bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome
Authors: Sze Marc A. , Schloss Patrick D. 
Published: August 2016

ABSTRACT

Two recent studies have reanalyzed previously published data and found that when data sets were analyzed independently, there was limited support for the widely accepted hypothesis that changes in the microbiome are associated with obesity. This hypothesis was reconsidered by increasing the number of data sets and pooling the results across the individual data sets. The preferred reporting items for systematic reviews and meta-analyses guidelines were used to identify 10 studies for an updated and more synthetic analysis. Alpha diversity metrics and the relative risk of obesity based on those metrics were used to identify a limited number of significant associations with obesity; however, when the results of the studies were pooled by using a random-effect model, significant associations were observed among Shannon diversity, the number of observed operational taxonomic units, Shannon evenness, and obesity status. They were not observed for the ratio of
Bacteroidetes
and
Firmicutes
or their individual relative abundances. Although these tests yielded small
P
values, the difference between the Shannon diversity indices of nonobese and obese individuals was 2.07%. A power analysis demonstrated that only one of the studies had sufficient power to detect a 5% difference in diversity. When random forest machine learning models were trained on one data set and then tested by using the other nine data sets, the median accuracy varied between 33.01 and 64.77% (median, 56.68%). Although there was support for a relationship between the microbial communities found in human feces and obesity status, this association was relatively weak and its detection is confounded by large interpersonal variation and insufficient sample sizes.

IMPORTANCE
As interest in the human microbiome grows, there is an increasing number of studies that can be used to test numerous hypotheses across human populations. The hypothesis that variation in the gut microbiota can explain or be used to predict obesity status has received considerable attention and is frequently mentioned as an example of the role of the microbiome in human health. Here we assessed this hypothesis by using 10 independent studies and found that although there is an association, it is smaller than can be detected by most microbiome studies. Furthermore, we directly tested the ability to predict obesity status on the basis of the composition of an individual’s microbiome and found that the median classification accuracy is between 33.01 and 64.77%. This type of analysis can be used to design future studies and expanded to explore other hypotheses.
A Full-Length Infectious cDNA Clone of Zika Virus from the 2015 Epidemic in Brazil as a Genetic Platform for Studies of Virus-Host Interactions and Vaccine Development
Authors: Tsetsarkin Konstantin A. , Kenney Heather , Chen Rubing , Liu Guangping , Manukyan Hasmik , Whitehead Stephen S. , Laassri Majid , Chumakov Konstantin , Pletnev Alexander G. 
Published: August 2016

ABSTRACT
An arthropod-borne virus, Zika virus (ZIKV), has recently emerged as a major human pathogen. Associated with complications during perinatal development and Guillain-Barré syndrome in adults, ZIKV raises new challenges for understanding the molecular determinants of flavivirus pathogenesis. This underscores the necessity for the development of a reverse genetic system based on an epidemic ZIKV strain. Here, we describe the generation and characterization in cell cultures of an infectious cDNA clone of ZIKV isolated from the 2015 epidemic in Brazil. The cDNA-derived ZIKV replicated efficiently in a variety of cell lines, including those of both neuronal and placental origin. We observed that the growth of cDNA-derived virus was attenuated compared to the growth of the parental isolate in most cell lines, which correlates with substantial differences in sequence heterogeneity between these viruses that were determined by deep-sequencing analysis. Our findings support the role of genetic diversity in maintaining the replicative fitness of viral populations under changing conditions. Moreover, these results indicate that caution should be exercised when interpreting the results of reverse-genetics experiments in attempts to accurately predict the biology of natural viruses. Finally, a Vero cell-adapted cDNA clone of ZIKV was generated that can be used as a convenient platform for studies aimed at the development of ZIKV vaccines and therapeutics.

