bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of miR-100 in regulating apoptosis of breast cancer cells
Authors: Gong Yi , He Tianliang , Yang Lu , Yang Geng , Chen Yulei , Zhang Xiaobo 
Published: July 2015

AbstractBreast cancer is a serious health problem worldwide. Inhibition of apoptosis plays a major role in breast cancer tumorigenesis. MicroRNAs (miRNAs) play crucial roles in the regulation of apoptosis. However, the regulation of breast cancer apoptosis by miRNAs has not been intensively investigated. To address this issue, the effect of miR-100 on the cell proliferation of different breast cancer cells was characterized in the present study. The results showed that miR-100 was significantly upregulated in SK-BR-3 cells compared with other human breast cancer cells (MCF7, MDA-MB-453, T47D, HCC1954 and SUM149). Silencing miR-100 expression with anti-miRNA-100 oligonucleotide (AMO-miR-100) initiated apoptosis of SK-BR-3 cells in vitro and in vivo. However, the overexpression of miR-100 led to the proliferation inhibition of the miR-100-downregulated breast cancer cells. Antagonism of miR-100 in SK-BR-3 cells increased the expression of MTMR3, a target gene of miR-100, which resulted in the activation of p27 and eventually led to G2/M cell-cycle arrest and apoptosis. The downregulation of miR-100 sensitized SK-BR-3 cells to chemotherapy. Therefore, our finding highlights a novel aspect of the miR-100-MTMR3-p27 pathway in the molecular etiology of breast cancer.
A simple methodological validation of the gas/particle fractionation of polycyclic aromatic hydrocarbons in ambient air
Authors: Kim Yong-Hyun , Kim Ki-Hyun 
Published: July 2015

AbstractThe analysis of polycyclic aromatic hydrocarbons (PAH) in ambient air requires the tedious experimental steps of both sampling and pretreatment (e.g., extraction or clean-up). To replace pre-existing conventional methods, a simple, rapid and novel technique was developed to measure gas-particle fractionation of PAH in ambient air based on ‘sorbent tube-thermal desorption-gas chromatograph-mass spectrometer (ST-TD-GC-MS)’. The separate collection and analysis of ambient PAHs were achieved independently by two serially connected STs. The basic quality assurance confirmed good linearity, precision and high sensitivity to eliminate the need for complicated pretreatment procedures with the detection limit (16 PAHs: 13.1 ± 7.04 pg). The analysis of real ambient PAH samples showed a clear fractionation between gas (two-three ringed PAHs) and particulate phases (five-six ringed PAHs). In contrast, for intermediate (four ringed) PAHs (fluoranthene, pyrene, benz[a]anthracene and chrysene), a highly systematic/gradual fractionation was established. It thus suggests a promising role of ST-TD-GC-MS as measurement system in acquiring a reliable database of airborne PAH.
The Inhibition of the Rayleigh-Taylor Instability by Rotation
Authors: Baldwin Kyle A. , Scase Matthew M. , Hill Richard J. A. 
Published: July 2015

AbstractIt is well-established that the Coriolis force that acts on fluid in a rotating system can act to stabilise otherwise unstable flows. Chandrasekhar considered theoretically the effect of the Coriolis force on the Rayleigh-Taylor instability, which occurs at the interface between a dense fluid lying on top of a lighter fluid under gravity, concluding that rotation alone could not stabilise this system indefinitely. Recent numerical work suggests that rotation may, nevertheless, slow the growth of the instability. Experimental verification of these results using standard techniques is problematic, owing to the practical difficulty in establishing the initial conditions. Here, we present a new experimental technique for studying the Rayleigh-Taylor instability under rotation that side-steps the problems encountered with standard techniques by using a strong magnetic field to destabilize an otherwise stable system. We find that rotation about an axis normal to the interface acts to retard the growth rate of the instability and stabilise long wavelength modes; the scale of the observed structures decreases with increasing rotation rate, asymptoting to a minimum wavelength controlled by viscosity. We present a critical rotation rate, dependent on Atwood number and the aspect ratio of the system, for stabilising the most unstable mode.
Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis
Authors: Bahbahani Hussain , Clifford Harry , Wragg David , Mbole-Kariuki Mary N , Van Tassell Curtis , Sonstegard Tad , Woolhouse Mark , Hanotte Olivier 
Published: July 2015

