bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with contraceptive ideation among urban men in Nigeria
Authors: Babalola Stella , Kusemiju Bola , Calhoun Lisa , Corroon Meghan , Ajao Bolanle 
Published: May 2015

AbstractObjectiveTo determine factors influencing the readiness of urban Nigerian men to adopt contraceptive methods.MethodsThe data were derived from a cross‐sectional household survey conducted in Ibadan and Kaduna between September and November 2012. The sample included 2358 men from both cities. An ideation framework was constructed and a multilevel analysis performed to identify factors associated with positive thinking about contraception.ResultsCorrelates of ideation operated at the individual, household, and community levels. There is considerable cluster‐level variability in ideation score. The key correlates included exposure to family planning promotion campaigns, education, age, religion, marital status, and community norms. Compared with no education, high education is associated with an approximately 6.7‐point increase in ideation score (P < 0.001). Men with a high level of NURHI program exposure had an average ideation score that was about 3.4 points higher than for their peers with no exposure (P < 0.001). The ideation score for Muslims was lower by approximately 1.7 points, on average, than for Christians (P < 0.001).ConclusionA comprehensive strategy of communication and behavior change activities surrounding contraceptive use should be tailored to meet the needs of specific groups of men. Community‐level interventions designed to mobilize community members and change social norms that hinder the spread of ideational characteristics that favor contraceptive use should be part of this comprehensive strategy.
A Comparison of Biceps Labrum Complex Findings in Patients with and without Superior Migration of the Humeral Head in Large or Massive Rotator Cuff Tears
Authors: Mura Nariyuki , Harada Mikio , Tsuruta Daisaku , Ogino Toshihiko , Takagi Michiaki 
Published: May 2015

Background The purpose of this study was to clarify the relationship between superior migration of the humeral head and findings of biceps labrum complex (BLC) in large or massive rotator cuff tears. Methods Forty-nine shoulders that underwent surgery for torn supraspinatus and infraspinatus tendons were included. Patients were divided into two groups according to the acromio—humeral interval (AHI). Arthroscopic findings of BLC were classified into five types; Type 0; normal shape, Type 1: fraying; Type 2: detachment; Type 3: attrition of BLC and superior glenoid; and Type 4: defect. Results The group without migration (AHI ≥ 7 mm) consisted of 21 shoulders and that with migration (AHI < 7 mm) was 28 shoulders. There were significantly more patients with Types 2, 3, and 4 in the group with migration than without migration. Conclusion This study indicates a potential relationship between BLC injury and superior humeral head migration accompanied by a rotator cuff tear.
Age and sedimentary record of inland eolian sediments in Lithuania, NE European Sand Belt
Authors: Kalińska-Nartiša Edyta , Thiel Christine , Nartišs Māris , Buylaert Jan-Pieter , Murray Andrew S. 
Published: May 2015

We present a study based on four inland eolian locations in Eastern, Central and Southeastern Lithuania belonging to the northeastern part of the ‘European Sand Belt’ (ESB). Although there have been several previous studies of the ESB, this north-eastern extension has not been investigated before in any detail. The sedimentary structural–textural features are investigated and a chronology was derived using optically stimulated luminescence on both quartz and feldspar. The sedimentary structures and the rounding and surface characteristics of the quartz grains argue for a predominance of eolian transport. Additionally, some structural alternations and a significant contribution of non-eolian grains are interpreted as inherited local glacial/glaciofluvial-bearing lithologies.Three main (glaciolacustrine–) eolian phases are distinguished based on the position in the landscape and the luminescence ages: (1) Anolder eolian seriesaround 15 to 16 ka, possibly correlated with the cold GS-2a event according to the GRIP stratigraphy, and (2) ayounger eolian seriesaround 14.0 ka, possibly representing the GI-1d and 1c events. Theolder eolian seriesis underlain by (3) aglaciolacustrine–eolian seriesfor which the period of deposition remains uncertain due to the significant discrepancy between the ages based on quartz and feldspar.
Perceptions relating to body size, weight loss and weight-loss interventions in black South African women: a qualitative study
Authors: Draper Catherine E , Davidowitz Kesiah J , Goedecke Julia H 
Published: May 2015