IMPORTANCE
The availability of genetic tools and laboratory models determines the progress in understanding mechanisms of virus emergence and pathogenesis. Recent large-scale outbreaks of Zika virus (ZIKV) that were linked to complications during perinatal development and Guillain-Barré syndrome in adults emphasize the urgency for the development of a reverse-genetics system based on an epidemic ZIKV strain. Here, we report a stable infectious cDNA clone for ZIKV isolated during the 2015 epidemic in Brazil, as well as a Vero cell-adapted version of it, which will be used for virus-host interaction studies and vaccine development.
How to make a transverse triple junction—New evidence for the assemblage of Gondwana along the Kaoko-Damara belts, Namibia
Authors: Passchier Cees , Trouw Rudolph , da Silva Schmitt Renata 
Published: August 2016

Abstract
T-shaped orogenic triple junctions between mobile belts usually form in two unrelated stages by subsequent and oblique continental collisions separated by a significant time span. Besides these “oblique triple junctions”, another type, named “transverse triple junctions”, may exist. Such junctions are created by a more complex mechanism of partly contemporaneous convergence of three cratons in a restricted time frame, involving strike slip. The Neoproterozoic–Cambrian Kaoko-Damara junction between the Rio de la Plata, Congo, and Kalahari cratons in Namibia is an example of such a transverse orogenic triple junction, formed by at least four subsequent but partly related deformation events. Initial north-south convergence between the Congo and Kalahari cratons was followed by east-west collision of the Rio de la Plata and Congo cratons. Subsequently, the Kalahari and Congo cratons collided, contemporaneous with sinistral strike-slip motion between the Congo and Rio de la Plata cratons and with the intrusion of large granite-syenite plutons, probably associated with slab detachment aided by the strike-slip movement. Other examples of transverse triple junctions may exist in Gondwana. Transcurrent shear zones, some possibly nucleated on transform faults from the pre-collision setting, are essential for the formation of transverse triple junctions.
The influence of vegetation on debris-flow initiation during extreme rainfall in the northern Colorado Front Range
Authors: Rengers Francis K. , McGuire Luke A. , Coe Jeffrey A. , Kean Jason W. , Baum Rex L. , Staley Dennis M. , Godt Jonathan W. 
Published: August 2016

Abstract
We explored regional influences on debris-flow initiation throughout the Colorado Front Range (Colorado, USA) by exploiting a unique data set of more than 1100 debris flows that initiated during a 5 day rainstorm in 2013. Using geospatial data, we examined the influence of rain, hillslope angle, hillslope aspect, and vegetation density on debris-flow initiation. In particular we used a greenness index to differentiate areas of high tree density from grass and bare soil. The data demonstrated an overwhelming propensity for debris-flow initiation on south-facing hillslopes. However, when the debris-flow density was analyzed with respect to total rainfall and greenness we found that most debris flows occurred in areas of high rainfall and low tree density, regardless of hillslope aspect. These results indicate that present-day tree density exerts a stronger influence on debris-flow initiation locations than aspect-driven variations in soil and bedrock properties that developed over longer time scales.
Development of cutoff-related knickpoints during early evolution of submarine channels
Authors: Sylvester Zoltán , Covault Jacob A. 
Published: August 2016

Abstract
Submarine channels are often thought of as having relatively simple geometries, with significant along-channel morphologic and stratigraphic continuity. Using high-resolution seismic reflection data from offshore Angola and a kinematic model of channel evolution, we present evidence that channels on the seafloor can develop slope variability as a result of meander cutoff events. When cutoffs develop, the shortened flow paths produce locally steep gradients, thus initiating knickpoints. Waves of knickpoint retreat and the related channel incision explain the occurrence of terraces and associated remnant channel deposits above the youngest channel thalweg. The simple processes of meander cutoff followed by knickpoint retreat are intrinsic to submarine channels and result in significant morphologic variability, erosion, and stratigraphic complexity, without any external forcing. These insights highlight the early evolution of submarine channels, a phase with a record that is commonly fragmented or completely absent as a result of subsequent erosion, and allow a better understanding of the autogenic controls on deep-marine stratigraphy.
Antibiotic use and clinical outcomes in the acute setting under management by an infectious diseases acute physician versus other clinical teams: a cohort study
Authors: Fawcett Nicola JK , Jones Nicola , Quan T Phuong , Mistry Vikash , Crook Derrick , Peto Tim , Walker A Sarah 
Published: August 2016

