bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between PPAR-γ2 Pro12Ala genotype and insulin resistance is modified by circulating lipids in Mexican children
Authors: Stryjecki Carolina , Peralta-Romero Jesus , Alyass Akram , Karam-Araujo Roberto , Suarez Fernando , Gomez-Zamudio Jaime , Burguete-Garcia Ana , Cruz Miguel , Meyre David 
Published: April 2016

AbstractThe Pro12Ala (rs1801282) polymorphism in peroxisome proliferator-activated receptor-γ2 (PPAR-γ2) has been convincingly associated with insulin resistance (IR) and type 2 diabetes (T2D) among Europeans, in interaction with a high-fat diet. Mexico is disproportionally affected by obesity and T2D however, whether the Pro12Ala polymorphism is associated with early metabolic complications in this population is unknown. We assessed the association of PPAR-γ2 Pro12Ala with metabolic traits in 1457 Mexican children using linear regression models. Interactions between PPAR-γ2 Pro12Ala and circulating lipids on metabolic traits were determined by adding an interaction term to regression models. We observed a high prevalence of overweight/obesity (49.2%), dyslipidemia (34.9%) and IR (11.1%). We detected nominally significant/significant interactions between lipids (total cholesterol, HDL-cholesterol, LDL-cholesterol), the PPAR-γ2 Pro12Ala genotype and waist-to-hip ratio, fasting insulin, HOMA-IR and IR (9.30 × 10−4  ≤ Pinteraction ≤ 0.04). Post-hoc subgroup analyses evidenced that the association between the PPAR-γ2 Pro12Ala genotype and fasting insulin, HOMA-IR and IR was restricted to children with total cholesterol or LDL-cholesterol values higher than the median (0.02 ≤ P ≤ 0.03). Our data support an association of the Pro12Ala polymorphism with IR in Mexican children and suggest that this relationship is modified by dyslipidemia.
DRAMP: a comprehensive data repository of antimicrobial peptides
Authors: Fan Linlin , Sun Jian , Zhou Meifeng , Zhou Jie , Lao Xingzhen , Zheng Heng , Xu Hanmei 
Published: April 2016

AbstractThe growing problem of antibiotic-resistant microorganisms results in an urgent need for substitutes to conventional antibiotics with novel modes of action and effective activities. Antimicrobial peptides (AMPs), produced by a wide variety of living organisms acting as a defense mechanism against invading pathogenic microbes, are considered to be such promising alternatives. AMPs display a broad spectrum of antimicrobial activity and a low propensity for developing resistance. Therefore, a thorough understanding of AMPs is essential to exploit them as antimicrobial drugs. Considering this, we developed a comprehensive user-friendly data repository of antimicrobial peptides (DRAMP), which holds 17349 antimicrobial sequences, including 4571 general AMPs, 12704 patented sequences and 74 peptides in drug development. Entries in the database have detailed annotations, especially detailed antimicrobial activity data (shown as target organism with MIC value) and structure information. Annotations also include accession numbers crosslinking to Pubmed, Swiss-prot and Protein Data Bank (PDB). The website of the database comes with easy-to-operate browsing as well as searching with sorting and filtering functionalities. Several useful sequence analysis tools are provided, including similarity search, sequence alignment and conserved domain search (CD-Search). DRAMP should be a useful resource for the development of novel antimicrobial peptide drugs.
Tristetraprolin inhibits gastric cancer progression through suppression of IL-33
Authors: Deng Kaiyuan , Wang Hao , Shan Ting , Chen Yigang , Zhou Hong , Zhao Qin , Xia Jiazeng 
Published: April 2016

AbstractTristetraprolin (TTP) is an adenine/uridine (AU)-rich element (ARE)-binding protein that can induce degradation of mRNAs. In this study, we report that TTP suppresses the expression of interleukin-33 (IL-33), a tumor-promoting inflammatory cytokine and thereby inhibits the progression of gastric cancer (GC). Overexpression of TTP decreased the level of IL-33, whereas knockdown of TTP increased IL-33 levels. We also discovered that TTP inhibited the proliferation, migration and invasion of GC cell lines through regulation of IL-33. Furthermore, TTP RNA and protein levels were remarkably reduced in GC and inversely correlated with IL-33 level and they were also closely associated with depth of invasion, lymph node metastasis, advanced TNM stage, as well as survival rate. Taken together, these findings identified TTP as a downregulator of IL-33 and further suggest that TTP can serve as a novel biomarker for the diagnosis of GC and as a potential therapeutic target for GC treatment.
Inter-polysomal coupling of termination and initiation during translation in eukaryotic cell-free system
Authors: Sogorin Evgeny A. , Agalarov Sultan Ch. , Spirin Alexander S. 
Published: April 2016

