bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR
Authors: Luo Jun , Li Junhua , Yang Hang , Yu Junping , Wei Hongping 
Published: July 2017

ABSTRACT

Accurate and rapid identification of methicillin-resistant
Staphylococcus aureus
(MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible
S. aureus
(MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of
nuc
and
mecA
markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers (
nuc
and
mecA
) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of
Escherichia coli
, MSSA, and other
mecA
-positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens.
The Translesion Polymerase Pol η Is Required for Efficient Epstein-Barr Virus Infectivity and Is Regulated by the Viral Deubiquitinating Enzyme BPLF1
Authors: Dyson Ossie F. , Pagano Joseph S. , Whitehurst Christopher B. 
Published: July 2017

ABSTRACT

Epstein-Barr virus (EBV) infection and lytic replication are known to induce a cellular DNA damage response. We previously showed that the virally encoded BPLF1 protein interacts with and regulates several members of the translesion synthesis (TLS) pathway, a DNA damage tolerance pathway, and that these cellular factors enhance viral infectivity. BPLF1 is a late lytic cycle gene, but the protein is also packaged in the viral tegument, indicating that BPLF1 may function both early and late during infection. The BPLF1 protein expresses deubiquitinating activity that is strictly conserved across the
Herpesviridae
; mutation of the active site cysteine results in a loss of enzymatic activity. Infection with an EBV BPLF1 knockout virus results in decreased EBV infectivity. Polymerase eta (Pol η), a specialized DNA repair polymerase, functions in TLS and allows for DNA replication complexes to bypass lesions in DNA. Here we report that BPLF1 interacts with Pol η and that Pol η protein levels are increased in the presence of functional BPLF1. BPLF1 promotes a nuclear relocalization of Pol η molecules which are focus-like in appearance, consistent with the localization observed when Pol η is recruited to sites of DNA damage. Knockdown of Pol η resulted in decreased production of infectious virus, and further, Pol η was found to bind to EBV DNA, suggesting that it may allow for bypass of damaged viral DNA during its replication. The results suggest a mechanism by which EBV recruits cellular repair factors, such as Pol η, to sites of viral DNA damage via BPLF1, thereby allowing for efficient viral DNA replication.

IMPORTANCE
Epstein-Barr virus is the causative agent of infectious mononucleosis and infects approximately 90% of the world's population. It causes lymphomas in individuals with acquired and innate immune disorders and is strongly associated with Hodgkin's lymphoma, Burkitt's lymphoma, diffuse large B-cell lymphomas, nasopharyngeal carcinoma (NPC), and lymphomas that develop in organ transplant recipients. Cellular DNA damage is a major determinant in the establishment of oncogenic processes and is well studied, but there are few studies of endogenous repair of viral DNA. This work evaluates how EBV's BPLF1 protein and its conserved deubiquitinating activity regulate the cellular DNA repair enzyme polymerase eta and recruit it to potential sites of viral damage and replication, resulting in enhanced production of infectious virus. These findings help to establish how EBV enlists and manipulates cellular DNA repair factors during the viral lytic cycle, contributing to efficient infectious virion production.
Simian T Lymphotropic Virus 1 Infection of Papio anubis:taxSequence Heterogeneity and T Cell Recognition
Authors: Termini James M. , Magnani Diogo M. , Maxwell Helen S. , Lauer William , Castro Iris , Pecotte Jerilyn , Barber Glen N. , Watkins David I. , Desrosiers Ronald C. 
Published: July 2017

