bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of a Reassortant Strain of Bluetongue Virus Serotype 23 from Western India
Authors: Maan Sushila , Maan Narender S. , Guimera Marc , Nomikou Kyriaki , Singh Karam Pal , Pullinger Gillian , Belaganahalli Manjunatha N. , Mertens Peter P. C. 
Published: May 2012

ABSTRACT
The full genome sequence (19,177 bp) of an Indian strain (IND1988/02) of bluetongue virus (BTV) serotype 23 was determined. This virus was isolated from a sheep that had been killed during a severe bluetongue outbreak that occurred in Rahuri, Maharashtra State, western India, in 1988. Phylogenetic analyses of these data demonstrate that most of the genome segments from IND1988/02 belong to the major “eastern” BTV topotype. However, genome segment 5 belongs to the major “western” BTV topotype, demonstrating that IND1988/02 is a reassortant. This may help to explain the increased virulence that was seen during this outbreak in 1988. Genome segment 5 of IND1988/02 shows >99% sequence identity with some other BTV isolates from India (e.g., BTV-3 IND2003/08), providing further evidence of the existence and circulation of reassortant strains on the subcontinent.
New PARP Gene with an Anti-Alphavirus Function
Authors: Atasheva Svetlana , Akhrymuk Maryna , Frolova Elena I. , Frolov Ilya 
Published: May 2012

ABSTRACT
Alphaviruses represent a highly important group of human and animal pathogens, which are transmitted by mosquito vectors between vertebrate hosts. The hallmark of alphavirus infection in vertebrates is the induction of a high-titer viremia, which is strongly dependent on the ability of the virus to interfere with host antiviral responses on both cellular and organismal levels. The identification of cellular factors, which are critical in orchestrating virus clearance without the development of cytopathic effect, may prove crucial in the design of new and highly effective antiviral treatments. To address this issue, we have developed a noncytopathic Venezuelan equine encephalitis virus (VEEV) mutant that can persistently replicate in cells defective in type I interferon (IFN) production or signaling but is cleared from IFN signaling-competent cells. Using this mutant, we analyzed (i) the spectrum of cellular genes activated by virus replication in the persistently infected cells and (ii) the spectrum of genes activated during noncytopathic virus clearance. By applying microarray-based technology and bioinformatic analysis, we identified a number of IFN-stimulated genes (ISGs) specifically activated during VEEV clearance. One of these gene products, the long isoform of PARP12 (PARP12L), demonstrated an inhibitory effect on the replication of VEEV, as well as other alphaviruses and several different types of other RNA viruses. Additionally, overexpression of two other members of the PARP gene superfamily was also shown to be capable of inhibiting VEEV replication.
An Epstein-Barr Virus (EBV) Mutant with Enhanced BZLF1 Expression Causes Lymphomas with Abortive Lytic EBV Infection in a Humanized Mouse Model
Authors: Ma Shi-Dong , Yu Xianming , Mertz Janet E. , Gumperz Jenny E. , Reinheim Erik , Zhou Ying , Tang Weihua , Burlingham William J. , Gulley Margaret L. , Kenney Shannon C. 
Published: May 2012

ABSTRACT
Immunosuppressed patients are at risk for developing Epstein-Barr Virus (EBV)-positive lymphomas that express the major EBV oncoprotein, LMP1. Although increasing evidence suggests that a small number of lytically infected cells may promote EBV-positive lymphomas, the impact of enhanced lytic gene expression on the ability of EBV to induce lymphomas is unclear. Here we have used immune-deficient mice, engrafted with human fetal hematopoietic stem cells and thymus and liver tissue, to compare lymphoma formation following infection with wild-type (WT) EBV versus infection with a “superlytic” (SL) mutant with enhanced BZLF1 (Z) expression. The same proportions (2/6) of the WT and SL virus-infected animals developed B-cell lymphomas by day 60 postinfection; the remainder of the animals had persistent tumor-free viral latency. In contrast, all WT and SL virus-infected animals treated with the OKT3 anti-CD3 antibody (which inhibits T-cell function) developed lymphomas by day 29. Lymphomas in OKT3-treated animals (in contrast to lymphomas in the untreated animals) contained many LMP1-expressing cells. The SL virus-infected lymphomas in both OKT3-treated and untreated animals contained many more Z-expressing cells (up to 30%) than the WT virus-infected lymphomas, but did not express late viral proteins and thus had an abortive lytic form of EBV infection. LMP1 and BMRF1 (an early lytic viral protein) were never coexpressed in the same cell, suggesting that LMP1 expression is incompatible with lytic viral reactivation. These results show that the SL mutant induces an “abortive” lytic infection in humanized mice that is compatible with continued cell growth and at least partially resistant to T-cell killing.
Progressive Loss of Memory T Cell Potential and Commitment to Exhaustion during Chronic Viral Infection
Authors: Angelosanto Jill M. , Blackburn Shawn D. , Crawford Alison , Wherry E. John 
Published: May 2012

