bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contact infection of infectious disease onboard a cruise ship
Authors: Zhang Nan , Miao Ruosong , Huang Hong , Chan Emily Y. Y. 
Published: December 2016

AbstractCruise tourism has become more popular. Long-term personal contact, complex population flows, a lack of medical care facilities, and defective infrastructure aboard most cruise ships is likely to result in the ship becoming an incubator for infectious diseases. In this paper, we use a cruise ship as a research scenario. Taking into consideration personal behavior, the nature and transfer route of the virus across different surfaces, virus reproduction, and disinfection, we studied contact infection of infectious disease on a cruise ship. Using gastroenteritis caused by the norovirus as an example, we analyzed the characteristics of infectious disease propagation based on simulation results under different conditions. We found hand washing are the most important factors affecting virus propagation and passenger infection. It also decides either the total number of virus microorganisms or the virus distribution in different functional areas. The transfer rate between different surfaces is a key factor influencing the concentricity of the virus. A high transfer rate leads to high concentricity. In addition, the risk of getting infected is effectively reduced when the disinfection frequency is above a certain threshold. The efficiency of disinfection of functional areas is determined by total virus number and total contact times of surfaces.
Neurodevelopment and Health-Related Quality of Life in Infants Born with Gastroschisis: A 6-Year Retrospective French Study
Authors: Zahed Meriem , Guimond Floriane , Baumstarck Karine , Faure Alice , Michel Fabrice , Claris Olivier , Massardier Jerome , Gire Catherine , Merrot Thierry , Tosello Barthelemy 
Published: December 2016

Introduction Quantify quality of life (QoL) outcomes in gastroschisis children is little assessed. The primary objective was to describe the long-term outcome of newborns with gastroschisis treated in three tertiary care hospitals of France in terms of neurodevelopment and QoL.
Materials and Methods The study reported was a cross-sectional, descriptive multicentric retrospective study assessing the outcome of newborns with gastroschisis, born between January 1, 2009, and December 31, 2014, treated at two large and French level III neonatal intensive care units. Long-term outcome data were assessed by questionnaires sent to the infants' parents. Questionnaires explored global health, neurological development, and quality of life (overall assessment including socio-economic and medical), Age & Stages Questionnaire, infants' quality of life (KIDSCREEN), and quality of parents' life (General Questionnaire Short Form-36).
Results In this study, 50% of the survivor's families answered the assessment form (n = 33). The average follow-up age was 40 months, ranging from 8 months to 6 years. Cases of simple gastroschisis more often had a normal score for “communication” (p = 0.033), while patients who received morphine for a longer duration had significantly lower scores for the items “communication” and “problem resolving” (p = 0.024 and p = 0.011, respectively). Children's QoL was significantly lower for patients with gestational age younger than 36 weeks (p = 0.023) and for patients born following “fetal cause delivery” (p = 0.022). Parents had a significantly higher physical composite score if their child underwent primary closure (p = 0.012).
Conclusion Our analyses confirm the idea that cases of complex gastroschisis and preterm delivery may lead to poorer outcome. Such hindsight (40 months in mean) allowed for an interesting assessment of development long after the patient's initial hospitalization and to confirm these results, a standardized neuropsychological evaluation of patients should be done when at least 6 years old. An accurate assessment of the social environment and its impact on the development and QoL of children will be fundamental to avoid selection bias.
Understanding the nature of atmospheric acid processing of mineral dusts in supplying bioavailable phosphorus to the oceans
Authors: Stockdale Anthony , Krom Michael D. , Mortimer Robert J. G. , Benning Liane G. , Carslaw Kenneth S. , Herbert Ross J. , Shi Zongbo , Myriokefalitakis Stelios , Kanakidou Maria , Nenes Athanasios 
Published: December 2016

