bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evasion of Short Interfering RNA-Directed Antiviral Silencing in Musa acuminata Persistently Infected with Six Distinct Banana Streak Pararetroviruses
Authors: Rajeswaran Rajendran , Seguin Jonathan , Chabannes Matthieu , Duroy Pierre-Olivier , Laboureau Nathalie , Farinelli Laurent , Iskra-Caruana Marie-Line , Pooggin Mikhail M. 
Published: July 2014

ABSTRACT
Vegetatively propagated crop plants often suffer from infections with persistent RNA and DNA viruses. Such viruses appear to evade the plant defenses that normally restrict viral replication and spread. The major antiviral defense mechanism is based on RNA silencing generating viral short interfering RNAs (siRNAs) that can potentially repress viral genes posttranscriptionally through RNA cleavage and transcriptionally through DNA cytosine methylation. Here we examined the RNA silencing machinery of banana plants persistently infected with six pararetroviruses after many years of vegetative propagation. Using deep sequencing, we reconstructed consensus master genomes of the viruses and characterized virus-derived and endogenous small RNAs. Consistent with the presence of endogenous siRNAs that can potentially establish and maintain DNA methylation, the banana genomic DNA was extensively methylated in both healthy and virus-infected plants. A novel class of abundant 20-nucleotide (nt) endogenous small RNAs with 5′-terminal guanosine was identified. In all virus-infected plants, 21- to 24-nt viral siRNAs accumulated at relatively high levels (up to 22% of the total small RNA population) and covered the entire circular viral DNA genomes in both orientations. The hotspots of 21-nt and 22-nt siRNAs occurred within open reading frame (ORF) I and II and the 5′ portion of ORF III, while 24-nt siRNAs were more evenly distributed along the viral genome. Despite the presence of abundant viral siRNAs of different size classes, the viral DNA was largely free of cytosine methylation. Thus, the virus is able to evade siRNA-directed DNA methylation and thereby avoid transcriptional silencing. This evasion of silencing likely contributes to the persistence of pararetroviruses in banana plants.

IMPORTANCE
We report that DNA pararetroviruses in
Musa acuminata
banana plants are able to evade DNA cytosine methylation and transcriptional gene silencing, despite being targeted by the host silencing machinery generating abundant 21- to 24-nucleotide short interfering RNAs. At the same time, the banana genomic DNA is extensively methylated in both healthy and virus-infected plants. Our findings shed light on the siRNA-generating gene silencing machinery of banana and provide a possible explanation why episomal pararetroviruses can persist in plants whereas true retroviruses with an obligatory genome-integration step in their replication cycle do not exist in plants.
Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses
Authors: Tokarz Rafal , Williams Simon Hedley , Sameroff Stephen , Sanchez Leon Maria , Jain Komal , Lipkin W. Ian 
Published: July 2014

ABSTRACT

A wide range of bacterial pathogens have been identified in ticks, yet the diversity of viruses in ticks is largely unexplored. In the United States,
Amblyomma americanum
,
Dermacentor variabilis
, and
Ixodes scapularis
are among the principal tick species associated with pathogen transmission. We used high-throughput sequencing to characterize the viromes of these tick species and identified the presence of Powassan virus and eight novel viruses. These included the most divergent nairovirus described to date, two new clades of tick-borne phleboviruses, a mononegavirus, and viruses with similarity to plant and insect viruses. Our analysis revealed that ticks are reservoirs for a wide range of viruses and suggests that discovery and characterization of tick-borne viruses will have implications for viral taxonomy and may provide insight into tick-transmitted diseases.