AbstractThe recording of the luciferase-generated luminescence in the eukaryotic cell-free translation system programmed with mRNA encoding firefly luciferase (Luc-mRNA) showed that the addition of free exogenous mRNAs into the translation reactor induces the immediate release of the functionally active protein from the polyribosomes of the translation system. The phenomenon did not depend on the coding specificity of the added free mRNA. At the same time it depended on the “initiation potential” of the added mRNA (including the features that ensure the successful initiation of translation, such as the presence of the cap structure and the sufficient concentration of the added mRNA in the translation mixture). The phenomenon also strictly depended on the presence of the stop codon in the translated mRNA. As the above-mentioned features of the added mRNA imply its activity in initiation of a new translation, the experimental data are found in agreement with the scenario where the molecules of the added mRNA interact by their 5′-ends with terminating and recycling ribosomes, stimulating the release of the complete polypeptides and providing for the initiation of a new translation.
Different extent in decline of infant mortality by region and cause in Shenyang, China
Authors: Huang Yan-Hong , Wu Qi-Jun , Li Li-Li , Li Da , Li Jing , Zhou Chen , Wu Lang , Zhu Jingjing , Gong Ting-Ting 
Published: April 2016

AbstractTo compare the pattern of cause of death of infant mortality rates by urban/rural areas as well as to generate knowledge for potential strategies to decrease this mortality, we carried out a study by analyzing the infant mortality data from the Shenyang Women and Children Health Care Centre. From 1997 to 2014, 970,583 live births and 6510 infant deaths were registered. Infant mortality rates, percent change, and annual percent change (APC) were calculated. The infant mortality significantly decreased by 5.92%, 7.41%, and 3.92% per year in overall, urban, and rural areas, respectively. Among the categories of causes of infant death, congenital anomalies (APC = −7.87%), asphyxia-related conditions (APC = −9.43), immaturity-related conditions (APC = −3.44%), diseases of the nervous system and sense organs (APC = −6.01%), and diseases of the respiratory system (APC = −6.29%) decreased significantly in the observational periods. Additionally, among selective causes of infant death, pneumonia, congenital heart disease, neural tube defects, preterm birth and low birth weight, birth asphyxia, and intracranial hemorrhage of the newborn significantly decreased by 5.45%, 5.45%, 16.47%, 2.18%, 10.95%, and 10.33% per year, respectively. In conclusion, infant mortality has been continuously decreased in Shenyang from 1997 to 2014, although further efforts are still needed to decrease the infant mortality in rural areas.
Associations of Exhaled Carbon Monoxide and Fractional Exhaled Nitric Oxide with Metabolic Syndrome: A Cohort Study
Authors: Guo Yanjun , Ma Jixuan , Lu Wei , He Jintong , Zhang Runbo , Yuan Jing , Chen Weihong 
Published: April 2016

AbstractExhaled carbon monoxide (eCO) and fractional exhaled nitric oxide (FeNO) could reflect underlying inflammatory and oxidative stresses, which play important roles in pathogenetic pathways of metabolic syndrome (MetS). However, epidemiologic evidence was limited. We conducted a study in Wuhan-Zhuhai (WHZH) cohort of 3649 community participants to investigate the association between eCO, FeNO and MetS in both cross-sectional and prospective ways. The results showed that higher eCO and FeNO were associated cross-sectionally with a higher prevalence of MetS. The multivariable-adjusted odds ratios for MetS at baseline were 1.22 (95% confidence interval [CI]: 1.11 to 1.35) associated with per log eCO and 1.14 (95% CI: 1.00 to 1.30) associated with per log FeNO. During a follow-up of 3 years, 358/2181 new developed MetS cases were identified. Compared with lowest quartile of eCO and FeNO, the multivariable-adjusted risk ratios (95% CI) for MetS were 1.48 (1.06 to 2.06) related to the highest quartile of eCO. These findings remained consistent across sex but not smoking status, eCO was only associated with MetS in non-smokers when stratified by smoking status. In conclusion, our study demonstrated that eCO and FeNO were independently and positively associated with the prevalence of MetS cross-sectionally, while only eCO was positively related with the incidence of MetS prospectively.
Cytotoxicity investigation of luminescent nanohybrids based on chitosan and carboxymethyl chitosan conjugated with Bi2S3 quantum dots for biomedical applications
Authors: Carvalho Sandhra M. , Mansur Herman S. , Ramanery Fábio P. , Mansur Alexandra A. P. , Lobato Zelia I. P. , Leite Maria F. 
Published: April 2016