ABSTRACT

T cell exhaustion and loss of memory potential occur during many chronic viral infections and cancer. We investigated when during chronic viral infection virus-specific CD8 T cells lose the potential to form memory. Virus-specific CD8 T cells from established chronic infection were unable to become memory CD8 T cells if removed from infection. However, at earlier stages of chronic infection, these virus-specific CD8 T cells retained the potential to partially or fully revert to a memory differentiation program after transfer to infection-free mice. Conversely, effector CD8 T cells primed during acute infection were not protected from exhaustion if transferred to a chronic infection. We also tested whether memory and exhausted CD8 T cells arose from different subpopulations of effector CD8 T cells and found that only the KLRG1
lo
memory precursor subset gave rise to exhausted CD8 T cells. Together, these studies demonstrate that CD8 T cell exhaustion is a progressive developmental process. Early during chronic infection, the fate of virus-specific CD8 T cells remains plastic, while later, exhausted CD8 T cells become fixed in their differentiation state. Moreover, exhausted CD8 T cells arise from the memory precursor and not the terminally differentiated subset of effector CD8 T cells. These studies have implications for our understanding of senescence versus exhaustion and for therapeutic interventions during chronic infection.
Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study
Authors: Huh Susanna Y , Rifas-Shiman Sheryl L , Zera Chloe A , Edwards Janet W Rich , Oken Emily , Weiss Scott T , Gillman Matthew W 
Published: May 2012

ObjectiveTo examine whether delivery by caesarean section is a risk factor for childhood obesity.DesignProspective prebirth cohort study (Project Viva).SettingEight outpatient multi-specialty practices based in the Boston, Massachusetts area.ParticipantsWe recruited women during early pregnancy between 1999 and 2002, and followed their children after birth. We included 1255 children with body composition measured at 3 years of age.Main outcome measuresBMI score, obesity (BMI for age and sex ≥95th percentile), and sum of triceps plus subscapular skinfold thicknesses at 3 years of age.Results284 children (22.6%) were delivered by caesarean section. At age 3, 15.7% of children delivered by caesarean section were obese compared with 7.5% of children born vaginally. In multivariable logistic and linear regression models adjusting for maternal prepregnancy BMI, birth weight, and other covariates, birth by caesarean section was associated with a higher odds of obesity at age 3 (OR 2.10, 95% CI 1.36 to 3.23), higher mean BMI z-score (0.20 units, 95% CI 0.07 to 0.33), and higher sum of triceps plus subscapular skinfold thicknesses (0.94 mm, 95% CI 0.36 to 1.51).ConclusionsInfants delivered by caesarean section may be at increased risk of childhood obesity. Further studies are needed to confirm our findings and to explore mechanisms underlying this association.
What stops hospital clinical staff from following protocols? An analysis of the incidence and factors behind the failure of bedside clinical staff to activate the rapid response system in a multi-campus Australian metropolitan healthcare service
Authors: Shearer Bill , Marshall Stuart , Buist Michael David , Finnigan Monica , Kitto Simon , Hore Tonina , Sturgess Tamica , Wilson Stuart , Ramsay Wayne 
Published: May 2012

ObjectiveTo explore the causes of failure to activate the rapid response system (RRS). The organisation has a recognised incidence of staff failing to act when confronted with a deteriorating patient and leading to adverse outcomes.DesignA multi-method study using the following: a point prevalence survey to determine the incidence of abnormal simple bedside observations and activation of the rapid response team by clinical staff; a prospective audit of all patients experiencing a cardiac arrest, unplanned intensive care unit admission or death over an 8-week period; structured interviews of staff to explore cognitive and sociocultural barriers to activating the RRS.SettingSouthern Health is a comprehensive healthcare network with 570 adult in-patient beds across four metropolitan teaching hospitals in the south-eastern sector of Melbourne.MeasurementsFrequency of physiological instability and outcomes within the in-patient hospital population. Qualitative data from staff interviews were thematically coded.ResultsThe incidence of physiological instability in the acute adult population was 4.04%. Nearly half of these patients (42%) did not receive an appropriate clinical response from the staff, despite most (69.2%) recognising their patient met physiological criteria for activating the RRS, and being ‘quite’, or ‘very’ concerned about their patient (75.8%). Structured interviews with 91 staff members identified predominantly sociocultural reasons for failure to activate the RRS.ConclusionsDespite an organisational commitment to the RRS, clinical staff act on local cultural rules within the clinical environment that are usually not explicit. Better understanding of these informal rules may lead to more appropriate activation of the RRS.
Design and trial of a new ambulance-to-emergency department handover protocol: ‘IMIST-AMBO’
Authors: Iedema Rick , Ball Chris , Daly Barbara , Young Jacinta , Green Tim , Middleton Paul M , Foster-Curry Catherine , Jones Marea , Hoy Sarah , Comerford Daniel 
Published: May 2012