SignificanceMineral dust is the most important external source of phosphorus (P), a key nutrient controlling phytoplankton productivity and carbon uptake, to the offshore ocean. The bioavailable P in dust exhibits considerable and poorly understood variability. Detailed laboratory experiments elucidate and quantify the major processes controlling P dissolution in the atmosphere. Dust exposure to acids is the main driver of P mineral transformations, and a simple direct proportionality is found between the amount of bioavailable P dissolved from the dust and acid exposure. Simulations suggest that dust acidification increases leachable P over large areas of the globe and explains much of its variability in important oceanic areas where primary productivity is limited by this nutrient (e.g., North Central Atlantic, Mediterranean).
Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography
Authors: Zhu Xiaohui , Hitchcock Adam P. , Bazylinski Dennis A. , Denes Peter , Joseph John , Lins Ulysses , Marchesini Stefano , Shiu Hung-Wei , Tyliszczak Tolek , Shapiro David A. 
Published: December 2016

SignificanceMagnetotactic bacteria are one of the simplest systems that perform biomineralization: organisms that create inorganic materials using biochemistry under genetic control. They synthesize magnetosomes, which are intracellular, membrane-bound nanoscale single crystals of magnetite, a magnetic iron oxide. We studied the magnetism of individual magnetosomes inside individual cells with spectro-ptychography, a new technique of high-resolution X-ray microscopy. Our results help us to understand how the cells biomineralize magnetosomes and their function in the cell ecophysiology. In addition to demonstrating a large improvement in spatial resolution relative to earlier nonptychography studies, the results presented provide insights into magnetosome biomineralization.
Sox2+ progenitors in sharks link taste development with the evolution of regenerative teeth from denticles
Authors: Martin Kyle J. , Rasch Liam J. , Cooper Rory L. , Metscher Brian D. , Johanson Zerina , Fraser Gareth J. 
Published: December 2016

SignificanceOral teeth and skin denticles share a deep, 450-million-year-old, evolutionary relationship among vertebrates. We investigate how teeth evolved from simpler denticles using sharks as an evolutionary developmental model. The striking ability of shark teeth to regenerate rapidly and continuously is not shared by denticles, and we suggest that this difference is related to the tooth-specific expression of the stem cell factor sox2. We show that epithelial progenitors of the shark dentition share a remarkable developmental relationship with taste buds. We suggest that teeth arose by combining the gene regulatory network for producing simple denticles with that for producing the highly regenerative taste buds in the oral cavity.
Janus effect of antifreeze proteins on ice nucleation
Authors: Liu Kai , Wang Chunlei , Ma Ji , Shi Guosheng , Yao Xi , Fang Haiping , Song Yanlin , Wang Jianjun 
Published: December 2016

Significance
In the past decades, a vast body of experimental and theoretical work has been undertaken to investigate the molecular level mechanism underlying heterogeneous ice nucleation. However, understanding of heterogeneous ice nucleation is still far from satisfactory. Antifreeze proteins (AFPs) are endowed with the unique ability to control freezing. Our research reveals the exact effect of AFPs on ice nucleation at the molecular level, which correlates ice nucleation with the surface chemistry and topography of different faces of AFPs. We also emphasize a critical role for the non–ice-binding face of AFPs and discover that the proper function of AFPs is realized only by synergistic effects of the non–ice-binding face and the ice-binding face.
Dopamine release from the locus coeruleus to the dorsal hippocampus promotes spatial learning and memory
Authors: Kempadoo Kimberly A. , Mosharov Eugene V. , Choi Se Joon , Sulzer David , Kandel Eric R. 
Published: December 2016

Significance
Successful completion of daily activities relies on the ability to select the relevant features of the environment to pay attention to and remember. Disruptions of these processes can lead to disorders, such as attention-deficit hyperactivity disorder and age-related memory loss. To devise therapeutic strategies, we must understand the neural circuits underlying normal cognition. One important pathway is the signaling of dopamine, a reinforcement-related neurotransmitter, in the hippocampus, a spatial learning and memory center. Surprisingly, the brain region supplying dopamine to the dorsal hippocampus is unclear. This study provides direct evidence that the noradrenergic locus coeruleus coreleases dopamine in the dorsal hippocampus and provides insight into dopamine function in selective attention and spatial learning and memory.
Estimating uncertainty in respondent-driven sampling using a tree bootstrap method
Authors: Baraff Aaron J. , McCormick Tyler H. , Raftery Adrian E. 
Published: December 2016

