bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular proteolysis in Atlantic salmon Salmo salar fingerlings (0+) from different biotopes in an Arctic river (Varzuga River, White Sea Basin)
Authors: Nemova Nina N. , Kaivarainen Elena I. , Krupnova Marina Y. , Veselov Aleksey E. , Murzina Svetlana A. , Pavlov Dmitry S. 
Published: January 2017

ABSTRACTThe activity of intracellular proteolytic enzymes was studied in Atlantic salmon (Salmo salar L.) fingerlings (0+) after hatching from spawning nests and dispersal in the Varzuga River main stem and its Pyatka tributary (Kola Peninsula, White Sea Basin). The study focused on calcium-dependent cytosolic proteinases (µ- and m-calpains), lysosomal proteinases (cathepsins В and D) and collagenase, and determined the free/protein-bound hydroxyproline ratio, which portrays collagenolytic activity. Compared to fingerlings from the Varzuga main stem, the intracellular proteolytic enzyme activity of cysteine proteinase and collagenase was higher in fingerlings from the Pyatka tributary, where current velocities and food availability were higher. These results indicate that there is a higher rate of intracellular protein metabolism in the juveniles from this phenotypic group.
An outbreak of norovirus GI-6 infection following a wedding in North West England
Authors: SMITH K. C. , INNS T. , DECRAENE V. , FOX A. , ALLEN D. J. , SHAH A. 
Published: January 2017

SUMMARYIn August 2015 a gastroenteritis outbreak occurred following a wedding. An outbreak investigation was undertaken and a cohort study was conducted using an online survey. Of 140 guests, 134 received the survey and 113 responded (84·3% response rate). Seventy respondents met the case definition of vomiting and/or diarrhoea within 72 h of the wedding (61·9% attack rate). Fifteen exposures were associated with illness; on stratification, all were confounded by the ham hock starter. Multivariable analysis showed a significant association with exposure to ham hock (risk ratio 6·62, 95% confidence interval 2·19–20·03). Eight guests and two catering staff submitted stool samples. All tested positive for norovirus GI-6 infection, including a food handler who had vomiting less than 48 h before the wedding. A single genotype was detected among all samples, suggesting a single source of contamination. The transmission pattern suggested point-source exposure. The most plausible cause of the outbreak was transmission from an infected food handler via contaminated food. This highlights the importance of appropriate exclusions for symptomatic food handlers. Additionally, the food handler's stool sample was submitted 7 days after symptom resolution. The potential for extended viral excretion, and the extremely low infective dose of norovirus, may mean that current exclusion guidelines are not of sufficient duration.
Natural language processing in mental health applications using non-clinical texts
Authors: CALVO RAFAEL A. , MILNE DAVID N. , HUSSAIN M. SAZZAD , CHRISTENSEN HELEN 
Published: January 2017

AbstractNatural language processing (NLP) techniques can be used to make inferences about peoples’ mental states from what they write on Facebook, Twitter and other social media. These inferences can then be used to create online pathways to direct people to health information and assistance and also to generate personalized interventions. Regrettably, the computational methods used to collect, process and utilize online writing data, as well as the evaluations of these techniques, are still dispersed in the literature. This paper provides a taxonomy of data sources and techniques that have been used for mental health support and intervention. Specifically, we review how social media and other data sources have been used to detect emotions and identify people who may be in need of psychological assistance; the computational techniques used in labeling and diagnosis; and finally, we discuss ways to generate and personalize mental health interventions. The overarching aim of this scoping review is to highlight areas of research where NLP has been applied in the mental health literature and to help develop a common language that draws together the fields of mental health, human-computer interaction and NLP.
Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides
Authors: Ma Wenting , Peng Donghai , Walker Sharon L. , Cao Bin , Gao Chun-Hui , Huang Qiaoyun , Cai Peng 
Published: January 2017

