bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited Utility of Dried-Blood- and Plasma Spot-Based Screening for Antiretroviral Treatment Failure with Cobas Ampliprep/TaqMan HIV-1 Version 2.0
Authors: Sawadogo Souleymane , Shiningavamwe Andreas , Chang Joy , Maher Andrew D. , Zhang Guoqing , Yang Chunfu , Gaeb Esegiel , Kaura Harold , Ellenberger Dennis , Lowrance David W. 
Published: August 2014

ABSTRACT
The 2013 WHO antiretroviral therapy (ART) guidelines recommend dried blood spots (DBS) as an alternative specimen type for viral load (VL) monitoring. We assessed the programmatic utility of screening for antiretroviral (ARV) treatment failure (TF) at 5,000 and 1,000 copies/ml using DBS and dried plasma spots (DPS) with a commonly used VL assay, the Roche Cobas Ampliprep/Cobas TaqMan V.2.0 (CAP/CTM). Plasma, DBS, and DPS were prepared from 839 whole-blood specimens collected from patients on ART for ≥6 months at three public facilities in Namibia. Using the CAP/CTM test, VL were measured in plasma, DBS, and DPS, and the results were compared using the plasma VL as the reference standard. The clinical sensitivities, specificities, and positive (PPV) and negative predictive values (NPV) of DBS at ARV TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml were 0.99, 0.55, 0.33, and 0.99 and 0.99, 0.26, 0.29, and 0.99, respectively, and for DPS at TF diagnostic thresholds of 5,000 copies/ml and 1,000 copies/ml, they were 0.88, 0.98, 0.92, and 0.97 and 0.91, 0.96, 0.89, and 0.97, respectively. The prevalences of TF were overestimated in DBS by 33% and 57% at these two thresholds, respectively. A high rate of false-positive results would occur if the CAP/CTM with DBS were to be used to screen for ARV TF. WHO recommendations for DBS-based VL monitoring should be specific to the VL assay version and type. Despite the better performance of DPS, the programmatic utility for TF screening may be limited by requirements for processing the whole blood at the collection site.
Development and Validation of a Sensitive and Specific
sodB
-Based Quantitative PCR Assay for Molecular Detection of Ehrlichia Species
Authors: Qurollo Barbara A. , Riggins Dana , Comyn Alaire , Zewde Merone T. , Breitschwerdt Edward B. 
Published: August 2014

ABSTRACT

We developed a sensitive and specific
sodB
-based quantitative PCR assay to detect
Ehrlichia
spp. The assay's limit of detection was 5 copies/reaction, and it did not amplify nonspecific DNA. Compared with a 16S rRNA gene PCR target, the
sodB
target may offer an improved molecular diagnostic assay to detect
Ehrlichia
spp.
Trafficking of Bluetongue Virus Visualized by Recovery of Tetracysteine-Tagged Virion Particles
Authors: Du Junzheng , Bhattacharya Bishnupriya , Ward Theresa H. , Roy Polly 
Published: August 2014

ABSTRACTBluetongue virus (BTV), a member of theOrbivirusgenus in theReoviridaefamily, is a double-capsid insect-borne virus enclosing a genome of 10 double-stranded RNA segments. Like those of other members of the family, BTV virions are nonenveloped particles containing two architecturally complex capsids. The two proteins of the outer capsid, VP2 and VP5, are involved in BTV entry and in the delivery of the transcriptionally active core to the cell cytoplasm. Although the importance of the endocytic pathway in BTV entry has been reported, detailed analyses of entry and the role of each protein in virus trafficking have not been possible due to the lack of availability of a tagged virus. Here, for the first time, we report on the successful manipulation of a segmented genome of a nonenveloped capsid virus by the introduction of tags that were subsequently fluorescently visualized in infected cells. The genetically engineered fluorescent BTV particles were observed to enter live cells immediately after virus adsorption. Further, we showed the separation of VP2 from VP5 during virus entry and confirmed that while VP2 is shed from virions in early endosomes, virus particles still consisting of VP5 were trafficked sequentially from early to late endosomes. Since BTV infects both mammalian and insect cells, the generation of tagged viruses will allow visualization of the trafficking of BTV farther downstream in different host cells. In addition, the tagging technology has potential for transferable application to other nonenveloped complex viruses.IMPORTANCELive-virus trafficking in host cells has been highly informative on the interactions between virus and host cells. Although the insertion of fluorescent markers into viral genomes has made it possible to study the trafficking of enveloped viruses, the physical constraints of architecturally complex capsid viruses have imposed practical limitations. In this study, we have successfully genetically engineered the segmented RNA genome of bluetongue virus (BTV), a complex nonenveloped virus belonging to theReoviridaefamily. The resulting fluorescent virus particles could be visualized in virus entry studies of both live and fixed cells. This is the first time a structurally complex capsid virus has been successfully genetically manipulated to generate virus particles that could be visualized in infected cells.
Immunogenicity Studies of Proteins Forming the T4 Phage Head Surface
Authors: Dąbrowska Krystyna , Miernikiewicz Paulina , Piotrowicz Agnieszka , Hodyra Katarzyna , Owczarek Barbara , Lecion Dorota , Kaźmierczak Zuzanna , Letarov Andrey , Górski Andrzej 
Published: August 2014