Abstract
Bioengineered hybrids are emerging as a new class of nanomaterials consisting of a biopolymer and inorganic semiconductors used in biomedical and environmental applications. The aim of the present work was to determine the cytocompatibility of novel water-soluble Bi2S3 quantum dots (QDs) functionalized with chitosan and O-carboxymethyl chitosan (CMC) as capping ligands using an eco-friendly aqueous process at room temperature. These hybrid nanocomposites were tested for cytocompatibility using a 3-(4,5-dimethylthiazol-2yl) 2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay with cultured human osteosarcoma cells (SAOS), human embryonic kidney cells (HEK293T cells) and a LIVE/DEAD® viability-cytotoxicity assay. The results of the in vitro assays demonstrated that the CMC and chitosan-based nanohybrids were not cytotoxic and exhibited suitable cell viability responses. However, despite the “safe by design” approach used in this research, we have proved that the impact of the size, surface charge and biofunctionalization of the nanohybrids on cytotoxicity was cell type-dependent due to complex mechanisms. Thus, these novel bionanocomposites offer promising prospects for potential biomedical and pharmaceutical applications as fluorescent nanoprobes.
Der zweite Gesundheitsmarkt aus Nachfragersicht: Ableitung eines Produkt-Marktraumes auf Basis von Konsumentenwahrnehmungen
Authors: Teichert T. , Mühlbach C. 
Published: April 2016

Zusammenfassung
Ziel der Studie: Ziel der Studie war eine Abbildung der individuellen Konsumentensicht auf den sehr speziellen Markt für Gesundheit bzw. Gesundheitsprodukte, den zweiten deutschen Gesundheitsmarkt. Eine visuelle Verortung der untersuchten Produktkategorien im Zuge einer Marktanalyse ergänzte diese Visualisierung.
Methodik: Eine großangelegte repräsentative Studie (N=1 033) ermittelte mit einer innovativen Adaption der Repertory-Grid-Methode die Konsumentensicht auf den betrachteten speziellen Markt. Grundlegende Fragen bzgl. der Gesundheitseinstellung sowie dem praktizierten gesunden Verhalten komplettierten die telefonisch umgesetzte Befragung.
Ergebnisse: Gesundheit stellt in gesättigten Märkten, vor allem auch unter dem Aspekt alternder Gesellschaften, einen Wachstumsmarkt dar, welcher sich bei Weitem nicht auf originäre medizinische Produkte beschränkt. In der hier vorgestellten Studie wurden Produktkategorien wie „Zahnpflege“, „Obst und Gemüse“ oder „Nüsse“ als gesunde Produkte klassifiziert.
Schlussfolgerung: Die Relevanz von Gesundheit, auch im gesamtwirtschaftlichen Kontext, ist lange unterschätzt worden. Nach wie vor nimmt Gesundheit für Konsumenten einen hohen Stellenwert ein. Eine Offenlegung der individuellen Wahrnehmungen im Gesundheitskontext bietet eine Möglichkeit der deutlich effektiveren Produktgestaltung. Die Identifikation gesunder Produktdimensionen aus Konsumentensicht bringt so Aufschluss über die tatsächlich gewünschten Produkteigenschaften und die daraus resultierenden vorhandenen Potenziale.
Die Entwicklung von Qualitätsstandards für die ambulante psychosoziale Krebsberatung – Ergebnisse einer Delphibefragung
Authors: Kuhnt S. , Mehnert A. , Giesler J. , Faust T. , Weis J. , Ernst J. 
Published: April 2016