AbstractClay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid–air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3–16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid–air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.
Spheroid arrays for high-throughput single-cell analysis of spatial patterns and biomarker expression in 3D
Authors: Ivanov Delyan P. , Grabowska Anna M. 
Published: January 2017

AbstractWe describe and share a device, methodology and image analysis algorithms, which allow up to 66 spheroids to be arranged into a gel-based array directly from a culture plate for downstream processing and analysis. Compared to processing individual samples, the technique uses 11-fold less reagents, saves time and enables automated imaging. To illustrate the power of the technology, we showcase applications of the methodology for investigating 3D spheroid morphology and marker expression and for in vitro safety and efficacy screens. First, spheroid arrays of 11 cell-lines were rapidly assessed for differences in spheroid morphology. Second, highly-positive (SOX-2), moderately-positive (Ki-67) and weakly-positive (βIII-tubulin) protein targets were detected and quantified. Third, the arrays enabled screening of ten media compositions for inducing differentiation in human neurospheres. Last, the application of spheroid microarrays for spheroid-based drug screens was demonstrated by quantifying the dose-dependent drop in proliferation and increase in differentiation in etoposide-treated neurospheres.
A novel HDAC inhibitor, CG200745, inhibits pancreatic cancer cell growth and overcomes gemcitabine resistance
Authors: Lee Hee Seung , Park Soo Been , Kim Sun A , Kwon Sool Ki , Cha Hyunju , Lee Do Young , Ro Seonggu , Cho Joong Myung , Song Si Young 
Published: January 2017

AbstractPancreatic cancer is predominantly lethal, and is primarily treated using gemcitabine, with increasing resistance. Therefore, novel agents that increase tumor sensitivity to gemcitabine are needed. Histone deacetylase (HDAC) inhibitors are emerging therapeutic agents, since HDAC plays an important role in cancer initiation and progression. We evaluated the antitumor effect of a novel HDAC inhibitor, CG200745, combined with gemcitabine/erlotinib on pancreatic cancer cells and gemcitabine-resistant pancreatic cancer cells. Three pancreatic cancer-cell lines were used to evaluate the antitumor effect of CG200745 combined with gemcitabine/erlotinib. CG200745 induced the expression of apoptotic proteins (PARP and caspase-3) and increased the levels of acetylated histone H3. CG200745 with gemcitabine/erlotinib showed significant growth inhibition and synergistic antitumor effects in vitro. In vivo, gemcitabine/erlotinib and CG200745 reduced tumor size up to 50%. CG200745 enhanced the sensitivity of gemcitabine-resistant pancreatic cancer cells to gemcitabine, and decreased the level of ATP-binding cassette-transporter genes, especially multidrug resistance protein 3 (MRP3) and MRP4. The novel HDAC inhibitor, CG200745, with gemcitabine/erlotinib had a synergistic anti-tumor effect on pancreatic cancer cells. CG200745 significantly improved pancreatic cancer sensitivity to gemcitabine, with a prominent antitumor effect on gemcitabine-resistant pancreatic cancer cells. Therefore, improved clinical outcome is expected in the future.
The anti-tumor activities of Neferine on cell invasion and oxaliplatin sensitivity regulated by EMT via Snail signaling in hepatocellular carcinoma
Authors: Deng Ganlu , Zeng Shan , Ma Junli , Zhang Yan , Qu Yanling , Han Ying , Yin Ling , Cai Changjing , Guo Cao , Shen Hong 
Published: January 2017

