bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Identification of Urinary Tract Pathogens from Urine Samples, Combining Urine Screening Methods and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Íñigo Melania , Coello Andreu , Fernández-Rivas Gema , Rivaya Belén , Hidalgo Jessica , Quesada María Dolores , Ausina Vicente 
Published: January 2016

ABSTRACT

Early diagnosis of urinary tract infections (UTIs) is essential to avoid inadequate or unnecessary empirical antibiotic therapy. Microbiological confirmation takes 24 to 48 h. The use of screening methods, such as cytometry and automated microscopic analysis of urine sediment, allows the rapid prediction of negative samples. In addition, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a widely established technique in clinical microbiology laboratories used to identify microorganisms. We evaluated the ability of MALDI-TOF MS to identify microorganisms from direct urine samples and the predictive value of automated analyzers for the identification of microorganisms in urine by MALDI-TOF MS. A total of 451 urine samples from patients with suspected UTIs were first analyzed using the Sysmex UF-1000
i
flow cytometer, an automatic sediment analyzer with microscopy (SediMax), culture, and then processed by MALDI-TOF MS with a simple triple-centrifuged procedure to obtain a pellet that was washed and centrifuged and finally applied directly to the MALDI-TOF MS plate. The organisms in 336 samples were correctly identified, mainly those with Gram-negative bacteria (86.10%). No microorganisms were misidentified, and no
Candida
spp. were correctly identified. Regarding the data from autoanalyzers, the best bacteriuria cutoffs were 1,000 and 200 U/μl for UF-1000
i
and SediMax, respectively. It was concluded that the combination of a urine screening method and MALDI-TOF MS provided a reliable identification from urine samples, especially in those containing Gram-negative bacteria.
Development and Validation of a Highly Accurate Quantitative Real-Time PCR Assay for Diagnosis of Bacterial Vaginosis
Authors: Hilbert David W. , Smith William L. , Chadwick Sean G. , Toner Geoffrey , Mordechai Eli , Adelson Martin E. , Aguin Tina J. , Sobel Jack D. , Gygax Scott E. 
Published: January 2016

ABSTRACT

Bacterial vaginosis (BV) is the most common gynecological infection in the United States. Diagnosis based on Amsel's criteria can be challenging and can be aided by laboratory-based testing. A standard method for diagnosis in research studies is enumeration of bacterial morphotypes of a Gram-stained vaginal smear (i.e., Nugent scoring). However, this technique is subjective, requires specialized training, and is not widely available. Therefore, a highly accurate molecular assay for the diagnosis of BV would be of great utility. We analyzed 385 vaginal specimens collected prospectively from subjects who were evaluated for BV by clinical signs and Nugent scoring. We analyzed quantitative real-time PCR (qPCR) assays on DNA extracted from these specimens to quantify nine organisms associated with vaginal health or disease:
Gardnerella vaginalis
,
Atopobium vaginae
, BV-associated bacteria 2 (BVAB2, an uncultured member of the order
Clostridiales
),
Megasphaera
phylotype 1 or 2,
Lactobacillus iners
,
Lactobacillus crispatus
,
Lactobacillus gasseri
, and
Lactobacillus jensenii
. We generated a logistic regression model that identified
G. vaginalis
,
A. vaginae
, and
Megasphaera
phylotypes 1 and 2 as the organisms for which quantification provided the most accurate diagnosis of symptomatic BV, as defined by Amsel's criteria and Nugent scoring, with 92% sensitivity, 95% specificity, 94% positive predictive value, and 94% negative predictive value. The inclusion of
Lactobacillus
spp. did not contribute sufficiently to the quantitative model for symptomatic BV detection. This molecular assay is a highly accurate laboratory tool to assist in the diagnosis of symptomatic BV.
Suppression of Type I Interferon Production by Human T-Cell Leukemia Virus Type 1 Oncoprotein Tax through Inhibition of IRF3 Phosphorylation
Authors: Yuen Chun-Kit , Chan Ching-Ping , Fung Sin-Yee , Wang Pei-Hui , Wong Wan-Man , Tang Hei-Man Vincent , Yuen Kit-San , Chan Chi-Ping , Jin Dong-Yan , Kok Kin-Hang 
Published: January 2016