ABSTRACTBaboons naturally infected with simian T lymphotropic virus (STLV) are a potentially useful model system for the study of vaccination against human T lymphotropic virus (HTLV). Here we expanded the number of available full-length baboon STLV-1 sequences from one to three and related the T cell responses that recognize the immunodominant Tax protein to thetaxsequences present in two individual baboons. Continuously growing T cell lines were established from two baboons, animals 12141 and 12752. Next-generation sequencing (NGS) of complete STLV genome sequences from these T cell lines revealed them to be closely related but distinct from each other and from the baboon STLV-1 sequence in the NCBI sequence database. Overlapping peptides corresponding to each unique Tax sequence and to the reference baboon Tax sequence were used to analyze recognition by T cells from each baboon using intracellular cytokine staining (ICS). Individual baboons expressed more gamma interferon and tumor necrosis factor alpha in response to Tax peptides corresponding to their own STLV-1 sequence than in response to Tax peptides corresponding to the reference baboon STLV-1 sequence. Thus, our analyses revealed distinct but closely related STLV-1 genome sequences in two baboons, extremely low heterogeneity of STLV sequences within each baboon, no evidence for superinfection within each baboon, and a ready ability of T cells in each baboon to recognize circulating Tax sequences. While amino acid substitutions that result in escape from CD8+T cell recognition were not observed, premature stop codons were observed in 7% and 56% oftaxsequences from peripheral blood mononuclear cells from animals 12141 and 12752, respectively.IMPORTANCEIt has been estimated that approximately 100,000 people suffer serious morbidity and 10,000 people die each year from the consequences associated with human T lymphotropic virus (HTLV) infection. There are no antiviral drugs and no preventive vaccine. A preventive vaccine would significantly impact the global burden associated with HTLV infections. Here we provide fundamental information on the simian T lymphotropic virus (STLV) naturally transmitted in a colony of captive baboons. The limited viral sequence heterogeneity in individual baboons, the identity of the viral gene product that is the major target of cellular immune responses, the persistence of viral amino acid sequences that are the major targets of cellular immune responses, and the emergencein vivoof truncated variants in the major target of cellular immune responses all parallel what are seen with HTLV infection of humans. These results justify the use of STLV-infected baboons as a model system for vaccine development efforts.
Predictive imaging biomarkers relevant for functional and anatomical outcomes during ranibizumab therapy of diabetic macular oedema
Authors: Gerendas Bianca S , Prager Sonja , Deak Gabor , Simader Christian , Lammer Jan , Waldstein Sebastian M , Guerin Tadhg , Kundi Michael , Schmidt-Erfurth Ursula Margarethe 
Published: July 2017

Background/aimsThe objective is to identify imaging biomarkers in optical coherence tomography predicting functional/anatomical outcomes in diabetic macular oedema (DMO).MethodsThe presented study is a post hoc analysis of the RESTORE/RESTORE-extension studies. Best-corrected visual acuity (BCVA) was analysed using general estimating equation models using treatment group/morphological features as predictor variables. In addition, linear multiple regression models analysed BCVA gain up to 12 and 36 months with BCVA/morphological baseline characteristics as independent predictor variables. The correlations between central retinal thickness (CRT)/BCVA were calculated as Spearman’s/Pearson’s correlation coefficients.ResultsA weak negative linear correlation between CRT/BCVA was observed in all study arms at baseline (r=−0.34, p<0.001) and at month 36 (r=−0.26, p<0.001). Patients with baseline height of intraretinal cystoid fluid (IRC) ≤380 µm had better baseline BCVA compared with patients with IRC height >380 µm (64.84±10.63 vs 61.66±9.92 letters; p=0.0071, respectively), which was maintained until the end of month 12 (70.5±12.33 vs 67.0±14.09 letters; p=0.0252, respectively). With laser, there was a trend for patients with subretinal fluid (SRF) at baseline to lose BCVA letters at month 12 (−5.38±16.54 vs 2.49±9.72 letters; p=0.1038), whereas ranibizumab patients trended towards higher BCVA gains (10.28±7.14 vs 6.76±7.67; p=0.0563), compared with those without SRF. With combined therapy, all patients had similar BCVA gains regardless of SRF (p=0.3768).ConclusionWith ranibizumab treatment, the height of IRC spaces at baseline was a better predictor of functional/anatomical improvement than CRT alone. There was also a trend for SRF to show a positive impact on ranibizumab therapy response and a negative impact on laser therapy response.
Sedentary time in older adults: a critical review of measurement, associations with health, and interventions
Authors: Copeland Jennifer L , Ashe Maureen C , Biddle Stuart JH , Brown Wendy J , Buman Matthew P , Chastin Sebastien , Gardiner Paul A , Inoue Shigeru , Jefferis Barbara J , Oka Koichiro , Owen Neville , Sardinha Luís B , Skelton Dawn A , Sugiyama Takemi , Dogra Shilpa 
Published: July 2017