IMPORTANCE
Ticks are implicated as vectors of a wide array of human and animal pathogens. To better understand the extent of tick-borne diseases, it is crucial to uncover the full range of microbial agents associated with ticks. Our current knowledge of the diversity of tick-associated viruses is limited, in part due to the lack of investigation of tick viromes. In this study, we examined the viromes of three tick species from the United States. We found that ticks are hosts to highly divergent viruses across several taxa, including ones previously associated with human disease. Our data underscore the diversity of tick-associated viruses and provide the foundation for further studies into viral etiology of tick-borne diseases.
Atomic Force Microscopy in Microbiology: New Structural and Functional Insights into the Microbial Cell Surface
Authors: Dufrêne Yves F. 
Published: July 2014

ABSTRACT
Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights.
An integrative framework for sensor-based measurement of teamwork in healthcare
Authors: Rosen Michael A , Dietz Aaron S , Yang Ting , Priebe Carey E , Pronovost Peter J 
Published: July 2014

AbstractThere is a strong link between teamwork and patient safety. Emerging evidence supports the efficacy of teamwork improvement interventions. However, the availability of reliable, valid, and practical measurement tools and strategies is commonly cited as a barrier to long-term sustainment and spread of these teamwork interventions. This article describes the potential value of sensor-based technology as a methodology to measure and evaluate teamwork in healthcare. The article summarizes the teamwork literature within healthcare, including team improvement interventions and measurement. Current applications of sensor-based measurement of teamwork are reviewed to assess the feasibility of employing this approach in healthcare. The article concludes with a discussion highlighting current application needs and gaps and relevant analytical techniques to overcome the challenges to implementation. Compelling studies exist documenting the feasibility of capturing a broad array of team input, process, and output variables with sensor-based methods. Implications of this research are summarized in a framework for development of multi-method team performance measurement systems. Sensor-based measurement within healthcare can unobtrusively capture information related to social networks, conversational patterns, physical activity, and an array of other meaningful information without having to directly observe or periodically survey clinicians. However, trust and privacy concerns present challenges that need to be overcome through engagement of end users in healthcare. Initial evidence exists to support the feasibility of sensor-based measurement to drive feedback and learning across individual, team, unit, and organizational levels. Future research is needed to refine methods, technologies, theory, and analytical strategies.
Directing the public to evidence-based online content
Authors: Cooper Crystale Purvis , Gelb Cynthia A , Vaughn Alexandra N , Smuland Jenny , Hughes Alexandra G , Hawkins Nikki A 
Published: July 2014

Abstract
To direct online users searching for gynecologic cancer information to accurate content, the Centers for Disease Control and Prevention's (CDC) ‘Inside Knowledge: Get the Facts About Gynecologic Cancer’ campaign sponsored search engine advertisements in English and Spanish. From June 2012 to August 2013, advertisements appeared when US Google users entered search terms related to gynecologic cancer. Users who clicked on the advertisements were directed to relevant content on the CDC website. Compared with the 3 months before the initiative (March–May 2012), visits to the CDC web pages linked to the advertisements were 26 times higher after the initiative began (June–August 2012) (p&lt;0.01), and 65 times higher when the search engine advertisements were supplemented with promotion on television and additional websites (September 2012–August 2013) (p&lt;0.01). Search engine advertisements can direct users to evidence-based content at a highly teachable moment—when they are seeking relevant information.
Preschoolers’ parent-rated health disparities are strongly associated with measures of adiposity in the Lifeways cohort study children
Authors: Shrivastava Aakash , Murrin Celine , Kelleher Cecily C 
Published: July 2014