ABSTRACT

Infection with human T-cell leukemia virus type 1 (HTLV-1) is associated with adult T-cell leukemia (ATL) and tropical spastic paraparesis. Type I interferons (IFNs) are key effectors of the innate antiviral response, and IFN-α combined with the nucleoside reverse transcriptase inhibitor zidovudine is considered the standard first-line therapy for ATL. HTLV-1 oncoprotein Tax is known to suppress innate IFN production and response but the underlying mechanisms remain to be fully established. In this study, we report on the suppression of type I IFN production by HTLV-1 Tax through interaction with and inhibition of TBK1 kinase that phosphorylates IRF3. Induced transcription of IFN-β was severely impaired in HTLV-1-transformed ATL cells and freshly infected T lymphocytes. The ability to suppress IRF3 activation was ascribed to Tax. The expression of Tax alone sufficiently repressed the induction of IFN production by RIG-I plus PACT, cGAMP synthase plus STING, TBK1, IKKε, IRF3, and IRF7, but not by IRF3-5D, a dominant-active phosphomimetic mutant. This suggests that Tax perturbs IFN production at the step of IRF3 phosphorylation. Tax mutants deficient for CREB or NF-κB activation were fully competent in the suppression of IFN production. Coimmunoprecipitation experiments confirmed the association of Tax with TBK1, IKKε, STING, and IRF3.
In vitro
kinase assay indicated an inhibitory effect of Tax on TBK1-mediated phosphorylation of IRF3. Taken together, our findings suggested a new mechanism by which HTLV-1 oncoprotein Tax circumvents the production of type I IFNs in infected cells. Our findings have implications in therapeutic intervention of ATL.

IMPORTANCE
Human T-cell leukemia virus type 1 (HTLV-1) is the cause of adult T-cell leukemia (ATL), an aggressive and fatal blood cancer, as well as another chronic disabling disease of the spinal cord. Treatments are unsatisfactory, and options are limited. A combination of antiviral cellular protein alpha interferon and zidovudine, which is an inhibitor of a viral enzyme called reverse transcriptase, has been recommended as the standard first-line therapy for ATL. Exactly how HTLV-1 interacts with the cellular machinery for interferon production and action is not well understood. Our work sheds light on the mechanism of action for the inhibition of interferon production by an HTLV-1 oncogenic protein called Tax. Our findings might help to improve interferon-based anti-HTLV-1 and anti-ATL therapy.
Induction of Epstein-Barr Virus Oncoprotein LMP1 by Transcription Factors AP-2 and Early B Cell Factor
Authors: Murata Takayuki , Noda Chieko , Narita Yohei , Watanabe Takahiro , Yoshida Masahiro , Ashio Keiji , Sato Yoshitaka , Goshima Fumi , Kanda Teru , Yoshiyama Hironori , Tsurumi Tatsuya , Kimura Hiroshi 
Published: January 2016

ABSTRACT
Latent membrane protein 1 (LMP1) is a major oncogene essential for primary B cell transformation by Epstein-Barr virus (EBV). Previous studies suggested that some transcription factors, such as PU.1, RBP-Jκ, NF-κB, and STAT, are involved in this expression, but the underlying mechanism is unclear. Here, we identified binding sites for PAX5, AP-2, and EBF in the proximal LMP1 promoter (ED-L1p). We first confirmed the significance of PU.1 and POU domain transcription factor binding for activation of the promoter in latency III. We then focused on the transcription factors AP-2 and early B cell factor (EBF). Interestingly, among the three AP-2-binding sites in the LMP1 promoter, two motifs were also bound by EBF. Overexpression, knockdown, and mutagenesis in the context of the viral genome indicated that AP-2 plays an important role in LMP1 expression in latency II in epithelial cells. In latency III B cells, on the other hand, the B cell-specific transcription factor EBF binds to the ED-L1p and activates LMP1 transcription from the promoter.