ObjectivesTo assess the magnitude of difference in antibiotic use between clinical teams in the acute setting and assess evidence for any adverse consequences to patient safety or healthcare delivery.DesignProspective cohort study (1 week) and analysis of linked electronic health records (3 years).SettingUK tertiary care centre.ParticipantsAll patients admitted sequentially to the acute medical service under an infectious diseases acute physician (IDP) and other medical teams during 1 week in 2013 (n=297), and 3 years 2012–2014 (n=47 585).Primary outcome measureAntibiotic use in days of therapy (DOT): raw group metrics and regression analysis adjusted for case mix.Secondary outcome measures30-day all-cause mortality, treatment failure and length of stay.ResultsAntibiotic use was 173 vs 282 DOT/100 admissions in the IDP versus non-IDP group. Using case mix-adjusted zero-inflated Poisson regression, IDP patients were significantly less likely to receive an antibiotic (adjusted OR=0.25 (95% CI 0.07 to 0.84), p=0.03) and received shorter courses (adjusted rate ratio (RR)=0.71 (95% CI 0.54 to 0.93), p=0.01). Clinically stable IDP patients of uncertain diagnosis were more likely to have antibiotics held (87% vs 55%; p=0.02). There was no significant difference in treatment failure or mortality (adjusted p>0.5; also in the 3-year data set), but IDP patients were more likely to be admitted overnight (adjusted OR=3.53 (95% CI 1.24 to 10.03), p=0.03) and have longer length of stay (adjusted RR=1.19 (95% CI 1.05 to 1.36), p=0.007).ConclusionsThe IDP-led group used 30% less antibiotic therapy with no adverse clinical outcome, suggesting antibiotic use can be reduced safely in the acute setting. This may be achieved in part by holding antibiotics and admitting the patient for observation rather than prescribing, which has implications for costs and hospital occupancy. More information is needed to indicate whether any such longer admission will increase or decrease risk of antibiotic-resistant infections.
African Breast Cancer—Disparities in Outcomes (ABC-DO): protocol of a multicountry mobile health prospective study of breast cancer survival in sub-Saharan Africa
Authors: McKenzie Fiona , Zietsman Annelle , Galukande Moses , Anele Angelica , Adisa Charles , Cubasch Herbert , Parham Groesbeck , Anderson Benjamin O , Abedi-Ardekani Behnoush , Schuz Joachim , dos Santos Silva Isabel , McCormack Valerie 
Published: August 2016

IntroductionSub-Saharan African (SSA) women with breast cancer (BC) have low survival rates from this potentially treatable disease. An understanding of context-specific societal, health-systems and woman-level barriers to BC early detection, diagnosis and treatment are needed.MethodsThe African Breast Cancer—Disparities in Outcomes (ABC-DO) is a prospective hospital-based study of overall survival, impact on quality of life (QOL) and delays along the journey to diagnosis and treatment of BC in SSA. ABC-DO is currently recruiting in Namibia, Nigeria, South Africa, Uganda and Zambia. Women aged 18 years or older who present at participating secondary and tertiary hospitals with a new clinical or histocytological diagnosis of primary BC are invited to participate. For consented women, tumour characteristics, specimen and treatment data are obtained. Over a 2-year enrolment period, we aim to recruit 2000 women who, in the first instance, will be followed for between 1 and 3 years. A face-to-face baseline interview obtains information on socioeconomic, cultural and demographic factors, QOL, health and BC attitudes/knowledge, and timing of all prediagnostic contacts with caregivers in orthodox health, traditional and spiritual systems. Responses are immediately captured on mobile devices that are fed into a tailored mobile health (mHealth) study management system. This system implements the study protocol, by prompting study researchers to phone women on her mobile phone every 3 months and, failing to reach her, prompts contact with her next-of-kin. At follow-up calls, women provide updated information on QOL, care received and disease impacts on family and working life; date of death is asked of her next-of-kin when relevant.Ethics and disseminationThe study was approved by ethics committees of all involved institutions. All participants provide written informed consent. The findings from the study will be published in peer-reviewed scientific journals, presented to funders and relevant local organisations and at scientific conferences.
Maternal morbidity and mortality from severe sepsis: a national cohort study
Authors: Acosta Colleen D , Harrison David A , Rowan Kathy , Lucas D Nuala , Kurinczuk Jennifer J , Knight Marian 
Published: August 2016