ObjectiveTo examine the relationship between lifecourse factors from preschoolers’ microecosystem and their parent-reported (mother-reported) health (PRH), following them prospectively from preconception to age 5 years. To investigate if preschoolers’ body mass index (BMI) and waist circumference were associated with preschoolers’ PRH when controlled for lifecourse predictors.DesignLifeways cross-generation cohort study.SettingIreland.ParticipantsOf 1082 families, 62% mothers responded on a health and lifestyle questionnaire at follow-up. Food frequency, BMI and waist circumference were measured. There were 547 family data sets available for analysis of children's PRH.Main outcome measureMother-reported children's PRH at age 5. Associations with child's individual and familial exposures from preconception to age 5 years examined using logistic regression.ResultsIn univariate analysis, relatively positive rating of children's PRH were associated with children's lower intake of fats (OR (95% CI) 2.2 (1.1 to 4.3)), higher intake of fruits/vegetables (OR (95% CI) 2.2 (1.1 to 4.3)); as well as familial socioeconomic characteristics {higher household income (OR (95% CI) 3.0 (1.6 to 5.9)), non-entitlement to means-tested healthcare (OR (95% CI) 2.1 (1.0 to 4.3)), mothers’ higher education (OR (95% CI) 1.9 (1.0 to 3.6))}, psychosocial characteristics {father's participation in study (OR (95% CI) 2.1 (1.0 to 4.3)), mothers’ perceiving better support from partner (OR (95% CI) 2.3 (1.2 to 4.3)), children (OR (95% CI) 1.9 (1.0 to 3.7)) or relatives (OR (95% CI) 2.2 (1.1 to 4.1))}, parents’ lifestyle {mothers’ lower intake of energy (OR (95% CI) 2.2 (1.1 to 4.3)), fathers’ non-smoking status (OR (95% CI) 2.2 (1.1 to 4.4))} and parents’ health {mothers’ self-rated health relatively positive (OR (95% CI) 5.1 (2.6 to 9.9)), fathers’ self-rated health relatively positive (OR (95% CI) 3.0 (1.5 to 6.0))}.In multivariable analysis (χ2=34.2, df=21, N=303, R2 = 0.26, p<0.05), one of the two strong predictors of children's relatively positive PRH was child not being obese by International Obesity Task Force classification (OR (95% CI) 5.5 (1.4 to 21.0)), observed also using BMI (kg/m2; OR (95% CI) 0.73 (0.58 to 0.93)) or waist circumference (cm; OR (95% CI) 0.89 (0.81 to 0.98)) as continuous variables. The other significant predictor was mothers’ self-rated health relatively positive (OR (95% CI) 4.2 (1.5 to 12.2)).ConclusionsPreschoolers’ health is adversely associated with obesity and this is independent of lifecourse and social and environmental inequalities. The findings suggest that reducing childhood obesity and improving maternal health may be useful ways to improve child's global health.
Visceral leishmaniasis-associated mortality in Bangladesh: a retrospective cross-sectional study
Authors: Huda M Mamun , Chowdhury Rajib , Ghosh Debashis , Dash Aditya Prasad , Bhattacharya Sujit Kumar , Mondal Dinesh 
Published: July 2014

ObjectiveTo investigate visceral leishmaniasis (VL) deaths and risk factors in two VL endemic areas of Bangladesh.DesignRetrospective cross-sectional.SettingTwo geographically and culturally different VL endemic subdistricts, Godagari in the district of Rajshahi and Trishal in the district of Mymensingh in Bangladesh, August 2009–December 2011.Participants51 094 inhabitants from randomly selected Unions in the two subdistricts.Main outcome measuresVL deaths, confirmed independently by qualified physicians using the verbal autopsy procedure ICD10 guideline.ResultsThe total number of people screened for VL deaths was 51 094 from 12 032 households from Godagari and Trishal subdistricts . About 16% of the people from Godagari were Tribals. The average age of the study population was 25.6 years (SD 18.4) and 49.7% were females. The VL case fatality rate averaged 6.12% (12/196) including 2/137 in Trishal and 10/59 in Godagari. Most of the VL deaths (9/12, 75%) occurred at home and the rest in tertiary hospitals. None of these deaths had been reported in the national VL surveillance system. The VL case fatality rate in the Tribal ethnic (22.2%) population was about 17 times higher than that in the Bangali ethnic (1.3%) population (p<0.0001). Tribal ethnicity had an 18 times (OR=18.1, 95% CI 3.6 to 90.6) higher risk for VL deaths compared with Bangali ethnicity (p<0.0001).ConclusionVL deaths were found to be high in the study areas and were under-reported. The Tribal ethnic population was at the highest risk for VL deaths. The national VL Elimination Programme should give special attention to the tribal community in the endemic areas, especially for those in Rajshahi, and should strengthen VL surveillance by including tertiary hospitals in the national surveillance system.
Prescription opioid injection and risk of hepatitis C in relation to traditional drugs of misuse in a prospective cohort of street youth
Authors: Hadland Scott E , DeBeck Kora , Kerr Thomas , Feng Cindy , Montaner Julio S , Wood Evan 
Published: July 2014