IMPORTANCE
Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) is crucial for B cell transformation and oncogenesis of other EBV-related malignancies, such as nasopharyngeal carcinoma and T/NK lymphoma. Its expression is largely dependent on the cell type or condition, and some transcription factors have been implicated in its regulation. However, these previous reports evaluated the significance of specific factors mostly by reporter assay. In this study, we prepared point-mutated EBV at the binding sites of such transcription factors and confirmed the importance of AP-2, EBF, PU.1, and POU domain factors. Our results will provide insight into the transcriptional regulation of the major oncogene LMP1.
Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism
Authors: Guo Peixuan , Noji Hiroyuki , Yengo Christopher M. , Zhao Zhengyi , Grainge Ian 
Published: January 2016

SUMMARY

The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (
http://rnanano.osu.edu/movie.html
), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including F
o
F
1
ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.
Can HIV reverse transcriptase activity assay be a low-cost alternative for viral load monitoring in resource-limited settings?
Authors: Gupta Soham , Palchaudhuri Riya , Neogi Ujjwal , Srinivasa Hiresave , Ashorn Per , De Costa Ayesha , Källander Clas , Shet Anita 
Published: January 2016

ObjectiveTo evaluate the performance and cost of an HIV reverse transcriptase-enzyme activity (HIV-RT) assay in comparison to an HIV-1 RNA assay for routine viral load monitoring in resource limited settings.DesignA cohort-based longitudinal study.SettingTwo antiretroviral therapy (ART) centres in Karnataka state, South India, providing treatment under the Indian AIDS control programme.ParticipantsA cohort of 327 HIV-1-infected Indian adult patients initiating first-line ART.Outcome measuresPerformance and cost of an HIV-RT assay (ExaVir Load V3) in comparison to a gold standard HIV-1 RNA assay (Abbott m2000rt) in a cohort of 327 Indian patients before (WK00) and 4 weeks (WK04) after initiation of first-line therapy.ResultsPlasma viral load was determined by an HIV-1 RNA assay and an HIV-RT assay in 629 samples (302 paired samples and 25 single time point samples at WK00) obtained from 327 patients. Overall, a strong correlation of r=0.96 was observed, with good correlation at WK00 (r=0.84) and at WK04 (r=0.77). Bland-Altman analysis of all samples showed a good level of agreement with a mean difference (bias) of 0.22 log10copies/mL. The performance of ExaVir Load V3 was not negatively affected by a nevirapine/efavirenz based antiretroviral regimen. The per test cost of measuring plasma viral load by the Abbott m2000rt and ExaVir Load V3 assays in a basic lab setting was $36.4 and $16.8, respectively.ConclusionsThe strong correlation between the HIV-RT and HIV-1 RNA assays suggests that the HIV-RT assay can be an affordable alternative option for monitoring patients on antiretroviral therapy in resource-limited settings.Trial registration numberISRCTN79261738.
Independent predictors of major adverse cardiovascular events in emergency department patients who are hospitalised with a suspected infection: a retrospective cohort study
Authors: de Groot Bas , van den Berg Stefanie , Kessler Joanne , Ansems Annemieke , Rijpsma Douwe 
Published: January 2016