AbstractObjectiveA higher tolerance for a larger body size has been associated with obesity in black South African (SA) women. The aim of the present study was to explore perceptions regarding body size and weight loss in a sample of black women from a low-income community in Cape Town, SA.DesignQualitative pilot study including five focus groups. Data were analysed using thematic analysis.SettingKhayelitsha, Cape Town, SA.SubjectsTwenty-one black SA women.ResultsThe majority of participants had positive perceptions of overweight/obesity, which were influenced by community and cultural perceptions, but some inconsistencies were observed as overweight/obesity was also associated with ill health. Participants identified many benefits to weight loss, but due to the association with sickness, they were concerned about being stigmatised in their community. Although participants had knowledge about healthy eating, the main barrier to eating healthily included the perceived higher cost of healthier food and food insecurity. All participants saw exercise as a strategy to lose weight and improve health, and were interested in participating in a community-based exercise intervention, but negative community perceptions and conflicting views regarding who should lead the intervention were identified as barriers.ConclusionsThese findings highlight the complexities surrounding participants’ perceptions regarding body size, weight loss and weight-loss interventions, and emphasise low socio-economic status as a barrier to change. The study also highlights the strong influence of cultural ideals and community perceptions on personal perceptions. These findings underscore the necessity for culturally appropriate weight-loss interventions in low-income, transitioning communities.
High-performance green flexible electronics based on biodegradable cellulose nanofibril paper
Authors: Jung Yei Hwan , Chang Tzu-Hsuan , Zhang Huilong , Yao Chunhua , Zheng Qifeng , Yang Vina W. , Mi Hongyi , Kim Munho , Cho Sang June , Park Dong-Wook , Jiang Hao , Lee Juhwan , Qiu Yijie , Zhou Weidong , Cai Zhiyong , Gong Shaoqin , Ma Zhenqiang 
Published: May 2015

AbstractToday’s consumer electronics, such as cell phones, tablets and other portable electronic devices, are typically made of non-renewable, non-biodegradable, and sometimes potentially toxic (for example, gallium arsenide) materials. These consumer electronics are frequently upgraded or discarded, leading to serious environmental contamination. Thus, electronic systems consisting of renewable and biodegradable materials and minimal amount of potentially toxic materials are desirable. Here we report high-performance flexible microwave and digital electronics that consume the smallest amount of potentially toxic materials on biobased, biodegradable and flexible cellulose nanofibril papers. Furthermore, we demonstrate gallium arsenide microwave devices, the consumer wireless workhorse, in a transferrable thin-film form. Successful fabrication of key electrical components on the flexible cellulose nanofibril paper with comparable performance to their rigid counterparts and clear demonstration of fungal biodegradation of the cellulose-nanofibril-based electronics suggest that it is feasible to fabricate high-performance flexible electronics using ecofriendly materials.
Photochemical degradation of the UV filter octyl methoxycinnamate in solution and in aggregates
Authors: Hanson Kerry M. , Narayanan Swathi , Nichols Valerie M. , Bardeen Christopher J. 
Published: May 2015

Abstract
The photodegradation of the ultraviolet (UV) filter octyl methoxycinnamate (OMC) is investigated in both dilute solution and in aggregated form. In dilute solution, the ratio of trans and cis isomers achieved at the photostationary state is solvent-dependent because of variations in the isomerization quantum yield. The two isomeric forms at the photostationary state are highly resistant to further photodegradation and no other UVA-absorbing species are formed. Aggregation of OMC, either in a neat film or in aqueous colloidal suspensions, leads to irreversible photodegradation of the molecule and the formation of multiple photoproducts. In addition to previously identified photoproducts like the UVB-absorbing cis and trans isomers and photodimers, we find photoproduct species whose absorption extends into the UVA. Characterization of the photophysical properties of these species indicates that they have long-lived excited-states (τ
f > 1 ns, 400 nm), unlike the isomeric forms of OMC (τ
f < 30 ps, 266 nm), and that excitation at 405 nm can sensitize the formation of singlet oxygen. These results show that the environment of OMC affects the photochemistry of the molecule and that the environmental conditions must be taken into account when considering the molecule’s stability. In particular, aggregation of OMC molecules results in complex photochemistry that can produce species whose absorption extends into UVA and are capable of generating reactive oxygen species.
Electric characteristics analysis on power drive system based on negative input‐resistance compensator
Authors: Wang Na , Zhou Yuanjun , Sun Jing , Bai Long 
Published: May 2015

