
Factors Influencing Amount of Weekly Exercise Time in Colorectal Cancer Survivors
Authors: Chou Yun-Jen , Lai Yeur-Hur , Lin Been-Ren , Liang Jin-Tung , Shun Shiow-Ching 
Published: April 2016

Background:Performing regular exercise of at least 150 minutes weekly has benefits for colorectal cancer survivors. However, barriers inhibit these survivors from performing regular exercise.Objectives:The aim of this study was to explore exercise behaviors and significant factors influencing weekly exercise time of more than 150 minutes in colorectal cancer survivors.Methods:A cross-sectional study design was used to recruit participants in Taiwan. Guided by the ecological model of health behavior, exercise barriers were assessed including intrapersonal, interpersonal, and environment-related barriers. A multiple logistic regression was used to explore the factors associated with the amount of weekly exercise.Results:Among 321 survivors, 57.0% of them had weekly exercise times of more than 150 minutes. The results identified multiple levels of significant factors related to weekly exercise times including intrapersonal factors (occupational status, functional status, pain, interest in exercise, and beliefs about the importance of exercise) and exercise barriers related to environmental factors (lack of time and bad weather). No interpersonal factors were found to be significant.Conclusions:Colorectal cancer survivors experienced low levels of physical and psychological distress. Multiple levels of significant factors related to exercise time including intrapersonal factors as well as exercise barriers related to environmental factors should be considered.Implications for Practice:Healthcare providers should discuss with their patients how to perform exercise programs; the discussion should address multiple levels of the ecological model such as any pain problems, functional status, employment status, and time limitations, as well as community environment.
Comparative Safety, Efficiency, and Nursing Preference Among 3 Methods for Intravenous Push Medication Preparation: A Randomized Crossover Simulation Study
Authors: Burger Maureen , Degnan Dan 
Published: April 2016

Objective
The aim of this study was to compare total time for drug preparation, associated errors, and nurses' preferences among 3 different intravenous (IV) push medication methods.

Research Design
A randomized crossover simulation design was used to compare total time for drug preparation and incidence of medication preparation errors between BD Simplist (BDS), Carpuject (CJ), and traditional vial-and-syringe process (TVSP). Three medication preparation areas were created to mimic a hospital setting. Twenty-four critical care nurses were asked to prepare an IV dose of diphenhydramine, ketorolac, and morphine in random order using BDS, CJ, and TVSP, also in random order. Total time for the preparation of each drug was measured. Medication preparation errors were noted. At the start of the study, nurses were surveyed about their stress levels regarding aspects of IV push medications. At completion, nurses were asked to rank order from the most to the least preferred administration method.

Results
Mean time in seconds for drug preparation was significantly shorter (P < 0.004) with BDS (28.7; 95% confidence interval [CI], 23.3–34.2) and CJ (28.3; 95% CI, 23.1–33.5) compared with TSVP (65.8; 95% CI, 57.7–73.9). The time difference between BDS and CJ was not statistically significant. Medication preparation errors were significantly reduced with BDS compared with both CJ and TVSP (1.4% versus 77.8% versus 73.6%; P < 0.001). The BDS was ranked by nurses as the most preferred method.

Conclusions
The BD Simplist system for IV push medications may offer nurses an opportunity to reduce steps and reduce errors during medication preparation.
Increased taxon sampling reveals thousands of hidden orthologs in flatworms
Authors: Martín-Durán José M. , Ryan Joseph F. , Vellutini Bruno C. , Pang Kevin , Hejnol Andreas 
Published: April 2016

AbstractGains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the complement of an organism consists of hidden orthologs, those with no apparent homology with common sequenced animal lineages –mistakenly considered new genes– but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify hidden orthologs in large transcriptomic databases. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3,427 hidden orthologs, some of them not identified by OrthoFinder, a common orthogroup inference algorithm. Unexpectedly, we do not observe a correlation between the number of hidden orthologs in a lineage and its ‘average’ evolutionary rate. Hidden orthologs do not show unusual sequence composition biases (e.g. GC content, average length, domain composition) that might account for systematic errors in sequence similarity searches. Instead, gene duplication and divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g. planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.