bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of a Highly Sensitive Mycobacterium tuberculosis Complex Real-Time PCR Assay for Diagnosis of Pulmonary Tuberculosis in a Low-Prevalence Setting: a Prospective Intervention Study
Authors: Vinuesa Víctor , Borrás Rafael , Briones María Luisa , Clari María Ángeles , Cresencio Vicenta , Giménez Estela , Muñoz Carmen , Oltra Rosa , Servera Emilio , Scheelje Talia , Tornero Carlos , Navarro David 
Published: March 2018

ABSTRACT

The potential impact of routine real-time PCR testing of respiratory specimens from patients with presumptive tuberculosis in terms of diagnostic accuracy and time to tuberculosis treatment inception in low-prevalence settings remains largely unexplored. We conducted a prospective intervention cohort study. Respiratory specimens from 1,020 patients were examined by acid-fast bacillus smear microscopy, tested by a real-time
Mycobacterium tuberculosis
complex PCR assay (Abbott RealTi
me
MTB PCR), and cultured in mycobacterial media. Seventeen patients tested positive by PCR (5 were acid-fast bacillus smear positive and 12 acid-fast bacillus smear negative), and
Mycobacterium tuberculosis
was recovered from cultures for 12 of them. Patients testing positive by PCR and negative by culture (
n
= 5) were treated and deemed to have responded to antituberculosis therapy. There were no PCR-negative/culture-positive cases, and none of the patients testing positive for nontuberculous mycobacteria (
n
= 20) yielded a positive PCR result. The data indicated that routine testing of respiratory specimens from patients with presumptive tuberculosis by the RealTi
me
MTB PCR assay improves the tuberculosis diagnostic yield and may reduce the time to antituberculosis treatment initiation. On the basis of our data, we propose a novel mycobacterial laboratory algorithm for tuberculosis diagnosis.
Infectious Bursal Disease Virus Hijacks Endosomal Membranes as the Scaffolding Structure for Viral Replication
Authors: Gimenez María Cecilia , Zanetti Flavia Adriana , Terebiznik Mauricio R. , Colombo María Isabel , Delgui Laura Ruth 
Published: March 2018

ABSTRACT

Birnaviruses are unconventional members of the group of double-stranded RNA (dsRNA) viruses that are characterized by the lack of a transcriptionally active inner core. Instead, the birnaviral particles organize their genome in ribonucleoprotein complexes (RNPs) composed by dsRNA segments, the dsRNA-binding VP3 protein, and the virally encoded RNA-dependent RNA polymerase (RdRp). This and other structural features suggest that birnaviruses may follow a completely different replication program from that followed by members of the
Reoviridae
family, supporting the hypothesis that birnaviruses are the evolutionary link between single-stranded positive RNA (+ssRNA) and dsRNA viruses. Here we demonstrate that infectious bursal disease virus (IBDV), a prototypical member of the
Birnaviridae
family, hijacks endosomal membranes of infected cells through the interaction of a viral protein, VP3, with the phospholipids on the cytosolic leaflet of these compartments for replication. Employing a mutagenesis approach, we demonstrated that VP3 domain PATCH 2 (P2) mediates the association of VP3 with the endosomal membranes. To determine the role of VP3 P2 in the context of the virus replication cycle, we used avian cells stably overexpressing VP3 P2 for IBDV infection. Importantly, the intra- and extracellular virus yields, as well as the intracellular levels of VP2 viral capsid protein, were significantly diminished in cells stably overexpressing VP3 P2. Together, our results indicate that the association of VP3 with endosomes has a relevant role in the IBDV replication cycle. This report provides direct experimental evidence for membranous compartments such as endosomes being required by a dsRNA virus for its replication. The results also support the previously proposed role of birnaviruses as an evolutionary link between +ssRNA and dsRNA viruses.