ObjectiveDespite dramatic increases in the misuse of prescription opioids, the extent to which their intravenous injection places drug users at risk of acquiring hepatitis C virus (HCV) remains unclear. We sought to compare risk of HCV acquisition from injection of prescription opioids to that from other street drugs among high-risk street youth.DesignProspective cohort study.SettingVancouver, British Columbia, Canada from September 2005 to November 2011.ParticipantsThe At-Risk Youth Study (ARYS) is a prospective cohort of drug-using adolescents and young adults aged 14–26 years. Participants were recruited through street-based outreach and snowball sampling.Primary outcome measureHCV antibody seroconversion, measured every 6 months during follow-up. Risk for seroconversion from injection of prescription opioids was compared with injection of other street drugs of misuse, including heroin, cocaine or crystal methamphetamine, using Cox proportional hazards regression controlling for age, gender and syringe sharing.ResultsBaseline HCV seropositivity was 10.6%. Among 512 HCV-seronegative youth contributing 860.2 person-years of follow-up, 56 (10.9%) seroconverted, resulting in an incidence density of 6.5/100 person-years. In bivariate analyses, prescription opioid injection (HR=3.48; 95% CI 1.57 to 7.70) predicted HCV seroconversion. However, in multivariate modelling, only injection of heroin (adjusted HR=4.56; 95% CI 2.39 to 8.70), cocaine (adjusted HR=1.88; 95% CI 1.00 to 3.54) and crystal methamphetamine (adjusted HR=2.91; 95% CI 1.57 to 5.38) remained independently associated with HCV seroconversion, whereas injection of prescription opioids did not (adjusted HR=0.94; 95% CI 0.40 to 2.21).ConclusionsAlthough misuse of prescription opioids is on the rise, traditional street drugs still posed the greatest threat of HCV transmission in this setting. Nonetheless, the high prevalence and incidence of HCV among Canadian street youth underscore the need for evidence-based drug prevention, treatment and harm reduction interventions targeting this vulnerable population.
‘This isn't what mine looked like’: a qualitative study of symptom appraisal and help seeking in people recently diagnosed with melanoma
Authors: Walter Fiona M , Birt Linda , Cavers Debbie , Scott Suzanne , Emery Jon , Burrows Nigel , Cavanagh Gina , MacKie Rona , Weller David , Campbell Christine 
Published: July 2014

ObjectiveTo explore symptom appraisal and help-seeking decisions among patients recently diagnosed with melanomas, and to compare experiences of people with ‘thinner’ (<1 mm) and ‘thicker’ (>2 mm) melanomas, as thickness at diagnosis is an important prognostic feature.MethodsIn-depth interviews with patients within 10 weeks of melanoma diagnosis explored the factors impacting on their pathways to diagnosis. Framework analysis, underpinned by the Model of Pathways to Treatment, was used to explore the data with particular focus on patients’ beliefs and experiences, disease factors, and healthcare professional (HCP) influences.Results63 patients were interviewed (29–93 years, 31 women, 30 thicker melanomas). All described their skin changes using rich lay vocabulary. Many included unassuming features such as ‘just a little spot’ as well as common features of changes in size, colour and shape. There appeared to be subtly different patterns of symptoms: descriptions of vertical growth, bleeding, oozing and itch were features of thicker melanomas irrespective of pathological type. Appraisal was influenced by explanations such as normal life changes, prior beliefs and whether skin changes matched known melanoma descriptions. Most decisions to seek help were triggered by common factors such as advice from family and friends. 11 patients reported previous reassurance about their skin changes by a HCP, with little guidance on monitoring change or when it would be appropriate to re-consult.ConclusionsPatients diagnosed with both thinner and thicker melanomas often did not initially recognise or interpret their skin changes as warning signs or prompts to seek timely medical attention. The findings provide guidance for melanoma awareness campaigns on more appropriate images, helpful descriptive language and the need to stress the often apparently innocuous nature of potentially serious skin changes. The importance of appropriate advice, monitoring and safety-netting procedures by HCPs for people presenting with skin changes is also highlighted.
Tea consumption and risk of type 2 diabetes mellitus: a systematic review and meta-analysis update
Authors: Yang Jian , Mao Qun-Xia , Xu Hong-Xia , Ma Xu , Zeng Chun-Yu 
Published: July 2014