AbstractThe small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics.
Functional BCL-2 regulatory genetic variants contribute to susceptibility of esophageal squamous cell carcinoma
Authors: Pan Wenting , Yang Jinyun , Wei Jinyu , Chen Hongwei , Ge Yunxia , Zhang Jingfeng , Wang Zhiqiong , Zhou Changchun , Yuan Qipeng , Zhou Liqing , Yang Ming 
Published: July 2015

AbstractB-cell lymphoma-2 (BCL-2) prevents apoptosis and its overexpression could promote cancer cell survival. Multiple functional BCL-2 genetic polymorphisms, such as rs2279115, rs1801018 and rs1564483, have been identified previously and might be involved in cancer development through deregulating BCL-2 expression. Therefore, we examined associations between these three polymorphisms and esophageal squamous cell carcinoma (ESCC) susceptibility as well as its biological function in vivo. Genotypes were determined in two independent case-control sets consisted of 1588 ESCC patients and 1600 controls from two regions of China. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression. The impact of the rs2279115 polymorphism on BCL-2 expression was detected using esophagus tissues. Our results demonstrated that the BCL-2 rs2279115 AA genotype was significantly associated with decreased ESCC risk compared with the CC genotype (OR = 0.72, 95% CI = 0.57–0.90, P = 0.005), especially in nonsmokers (OR = 0.42, 95% CI = 0.29–0.59, P = 0.001) or nondrinkers (OR = 0.44, 95% CI = 0.32–0.62, P = 0.002). Genotype-phenotype correlation studies demonstrated that subjects with the rs2279115 CA and AA genotypes had a statistically significant decrease of BCL-2 mRNA expression compared to the CC genotype in both normal and cancerous esophagus tissues. Our results indicate that the BCL-2 rs2279115 polymorphism contributes to ESCC susceptibility in Chinese populations.
Folic acid supplements and colorectal cancer risk: meta-analysis of randomized controlled trials
Authors: Qin Tingting , Du Mulong , Du Haina , Shu Yongqian , Wang Meilin , Zhu Lingjun 
Published: July 2015

AbstractNumerous studies have investigated the effects of folic acid supplementation on colorectal cancer risk, but conflicting results were reported. We herein performed a meta-analysis based on relevant studies to reach a more definitive conclusion. The PubMed and Embase databases were searched for quality randomized controlled trials (RCTs) published before October 2014. Eight articles met the inclusion criteria and were subsequently analyzed. The results suggested that folic acid treatment was not associated with colorectal cancer risk in the total population (relative risk [RR] = 1.00, 95% confidence interval [CI] = 0.82–1.22, P = 0.974). Moreover, no statistical effect was identified in further subgroup analyses stratified by ethnicity, gender, body mass index (BMI) and potential confounding factors. No significant heterogeneity or publication bias was observed. In conclusion, our meta-analysis demonstrated that folic acid supplementation had no effect on colorectal cancer risk. However, this finding must be validated by further large studies.
Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape
Authors: Nguyen Lam T. , Gumbart James C. , Beeby Morgan , Jensen Grant J. 
Published: July 2015

Significance
The rod shape of walled bacteria is determined by the peptidoglycan (PG) sacculus, but how rod shape is maintained as cells grow remains a fundamental question in bacterial cell biology. We have developed a coarse-grained modeling method to study rod shape maintenance. Individual PG remodeling enzymes, including transglycosylases, transpeptidases, and endopeptidases, are for the first time, to our knowledge, explicitly modeled to explore how they can coordinate to remodel a sacculus several orders of magnitude larger than the enzymes themselves. Rather than requiring top-down regulation of new PG insertion sites, our work shows that local coordination of the PG remodeling enzymes within discrete complexes can be sufficient to maintain the integrity and rod shape of the sacculus.
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function
Authors: Pietal Michal J. , Bujnicki Janusz M. , Kozlowski Lukasz P. 
Published: July 2015