IMPORTANCE
Infectious bursal disease (IBD; also called Gumboro disease) is an acute, highly contagious immunosuppressive disease that affects young chickens and spreads worldwide. The etiological agent of IBD is infectious bursal disease virus (IBDV). This virus destroys the central immune organ (bursa of Fabricius), resulting in immunosuppression and reduced responses of chickens to vaccines, which increase their susceptibility to other pathogens. IBDV is a member of
Birnaviridae
family, which comprises unconventional members of dsRNA viruses, whose replication strategy has been scarcely studied. In this report we show that IBDV hijacks the endosomes of the infected cells for establishing viral replication complexes via the association of the ribonucleoprotein complex component VP3 with the phospholipids in the cytosolic leaflet of endosomal membranes. We show that this interaction is mediated by the VP3 PATCH 2 domain and demonstrate its relevant role in the context of viral infection.
Vaccinia Virus Phospholipase Protein F13 Promotes Rapid Entry of Extracellular Virions into Cells
Authors: Bryk Peter , Brewer Matthew G. , Ward Brian M. 
Published: March 2018

ABSTRACT

The vaccinia virus protein F13, encoded by the F13L gene, is conserved across the subfamily
Chordopoxvirinae
and is critical among orthopoxviruses to produce the wrapped form of virus that is required for cell-to-cell spread. F13 is the major envelope protein on the membrane of extracellular forms of virus; however, it is not known if F13 is required in steps postwrapping. In this report, we utilize two temperature-sensitive vaccinia virus mutants from the Condit collection of temperature-sensitive viruses whose small plaque phenotypes have been mapped to the F13L gene. Despite the drastic reduction in plaque size, the temperature-sensitive viruses were found to produce levels of extracellular virions similar to those of the parental strain, Western Reserve (WR), at the permissive and nonpermissive temperatures, suggesting that they are not defective in extracellular virion formation. Analyses of extracellular virions produced by one temperature-sensitive mutant found that those produced at the nonpermissive temperature had undetectable levels of F13 and bound cells with efficiency similar to that of WR but displayed delayed cell entry kinetics. Additionally, low-pH treatment of cells bound by extracellular virions produced at the nonpermissive temperature by the temperature-sensitive reporter virus was unable to overcome a block in infection by bafilomycin A1, suggesting that these virions display increased resistance to dissolution of the extracellular virion envelope. Taken together, our results suggest that F13 plays a role both in the formation of extracellular virions and in the promotion of their rapid entry into cells by enhancing the sensitivity of the membrane to acid-induced dissolution.

IMPORTANCE
Vaccinia virus (VACV) is an orthopoxvirus and produces two infectious forms, mature virions (MV) and extracellular virions (EV). EV are derived from MV and contain an additional membrane that must first be removed prior to cell entry. F13 is critical for the formation of EV, but a postenvelopment role has not been described. Here, two temperature-sensitive VACV mutants whose deficiencies were previously mapped to the F13L locus are characterized. Both viruses produced EV at the nonpermissive temperature at levels similar to those of a virus that has F13L, yet they had a small plaque phenotype and rate of spread similar to that of an F13L deletion virus. F13 was undetectable on the EV membrane at the nonpermissive temperature, and these EV exhibited delayed cell entry kinetics compared to EV containing F13. This study is the first to conclusively demonstrate a novel role for F13 in cell entry of the EV form of the virus.
Elevated platelet counts in a cohort of children with moderate-severe osteogenesis imperfecta suggest that inflammation is present
Authors: Salter Lois , Offiah Amaka C , Bishop Nicholas 
Published: March 2018