A power drive system is a typical load for the 270 V DC power distribution systems of more electric aircraft. It may cause instability of power grid, including voltage transients and current transients. A negative input‐resistance compensator with current limitation is proposed to solve the stability problem as well as to decrease both voltage transients and current transients. The main emphasis is placed on the transient characteristics research of power drive system with the proposed compensator. A dc network admittance model is established to select proper parameters for the compensator. Simulation and experiments show that the designed compensator increases system stability while satisfying the transient requirements of the power distribution system.
Does Government‐sponsored Advertising Increase Social Welfare? A Theoretical and Empirical Investigation
Authors: Carpio Carlos E. , Isengildina‐Massa Olga 
Published: May 2015

AbstractThe main objective of this study was to analyze the effect of advertising on social welfare in a perfectly competitive market where the level of advertising is chosen by a social planner. The theoretical model revealed that social planner‐sponsored advertising that increases the equilibrium price of the advertised good can increase society's welfare if the effect of advertising in consumers' utility is higher than the consumer welfare‐reducing price effect. The empirical illustration focuses on the U.S. state of South Carolina's “buy local” food products campaign. The findings suggest that this government‐sponsored advertising campaign increases total welfare.
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach
Authors: Henriques David , Rocha Miguel , Saez-Rodriguez Julio , Banga Julio R. 
Published: May 2015

Abstract
Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters.
Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: julio@iim.csic.es or saezrodriguez@ebi.ac.uk
Bayesian mixture analysis for metagenomic community profiling
Authors: Morfopoulou Sofia , Plagnol Vincent 
Published: May 2015

AbstractMotivation: Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture.Results: We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures.Availability and implementation: metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMixContact: sofia.morfopoulou.10@ucl.ac.ukSupplementary information: Supplementary data are available at Bionformatics online.
tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation
Authors: Chambaz Antoine , Neuvial Pierre 
Published: May 2015

Abstract
Summary: We describe the implementation of the method introduced by Chambaz et al. in 2012. We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers.
Availability and implementation: An open-source R package tmle.npvi is available from CRAN (http://cran.r-project.org/).
Contact: pierre.neuvial@genopole.cnrs.fr
pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge
Authors: Wachter Astrid , Beißbarth Tim 
Published: May 2015

Abstract
Summary: Characterization of biological processes is progressively enabled with the increased generation of omics data on different signaling levels. Here we present a straightforward approach for the integrative analysis of data from different high-throughput technologies based on pathway and interaction models from public databases. pwOmics performs pathway-based level-specific data comparison of coupled human proteomic and genomic/transcriptomic datasets based on their log fold changes. Separate downstream and upstream analyses results on the functional levels of pathways, transcription factors and genes/transcripts are performed in the cross-platform consensus analysis. These provide a basis for the combined interpretation of regulatory effects over time. Via network reconstruction and inference methods (Steiner tree, dynamic Bayesian network inference) consensus graphical networks can be generated for further analyses and visualization.
Availability and implementation: The R package pwOmics is freely available on Bioconductor (http://www.bioconductor.org/).
Contact: astrid.wachter@med.uni-goettingen.de
PopGeV: a web-based large-scale population genome browser
Authors: Shi Xinyi , Peng Jing , Yu Xiaohan , Zhang Xiaohong , Li Dongye , Liu Baohui , Kong Fanjiang , Yuan Xiaohui 
Published: May 2015

Abstract
Motivation: The development of high-throughput sequencing technology has made it possible for more and more researchers to use population sequencing data to mine genes associated with specific traits. However, the massive amounts of sequencing data have also brought new challenges to the researchers. The question of how to browse population genomic data in an easy and intuitive manner must be addressed. Web-based genome browsers allow user to conveniently view the results of genomic analyses, but heavy usage can reduce the response speed of the webpage, which limits its usefulness in the display of large-scale genome data. IndexedDB technology is a good solution to this problem; it supports web browsers and so creates local databases. In this way, data can be read from the local storage, achieving a smooth display of population genomic data.
Results: PopGeV has the following characteristics. First, it uses a new encoding method for compression of population SNP and INDEL data. IndexedDB technology is used to download the results to local storage so that users can browse the results smoothly even when the network traffic is heavy. Second, PopGeV identify similar genomic regions between two individuals based on SNP data. Population diversity indexes are calculated when comparing two populations. Third, user defined annotation information can be integrated for user-friendly mining of gene functions. Simulation shows that PopGeV can smoothly display analysis results of population genome containing over 500 individuals with 2 millions SNP data.
Availability and implementation: PopGeV is available at www.soyomics.com/popgev/
Contact: yuanxh@iga.ac.cn
Diffusion maps for high-dimensional single-cell analysis of differentiation data
Authors: Haghverdi Laleh , Buettner Florian , Theis Fabian J. 
Published: May 2015