ObjectiveEmergency department (ED) patients hospitalised with a suspected infection have an increased risk for major adverse cardiovascular events (MACE). This study aims to identify independent predictors of MACE after hospital admission which could be used for identification of high-risk patients who may benefit from preventive strategies.SettingDutch tertiary care centre and urban hospital.ParticipantsConsecutive, hospitalised, ED patients with a suspected infection.DesignThis was a secondary analysis using an existing database in which consecutive, hospitalised, ED patients with a suspected infection were prospectively enrolled. Potential independent predictors, including illness severity, as assessed by the Predisposition, Infection, Response, Organ failure (PIRO) score, and classic cardiac risk factors were analysed by multivariable binary logistic regression. Prognostic and discriminative performance of the model was quantified by the Hosmer-Lemeshow test and receiver operator characteristics with area under the curve (AUC) analyses, respectively. Maximum sensitivity and specificity for identification of MACE were calculated.Primary outcomeMACE within 90 days after hospital admission.Results36 (2.1%) of the 1728 included patients developed MACE <90 days after ED presentation. Independent predictors of MACE were the RO components of the PIRO score, reflecting acute organ failure, with a corrected OR (OR (95% CI) 1.1 (1.0 to 1.3) per point increase), presence of atrial fibrillation/flutter; OR 3.9 (2.0 to 7.7) and >2 classic cardiovascular risk factors; 2.2 (1.1 to 4.3). The AUC was 0.773, and the goodness-of-fit test had a p value of 0.714. These predictors identified MACE with 75% sensitivity and 70% specificity.ConclusionsBesides the classical cardiovascular risk factors, atrial fibrillation and signs of acute organ failure were independent risk factors of MACE in ED patients hospitalised with a suspected infection. Future studies should investigate whether preventive measures like antiplatelet therapy should be initialised in hospitalised ED patients with suspected infection and high risk for MACE.
Psychological interventions to improve psychological well-being in people with dementia or mild cognitive impairment: systematic review and meta-analysis protocol
Authors: Farrand Paul , Matthews Justin , Dickens Chris , Anderson Martin , Woodford Joanne 
Published: January 2016

IntroductionDementia and mild cognitive impairment are associated with an increased risk of depression, anxiety, psychological distress and poor mental health-related quality of life. However, there is a lack of research examining the evidence base for psychological interventions targeting general psychological well-being within this population. Furthermore, there is little research relating to the design of randomised controlled trials examining psychological interventions for dementia and mild cognitive impairment, such as effective recruitment techniques, trial eligibility and appropriate comparators.Methods and analysisSystematic review of electronic databases (CINAHL; EMBASE; PsychInfo; MEDLINE; ASSIA and CENTRAL), supplemented by expert contact, reference and citation checking, and grey literature searches. Published and unpublished studies will be eligible for inclusion with no limitations placed on year of publication. Primary outcomes of interest will be standardised measurements of depression, anxiety, psychological distress or mental health-related quality of life. Eligibility and randomisation proportions will be calculated as secondary outcomes. If data permits, meta-analytical techniques will examine: (1) overall effectiveness of psychological interventions for people with dementia or mild cognitive impairment in relation to outcomes of depression, anxiety, psychological distress or mental health-related quality of life; (2) clinical and methodological moderators associated with effectiveness; (3) proportions eligible, recruited and randomised.Ethics and disseminationEthical approval is not required for the present systematic review. Results will inform the design of a feasibility study examining a new psychological intervention for people with dementia and depression, with dissemination through publication in peer-reviewed journals and presentations at relevant conferences.Trial registration numberCRD42015025177.
School-based intervention for the prevention of HPV among adolescents: a cluster randomised controlled study
Authors: Grandahl Maria , Rosenblad Andreas , Stenhammar Christina , Tydén Tanja , Westerling Ragnar , Larsson Margareta , Oscarsson Marie , Andrae Bengt , Dalianis Tina , Nevéus Tryggve 
Published: January 2016