ABSTRACTAdvances in phage therapy and novel applications of phages in biotechnology encourage interest in phage impact on human and animal immunity. Here we present comparative studies of immunogenic properties of T4 phage head surface proteins gp23*, gp24*, Hoc, and Soc, both as elements of the phage capsid and as isolated agents. Studies comprise evaluation of specific antibodies in the human population, analysis of the proteins' impact on the primary and secondary responses in mice, and the effect of specific antibodies on phage antibacterial activityin vitroandin vivoin mice. In humans, natural antibodies specific to T4-like phages were abundant (81% of investigated sera). Among those, significantly elevated levels of IgG antibodies only against major head protein (gp23*) were found, which probably reflected cross-reactions of T4 with antibodies induced by other T4-like phages. Both IgM and IgG antibodies were induced mostly by gp23* and Hoc, while weak (gp24*) and very weak (Soc) reactivities of other head proteins were noticed. Thus, T4 head proteins that markedly contribute to immunological memory to the phage are highly antigenic outer capsid protein (Hoc) and major capsid protein (gp23*). Specific anti-gp23* and anti-Hoc antibodies substantially decreased T4 phage activityin vitroand to some extentin vivo. Cooperating with antibodies, the immune complement system also contributed to annihilating phages.IMPORTANCECurrent descriptions of phage immunogenicity and its biological consequences are still vague and incomplete; thus, the central problem of this work is timely and may have strong practical implications. Here is presented the very first description of the contribution of bacteriophage proteins to immunological memory of the phage. Understanding of interactions between phages and mammalian immunology may help in biotechnological adaptations of phages for therapeutic requirements as well as for better appreciation of phage ecology and their role in the biosphere.
Comprehensive Analysis of Herpes Simplex Virus 1 (HSV-1) Entry Mediated by Zebrafish 3-
O
-Sulfotransferase Isoforms: Implications for the Development of a Zebrafish Model of HSV-1 Infection
Authors: Yakoub Abraam M. , Rawal Nistha , Maus Erika , Baldwin John , Shukla Deepak , Tiwari Vaibhav 
Published: August 2014

ABSTRACT

Binding of herpes simplex virus 1 (HSV-1) envelope glycoprotein D (gD) to the receptor 3-
O
-sulfated heparan sulfate (3-
O
S HS) mediates viral entry. 3-
O
-Sulfation of HS is catalyzed by the 3-
O
-sulfotransferase (3-
O
ST) enzyme. Multiple isoforms of 3-
O
ST are differentially expressed in tissues of zebrafish (ZF) embryos. Here, we performed a comprehensive analysis of the role of ZF 3-
O
ST isoforms (3-
O
ST-1, 3-
O
ST-5, 3-
O
ST-6, and 3-
O
ST-7) in HSV-1 entry. We found that a group of 3-
O
ST gene family isoforms (3-
O
ST-2, -3, -4, and -6) with conserved catalytic and substrate-binding residues of the enzyme mediates HSV-1 entry and spread, while the other group (3-
O
ST-1, -5, and -7) lacks these properties. These results demonstrate that HSV-1 entry can be recapitulated by certain ZF 3-
O
ST enzymes, a significant step toward the establishment of a ZF model of HSV-1 infection and tissue-specific tropism.
APOBEC3F Determinants of HIV-1 Vif Sensitivity
Authors: Land Allison M. , Shaban Nadine M. , Evans Leah , Hultquist Judd F. , Albin John S. , Harris Reuben S. 
Published: August 2014