Sedentary time (ST) is an important risk factor for a variety of health outcomes in older adults. Consensus is needed on future research directions so that collaborative and timely efforts can be made globally to address this modifiable risk factor. In this review, we examined current literature to identify gaps and inform future research priorities on ST and healthy ageing. We reviewed three primary topics:(1) the validity/reliability of self-report measurement tools, (2) the consequences of prolonged ST on geriatric-relevant health outcomes (physical function, cognitive function, mental health, incontinence and quality of life) and(3) the effectiveness of interventions to reduce ST in older adults.MethodsA trained librarian created a search strategy that was peer reviewed for completeness.ResultsSelf-report assessment of the context and type of ST is important but the tools tend to underestimate total ST. There appears to be an association between ST and geriatric-relevant health outcomes, although there is insufficient longitudinal evidence to determine a dose–response relationship or a threshold for clinically relevant risk. The type of ST may also affect health; some cognitively engaging sedentary behaviours appear to benefit health, while time spent in more passive activities may be detrimental. Short-term feasibility studies of individual-level ST interventions have been conducted; however, few studies have appropriately assessed the impact of these interventions on geriatric-relevant health outcomes, nor have they addressed organisation or environment level changes. Research is specifically needed to inform evidence-based interventions that help maintain functional autonomy among older adults.This consensus statement has been endorsed by the following societies: Academy of Geriatric Physical Therapy, Exercise & Sports Science Australia, Canadian Centre for Activity and Aging, Society of Behavioral Medicine, and the National Centre for Sport and Exercise Medicine.
Elevated incidence rates of diabetes in Peru: report from PERUDIAB, a national urban population-based longitudinal study
Authors: Seclen Segundo Nicolas , Rosas Moises Ernesto , Arias Arturo Jaime , Medina Cecilia Alexandra 
Published: July 2017

ObjectiveA recent report from a non-nationally representative, geographically diverse sample in four separate communities in Peru suggests an unusually high diabetes incidence. We aimed to estimate the national diabetes incidence rate using PERUDIAB, a probabilistic, national urban population-based longitudinal study.Research design and methods662 subjects without diabetes, selected by multistage, cluster, random sampling of households, representing the 24 administrative and the 3 (coast, highlands and jungle) natural regions across the country, from both sexes, aged 25+ years at baseline, enrolled in 2010–2012, were followed for 3.8 years. New diabetes cases were defined as fasting blood glucose ≥126 mg/dL or on medical diabetes treatment.ResultsThere were 49 cases of diabetes in 2408 person-years follow-up. The weighted cumulative incidence of diabetes was 7.2% while the weighted incidence rate was estimated at 19.5 (95% CI 13.9 to 28.3) new cases per 1000 person-years. Older age, obesity and technical or higher education were statistically associated with the incidence of diabetes.ConclusionOur results confirm that the incidence of diabetes in Peru is among the highest reported globally. The fast economic growth in the last 20 years, high overweight and obesity rates may have triggered this phenomenon.
Evaluation of a pilot police-led suicide early alert surveillance strategy in the UK
Authors: McGeechan Grant James , Richardson Catherine , Weir Kevin , Wilson Lynn , O’Neill Gillian , Newbury-Birch Dorothy 
Published: July 2017