Abstract
Motivation: To date, only a few distinct successful approaches have been introduced to reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a 2D contact map). Current algorithms can infer structures from information-rich contact maps that contain a limited fraction of erroneous predictions. However, it is difficult to reconstruct 3D structures from predicted contact maps that usually contain a high fraction of false contacts.
Results: We describe a new, multi-step protocol that predicts protein 3D structures from the predicted contact maps. The method is based on a novel distance function acting on a fuzzy residue proximity graph, which predicts a 2D distance map from a 2D predicted contact map. The application of a Multi-Dimensional Scaling algorithm transforms that predicted 2D distance map into a coarse 3D model, which is further refined by typical modeling programs into an all-atom representation. We tested our approach on contact maps predicted de novo by MULTICOM, the top contact map predictor according to CASP10. We show that our method outperforms FT-COMAR, the state-of-the-art method for 3D structure reconstruction from 2D maps. For all predicted 2D contact maps of relatively low sensitivity (60–84%), GDFuzz3D generates more accurate 3D models, with the average improvement of 4.87 Å in terms of RMSD.
Availability and implementation: GDFuzz3D server and standalone version are freely available at http://iimcb.genesilico.pl/gdserver/GDFuzz3D/.
Contact: iamb@genesilico.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites
Authors: Yang Jichen , Ramsey Stephen A. 
Published: July 2015

Abstract
Motivation: The position-weight matrix (PWM) is a useful representation of a transcription factor binding site (TFBS) sequence pattern because the PWM can be estimated from a small number of representative TFBS sequences. However, because the PWM probability model assumes independence between individual nucleotide positions, the PWMs for some TFs poorly discriminate binding sites from non-binding-sites that have similar sequence content. Since the local three-dimensional DNA structure (‘shape’) is a determinant of TF binding specificity and since DNA shape has a significant sequence-dependence, we combined DNA shape-derived features into a TF-generalized regulatory score and tested whether the score could improve PWM-based discrimination of TFBS from non-binding-sites.
Results: We compared a traditional PWM model to a model that combines the PWM with a DNA shape feature-based regulatory potential score, for accuracy in detecting binding sites for 75 vertebrate transcription factors. The PWM + shape model was more accurate than the PWM-only model, for 45% of TFs tested, with no significant loss of accuracy for the remaining TFs.
Availability and implementation: The shape-based model is available as an open-source R package at that is archived on the GitHub software repository at https://github.com/ramseylab/regshape/.
Contact: stephen.ramsey@oregonstate.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Cognitive Function Does Not Impact Self-reported Health-Related Quality of Life in Heart Failure Patients
Authors: Gathright Emily C. , Fulcher Michael J. , Dolansky Mary A. , Gunstad John , Redle Joseph D. , Josephson Richard , Moore Shirley M. , Hughes Joel W. 
Published: July 2015

Background:
Adults with heart failure (HF) often demonstrate impairment across multiple domains of cognitive functioning and report poor health-related quality of life (HRQoL). Previous researchers have found that cognitive deficits were generally not associated with HRQoL in a carefully evaluated sample. The exception was memory, which was only weakly associated with HRQoL. However, cognitive deficits interfere with self-care and disease self-management, which could be expected to affect HRQoL.

Objective:
We sought to verify this counterintuitive finding in a large well-characterized sample of HF patients using a well-validated neuropsychological battery.

Methods:
Participants were 302 adults (63% male) predominately white (72.5%) HF patients (68.7 ± 9.6 years) recruited from 2 medical centers. Self-reported HRQoL was assessed using the Kansas City Cardiomyopathy Questionnaire. Participants completed a neuropsychological battery examining attention, executive function, memory, and visuospatial functioning. Hierarchical multiple linear regression was used for analyses.

Results:
Mild global cognitive impairment was observed in 29.5% of the sample (Modified Mini-Mental State [3MS] Examination score <90). Controlling for gender, depression, HF severity, premorbid IQ, comorbidities, and education, only executive function predicted HRQoL, β = .17, P < .05. However, executive function accounted for only 0.6% of the variance in HRQoL.

Conclusion:
Cognitive function generally did not predict HRQoL in HF patients. The correlates of HRQoL in HF do not appear to include mild cognitive impairment. Other factors may play a bigger role such as disease severity, age, and depressive symptoms. Future studies should investigate modifiable determinants of HRQoL in HF patients, toward the goal of finding interventions that preserve HRQoL during this chronic illness.
Lactobacillus vespulae sp. nov., isolated from gut of a queen wasp (Vespula vulgaris)
Authors: Hoang Van-An , Kim Yeon-Ju , Nguyen Ngoc-Lan , Kim Si-Kwan , Yang Deok-Chun 
Published: July 2015