Significance
Some hidden or hard-to-reach populations of interest to researchers are difficult to study with standard statistical methods because there is not a reliable list of members from which samples can be drawn. Respondent-driven sampling (RDS) is a common way to reach members of these populations by allowing a small number of respondents to recruit further respondents in the target population from their personal contacts. However, estimates derived from RDS are known to have a high degree of uncertainty, for which current methods do not fully account. We present a method that overcomes this problem and allows for better statistical inference from RDS data.
Improved orthology inference with Hieranoid 2
Authors: Kaduk Mateusz , Sonnhammer Erik 
Published: December 2016

Abstract

Motivation
The initial step in many orthology inference methods is the computationally demanding establishment of all pairwise protein similarities across all analysed proteomes. The quadratic scaling with proteomes has become a major bottleneck. A remedy is offered by the Hieranoid algorithm which reduces the complexity to linear by hierarchically aggregating ortholog groups from InParanoid along a species tree.

Results
We have further developed the Hieranoid algorithm in many ways. Major improvements have been made to the construction of multiple sequence alignments and consensus sequences. Hieranoid version 2 was evaluated with standard benchmarks that reveal a dramatic increase in the coverage/accuracy tradeoff over version 1, such that it now compares favourably with the best methods. The new parallelized cluster mode allows Hieranoid to be run on large data sets in a much shorter timespan than InParanoid, yet at similar accuracy.

Availability and Implementation
Perl code freely available at http://hieranoid.sbc.su.se/.

Supplementary information
Supplementary data are available at Bioinformatics online.
AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins
Authors: Colledge Matthew , Wallace B A 
Published: December 2016

Abstract

Summary
Integral membrane proteins that form helical pores and bundles constitute major drug targets, and many of their structures have been defined by crystallography and cryo-electron microscopy. The gating of channels and ligand binding of transporters generally involve changes in orientation of one or more the constituent helices in the structures. At present there is no standard easily accessible means for defining the orientation of a helix in a membrane protein structure. AnglerFish is a web-based tool for parameterising the angles of transmembrane helices based on PDB coordinates, with the helical orientations defined by the angles ‘tilt’ and ‘swing’. AnglerFish is particularly useful for defining changes in structure between different states, including both symmetric and asymmetric transitions, and can be used to quantitate differences between related structures or different subunits within the same structure.

Availability and Implementation
AnglerFish is freely available at http://anglerfish.cryst.bbk.ac.uk. The website is implemented in Perl-cgi and Apache and operation in all major browsers is supported. The source code is available at GitHub.

Supplementary information
Supplementary data are available at Bioinformatics online.
Analyzing user-generated online content for drug discovery: development and use of MedCrawler
Authors: Helfenstein Andreas , Tammela Päivi 
Published: December 2016

AbstractMotivationEthnopharmacology, or the scientific validation of traditional medicine, is a respected starting point in drug discovery. Home remedies and traditional use of plants are still widespread, also in Western societies. Instead of perusing ancient pharmacopeias, we developed MedCrawler, which we used to analyze blog posts for mentions of home remedies and their applications. This method is free and accessible from the office computer.ResultsWe developed MedCrawler, a data mining tool for analyzing user-generated blog posts aiming to find modern ‘traditional’ medicine or home remedies. It searches user-generated blog posts and analyzes them for correlations between medically relevant terms. We also present examples and show that this method is capable of delivering both scientifically validated uses as well as not so well documented applications, which might serve as a starting point for follow-up research.Availability and ImplementationSource code is available on GitHub at {{https://github.com/a-hel/medcrawler}}Supplementary informationSupplementary data are available at Bioinformatics online.
ACTG: novel peptide mapping onto gene models
Authors: Choi Seunghyuk , Kim Hyunwoo , Paek Eunok 
Published: December 2016

Abstract

Summary
In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model. Mapping potentially novel peptides to genome sequences, while allowing certain genomic variations, requires introducing novel gene models when aligning peptide sequences to gene structures. We have developed a new tool called ACTG (Amino aCids To Genome), which maps peptides to genome, assuming all possible single exon skipping, junction variation allowing three edit distances from the original splice sites, exon extension and frame shift. In addition, it can also consider SNVs (single nucleotide variations) during mapping phase if a user provides the VCF (variant call format) file as an input.