ObjectivesTo describe the incidence, characteristics and risk factors for critical care admission with severe maternal sepsis in the UK.DesignNational cohort study.Setting198 critical care units in the UK.Participants646 pregnant and recently pregnant women who had severe sepsis within the first 24 hours of admission in 2008–2010.Primary and secondary outcome measuresSeptic shock, mortality.ResultsOf all maternal critical care admissions, 14.4% (n=646) had severe sepsis; 10.6% (n=474) had septic shock. The absolute risk of maternal critical care admission with severe sepsis was 4.1/10 000 maternities. Pneumonia/respiratory infection (irrespective of the H1N1 pandemic influenza strain) and genital tract infection were the most common sources of sepsis (40% and 24%, respectively). We identified a significant gradient in the risk of severe maternal sepsis associated with increasing deprivation (RR=6.5; 95% CI 4.9 to 8.5 most deprived compared with most affluent women). The absolute risk of mortality was 1.8/100 000 maternities. The most common source of infection among women who died was pneumonia/respiratory infection (41%). Known risk factors for morbidity supported by this study were: younger age, multiple gestation birth and caesarean section. Significant risk factors for mortality in unadjusted analysis were: age ≥35 years (unadjusted OR (uOR)=3.5; 95% CI 1.1 to 10.6), ≥3 organ system dysfunctions (uOR=12.7; 95% CI 2.9 to 55.1), respiratory dysfunction (uOR=6.5; 95% CI1.9 to 21.6), renal dysfunction (uOR=5.6; 95% CI 2.3 to 13.4) and haematological dysfunction (uOR=6.5; 95% CI 2.9 to 14.6).ConclusionsThis study suggests a need to improve timely recognition of severe respiratory tract and genital tract infection in the obstetric population. The social gradient associated with the risk of severe sepsis morbidity and mortality raises important questions regarding maternal health service provision and usage.
Advanced imaging in colonoscopy: contemporary approach to dysplasia surveillance in inflammatory bowel disease
Authors: Beintaris Iosif , Rutter Matt 
Published: August 2016

Inflammatory bowel disease (IBD) (ulcerative colitis (UC) and Crohn’s disease (CD)) is a chronic relapsing/remitting condition characterised by intestinal inflammation. One of the main concerns in patients with longstanding ulcerative and Crohn’s colitis is development of colonic dysplasia and colorectal cancer (CRC), a risk higher than that of the general population. Colonoscopy surveillance programmes have been developed by major societies worldwide to improve early dysplasia detection and treatment, thus preventing progression to colorectal cancer.Colonoscopy is an imperfect tool as lesions can be missed, an issue even more relevant to colitic patients, where mucosal inspection and lesion recognition may prove challenging. Extensive research has been undertaken on performance improvement in this area while technical advances in optical imaging, such as high-definition, have made their way into modern endoscopy units.Techniques and technologies available to enhance optical diagnosis of dysplasia in inflammatory bowel disease are reviewed in this paper, focusing on those that are realistic, widely available and feasible for everyday practice.
The impact of gestational weight gain in different trimesters of pregnancy on glucose challenge test and gestational diabetes
Authors: Hantoushzadeh Sedigheh , Sheikh Mahdi , Bosaghzadeh Zeynab , Ghotbizadeh Fahimeh , Tarafdari Azam , Panahi Zahra , Shariat Mamak 
Published: August 2016