ABSTRACT
HIV-1 Vif counteracts restrictive APOBEC3 proteins by targeting them for proteasomal degradation. To determine the regions mediating sensitivity to Vif, we compared human APOBEC3F, which is HIV-1 Vif sensitive, with rhesus APOBEC3F, which is HIV-1 Vif resistant. Rhesus-human APOBEC3F chimeras and amino acid substitution mutants were tested for sensitivity to HIV-1 Vif. This approach identified the α3 and α4 helices of human APOBEC3F as important determinants of the interaction with HIV-1 Vif.
Robotic-assisted laparoscopic management of a caliceal diverticular calculus
Authors: Torricelli Fabio Cesar Miranda , Batista Lucas T , Colombo Jose Roberto , Coelho Rafael Ferreira 
Published: August 2014

PurposeTo report the first case of robotic-assisted laparoscopic management of a symptomatic caliceal diverticular calculus and review the literature on laparoscopic treatment for this condition.Case reportA 33-year-old obese woman with a 2×1 cm calculus within an anterior caliceal diverticulum located in the middle pole of the left kidney was referred to our service. She had already undergone two flexible ureterorenoscopies without success. We considered that a percutaneous approach would be very challenging due to stone location, thus we elected to perform a robotic-assisted laparoscopic procedure for stone removal and diverticulum fulguration. The procedure was uneventfully performed with no intraoperative or postoperative complications. The patient was discharged from the hospital on the second postoperative day and after 1.5 years of follow-up she is asymptomatic with no recurrence.ConclusionsThe robotic-assisted laparoscopic approach to caliceal diverticular calculi is feasible and safe, providing one more option for treatment of stones in challenging locations.
Prospective analysis of the accuracy of diagnosis of carpal tunnel syndrome using a web-based questionnaire
Authors: Bland Jeremy D P , Rudolfer Stephan , Weller Peter 
Published: August 2014

ObjectiveTo confirm the accuracy of a diagnostic questionnaire for carpal tunnel syndrome (CTS) when presented via a public website rather than on paper.DesignProspective comparison of the probability of CTS as assessed by the web-based questionnaire athttp://www.carpal-tunnel.netwith the results of nerve conduction studies.SettingSubregional neurophysiology laboratory serving a population of 700 000 in East Kent, UK.Participants2821 individuals who were able to complete an online diagnostic questionnaire out of 4899 referred for initial diagnostic testing for new presentations with suspected CTS from April 2011 to March 2013. No exclusions were made on grounds of age, gender or coincident pathology.Main outcome measure—nerve conduction results confirming CTS. The severity of median nerve impairment demonstrated was also assessed using a validated neurophysiological scale.ResultsThe web-based questionnaire accurately estimates the probability of CTS being confirmed on nerve conduction studies. Using a website diagnostic score of ≥40% as an example cut-off value the questionnaire achieves 78% sensitivity and 68% specificity in predicting the finding of evidence of CTS on nerve conduction studies. The web-based version of the diagnostic questionnaire was as accurate as the original paper version with an area under the receiver operating characteristic curve of 0.79. There was also a significant correlation between the diagnostic score given by the website and the severity of CTS with higher scores being associated with greater nerve dysfunction (r=0.3, p<0.00001).ConclusionsCompletion of the symptom questionnaire on the website by patients at home provides a prediction of the likelihood of CTS which is sufficiently accurate to be used in initial planning of investigation and treatment.
The effects of financial incentives for case finding for depression in patients with diabetes and coronary heart disease: interrupted time series analysis
Authors: McLintock Kate , Russell Amy M , Alderson Sarah L , West Robert , House Allan , Westerman Karen , Foy Robbie 
Published: August 2014

ObjectiveTo evaluate the effects of Quality and Outcomes Framework (QOF) incentivised case finding for depression on diagnosis and treatment in targeted and non-targeted long-term conditions.DesignInterrupted time series analysis.SettingGeneral practices in Leeds, UK.Participants65 (58%) of 112 general practices shared data on 37 229 patients with diabetes and coronary heart disease targeted by case finding incentives, and 101 008 patients with four other long-term conditions not targeted (hypertension, epilepsy, chronic obstructive pulmonary disease and asthma).InterventionIncentivised case finding for depression using two standard screening questions.Main outcome measuresClinical codes indicating new depression-related diagnoses and new prescriptions of antidepressants. We extracted routinely recorded data from February 2002 through April 2012. The number of new diagnoses and prescriptions for those on registers was modelled with a binomial regression, which provided the strength of associations between time periods and their rates.ResultsNew diagnoses of depression increased from 21 to 94/100 000 per month in targeted patients between the periods 2002–2004 and 2007–2011 (OR 2.09; 1.92 to 2.27). The rate increased from 27 to 77/100 000 per month in non-targeted patients (OR 1.53; 1.46 to 1.62). The slopes in prescribing for both groups flattened to zero immediately after QOF was introduced but before incentivised case finding (p<0.01 for both). Antidepressant prescribing in targeted patients returned to the pre-QOF secular upward trend (Wald test for equivalence of slope, z=0.73, p=0.47); the slope was less steep for non-targeted patients (z=−4.14, p<0.01).ConclusionsIncentivised case finding increased new depression-related diagnoses. The establishment of QOF disrupted rising trends in new prescriptions of antidepressants, which resumed following the introduction of incentivised case finding. Prescribing trends are of concern given that they may include people with mild-to-moderate depression unlikely to respond to such treatment.
Lung ultrasonography: an effective way to diagnose community-acquired pneumonia
Authors: Liu Xiao-lei , Lian Rui , Tao Yong-kang , Gu Cheng-dong , Zhang Guo-qiang 
Published: August 2014