BackgroundElevated platelet counts are observed in cancer, autoimmunity and inflammation with concurrent illness. Proinflammatory cytokines are elevated in murine osteogenesis imperfecta (OI) models. We hypothesised that platelet counts might be elevated in children with moderate-severe OI.MethodsWe reviewed the hospital records of 71 children with moderate-severe OI, treated in the Sheffield Children’s Hospital’s Severe, Complex and Atypical Osteogenesis Imperfecta Highly Specialised Service. Data relating platelet count (below/above average, above upper limit) to prior and concurrent events were summarised as event proportions per child. Additionally, we created platelet SD scores to assess age and time-related trends, and relationship with OI type.Results1206 platelet counts were recorded. Platelet SD scores were right-shifted by 0.89 SD overall. 49 of 71 (69%) patients had at least one platelet count above the normal range and 246 (20.4%) of all counts were above the upper limit of normal. Of these, 101 (41%) were high despite no confounding factors being present. For the 47 children with data at age less than 2 years, 89 (30.0%) platelet counts were above the upper limit of normal and 39 (44%) had no associated confounding factor. Elevated platelet counts were recorded most often for children with new or existing vertebral fractures.ConclusionsRaised platelet counts were observed in association with new and healing vertebral fractures, but also (41%–44%) in the absence of identified proinflammatory factors or events. We speculate that these findings are evidence for a proinflammatory component to OI that could be a target for therapeutic intervention.
Feasibility of using touch screen technology for early cognitive assessment in children
Authors: Twomey Deirdre M , Wrigley Conal , Ahearne Caroline , Murphy Raegan , De Haan Michelle , Marlow Neil , Murray Deirdre M 
Published: March 2018

ObjectiveTo explore the feasibility of using a touch screen assessment tool to measure cognitive capacity in toddlers.Design112 typically developing children with a median age of 31 months (IQR: 26–34) interacted with a touch screen cognitive assessment tool. We examined the sensitivity of the tool to age-related changes in cognition by comparing the number of items completed, speed of task completion and accuracy in two age groups; 24–29 months versus 30–36 months.ResultsChildren aged 30–36 months completed more tasks (median: 18, IQR: 18–18) than those aged 24–29 months (median: 17, IQR: 15–18). Older children also completed two of the three working memory tasks and an object permanence task faster than their younger peers. Children became faster at completing the working memory items with each exposure and registered similar completion times on the hidden object retrieval items, despite task demands being twofold on the second exposure. A novel item required children to integrate what they had learnt on preceding items. The older group was more likely to complete this item and to do so faster than the younger group.ConclusionsChildren as young as 24 months can complete items requiring cognitive engagement on a touch screen device, with no verbal instruction and minimal child–administrator interaction. This paves the way for using touch screen technology for language and administrator independent developmental assessment in toddlers.
Subannular reconstruction in secondary mitral regurgitation: a meta-analysis
Authors: Harmel Eva Karolina , Reichenspurner Hermann , Girdauskas Evaldas 
Published: March 2018

ObjectiveMitral valve repair using an undersized complete annuloplasty ring in secondary mitral regurgitation with restricted leaflet motion during systole (Carpentier’s surgical classification of mitral valve pathology: type IIIb) only inadequately addresses the underlying left ventricular disease. This may lead to an ongoing ventricular remodelling and progressive papillary muscle displacement with increasing leaflet tethering. Several subannular techniques have been proposed to counteract the reoccurrence of mitral regurgitation after mitral valve repair. We aimed to evaluate the potential additive effect of such subannular techniques on the late reoccurrence rate of secondary mitral regurgitation.MethodsSystematic literature review and meta-analysis were performed on PubMed, Embase and Google Scholar for studies published up to March 2016 and reporting late reoccurrence of mitral regurgitation after mitral valve repair using standard annuloplasty (control group) versus annuloplasty with subannular correction (study group) cohorts. Primary endpoint was late reoccurrence of mitral regurgitation ≥2 after surgical mitral valve repair, as defined by follow-up echocardiography.ResultsThe cumulative number of 1093 patients in 12 included studies served as our study population. A total of 743 patients underwent combined mitral valve repair including annuloplasty and subannular manoeuvre (ie, study group), while the remaining 350 patients underwent an isolated ring annuloplasty (ie, control group). Secondary mitral regurgitation was caused by ischaemic heart disease in 733/743 patients in the study group and 334/350 patients in the control group. Mean echocardiographic follow-up was 42.7±13.9 months. Pooled outcome analysis demonstrated that the combination of subannular repair with ring annuloplasty was associated with a significantly lower reoccurrence rate of mitral regurgitation ≥2 as compared with annuloplasty alone (OR 0.27, 95% CI 0.19 to 0.38, P=0.0001).ConclusionThe combination of subannular reconstruction and mitral valve annuloplasty is associated with a lower late reoccurrence of mitral regurgitation after surgical mitral valve repair, as compared with annuloplasty alone.
Effectiveness of new antiplatelets in the prevention of recurrent myocardial infarction
Authors: Grimaldi-Bensouda Lamiae , Danchin Nicolas , Dallongeville Jean , Falissard Bruno , Furber Alain , Cottin Yves , Bonello Laurent , Morel Olivier , Leclercq Florence , Puymirat Etienne , Ghanem Fahmi , Delarche Nicolas , Benichou Jacques , Abenhaim Lucien 
Published: March 2018