BackgroundInformation communicated by ambulance paramedics to Emergency Department (ED) staff during handover of patients has been found to be inconsistent and incomplete, and yet has major implications for patients' subsequent hospital treatment and trajectory of care.AimThe study's aims were to: (1) identify the existing structure of paramedic-to-emergency staff handovers by video recording and analysing them; (2) involve practitioners in reflecting on practice using the footage; (3) combine those reflections with formal analyses of these filmed handovers to design a handover protocol; (4) trial-run the protocol; and (5) assess the protocol's enactment.MethodThe study was a ‘video-reflexive ethnography’ involving: structured analysis of videoed handovers (informed by ED clinicians' and ambulance paramedics' comments); ED clinicians and ambulance paramedics viewing their own practices; and rapid at-work training and feedback for paramedics. A five-question pre- and post-survey measured ED triage nurses' perceptions of the new protocol's impact. In total, 137 pre- and post-handovers were filmed involving 291 staff, and 368 staff were educated in the use of the new protocol.ResultsThere was agreement thatIdentification of the patient,Mechanism/medical complaint,Injuries/information relative to the complaint,Signs, vitals and GCS,Treatment and trends/response to treatment,Allergies,Medications,Background history andOther (social) information (IMIST-AMBO) was the preferred protocol for non-trauma and trauma handovers. Uptake of IMIST-AMBO showed improvements: a greater volume of information per handover that was more consistently ordered; fewer questions from ED staff; a reduction in handover duration; and fewer repetitions by both paramedics and ED clinicians that may suggest improved recipient comprehension and retention.ConclusionIMIST-AMBO shows promise for improving the ambulance-ED handover communication interface. Involving paramedics and ED clinicians in its development enhanced the resulting protocol, strengthened ED clinicians' and ambulance paramedics' sense of ownership over the protocol and bolstered their peers' willingness to adopt it.
Male IDUs who have sex with men in England, Wales and Northern Ireland: are they at greater risk of bloodborne virus infection and harm than those who only have sex with women?
Authors: Marongiu Andrea , Hope Vivian D , Parry John V , Ncube Fortune 
Published: May 2012

ObjectivesIn the UK, although transmission of HIV among injecting drug user (IDUs) has been limited since the 1980s, IDUs and men who have sex with men (MSM) have higher HIV and hepatitis C virus (HCV) prevalences than the general population. MSM who are also IDUs (MSM-IDUs) may therefore have a higher risk of infection than male IDUs who only have sex with women.MethodsAnalysis of data from a national survey of IDUs attending services (England, Wales and Northern Ireland) between 1998 and 2007, which collected demographic and behavioural data and oral fluid samples for HIV and HCV antibody testing.ResultsOf the 8671 men who reported injecting drugs and having sex during the preceding year, 96% (8354) were men who only had sex with women (MSW). MSM-IDUs and MSW-IDUs had similar age and number of years of injecting. MSM-IDUs had a higher prevalence of HIV (adjusted OR=4.08, 95% CI 1.9 to 8.5) and of HCV (adjusted OR =1.34, 95% CI 1.1 to 1.8) and were about four times (adjusted OR =3.78, 95% CI 2.9 to 4.9) more likely to have unprotected sex with multiple partners. Among those who injected in the 4 weeks prior to participation, the MSM-IDUs had a higher level of needle/syringe sharing (adjusted OR =1.72, 95% CI 1.3 to 2.2).DiscussionMSM-IDUs have a fourfold higher risk of HIV; HCV prevalence in MSM-IDUs is a third higher than among MSW-IDUs, suggesting elevated risk from injecting and possibly sexual transmission. These findings emphasise the need for public health interventions specifically targeted at MSM-IDUs.
O1 Rapid automated white cell urinalysis is more accurate than urethral smear for predicting chlamydia infection in men
Authors: Pond M J , Patel S , Butcher P D , Hay P E , Sadiq S T 
Published: May 2012