PurposeTo analyse the ultrasonographic findings of community-acquired pneumonia (CAP) and its efficacy for diagnosis of CAP compared with chest X-ray (CXR).MethodsPatients who presented to the Emergency Department with suspected CAP were included in the study. Bedside ultrasonography was performed at each intercostal space in the midclavicular, anterior axillary, midaxillary and paravertebral lines. Any pulmonary consolidation, focal interstitial pattern, pleural-line abnormalities and subpleural lesions were recorded, and the numbers of subpleural lesions and intercostal spaces with pleural-line abnormalities were counted. All patients received bedside CXR and CT. Using CT scan as the gold standard, ultrasonography findings were compared between CAP group and non-CAP group, and between CAP patients with CT showing consolidation or diffuse ground-glass opacification. The sensitivity of ultrasonography was compared with CXR for the diagnosis of CAP.ResultsOf 179 patients included in the study, 112 were diagnosed with CAP by CT. Patients in CAP group were more likely to have consolidation (p<0.001), focal interstitial pattern (p<0.001) and had higher number of subpleural lesions (p<0.001) and intercostal spaces with pleural-line abnormalities (p<0.001) on ultrasound than those without CAP. CAP patients whose CT showed consolidation were more likely to have consolidation (p<0.001) and had lower numbers of subpleural lesions (p<0.001) and intercostal spaces with pleural-line abnormalities (p<0.001) compared to CAP patients whose CT showed diffuse ground-glass opacification. The diagnostic sensitivity, specificity, and accuracy for ultrasonography and CXR were 94.6% versus 77.7% (p<0.001), 98.5% versus 94.0% (p=0.940) and 96.1% versus 83.8% (p<0.001), respectively.ConclusionsLung ultrasonography has a better diagnostic sensitivity and accuracy for diagnosing CAP compared with CXR.
Rising inequality in mortality among working-age men and women in Sweden: a national registry-based repeated cohort study, 1990–2007
Authors: Kondo Naoki , Rostila Mikael , Åberg Yngwe Monica 
Published: August 2014

BackgroundIn the past two decades, health inequality has persisted or increased in states with comprehensive welfare.MethodsWe conducted a national registry-based repeated cohort study with a 3-year follow-up between 1990 and 2007 in Sweden. Information on all-cause mortality in all working-age Swedish men and women aged between 30 and 64 years was collected. Data were subjected to temporal trend analysis using joinpoint regression to statistically confirm the trajectories observed.ResultsAmong men, age-standardised mortality rate decreased by 38.3% from 234.9 to 145 (per 100 000 population) over the whole period in the highest income quintile, whereas the reduction was only 18.3% (from 774.5 to 632.5) in the lowest quintile. Among women, mortality decreased by 40% (from 187.4 to 112.5) in the highest income group, but increased by 12.1% (from 280.2 to 314.2) in the poorest income group. Joinpoint regression identified that the differences in age-standardised mortality between the highest and the lowest income quintiles decreased among men by 18.85 annually between 1990 and 1994 (p trend=0.02), whereas it increased later, with a 2.88 point increase per year (p trend <0.0001). Among women, it continuously increased by 9.26/year (p trend <0.0001). In relative terms, age-adjusted mortality rate ratios showed a continuous increase in both genders.ConclusionsIncome-based inequalities among working-age male and female Swedes have increased since the late 1990s, whereas in absolute terms the increase was less remarkable among men. Structural and behavioural factors explaining this trend, such as the economic recession in the early 1990s, should be studied further.
Percutaneous coronary intervention causes a rapid but transient mobilisation of CD34+CD45−cells
Authors: Padfield Gareth J , Tura-Ceide Olga , Freyer Elizabeth , Barclay G Robin , Turner Marc , Newby David E , Mills Nicholas L 
Published: August 2014