ObjectiveTea has been suggested to decrease blood glucose levels and protect pancreatic β cells in diabetic mice. However, human epidemiological studies showed inconsistent results for the association between tea consumption and type 2 diabetes mellitus (T2DM) risk. The aim of this study was to conduct a meta-analysis to further explore the association between tea consumption and incidence of T2DM.DesignSystematic review and meta-analysis.MethodsWe performed a systematic literature search up to 30 August 2013 in PubMed, EMBASE, Chinese Wanfang Database and CNKI database. Pooling relative risks (RRs) were estimated by random-effect models. Two kinds of subgroup analyses (according to sex and regions) were performed. Sensitive analyses were performed according to types of tea.ResultsOverall, no statistically significant relationship between tea consumption and risk of T2DM was found based on 12 eligible studies (pooling RR 0.99, 95% CI 0.95 to 1.03). Compared with the lowest/non-tea group, daily tea consumption (≥3 cups/day) was associated with a lower T2DM risk (RR 0.84, 95% CI 0.73 to 0.97). Subgroup analyses showed a difference between men and women. Overall, the RRs (95% CI) were 0.92 (0.84 to 1.00) for men, and 1.00 (0.96 to 1.05) for women, respectively. Tea consumption of ≥3 cups/day was associated with decreased T2DM risk in women (RR 0.84, 95% CI 0.71 to 1.00). Overall, the RRs (95% CIs) were 0.84 (0.71 to 1.00) for Asians, and 1.00 (0.97 to 1.04) for Americans and Europeans, respectively. No obvious change was found in sensitivity analyses.ConclusionsThe results suggest that daily tea consumption (≥3 cups/day) is associated with a lower T2DM risk. However, further studies are needed to enrich related evidence, especially with regard to types of tea or sex.
A combined teamwork training and work standardisation intervention in operating theatres: controlled interrupted time series study
Authors: Morgan Lauren , Pickering Sharon P , Hadi Mohammed , Robertson Eleanor , New Steve , Griffin Damian , Collins Gary , Rivero-Arias Oliver , Catchpole Ken , McCulloch Peter 
Published: July 2014

BackgroundTeamwork training and system standardisation have both been proposed to reduce error and harm in surgery. Since the approaches differ markedly, there is potential for synergy between them.MethodsDesign:Controlled interrupted time series with a 3 month intervention and observation phases before and after.Setting:Operating theatres conducting elective orthopaedic surgery in a single hospital system (UK Hospital Trust).Intervention:Teamwork training based on crew resource management plus training and follow-up support in developing standardised operating procedures. Focus of subsequent standardisation efforts decided by theatre staff.Measures:Paired observers watched whole procedures together. We assessed non-technical skills using NOTECHS II, technical performance using glitch rate and compliance with WHO checklist using a simple quality tool. We measured complication and readmission rates and hospital stay using hospital administrative records. Before/after change was compared in the active and control groups using two-way ANOVA and regression models.Results1121 patients were operated on before and 1100 after intervention. 44 operations were observed before and 50 afterwards. Non-technical skills (p=0.002) and WHO compliance (p<0.001) improved significantly after the intervention in the active versus the control group. Glitch count improved in both groups and there was no significant effect on clinical outcomes.DiscussionCombined training in teamwork and system improvement causes marked improvements in team behaviour and WHO performance, but not technical performance or outcome. These findings are consistent with the synergistic hypothesis, but larger controlled studies with a strong implementation strategy are required to test potential outcome effects.