AbstractTumor invasion and chemotherapy resistance, which are associated with epithelial-mesenchymal transition (EMT), remain as major challenges in hepatocellular carcinoma (HCC) treatment. Neferine, a natural component of Nelumbo nucifera, have been proven the antitumor efficiency in cancer, but the effects of Neferine on HCC invasion and chemosensitivity need to be elucidated. Applying multiple assays of cell proliferation, flow cytometry, immunofluorescence staining, qRT-PCR, Western blot, fluorescence molecular tomography imaging, the influences of Neferine on EMT-regulated viability, apoptosis, invasion, and oxaliplatin (OXA) sensitivity were assessed in HCC cells of HepG2 and Bel-7402, as well as in xenograft animal models in vivo. Here, we reported that Neferine had no obvious effects on HCC cells proliferation, but significantly enhanced cytotoxicity and apoptosis caused by OXA in vitro and in vivo. Through an upregulation of E-cadherin and downregulation of Vimentin, Snail and N-cadherin, Neferine suppressed EMT-induced migration and invasion abilities of HCC cells. TGF-β1 cancelled the effects of Neferine on the migration and invasion of HCC cells. Snail overexpression or TGF-β1-induced EMT attenuated Neferine-mediated OXA sensitization in HCC. Together, our data suggest that Neferine enhances oxaliplatin sensitivity through an inhibition of EMT in HCC cells. Neferine may be used as an OXA sensitizer in HCC chemotherapy.
Effects of light on quantum phases and topological properties of two-dimensional Metal-organic frameworks
Authors: Wang Yunhua , Liu Yulan , Wang Biao 
Published: January 2017

AbstractPeriodically driven nontrivial quantum states open another door to engineer topological phases in solid systems by light. Here we show, based on the Floquet-Bloch theory, that the on-resonant linearly and circularly polarized infrared light brings in the exotic Floquet quantum spin Hall state and half-metal in two-dimensional Metal-organic frameworks (2D MOFs) because of the unbroken and broken time-reversal symmetry, respectively. We also observe that the off-resonant light triggers topological quantum phase transitions and induces semimetals with pseudospin-1 Dirac-Weyl fermions via the photon-dressed topological band structures of 2D MOFs. This work paves a way to design light-controlled spintronics and optoelectronics based on 2D MOFs.
Cortical Brain Functions – The Brodmann Legacy in the 21st Century
Authors: Damiani Daniel , Nascimento Anna Maria , Pereira Leticia Kühl 
Published: January 2017

AbstractIn 1909, Korbinian Brodmann described 52 functional brain areas, 43 of them found in the human brain. More than a century later, his devoted functional map was incremented by Glasser et al in 2016, using functional nuclear magnetic resonance imaging techniques to propose the existence of 180 functional areas in each hemisphere, based on their cortical thickness, degree of myelination (cortical myelin content), neuronal interconnection, topographic organization, multitask answers, and assessment in their resting state. This opens a huge possibility, through functional neuroanatomy, to understand a little more about normal brain function and its functional impairment in the presence of a disease.
A Simplified Technique for Drainage of Chronic Calcified Pleural Empyema
Authors: Younssa Hama , Didier James , Ibrahim Magagi , Harissou Adamou , Adakal Ousseini , Sani Rachid , Rabiou Sani 
Published: January 2017

AbstractChronic pleural pocket has well-known diagnosis and treatment principles since first described by Hippocrates 2,400 years ago. However, its treatment remains constant even though its causes, severity during management, and terrain vary considerably. In well-structured health care systems, posttuberculous empyema has become rare; its well-codified medical treatment relies on early diagnosis and adapted antibiotherapy, punctures/drainage, and appropriate intrapleural antifibrinolytics. In developing countries, a poor health organizational system increases the incidence of pleural pocket, which can progress until surgery is indicated. In such a context, the general principles of treatment include pleural decortication along with pulmonary resection. This technique remains difficult, risky, and, sometimes, impossible due to the chronicity of the lesion. In patients debilitated by several months of septic evolution, a simplified thoracostomy technique permits complete resection of the pocket.
The impact of face systems on the pragmalinguistic features of academic e-mail requests
Authors: Aslan Erhan 
Published: January 2017