Availability and Implementation
Available at http://prix.hanyang.ac.kr/ACTG/search.jsp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Intraseason Waning of Influenza Vaccine Protection: Evidence From the US Influenza Vaccine Effectiveness Network, 2011–2012 Through 2014–2015
Authors: Ferdinands Jill M. , Fry Alicia M. , Reynolds Sue , Petrie Joshua G. , Flannery Brendan , Jackson Michael L. , Belongia Edward A. 
Published: December 2016

Abstract

Background.
Recent studies suggest that influenza vaccine effectiveness (VE) may wane over the course of an influenza season, leading to suboptimal VE during late influenza seasons.

Methods.
We examined the association between influenza VE and time since vaccination among patients ≥9 years old with medically attended acute respiratory illness in the US Influenza Vaccine Effectiveness Network using data pooled from the 2011–2012 through 2014–2015 influenza seasons. We used multivariate logistic regression with polymerase chain reaction–confirmed influenza infection as the outcome and vaccination status defined by days between vaccination and symptom onset as the predictor. Models were adjusted for calendar time and other potential confounding factors.

Results.
We observed decreasing VE with increasing time since vaccination for influenza A(H3N2) (P = .004), influenza A(H1N1)pdm09 (P = .01), and influenza B viruses (P = .04). Maximum VE was observed shortly after vaccination, followed by a decline in VE of about 7% (absolute) per month for influenza A(H3N2) and influenza B and 6%–11% per month for influenza A(H1N1)pdm09 viruses. VE remained greater than zero for at least 6 months for influenza A(H1N1)pdm09 and influenza B and at least 5 months for influenza A(H3N2) viruses. Decline in VE was more pronounced among patients with prior-season influenza vaccination. A similar pattern of increasing influenza risk with increasing time since vaccination was seen in analyses limited to vaccinees.

Conclusions.
We observed decreasing influenza vaccine protection with increasing time since vaccination across influenza types/subtypes. This association is consistent with intraseason waning of host immunity, but bias or residual confounding could explain these findings.
Combatting Global Infectious Diseases: A Network Effect of Specimen Referral Systems
Authors: Fonjungo Peter N. , Alemnji George A. , Kebede Yenew , Opio Alex , Mwangi Christina , Spira Thomas J. , Beard R. Suzanne , Nkengasong John N. 
Published: December 2016

Abstract
The recent Ebola virus outbreak in West Africa clearly demonstrated the critical role of laboratory systems and networks in responding to epidemics. Because of the huge challenges in establishing functional laboratories at all tiers of health systems in developing countries, strengthening specimen referral networks is critical. In this review article, we propose a platform strategy for developing specimen referral networks based on 2 models: centralized and decentralized laboratory specimen referral networks. These models have been shown to be effective in patient management in programs in resource-limited settings. Both models lead to reduced turnaround time and retain flexibility for integrating different specimen types. In Haiti, decentralized specimen referral systems resulted in a 182% increase in patients enrolling in human immunodeficiency virus treatment programs within 6 months. In Uganda, cost savings of up to 62% were observed with a centralized model. A platform strategy will create a network effect that will benefit multiple disease programs.
HLA-B*57 and IFNL4-Related Polymorphisms Are Associated With Protection Against HIV-1 Disease Progression in Controllers
Authors: Dominguez-Molina Beatriz , Tarancon-Diez Laura , Hua Stephane , Abad-Molina Cristina , Rodriguez-Gallego Esther , Machmach Kawthar , Vidal Francesc , Tural Cristina , Moreno Santiago , Goñi María José , Ramírez de Arellano Elena , del Val Margarita , Gonzalez-Escribano María Francisca , Del Romero Jorge , Rodriguez Carmen , Capa Laura , Viciana Pompeyo , Alcamí José , Yu Xu G. , Walker Bruce D. , Leal Manuel , Lichterfeld Mathias , Ruiz-Mateos Ezequiel ,   for the Spanish AIDS Research Network HIV-Controllers Cohort integrated in the Spanish AIDS Research Network
Published: December 2016

Abstract

Background.
Human immunodeficiency virus type 1 (HIV-1) controllers maintain HIV-1 viremia at low levels (normally &lt;2000 HIV-RNA copies/mL) without antiretroviral treatment. However, some HIV-1 controllers have evidence of immunologic progression with marked CD4+ T-cell decline. We investigated host genetic factors associated with protection against CD4+ T-cell loss in HIV-1 controllers.