ObjectiveTo compare ticagrelor and prasugrel with clopidogrel for recurrent fatal and non-fatal myocardial infarction (reMI) in real-life conditions.MethodsCase-referent study using the Pharmacoepidemiological General Research eXtension (PGRx)-acute coronary syndrome (ACS) registry. Cases were patients with reMI from a cohort with index ACS or external to the cohort (same sites). Referents from the cohort, without recurrent event, were matched on index ACS type and date, age and sex with reMI cases. Multivariate conditional logistic regression assessed the OR (95% CI) for reMI associated with ticagrelor and prasugrel vs clopidogrel, adjusted for aspirin use and cardiovascular risk factors.Results1047 cases and 2234 matched referents were included. Compared with clopidogrel, ticagrelor and prasugrel were associated with respective ORs of 0.65 (95% CI 0.52 to 0.81) and 0.71 (95% CI 0.53 to 0.96) for reMI occurrence. ORs for ticagrelor and prasugrel vs clopidogrel were: 0.50 (95% CI 0.38 to 0.67) and 0.66 (95% CI 0.45 to 0.95), 0.39 (95% CI 0.24 to 0.62) and 0.44 (95% CI 0.26 to 0.75), 0.63 (95% CI 0.43 to 0.92) and 1.20 (95% CI 0.69 to 2.07), 1.11 (95% CI 0.72 to 1.72) and 0.82 (95% CI 0.44 to 1.54) when index ACS was a first MI, a first ST-elevated MI (STEMI), a first non-STEMI and a recurrent ACS, respectively, and 0.63 (95% CI 0.45 to 0.87) and 0.77 (95% CI 0.41 to 1.45) for patients aged ≥70  years.ConclusionsThis real-world study showed a significant reduction of reMI with new antiplatelets compared with clopidogrel, ticagrelor being associated with a greater decrease of risk notably for first, either STEMI or non-STEMI. The larger magnitude of effect may be attributed to potential residual confounding or higher effectiveness compared with efficacy reported in trials (EMA Post Authorisation Study Registry Number EUPAS5905).
Short preheating at 41°C leads to a red blood cells count comparable to that in RET channel of Sysmex analysers in samples showing cold agglutination
Authors: La Gioia Antonio , Fumi Maurizio , Fiorini Fabiana , Pezzati Paola , Balboni Fiamma , Bombara Maria , Marini Alessandra , Pancione Ylenia , Solarino Leonardo , Marchese Elisa , Sale Silvia , Rocco Vincenzo , Fiorini Marcello 
Published: March 2018

AimsThe presence of cold agglutinin in blood samples can cause a spontaneous agglutination of red blood cells (RBCs) when low temperature occurs. This phenomenon causes a spurious lowering of RBC count on the automated haematological analysers that are detected by incongruous values (≥370 g/L) of the mean cellular haemoglobi concentration (MCHC). A preheating at 37°C can remove the RBC agglutination generally resulting in a reliable count. It has been reported that the same result can be reached by using the optical reticulocyte (RET) channel of Sysmex analysers where the RBC count is not influenced by the presence of cold agglutinin. This study aims to evaluate these data in a larger population, with regard to environmental conditions on Sysmex analysers. We have also evaluated the influence of different thermal pretreatments on the RBC count.MethodsThis study was performed on 96 remnants of peripheral blood samples (48 with MCHC in normal range and 48 with MCHC>370 g/L) which have been analysed in different preanalytical conditions on the Sysmex analysers.ResultsA preheating of samples at 41°C for 1 min leads to a reversibility of the cold agglutination comparable to the one observed in the RET channel and yields better results compared with 37°C for 2 hours.ConclusionsNone of described procedures assure the complete cold agglutination reversibility in every case. Consequently, since the haematological analysers not yet provide reliable parameters to confirm the complete resolution of agglutination, further verification of RBC count accuracy needs to be performed.
Breast cancer histologic grading using digital microscopy: concordance and outcome association
Authors: Rakha Emad A , Aleskandarani Mohamed , Toss Michael S , Green Andrew R , Ball Graham , Ellis Ian O , Dalton Leslie W 
Published: March 2018