AbstractThis study investigates the impact of power/distance (PD) variables operationalized as face systems on the pragmalinguistic features of academic e-mail requests. A corpus of 90 academic e-mails was classified into four face system groups: hierarchical (sender +P), hierarchical (recipient +P), deference, and solidarity. Request perspectives, strategies, and mitigating supportive moves were analyzed. The analysis revealed that the speaker and hearer dominance were the most frequent request perspectives in the hierarchical (recipient+P) and deference groups. The impersonal perspective was more common in the hierarchical (sender+P) group. The preparatory was the dominant request strategy in all groups, relatively more frequent in the hierarchical (recipient+P) and deference groups. The most common supportive move was the grounder, which occurred more frequently than other supportive moves. The findings of the study indicate that face systems influence the request patterns in academic e-mail communication. The study has implications for future research on pragmatics of computer-mediated communication (CMC).
Association of Maternal Plasma Folate and Cardiometabolic Risk Factors in Pregnancy with Elevated Blood Pressure of Offspring in Childhood
Authors: Wang Hongjian , Mueller Noel T. , Li Jianping , Sun Ninglin , Huo Yong , Ren Fazheng , Wang Xiaobin 
Published: January 2017

Abstract

BACKGROUND
The prevalence of childhood elevated blood pressure (BP) has increased in the United States, particularly among African Americans. The influence of maternal plasma folate levels, alone or in combination with maternal cardiometabolic risk factors (hypertensive disorders, diabetes, and prepregnancy obesity), on child systolic BP (SBP) has not been examined in a prospective birth cohort. We hypothesize that adequate maternal folate levels can reduce the risk of elevated SBP in children born to mothers with cardiometabolic risk factors.

METHODS
This study included 1,290 mother–child dyads (875 African Americans (67.8%)) recruited at birth and followed prospectively up to age 9 years from 2003 to 2014 at the Boston Medical Center. Child SBP percentile was calculated according to US reference data and elevated SBP was defined as SBP ≥75th percentile.

RESULTS
Maternal folate levels, overall, were not associated with child SBP. However, we found a significant multiplicative interaction between maternal cardiometabolic risk factors and maternal folate levels (Pinteraction = 0.015) on childhood elevated SBP. Among children born to mothers with any cardiometabolic risk factors, those whose mothers had folate levels above (vs. below) the median had 40% lower odds of elevated childhood SBP (odds ratio = 0.60, 95% confidence interval: 0.40–0.90). The associations did not differ appreciably in analyses restricted to African Americans, and they were not explained by gestational age, size at birth, prenatal folate intake, or breastfeeding.

CONCLUSIONS
Findings from our urban minority birth cohort suggest that higher levels of maternal folate may help counteract the adverse associations of maternal cardiometabolic risk factors on child SBP.
Health Insurance Type and Control of Hypertension Among US Women Living With and Without HIV Infection in the Women’s Interagency HIV Study
Authors: Ludema Christina , Cole Stephen R. , Eron Joseph J. , Holmes G. Mark , Anastos Kathryn , Cocohoba Jennifer , Cohen Marge H. , Cooper Hannah L.F. , Golub Elizabeth T. , Kassaye Seble , Konkle-Parker Deborah , Metsch Lisa , Milam Joel , Wilson Tracey E. , Adimora Adaora A. 
Published: January 2017

Abstract

BACKGROUND
Health care access is an important determinant of health. We assessed the effect of health insurance status and type on blood pressure control among US women living with (WLWH) and without HIV.

METHODS
We used longitudinal cohort data from the Women’s Interagency HIV Study (WIHS). WIHS participants were included at their first study visit since 2001 with incident uncontrolled blood pressure (BP) (i.e., BP ≥140/90 and at which BP at the prior visit was controlled (i.e., &lt;135/85). We assessed time to regained BP control using inverse Kaplan–Meier curves and Cox proportional hazard models. Confounding and selection bias were accounted for using inverse probability-of-exposure-and-censoring weights.