Methods.
We analyzed the association of interferon-lambda 4 (IFNL4)–related polymorphisms and human leukocyte antigen (HLA)-B haplotypes within long-term nonprogressor HIV-1 controllers (LTNP-Cs; defined by maintaining CD4+ T-cells counts &gt;500 cells/mm3 for more than 7 years after HIV-1 diagnosis) vs non-LTNP-Cs who developed CD4+ T-cell counts &lt;500 cells/mm3. Both a Spanish study cohort (n = 140) and an international validation cohort (n = 914) were examined. Additionally, in a subgroup of individuals, HIV-1–specific T-cell responses and soluble cytokines were analyzed.

Results.
HLA-B*57 was independently associated with the LTNP-C phenotype (odds ratio [OR], 3.056 [1.029–9.069]; P = .044 and OR, 1.924 [1.252–2.957]; P = .003) while IFNL4 genotypes represented independent factors for becoming non-LTNP-C (TT/TT, ss469415590; OR, 0.401 [0.171–0.942]; P = .036 or A/A, rs12980275; OR, 0.637 [0.434–0.934]; P = .021) in the Spanish and validation cohorts, respectively, after adjusting for sex, age at HIV-1 diagnosis, IFNL4-related polymorphisms, and different HLA-B haplotypes. LTNP-Cs showed lower plasma induced protein 10 (P = .019) and higher IFN-γ (P = .02) levels than the HIV-1 controllers with diminished CD4+ T-cell numbers. Moreover, LTNP-Cs exhibited higher quantities of interleukin (IL)2+CD57- and IFN-γ +CD57- HIV-1–specific CD8+ T cells (P = .002 and .041, respectively) than non-LTNP-Cs.

Conclusions.
We defined genetic markers able to segregate stable HIV-1 controllers from those who experience CD4+ T-cell decline. These findings allow for identification of HIV-1 controllers at risk for immunologic progression and provide avenues for personalized therapeutic interventions and precision medicine for optimizing clinical care of these individuals.
Diabetes Mellitus and Latent Tuberculosis Infection: A Systemic Review and Metaanalysis
Authors: Lee Meng-Rui , Huang Ya-Ping , Kuo Yu-Ting , Luo Chen-Hao , Shih Yun-Ju , Shu Chin-Chung , Wang Jann-Yuan , Ko Jen-Chung , Yu Chong-Jen , Lin Hsien-Ho 
Published: December 2016

Abstract

Background.
Despite the well-documented association between diabetes and active tuberculosis, evidence of the association between diabetes and latent tuberculosis infection (LTBI) remains limited and inconsistent.

Methods.
We included observational studies that applied either the tuberculin skin test or the interferon gamma release assay for diagnosis of LTBI and that provided adjusted effect estimate for the association between diabetes and LTBI. We searched PubMed and EMBASE through 31 January 2016. The risk of bias of included studies was assessed using a quality assessment tool modified from the Newcastle-Ottawa scale.

Results.
Thirteen studies (1 cohort study and 12 cross-sectional studies) were included, involving 38263 participants. The cohort study revealed an increased but nonsignificant risk of LTBI among diabetics (risk ratio, 4.40; 95% confidence interval [CI], 0.50–38.55). For the cross-sectional studies, the pooled odds ratio from the random-effects model was 1.18 (95% CI, 1.06–1.30), with a small statistical heterogeneity across studies (I2, 3.5%). The risk of bias assessment revealed several methodological issues, but the overall direction of biases would reduce the positive causal association between diabetes and LTBI.

Conclusions.
Diabetes was associated with a small but statistically significant risk for LTBI. Findings from this review could be used to inform future cost-effectiveness analysis on the impact of LTBI screening programs among diabetics.