IntroductionThose bereaved by suicide are at increased risk of psychological harm, which can be reduced with the provision of timely support. This paper outlines an evaluation of a pilot police-led suicide strategy, in comparison to a coroner-led suicide strategy looking at the number, and length of time it takes for deaths to be recorded for each strategy. Additionally, the police-led strategy offers timely contact from support services for bereaved individuals. We examined what impact this offer of support had on the capacity of support services.MethodsA mixed methods evaluation compared how long it took for suspected suicides to be recorded using both strategies. The number of referrals received by support services during the pilot strategy were compared with those from previous years. A feedback focus group, and interviews, were held with key stakeholders.ResultsThe coroner strategy was more consistent at identifying suspected suicides; however, reports were filed quicker by the police. Bereaved individuals were willing to share contact details with police officers and consent for referral to support services which lead to increased referrals. The focus group and interviews revealed that the pilot police strategy needs better integration into routine police practice.ConclusionsThis strategy has the potential to deliver a real benefit to those bereaved by suicide; however, there are still aspects which could be improved.
Absence of transforming growth factor beta 1 in murine platelets reduces neointima formation without affecting arterial thrombosis
Authors: Schütz Eva , Bochenek Magdalena L. , Riehl Dennis R. , Bosmann Markus , Münzel Thomas , Konstantinides Stavros , Schäfer Katrin 
Published: July 2017

SummaryPlatelet degranulation at the site of vascular injury prevents bleeding and may affect the chronic vascular wound healing response. Transforming Growth Factor (TGF)-β1 is a major component of platelet α-granules known to accumulating in thrombi. It was our aim to determine the role of TGFβ1 released from activated platelets for neointima formation following arterial injury and thrombosis. Mice with platelet-specific deletion of TGFβ1 (Plt.TGFβ-KO) underwent carotid artery injury. Immunoassays confirmed the absence of active TGFβ1 in platelet releasates and plasma of Plt.TGFβ-KO mice. Whole blood analyses revealed similar haematological parameters, and tail cut assays excluded major bleeding defects. Platelet aggregation and the acute thrombotic response to injury in vivo did not differ between Plt.TGFβ-KO and Plt.TGFβ-WT mice. Morphometric analysis revealed that absence of TGFβ1 in platelets resulted in a significant reduction of neointima formation with lower neointima area, intima-to-media ratio, and lumen stenosis. On the other hand, the media area was enlarged in mice lacking TGFβ1 in platelets and contained increased amounts of proteases involved in latent TGFβ activation, including MMP2, MMP9 and thrombin. Significantly increased numbers of proliferating cells and cells expressing the mesenchymal markers platelet-derived growth factor receptor-β or fibroblast-specific protein-1, and the macrophage antigen F4/80, were observed in the media of Plt.TGFβ-KO mice, whereas the medial smooth muscle-actin-immuno-positive area and collagen content did not differ between genotypes. Our findings support an essential role for platelet-derived TGFβ1 for the vascular remodelling response to arterial injury, apparently independent from the role of platelets in thrombosis or haemostasis.Supplementary Material to this article is available online at www.thrombosis-online.com.
Precipitation Characteristics over East Asia in Early Summer: Effects of the Subtropical Jet and Lower-Tropospheric Convective Instability
Authors: Yokoyama Chie , Takayabu Yukari N. , Horinouchi Takeshi 
Published: July 2017

Abstract
A quasi-stationary front, called the baiu front, often appears during the early-summer rainy season in East Asia (baiu in Japan). The present study examines how precipitation characteristics during the baiu season are determined by the large-scale environment, using satellite observation three-dimensional precipitation data. Emphasis is placed on the effect of subtropical jet (STJ) and lower-tropospheric convective instability (LCI).
A rainband appears together with a deep moisture convergence to the south of the STJ. Two types of mesoscale rainfall events (REs; contiguous rainfall areas), which are grouped by the stratiform precipitation ratio (SPR; stratiform precipitation over total precipitation), are identified: moderately stratiform REs (SPR of 0%–80%) representing tropical organized precipitation systems and highly stratiform REs (SPR of 80%–100%) representing midlatitude precipitation systems associated with extratropical cyclones. As the STJ becomes strong, rainfall from both types of mesoscale precipitation systems increases, with a distinct eastward extension of a midtropospheric moist region. In contrast, small systems appear regardless of the STJ, with high dependency on the LCI.
The results indicate that the STJ plays a role in moistening the midtroposphere owing to ascent associated with secondary circulation to the south of the STJ, producing environments favorable for organized precipitation systems in the southern part of the rainband. The horizontal moisture flux convergence may also contribute to precipitation just along the STJ. On the other hand, the LCI plays a role in generating shallow convection. In high-LCI conditions, deep convection can occur without the aid of mesoscale organization.
Weakening of the Tropical Atmospheric Circulation Response to Local Sea Surface Temperature Anomalies under Global Warming
Authors: Huang Ping , Chen Dong , Ying Jun 
Published: July 2017