RESULTS
Most of the 1,130 WLWH and 422 HIV-uninfected WIHS participants who had an elevated systolic or diastolic measurement were insured via Medicaid, were African-American, and had a yearly income ≤$12,000. Among participants living with HIV, comparing the uninsured to those with Medicaid yielded an 18-month BP control risk difference of 0.16 (95% CI: 0.10, 0.23). This translates into a number-needed-to-treat (or insure) of 6; to reduce the caseload of WLWH with uncontrolled BP by one case, five individuals without insurance would need to be insured via Medicaid. Blood pressure control was similar among WLWH with private insurance and Medicaid. There were no differences observed by health insurance status on 18-month risk of BP control among the HIV-uninfected participants.

CONCLUSIONS
These results underscore the importance of health insurance for hypertension control—especially for people living with HIV.
‘COV’COP’ allows to detect CNVs responsible for inherited diseases among amplicons sequencing data
Authors: Derouault P , Parfait B , Moulinas R , Barrot C.-C , Sturtz F , Merillou S , Lia A.-S 
Published: January 2017

Abstract

Summary
In order to help molecular geneticists to rapidly identify CNVs responsible for inherited diseases among amplicons sequencing data generated by NGS, we designed a user-friendly tool ‘Cov’Cop’. Using the run’s coverage file provided by the sequencer, Cov’Cop simultaneously analyzes all the patients of the run using a two-stage algorithm containing correction and normalization levels and provides an easily understandable output, showing with various colors, potentially deleted and duplicated amplicons.

Availability and Implementation
https://git.unilim.fr/merilp02/CovCop

Supplementary information
Supplementary data are available at Bioinformatics online.
Large-scale 16S gene assembly using metagenomics shotgun sequences
Authors: Zeng Feng , Wang Zicheng , Wang Ying , Zhou Jizhong , Chen Ting 
Published: January 2017

Abstract

Motivation
Combining a 16S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identification of known and novel microbes.

Results
To achieve this, we herein report reference-based ribosome assembly (RAMBL), a computational pipeline, which integrates taxonomic tree search and Dirichlet process clustering to reconstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy. By benchmarking against the synthetic and real shotgun sequences, we demonstrated that full-length 16S gene assemblies of RAMBL were a good proxy for known and putative microbes, including Candidate Phyla Radiation. We found that 30–40% of bacteria genera in the terrestrial and intestinal biomes have no closely related genome sequences. We also observed that RAMBL was able to generate a more accurate determination of environmental microbial diversity and yield better disease classification, suggesting that full-length 16S gene assemblies are a powerful alternative to marker gene set and 16S short reads. RAMBL first realizes the access to full-length 16S gene sequences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve metagenomic data analysis and interpretation.

Availability and Implementation
RAMBL is available at https://github.com/homopolymer/RAMBL for academic use.

Supplementary information
Supplementary data are available at Bioinformatics online.
LOCUST: a custom sequence locus typer for classifying microbial isolates
Authors: Brinkac Lauren M , Beck Erin , Inman Jason , Venepally Pratap , Fouts Derrick E , Sutton Granger 
Published: January 2017

Abstract

Summary
LOCUST is a custom sequence locus typer tool for classifying microbial genomes. It provides a fully automated opportunity to customize the classification of genome-wide nucleotide variant data most relevant to biological research.

Availability and Implementation
Source code, demo data, and detailed documentation are freely available at http://sourceforge.net/projects/locustyper.

Supplementary information
Supplementary data are available at Bioinformatics online.
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
Authors: Kyle Jennifer E , Crowell Kevin L , Casey Cameron P , Fujimoto Grant M , Kim Sangtae , Dautel Sydney E , Smith Richard D , Payne Samuel H , Metz Thomas O 
Published: January 2017

Abstract

Summary
We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS-based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species. LIQUID was compared to other freely available software commonly used to identify lipids and other small molecules (e.g. CFM-ID, MetFrag, GNPS, LipidBlast and MS-DIAL), and was found to have a faster processing time to arrive at a higher number of validated lipid identifications.

Availability and Implementation
LIQUID is available at http://github.com/PNNL-Comp-Mass-Spec/LIQUID.

Supplementary information
Supplementary data are available at Bioinformatics online.