BackgroundThe cut-off of ≥5 polymorphs/high power field (p/hpf) in a Gram stained male urethral smear (GSUS) for diagnosing non-gonococcal urethritis derives from evaluations using Chlamydia trachomatis (CT) culture as gold standard. There is also significant observer variation in performing microscopy.ObjectiveTo compare automated flow cytometry of first void urine white cell count (FVU-UWC) to GSUS for prediction of CT infection in men.MethodsFirst void urines from 227 symptomatic male patients, all undergoing GSUS, were collected and patients stratified into: those treated for urethritis, diagnosed by GSUS result, history and examination (n=114) and; those not thought to have urethritis (n=113). First void urines were analysed by automated flow cytometry using the bench-top Sysmex UF-100 Analyser.ResultsCT was found in 11.6% and 6.2% urethritis and non-urethritis patients respectively and gonorrhoea (GC) in 3.6% and 1.1% respectively. There was no difference in UWC between urethritis and non-urethritis (p=0.690) nor association between GSUS grade and UWC (p=0.933). Median GSUS was higher for CT positive compared to negative patients (≥5/hpf vs 0). UWC were higher in CT (p=0.001) and GC (p≤0.001) positives. ROC area under the curve (AUC) for predicting CT was 0.844 (p≤0.001) with an optimal cut-off of >29 UWC/μl giving sensitivity of 90% and specificity of 76%. For predicting CT in urethritis and non-urethritis: the positive predictive values using the >29 UWC/μl cut-off were 20% (95%CI 9.1% to 37.5%) and 34.4% (19.2% to 53.2%) and the negative predictive values NPVs 100% (94.2% to 100%) and 97.5% (90.4% to 99.6%) respectively; for GSUS, using ≥5/hpf, positive predictive values were 10.5% (5.4% to 18.9%) and 0% (0% to 60.4%) and negative predictive values were 82.4% (55.8% to 95.3%) and 93.6% (86.8% to 97.2%) respectively.ConclusionUWC is (1) higher in CT and GC infection; (2) is a better predictor of urethral CT than GSUS and; (3) possibly more useful for determining non-gonococcal urethritis. Automated rapid flow cytometry may offer significantly improved utility over microscopy in the clinic.
O11 Health promotional messages in short message service (SMS) follow-up of GU medicine clinic defaulters; a tool to improve subsequent attendance rates?
Authors: Rutland E , Roe H , Weaver A 
Published: May 2012

BackgroundPatients who do not attend (DNA) booked GU medicine (GUM) clinics waste resources and may pose a public health risk through onward transmission of sexually transmitted infections. Short message services (SMS) appointment reminders improve attendance rates, however the impact of their use in patients who have already DNA'd is unknown. In addition, health promotional tools are frequently used to improve STI awareness however there is little evidence for their effect on GUM clinic attendance.AimsTo determine whether SMS follow-up of patients who DNA booked GUM appointments improves subsequent re-attendance rates and to assess the impact of inclusion of a health promotional message on re-attendance rates.MethodsThis prospective randomised control study included all patients aged 16–30 yrs who DNA a booked GUM appointment during the 6 month study period. Subjects were randomised to: (1) no intervention; (2) SMS notification of the defaulted appointment and invitation to attend clinic; (3) as per arm 2 including a health promotional message about Chlamydia. All SMS were sent 1 week after the defaulted appointment. Patients re-booking or attending prior to this time were excluded. The proportion of patients who re-attend within 4 weeks of the defaulted appointment were compared using the Fisher's Exact test.Results252 patients were included. 4.5% (4/88) in the control group re-attended clinic compared to 8.2% (7/85) receiving a text reminder (p=0.36) and 15.2% (12/79) when a health promotional message (p=0.032). None of those re attending in the control group were diagnosed with an STI compared to 29% in group 2 (Gonorrhoea and Chlamydia) and 25% in group 3 (2 × Chlamydia and 1 Herpes).DiscussionSMS follow-up of clinic defaulters improves subsequent re-attendance rates if a health promotional message is included. The addition of a health promotional message to current routine clinic reminder texts may reduce DNA rates and warrants further study.
O2 Who should have gonorrhoea cultures in addition to gonorrhoea and chlamydia nucleic acid amplification tests? Cost effectiveness study
Authors: Hulme C , Stewart C M W , Schoeman S A , Wilcox M H , Wilson J D 
Published: May 2012