Abstract
Motivation: Single-cell technologies have recently gained popularity in cellular differentiation studies regarding their ability to resolve potential heterogeneities in cell populations. Analyzing such high-dimensional single-cell data has its own statistical and computational challenges. Popular multivariate approaches are based on data normalization, followed by dimension reduction and clustering to identify subgroups. However, in the case of cellular differentiation, we would not expect clear clusters to be present but instead expect the cells to follow continuous branching lineages.
Results: Here, we propose the use of diffusion maps to deal with the problem of defining differentiation trajectories. We adapt this method to single-cell data by adequate choice of kernel width and inclusion of uncertainties or missing measurement values, which enables the establishment of a pseudotemporal ordering of single cells in a high-dimensional gene expression space. We expect this output to reflect cell differentiation trajectories, where the data originates from intrinsic diffusion-like dynamics. Starting from a pluripotent stage, cells move smoothly within the transcriptional landscape towards more differentiated states with some stochasticity along their path. We demonstrate the robustness of our method with respect to extrinsic noise (e.g. measurement noise) and sampling density heterogeneities on simulated toy data as well as two single-cell quantitative polymerase chain reaction datasets (i.e. mouse haematopoietic stem cells and mouse embryonic stem cells) and an RNA-Seq data of human pre-implantation embryos. We show that diffusion maps perform considerably better than Principal Component Analysis and are advantageous over other techniques for non-linear dimension reduction such as t-distributed Stochastic Neighbour Embedding for preserving the global structures and pseudotemporal ordering of cells.
Availability and implementation: The Matlab implementation of diffusion maps for single-cell data is available at https://www.helmholtz-muenchen.de/icb/single-cell-diffusion-map.
Contact: fbuettner.phys@gmail.com, fabian.theis@helmholtz-muenchen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Prenatal Transmission of Syphilis and Human Immunodeficiency Virus in Brazil: Achieving Regional Targets for Elimination
Authors: Cerda Rodrigo , Perez Freddy , Domingues Rosa Maria S.M. , Luz Paula M. , Grinsztejn Beatriz , Veloso Valdilea G. , Caffe Sonja , Francke Jordan A. , Freedberg Kenneth A. , Ciaranello Andrea L. 
Published: May 2015

AbstractBackground.  The Pan-American Health Organization has called for reducing (1) human immunodeficiency virus (HIV) mother-to-child transmission (MTCT) to ≤0.30 infections/1000 live births (LB), (2) HIV MTCT risk to ≤2.0%, and (3) congenital syphilis (CS) incidence to ≤0.50/1000 LB in the Americas by 2015.Methods.  Using published Brazilian data in a mathematical model, we simulated a cohort of pregnant women from antenatal care (ANC) through birth. We investigated 2 scenarios: “current access” (89.1% receive one ANC syphilis test and 41.1% receive 2; 81.7% receive one ANC HIV test and 18.9% receive birth testing; if diagnosed, 81.0% are treated for syphilis and 87.5% are treated for HIV) and “ideal access” (95% of women undergo 2 HIV and syphilis screenings; 95% receive appropriate treatment). We conducted univariate and multivariate sensitivity analyses on key inputs.Results.  With current access, we projected 2.95 CS cases/1000 LB, 0.29 HIV infections/1000 LB, 7.1% HIV MTCT risk, and 11.11 intrauterine fetal demises (IUFD)/1000 pregnancies, with significant regional variation. With ideal access, we projected improved outcomes: 1.00 CS cases/1000 LB, 0.10 HIV infections/1000 LB, HIV MTCT risk of 2.4%, and 10.65 IUFD/1000 pregnancies. Increased testing drove the greatest improvements. Even with ideal access, only HIV infections/1000 LB met elimination goals. Achieving all targets required testing and treatment &gt;95% and reductions in prevalence and incidence of HIV and syphilis.Conclusions.  Increasing access to care and HIV and syphilis antenatal testing will substantially reduce HIV and syphilis MTCT in Brazil. In addition, regionally tailored interventions reducing syphilis incidence and prevalence and supporting HIV treatment adherence are necessary to completely meet elimination goals.