A Gram-stain-positive, oxidase- and catalase-negative, rod-shaped, facultatively anaerobic bacterial strain, DCY75T, was isolated from a queen wasp (Vespula vulgaris). Growth occurred at 4–37 °C (optimum, 30 °C), at pH 3.5–8.0 (optimum, pH 5.0–6.0) and with ≤ 7.0 % (w/v) NaCl. Strain DCY75T produced gas during growth on glucose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DCY75T belonged to the genus Lactobacillus and was closely related to Lactobacillus sanfranciscensis ATCC 27651T and Lactobacillus lindneri DSM 20690T at sequence similarities of 96.7 and 96.4 %, respectively. A comparison of two housekeeping genes, pheS and rpoA, revealed that strain DCT75T was well separated from other species of the genus Lactobacillus. Strain DCY75T produced d- and l-lactic acid isomers in a ratio of 22.5 : 77.5 (v/v). The major fatty acids were summed feature 8 (comprising C18 :
1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω9c and C18 : 0.The peptidoglycan structure was of the A4α (l-Lys–d-Asp) type. Cell-wall sugars were glucose, galactose and ribose. The DNA G+C content was 35.5 ± 1.3 mol%. Based on phenotypic and genotypic properties, strain DCY75T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus vespulae sp. nov. is proposed. The type strain is DCY75T ( = KCTC 21023T = JCM 19742T).
Publishing descriptions of non-public clinical datasets: guidance for researchers, repositories, editors and funding organisations
Authors: Hrynaszkiewicz Iain , Khodiyar Varsha , Hufton Andrew L , Sansone Susanna-Assunta 
Published: July 2015

AbstractSharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles – where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. We propose changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs).
Clustering of mRNA-Seq data for detection of alternative splicing patterns
Authors: Johnson Marla , Purdom Elizabeth 
Published: July 2015

AbstractCurrent sequencing of mRNA can provide estimates of the levels of individual isoforms within the cell, where isoforms are the different distinct mRNA products or proteins created by a gene. It remains to adapt many standard statistical methods commonly used for analyzing gene expression levels to take advantage of this additional information. One novel question is whether we can find groupings or clusters of samples that are distinguished not by their gene expression but by their isoform usage. Such clusters in tumors, for example, could be the result of shared disruption to the splicing system that creates the different isoforms. We propose a novel approach to clustering mRNA-Seq data that identifies clusters of samples with common isoform usage. We show via simulation that our methods are more sensitive to finding clusters of similar alternative splicing patterns than standard clustering techniques applied directly to the estimates of isoform levels. We further demonstrate that clustering on isoform usage is more accurate than clustering directly on isoform levels by examining real data that contains a technical artifact that resulted in different batches having different isoform usage patterns. Clustering, mRNA-Seq, Alternative splicing
Development of a leagile transformation methodology for product development
Authors: Lemieux Andree-Anne , Lamouri Samir , Pellerin Robert , Tamayo Simon 
Published: July 2015

Purpose– The purpose of this paper is to propose a leagile transformation model for product development that guides manufacturers in the construction of a road map and the management of its deployment in line with both lean and agile improvement objectives.Design/methodology/approach– An intervention qualitative and transformative research approach was adopted in order to develop required knowledge to theorise professional practice made from rigorous observations of facts. The research project took place over a period of two and a half years, in partnership with an international firm that develops and produces a wide range of luxury products.Findings– The application of the methodology proved that a lean transformation does not have to be generated only by the field needs but it can follow a mixed approach where a top-down transformation management linked with strategic objectives is deployed without compromising implication and needs from people on the field. The right balance can be found between the strategic aspect of transformation and the incremental aspect on the field of lean paradigms.Research limitations/implications– For complete validation and widespread scientific application, the model should be tested in other sectors and industries.Practical implications– The application case of the leagile model in several divisions of a luxury organisation proved that the proposed approach can be used as a guide for manufacturer in the construction of an improvement road map and in the management of its deployment. The application cases enabled a number of positive results to be generated and measured on quantitative indicators such as service ratio for new products for which, one of the divisions saw an increase of 30 per cent. The approach created a positive revolution among development team members by its potential in terms of communication, steering, benchmarking and knowledge system.Originality/value– The model supports the identification and prioritisation of improvement initiatives by focusing on the levers for improvement that meet the needs and objectives of transformation, as well as the organisation’s maturity level.