AbstractPurposeAssessing the effects of excessive weight gain before pregnancy, in the first and second trimesters and in the month preceding glucose challenge test (GCT) on GCT results and gestational diabetes mellitus (GDM).Study designThis prospective cohort study evaluated 1279 pregnant women who were referred for their first prenatal visit in 2012–2015. Mother's body mass index (BMI) was recorded before pregnancy, during the first visit and every 4 weeks until 28 gestational weeks. All mothers underwent GCT at 28 weeks and when 1 h glucose ≥140 mg/dL (≥7.8 mmol/L), they were referred for a 100 g fasting glucose 3 h glucose tolerance test.ResultsObesity and being overweight prior to pregnancy were associated with 2.8-fold and 1.5-fold higher rates of developing GDM (p&lt;0.001, p=0.04) and 1.9-fold and 1.8-fold higher rates of having false-positive GCT results (p&lt;0.001). First-trimester excessive weight gain was significantly associated with false-positive GCT in women who were lean, overweight and obese before pregnancy (all p&lt;0.001). When these women kept gaining excessive weight during the subsequent period the risk of developing GDM was significantly increased regardless of their pre-pregnancy BMI (p=0.03). When these women adhered to the recommended weight gain during the subsequent period, the risk of developing GDM was not increased, however the risk of having false-positive GCT remained high (p&lt;0.001).ConclusionsElevated pre-pregnancy BMI independently increases the risk of GDM and false-positive GCT. First trimester weight gain is the most important predictor of GCT and GDM regardless of pre-pregnancy BMI. The weight gain during the subsequent period affects the risk of developing GDM only in women with excessive first-trimester weight gain.
Association between blood lead levels and blood pressures in a non-smoking healthy Korean population
Authors: Lee Kyu Rae , Ko Ki Dong , Hwang In Cheol , Suh Heuy Sun , Kim Kyoung Kon 
Published: August 2016

ABSTRACTObjectiveThe Korea National Health and Nutrition Examination Survey (KNHANES) has been performed every 3 years in Korea to help prevent cardiovascular mortality in the general population. Previous studies showed an association between blood lead levels and cardiovascular mortality. In order to assess the relationship between blood lead concentration and blood pressure in the healthy general population, we investigated whether blood lead levels were related to blood pressure in a non-smoking healthy population without any known medical diseases in the 2013 KNHANES.Methods896 (mean age 40.55±13.83 years; body mass index 23.06±3.33 kg/m2) subjects who had no known diseases were included among 8018 subjects. Exclusion criteria were: hypertension, diabetes, hyperlipidaemia, cerebrovascular events, renal insufficiency, liver cirrhosis, thyroid dysfunction, any cardiovascular or renal disease, and any malignancy. Blood pressures were measured three times by sphygmomanometers, 5 min apart. Blood pressures were then expressed as the average between the second and third values. Height, weight, waist circumferences and blood pressure, as well as total cholesterol, high density lipoprotein cholesterol, triglycerides, low density lipoprotein cholesterol, aspartate aminotransferase (AST), alanine aminotransferase (ALT), white blood cell count and blood lead levels were measured. In addition, dietary components were analysed by 24 hour recall.ResultsThe association between log blood lead levels and systolic/diastolic pressure was stronger after it was controlled for age, sex, education, body mass index (BMI), waist circumference and fasting plasma glucose (FPG) (p=0.048, 0.002). Furthermore, the association between log blood lead levels and systolic pressure (p=0.048) and diastolic pressure (p=0.002) was more evident when controlled for age, sex, education, BMI, waist circumference, FPG, AST and ALT.ConclusionsBlood lead levels are significant determinants of systolic and diastolic blood pressure in a healthy Korean population, irrespective of sociodemographic factors and metabolic derangements.
Understanding the masses and mixings of one-zero textures in 3+1 scenario
Authors: Nath Newton , Ghosh Monojit , Gupta Shivani 
Published: August 2016

We present a detailed analysis and phenomenological consequences of neutrino mass matrix, [Formula: see text], with one-zero texture in the flavor basis where the active neutrino sector is extended by one sterile neutrino (3[Formula: see text]+[Formula: see text]1 case). In particular, our aim is to explore behavior of the sterile mixing parameters in detail when one of the elements of the neutrino mass matrix goes to zero. To study this, we consider two distinct mass spectrum of the active neutrinos: (i) completely hierarchical mass spectrum with a vanishing neutrino mass and (ii) completely quasidegenerate mass spectrum. In 3[Formula: see text]+[Formula: see text]1 scenario, the low energy neutrino mass matrix, [Formula: see text], is a [Formula: see text] matrix and has 10 independent elements. Thus it can have 10 possible one-zero textures. From the earlier studies it can be inferred that, if one assumes one vanishing neutrino mass, then only seven of these [Formula: see text] are phenomenologically allowed by the current neutrino oscillation data. On the other hand, if the neutrinos are quasidegenerate then there are eight phenomenologically viable one-zero textures. In this paper, we study the correlations between the sterile mixing parameters for each of these allowed textures for both mass spectrum and also their implications on the effective Majorana mass.