BackgroundNucleic acid amplification tests (NAATs) can now detect chlamydia (CT) and gonorrhoea (GC) but cultures are needed in GC NAAT positive people prior to treatment. This necessitates re-evaluation, examination and culture if cultures have not been taken initially.Aim/ObjectiveTo discover if it is more cost-effective to perform a NAAT plus GC culture or just a NAAT followed by recall of GC positives for culture.Methods3973 women performed a self-taken vulvo-vaginal swab (VVS) then clinicians took urethral and endocervical samples for GC culture. The VVSs were analysed for GC/CT by Aptima Combo 2 (AC2). Cost effectiveness was analysed using incremental cost effectiveness ratios using correct detection of GC/CT as the primary endpoint. Costs were estimated from a sub-sample of 92 patients in July 2009 and included costs of clinic time and laboratory costs. Comparisons were made of GC cultures plus a CT NAAT vs VVSs analysed by AC2 in various subgroups.ResultsVVS GC/CT NAAT with subsequent culture of GC positives was more cost-effective (8% cost-saving). The greatest saving was in women not requiring examination (37% cost saving). Cost of time taken explaining a self-taken swab was 11% of cost of examination. Savings also accrued by using AC2 rather than GC culture and CT NAAT. In contacts of GC, it was more cost-effective to include GC culture at first examination (15% cost saving).ConclusionsVVS analysed by AC2 for GC/CT is more cost-effective and detects more infections than GC culture plus CT NAAT. In women with no symptoms self-taken VVSs give cost savings of 37%. In women with symptoms VVSs remain cost-effective unless the prevalence of GC is above 10%. We would recommend including GC culture at first examination for women who are GC contacts (see abstract O2 table 1), those with pelvic inflammatory disease or cervicitis and in other circumstances where immediate antibiotic treatment is given.Abstract O2 Table 1Costs of different testing strategies in whole group and subgroupsSubgroupGonorrhoea prevalenceTotal cost GC culture + CT NAATTotal cost GC/CT NAAT and subsequent GC culture if GC +veAll women n=39732.5%£199 285.68£182 769.12Symptomatic for bacterial STI n=16773.4%£84 118.32£77 650.50Asymptomatic for bacterial STI but requiring examination n=9003.4%£45 144.00£41 625.49Asymptomatic and not requiring examination n=13960.9%£70 023.36£44 230.22GC contacts n=4450%£2940.52£3382.06Previous GC n=1627%£10 826.46£10 365.43Cervicitis n=21810%£14 568.94£14 163.10Pelvic inflammatory disease n=1698.3%£11 294.27£10 888.58
O3 Gonorrhoea test of cure: outcomes in a large urban sexual health service
Authors: Cheserem E , Stevenson J , Evason R , Brady M 
Published: May 2012

BackgroundNew British Association for Sexual Health and HIV guidelines for the management of gonorrhoea in adults were introduced in June 2011. First line therapy was changed to ceftriaxone 500 mg intramuscularly plus azithromycin 1 g orally, with a test of cure (TOC) recommended for all patients at 2 weeks. Our clinic policy changed to reflect these guidelines. TOC, previously performed in selected cases, was recommended in all cases.AimsTo identify the proportion of cases correctly treated following the change in guidelines and analyse TOC outcomes.MethodsA retrospective case notes review was carried out from 17 June to 22 November 2011. Diagnosis of gonorrhoea was from microscopy, nucleic acid amplification tests (NAAT) and culture. The NAAT test used was Gen-Probe APTIMA Combo 2, confirmed by the Aptima GC mono-assay.Results152 cases were identified; 63% of cases were in men, 75% were heterosexual. The median age was 25 years (IQR 20–33.5). 24% had previously had gonorrhoea, 29% had concurrent sexually transmitted infections and 5% had HIV co-infection. 88% of patients received correct treatment as per British Association for Sexual Health and HIV guidelines. 76% were offered TOC; of these, 43% attended for TOC. TOC was negative in all patients tested (NAAT and/or culture). 4% of patients attending TOC were retreated because of re-infection risk. 22% (82/369) of partners were tested and treated for gonorrhoea; however, written or official verification of this was limited.DiscussionOur data show that a high proportion, though not all, of patients are offered correct treatment at our centre, but only 43% return for TOC. Of those who return, persistent infection, to date, has not been detected at our centre. This may indicate that guidelines can be refined to direct TOC towards populations at greater risk of persistent or resistant gonorrhoea infection. More data regarding the best time to offer TOC is also required, as earlier TOC may improve uptake.