ObjectiveTo improve primary prevention of human papillomavirus (HPV) infection by promoting vaccination and increased condom use among upper secondary school students.DesignCluster randomised controlled trial.Setting18 upper secondary schools in Sweden.ParticipantsSchools were first randomised to the intervention or the control group, after which individual classes were randomised so as to be included or not. Of the 832 students aged 16 years invited to participate during the regular individual health interview with the school nurse, 751 (90.2%) agreed to participate and 741 (89.1%) students completed the study.InterventionsThe intervention was based on the Health Belief Model (HBM). According to HBM, a person's health behaviour can be explained by individual beliefs regarding health actions. School nurses delivered 30 min face-to-face structured information about HPV, including cancer risks and HPV prevention, by propagating condom use and HPV vaccination. Students in the intervention and the control groups completed questionnaires at baseline and after 3 months.Main outcome measuresIntention to use condom with a new partner and beliefs about primary prevention of HPV, and also specifically vaccination status and increased condom use.ResultsAll statistical analyses were performed at the individual level. The intervention had a significant effect on the intention to use condom (p=0.004). There was also a significant effect on HBM total score (p=0.003), with a 2.559 points higher score for the intervention group compared to the controls. The influence on the HBM parameterssusceptibilityandseveritywas also significant (p<0.001 for both variables). The intervention also influenced behaviour: girls in the intervention group chose to have themselves vaccinated to a significantly higher degree than the controls (p=0.02). No harms were reported.ConclusionsThe school-based intervention had favourable effects on the beliefs about primary prevention of HPV, and increased the HPV vaccination rates in a diverse population of adolescents.Trial registration numberNCT02280967; Results.
Decisions about the use of psychotropic medication during pregnancy: a qualitative study
Authors: Stevenson Fiona , Hamilton Sarah , Pinfold Vanessa , Walker Charlotte , Dare Ceri R J , Kaur Harminder , Lambley Ruth , Szymczynska Paulina , Nicolls Vicky , Petersen Irene 
Published: January 2016

ObjectiveTo understand the perspectives of women with severe mental illness concerning the use of psychotropic medicines while pregnant.DesignInterviews conducted by female peer researchers with personal experience of making or considering decisions about using psychotropic medicines in pregnancy, supported by professional researchers.Participants12 women who had had a baby in the past 5 years and had taken antipsychotics or mood-stabilisers for severe mental illness within the 12-month period immediately prior to that pregnancy. Recruitment to the study was via peer networks and the women interviewed came from different regions of England.SettingInterviews were arranged in places where women felt comfortable and that accommodated their childcare needs including their home, local library and the research office.ResultsThe views expressed demonstrated complex attempts to engage with decision-making about the use of psychotropic medicines in pregnancy. In nearly all cases, the women expressed the view that healthcare professionals had access to limited information leaving women to rely on experiential and common sense evidence when making decisions about medicine taking during pregnancy.ConclusionsThe findings complement existing work using electronic health records by providing explanations for the discontinuation of psychotropic medicines in pregnancy. Further work is necessary to understand health professionals’ perspectives on the provision of services and care to women with severe mental illness during pregnancy.
Intravascular optical coherence tomography for the evaluation of arterial bifurcations covered by flow diverters
Authors: Iosif Christina , Saleme Suzana , Ponsonnard Sebastien , Carles Pierre , Silveira Eduardo Pedrolo , Waihrich Eduardo , Trolliard Gilles , Yardin Catherine , Mounayer Charbel 
Published: January 2016

Background and objectiveDue to its high spatial resolution, intravascular optical coherence tomography (OCT) has been used as a valid method for in vivo evaluation of several types of coronary stents at straight lumen and bifurcation sites. We sought to evaluate its effectiveness for flow diverting stents deployed in arterial bifurcation sites involving jailing of a side branch.MethodsFour large white swine were stented with flow diverting stents covering the right common carotid artery–ascending pharyngeal artery bifurcation. After 12 weeks of follow-up the animals were evaluated by digital subtraction angiography and intravascular OCT and subsequently sacrificed. Neointimal thickness on the parent arteries and the free segments of the stent were measured. The stented arteries were harvested and underwent scanning electron microscopy (SEM) imaging. Ostia surface values were measured with OCT three-dimensional (3D) reconstructions and SEM images.ResultsAll endovascular procedures and OCT pullback runs were feasible. Stent apposition was satisfactory on the immediate post-stent OCT reconstructions. At 12-week controls, all stents and jailed branches were patent. Mean neointimal thickness was 0.11±0.04 mm on the free segments of the stent. The mean ostia surface at 12 weeks was 319 750±345 533 μm2with 3D-OCT reconstructions and 351 198±396 355 μm2with SEM image-derived calculations. Good correlation was found for ostia surface values between the two techniques; the values did not differ significantly in this preliminary study.ConclusionsIntravascular OCT appears to be a promising technique for immediate and follow-up assessment of the orifice of arterial branches covered by flow diverting stents.