Abstract
In the tropics, the atmospheric circulation response to sea surface temperature (SST) anomalies is a crucial part of the tropical air–sea interaction—the primary process of tropical climate. How it will change under global warming is of great importance to tropical climate change. Here, it is shown that the atmospheric vertical circulation response to local SST anomalies will likely be weakened under global warming using 28 selected models from phase 5 of the Coupled Model Intercomparison Project. The weakening of the circulation response to SST anomalies is closely tied to the increased atmospheric stability under global warming, which increases at the same rate as the circulation response decreases—around 8% for 1 K of tropical-mean SST warming. The spatial pattern of background warming can modify—especially in the equatorial central-eastern Pacific—the spatial distribution of the changes in the circulation response. The atmospheric response to SST anomalies may increase where the local background warming is pronouncedly greater than the tropical mean. The general weakening of the atmospheric circulation response to SST anomalies leads to a decreased circulation response to the structured variability of tropical SST anomalies, such as the El Niño–Southern Oscillation and the Indian Ocean dipole. The decreased circulation response will offset some of the enhancement of the tropical rainfall response to these SST modes as a result of global-warming-induced moisture increase and also implies a decreased amplitude of the tropical air–sea interaction modes.
Multifractal Analysis of Snowfall Recorded Using a 2D Video Disdrometer
Authors: Raupach Timothy H. , Gires Auguste , Tchiguirinskaia Ioulia , Schertzer Daniel , Berne Alexis 
Published: July 2017

Abstract
Universal multifractal (UM) analysis was used to investigate the scaling properties of snowfall at high temporal and spatial resolutions. Snowfall data were recorded using a 2D video disdrometer (2DVD) in the Swiss Alps. Six 1-h-long periods of snowfall, half in calm and half in light wind conditions, were selected for analysis. UM analysis was performed on reconstructed 35-m vertical columns of snowfall structure, snowfall time series at 100-ms resolution, and two-dimensional snowflake accumulation maps over a 5.12 5.12 cm2 area. Multifractal scaling was observed for the vertical structure of snow particle number concentration, for scales between about 35 and 4.4 m, and sometimes down to about 0.5 m. At smaller scales, no scaling was observed. In high-resolution time series of snowfall, evidence of scaling was found for scales between about 7 min and ~26 s in most of the analyzed hours. Snowflake accumulations within a subset of the small sampling area of the 2DVD showed no scaling properties, suggesting homogeneous structure in snowfall at the very small (~5 cm) scale, which agrees with the results for vertical structure and time series.
A Fetch-Based Statistical Method to Bias Correct and Downscale Wind Speed over Unresolved Water Bodies
Authors: Holman Bryan P. , Lazarus Steven M. , Splitt Michael E. 
Published: July 2017

Abstract
This paper presents a method to bias correct and downscale wind speed over water bodies that are unresolved by numerical weather prediction (NWP) models and analyses. The dependency of wind speeds over water bodies to fetch length is investigated as a predictor of model wind speed error. Because model bias is found to be related to the forecast wind direction, a statistical method that uses the forecast fetch to remove wind speed bias is developed and tested. The method estimates wind speed bias using recent forecast errors from similar stations (i.e., those with comparable fetch lengths). As a result, the bias correction is not tied to local observations but instead to locations with similar land–water characteristics. Thus, it can also be used to downscale wind fields over inland and coastal water bodies. The fetch method is compared to four reference bias correction methods using one year’s worth of wind speed output from three NWP analyses in Florida. The fetch method yields a bias error near zero and results in a reduction of the mean absolute error that is comparable to the reference methods. The fetch method is then used to bias correct and downscale a coarse analysis to 500-m grid spacing over a coastal estuary in central Florida.