ObjectiveCirculating CD34+CD45−cell concentrations are increased in patients with coronary artery disease, however their pathophysiological significance is unknown. We determined CD34+CD45−cell concentrations following percutaneous coronary intervention (PCI) in order to explore their role in acute vascular injury.MethodsIn a prospective time-course analysis, we quantified using flow cytometry circulating CD34+CD45−cells, traditional CD34+VEGFR-2+putative endothelial progenitor cells (EPCs), CD14+VEGFR−2+Tie-2+angiogenic monocytes and intercellular adhesion molecule expression (CXCR-4 and CD18) in patients, before and during the first week following diagnostic angiography (n=13) or PCI (n=23). Vascular endothelial growth factor-A (VEGF-A) and C reactive protein (CRP) were quantified by ELISA.ResultsUnlike diagnostic angiography, PCI increased circulating neutrophil and CRP concentrations at 24 and 48 h, respectively (p<0.002 for both). CD34+CD45−cell concentrations were unaffected by angiography (p>0.4), but were transiently increased 6 h following PCI (median (IQR) 0.93 (0.43–1.49) vs 1.51 (0.96–2.15)×106 cells/L; p=0.01), returning to normal by 24 h.This occurred in the absence of any change in serum VEFG-A concentration, adhesion molecule expression on CD34+cells, or mobilisation of traditional EPCs or angiogenic monocytes (p>0.1 for all).ConclusionsPCI transiently increases circulating CD34+CD45−cells, without increasing CD34+adhesion molecule expression or VEGF-A concentrations, suggesting that CD34+CD45−cells may be mobilised from the vessel wall directly as a result of mechanical injury. Traditional putative EPC and angiogenic monocytes are unaffected by PCI, and are unlikely to be important in the acute response to vascular injury.
Obesity, Physical Activity, and Their Interaction in Incident Atrial Fibrillation in Postmenopausal Women
Authors: Azarbal Farnaz , Stefanick Marcia L. , Salmoirago‐Blotcher Elena , Manson JoAnn E. , Albert Christine M. , LaMonte Michael J. , Larson Joseph C. , Li Wenjun , Martin Lisa W. , Nassir Rami , Garcia Lorena , Assimes Themistocles L. , Tharp Katie M. , Hlatky Mark A. , Perez Marco V. 
Published: August 2014

Background

Atrial fibrillation (
AF
) is the most common cardiac arrhythmia and is associated with increased risk of stroke and death. Obesity is an independent risk factor for
AF
, but modifiers of this risk are not well known. We studied the roles of obesity, physical activity, and their interaction in conferring risk of incident
AF
.

Methods and Results

The Women's Health Initiative (
WHI
) Observational Study was a prospective observational study of 93 676 postmenopausal women followed for an average of 11.5 years. Incident
AF
was identified using
WHI
‐ascertained hospitalization records and diagnostic codes from Medicare claims. A multivariate Cox's hazard regression model adjusted for demographic and clinical risk factors was used to evaluate the interaction between obesity and physical activity and its association with incident
AF
. After exclusion of women with prevalent
AF
, incomplete data, or underweight body mass index (
BMI
), 9792 of the remaining 81 317 women developed
AF
. Women were, on average, 63.4 years old, 7.8% were African American, and 3.6% were Hispanic. Increased
BMI
(hazard ratio [
HR
], 1.12 per 5‐kg/m
2
increase; 95% confidence interval [
CI
], 1.10 to 1.14) and reduced physical activity (>9 vs. 0 metabolic equivalent task hours per week;
HR
, 0.90; 95%
CI
, 0.85 to 0.96) were independently associated with higher rates of
AF
after multivariate adjustment. Higher levels of physical activity reduced the
AF
risk conferred by obesity (interaction
P
=0.033).

Conclusions

Greater physical activity is associated with lower rates of incident
AF
and modifies the association between obesity and incident
AF
.
International Criminal Law, Causation, and Responsibility
Authors: Mayr Erasmus 
Published: August 2014

In this article, I explore the question whether criminal responsibility, within the international criminal law, should be considered as a causal notion. I start off with the connection between causation and criminal responsibility in general and introduce three more specific claims about this connection (Sections 1 and 2). Afterwards, I go on to examine a much-discussed case in international criminal law, the case of command responsibility from failure to punish, where responsibility for harmful effects is apparently attributed without causal control on the agent’s part (Section 3). I argue that, even in this case, the notion of responsibility must remain linked to causation in the ways discussed earlier, but try to show that the constraints arising from these links can be met.