AimsVirtual microscopy utilising digital whole slide imaging (WSI) is increasingly used in breast pathology. Histologic grade is one of the strongest prognostic factors in breast cancer (BC). This study aims at investigating the agreement between BC grading using traditional light microscopy (LM) and digital WSI with consideration of reproducibility and impact on outcome prediction.MethodsA large (n=1675) well-characterised cohort of BC originally graded by LM was re-graded using WSI. Two separate virtual-based grading sessions (V1 and V2) were performed with a 3-month washout period. Outcome was assessed using BC-specific and distant metastasis-free survival.ResultsThe concordance between LM grading and WSI was strong (LM/WSI Cramer’s V: V1=0.576, and V2=0.579). The agreement regarding grade components was as follows: tubule formation=0.538, pleomorphism=0.422 and mitosis=0.514. Greatest discordance was observed between adjacent grades, whereas high/low grade discordance was uncommon (1.5%). The intraobserver agreement for the two WSI sessions was substantial for grade (V1/V2 Cramer’s V=0.676; kappa=0.648) and grade components (Cramer’s V T=0.628, p=0.573 and M=0.580). Grading using both platforms showed strong association with outcome (all p values <0.001). Although mitotic scores assessed using both platforms were strongly associated with outcome, WSI tends to underestimate mitotic counts.ConclusionsVirtual microscopy is a reliable and reproducible method for assessing BC histologic grade. Regardless of the observer or assessment platform, histologic grade is a significant predictor of outcome. Continuing advances in imaging technology could potentially provide improved performance of WSI BC grading and in particular mitotic count assessment.
The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics
Authors: Fumagalli Caterina , Vacirca Davide , Rappa Alessandra , Passaro Antonio , Guarize Juliana , Rafaniello Raviele Paola , de Marinis Filippo , Spaggiari Lorenzo , Casadio Chiara , Viale Giuseppe , Barberis Massimo , Guerini-Rocco Elena 
Published: March 2018

BackgroundMolecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously.AimsTo evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC.MethodsA single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes.Results441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed inKRAS,TP53,EGFR,STK11andMETgenes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairingKRASor EGFR in association withTP53alterations.ConclusionsThe study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.
Castor bean cake detoxified with calcium hydroxide in diets for pigs at growing and finishing phases
Authors: Gomes da Silva Taisa Rocha , Pascoal Leonardo Augusto Fonseca , Costa Fernando Guilherme Perazzo , Watanabe Pedro Henrique , Dantas Martins Terezinha Domiciano 
Published: March 2018

The present study was aimed to evaluate the use of increasing levels of castor bean cake detoxified with calcium hydroxide in diets for pigs at growing and finishing phases on performance, diet digestibility, weight of digestive organs, carcass traits, and economic evaluation. A total of 40 barrows with 44.59 ± 5.16 kg initial weight were fed diets with 0%, 7%, 14%, and 21% detoxified castor bean cake. Increasing levels of detoxified castor bean cake in diets resulted in linear worsening in the average daily gain of the pigs. Dry matter, crude protein, and gross energy digestibilities were adversely affected by the levels of detoxified castor bean cake. A linear decrease in loin eye area and ham yield was detected depending on detoxified castor bean cake inclusion levels. Although the detoxified castor bean cake had no effect on the assessed economic variables, its use in diets for growing and finishing pigs is not recommended.