Zusammenfassung
Hintergrund: Die ambulante psychosoziale Versorgung von Krebspatienten und deren Angehörigen ist ein zentraler Bestandteil der onkologischen Versorgung. Bislang sind die Angebote ambulanter Versorgung unter den Aspekten des erbrachten Leistungsspektrums und der Qualitätssicherung sehr heterogen und schwer vergleichbar.
Fragestellung: Ziel der Studie war die Entwicklung von Qualitätsstandards für die ambulante psychosoziale Krebsberatung in der Form eines mehrdimensionalen Klassifikationssystems.
Material und Methoden: Auf der Basis einer Delphierhebung (3 Befragungsrunden) mit 97 Experten aus mehr als 10 unterschiedlichen Tätigkeitsfeldern bzw. institutionellen Kontexten (z. B. ambulante und stationäre psychosoziale Versorgung, Krebs- und Fachgesellschaften, Medizin, Wissenschaft und Selbsthilfe) wurden insgesamt 134 Einzelkriterien zu 9 Qualitätsbereichen (z. B. Personalstruktur, Leistungsangebot, Dokumentation) erstellt und hinsichtlich der Relevanz, Eindeutigkeit, Vollständigkeit und dem Grad der Verbindlichkeit beurteilt.
Ergebnis: 119 Einzelkriterien (88,8%) wurden als konsensfähige Qualitätsmerkmale angenommen, davon 94 als Basiskriterium (79%) und 25 als optionales Kriterium (21%). Die höchste Anzahl an Einzelkriterien entfallen auf die Qualitätsbereiche Beratungsangebot (26 Einzelkriterien), Dokumentation (21) sowie Personal bzw. Erreichbarkeit (jeweils 16). Insgesamt 15 Kriterien (11,2%) erreichten über die 3 Delphirunden keinen Konsens und wurden entfernt.
Schlussfolgerung: Mit den im Expertenkonsens erarbeiteten Qualitätskriterien liegen erstmals Standards für die ambulante psychosoziale Krebsberatung vor, die eine vergleichbare Beurteilung der Leistungsangebote ambulanter Krebsberatungsstellen ermöglichen.
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
Authors: Vandenbon Alexis , Dinh Viet H. , Mikami Norihisa , Kitagawa Yohko , Teraguchi Shunsuke , Ohkura Naganari , Sakaguchi Shimon 
Published: April 2016

Significance
Correlation of expression between genes can offer useful hints regarding their function or underlying regulatory mechanism. Today, large amounts of expression data are publicly available, allowing researchers to estimate expression correlation over thousands of samples. However, extracting information from correlation data is not straightforward, because underlying expression data are generated by different laboratories working on different cell types and under different conditions. Here we present Immuno-Navigator, a database for correlation of expression in cells of the immune system, which addresses these issues. We present examples of ways our database can be used for generating hypotheses for further experimental analysis. We demonstrate how it recapitulates known facts in immunology and successfully predicts key regulators in naturally occurring regulatory T cells.
Quantifying Recruitment Compensation in Florida Largemouth Bass, with Implications for Fisheries
Authors: Shaw Stephanie L. , Allen Micheal S. 
Published: April 2016

AbstractFish populations that undergo heavy exploitation and those for which the act of fishing can influence individual brood success are at risk of recruitment effects due to angling. The angling of brood‐guarding male black bass Micropterus spp. has been shown to decrease brood success, although there is no evidence that a loss of individual broods has population‐level impacts. Therefore, some level of recruitment compensation may influence juvenile bass survival. We sought to measure recruitment compensation and the form of the stock–recruit relationship for a brood‐guarding species, the Florida Largemouth Bass M. salmoides floridanus (hereafter, Florida Bass). The study was conducted in four north‐central Florida lakes during 4 years (2010–2013). We quantified adult stock density by using mark–recapture electrofishing surveys. The estimated broods produced in each spawning season, the number of those broods that were successful, and the age‐1 recruit density were quantified via snorkel surveys. We evaluated three models for describing the effects of stock density or successful brood density on recruitment: a proportional (linear; i.e., no compensation) model, a Ricker (dome‐shaped) model, and a Beverton–Holt (asymptotic) model. Recruit density was better indicated by the number of successful broods produced than by spawning stock density. Model comparisons indicated that the density‐dependent models had the most support, whereas there was no apparent support for the proportional or density‐independent model. The Ricker model had the most empirical support overall (estimated parameters: a = 2.2, b = 0.009). Our results indicate that the number of successful broods would have to fall below about 5 broods/ha to generate direct declines in observed average recruitment of Florida Bass.Received August 5, 2015; accepted December 9, 2015 Published online April 14, 2016
Production of a thermal stress resistant mutant Euglena gracilis strain using Fe-ion beam irradiation
Authors: Yamada Koji , Kazama Yusuke , Mitra Sharbanee , Marukawa Yuka , Arashida Ryo , Abe Tomoko , Ishikawa Takahiro , Suzuki Kengo 
Published: April 2016

Abstract
Euglena gracilis is a common phytoplankton species, which also has motile flagellate characteristics. Recent research and development has enabled the industrial use of E. gracilis and selective breeding of this species is expected to further expand its application. However, the production of E. gracilis nuclear mutants is difficult because of the robustness of its genome. To establish an efficient mutation induction procedure for E. gracilis, we employed Fe-ion beam irradiation in the RIKEN RI beam factory. A decrease in the survival rate was observed with the increase in irradiation dose, and the upper limit used for E. gracilis selective breeding was around 50 Gy. For a practical trial of Fe-ion irradiation, we conducted a screening to isolate high-temperature-tolerant mutants. The screening yielded mutants that proliferated faster than the wild-type strain at 32 °C. Our results demonstrate the effectiveness of heavy-ion irradiation on E. gracilis selective breeding.
PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences
Authors: Peng Yousong , Yang Lei , Li Honglei , Zou Yuanqiang , Deng Lizong , Wu Aiping , Du Xiangjun , Wang Dayan , Shu Yuelong , Jiang Taijiao 
Published: April 2016

Abstract
Motivation: Timely surveillance of the antigenic dynamics of the influenza virus is critical for accurate selection of vaccine strains, which is important for effective prevention of viral spread and infection.
Results: Here, we provide a computational platform, called PREDAC-H3, for antigenic surveillance of human influenza A(H3N2) virus based on the sequence of surface protein hemagglutinin (HA). PREDAC-H3 not only determines the antigenic variants and antigenic cluster (grouped for similar antigenicity) to which the virus belongs, based on HA sequences, but also allows visualization of the spatial distribution and temporal dynamics of antigenic clusters of viruses isolated from around the world, thus assisting in antigenic surveillance of human influenza A(H3N2) virus.
Availability and Implementation: It is publicly available from: http://biocloud.hnu.edu.cn/influ411/html/index.php.
Contacts: yshu@cnic.org.cn or taijiao@moon.ibp.ac.cn
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
Authors: Pliatsika Venetia , Loher Phillipe , Telonis Aristeidis G. , Rigoutsos Isidore 
Published: April 2016

Abstract
Motivation: It has been known that mature transfer RNAs (tRNAs) that are encoded in the nuclear genome give rise to short molecules, collectively known as tRNA fragments or tRFs. Recently, we reported that, in healthy individuals and in patients, tRFs are constitutive, arise from mitochondrial as well as from nuclear tRNAs, and have composition and abundances that depend on a person’s sex, population origin and race as well as on tissue, disease and disease subtype. Our findings as well as similar work by other groups highlight the importance of tRFs and presage an increase in the community’s interest in elucidating the roles of tRFs in health and disease.
Results: We created MINTbase, a web-based framework that serves the dual-purpose of being a content repository for tRFs and a tool for the interactive exploration of these newly discovered molecules. A key feature of MINTbase is that it deterministically and exhaustively enumerates all possible genomic locations where a sequence fragment can be found and indicates which fragments are exclusive to tRNA space, and thus can be considered as tRFs: this is a very important consideration given that the genomes of higher organisms are riddled with partial tRNA sequences and with tRNA-lookalikes whose aberrant transcripts can be mistaken for tRFs. MINTbase is extremely flexible and integrates and presents tRF information from multiple yet interconnected vantage points (‘vistas’). Vistas permit the user to interactively personalize the information that is returned and the manner in which it is displayed. MINTbase can report comparative information on how a tRF is distributed across all anticodon/amino acid combinations, provides alignments between a tRNA and multiple tRFs with which the user can interact, provides details on published studies that reported a tRF as expressed, etc. Importantly, we designed MINTbase to contain all possible tRFs that could ever be produced by mature tRNAs: this allows us to report on their genomic distributions, anticodon/amino acid properties, alignments, etc. while giving users the ability to at-will investigate candidate tRF molecules before embarking on focused experimental explorations. Lastly, we also introduce a new labeling scheme that is tRF-sequence-based and allows users to associate a tRF with a universally unique label (‘tRF-license plate’) that is independent of a genome assembly and does not require any brokering mechanism.
Availability and Implementation: MINTbase is freely accessible at http://cm.jefferson.edu/MINTbase/. Dataset submissions to MINTbase can be initiated at http://cm.jefferson.edu/MINTsubmit/.
Contact: isidore.rigoutsos@jefferson.edu
Supplementary information: Supplementary data are available at Bioinformatics online.