bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Evaluation of the MALDI Sepsityper and Verigene BC-GN Assays for Rapid Identification of Gram-Negative Bacilli from Positive Blood Cultures
Authors: Arroyo Miguel A. , Denys Gerald A. 
Published: June 2017

ABSTRACT

Rapid identification of microorganisms from positive blood cultures has improved clinical management and antimicrobial stewardship. The advent of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has reduced the time to identification of cultured isolates and is now often the definitive method used in the clinical microbiology laboratory. The commercial
in vitro
diagnostic MALDI Sepsityper (Sepsityper) kit has the potential for standardization and clinical routine use for the rapid identification of a broad range of bacteria from positive blood cultures. In this study, we performed a parallel evaluation of the Sepsityper (Bruker Daltonics, Billerica, MA) and the Verigene BC-GN (BC-GN) assays (Nanosphere, Inc., Northfield, IL) for the identification of Gram-negative bacilli. A total of 210 Bactec bottles demonstrating Gram-negative bacilli were prospectively enrolled for this study. Among these, 200 monomicrobial cultures were included in the comparative analysis. For monomicrobial cultures, the BC-GN detected 85% (170/200) compared to that detected by routine culture while the Sepsityper detected 94% (188/200) and 91% (181/200) to the genus and species levels, respectively. Comparable positive percentage agreement and negative percentage agreement were observed between the Sepsityper (96.5% and 98.8%, respectively) and the BC-GN (99.4% and 99.8%, respectively) when only (
n
= 170, 85%) organisms targeted by the latter test were included in the analysis. In conclusion, the two methods evaluated in this study showed excellent performance characteristics for the identification of Gram-negative bacilli commonly isolated from blood cultures. The Sepsityper showed a broader identification range capability that may further improve clinical management and antimicrobial stewardship in patients with less frequent Gram-negative bacilli bloodstream infections.
Differential Requirement of Human Cytomegalovirus UL112-113 Protein Isoforms for Viral Replication
Authors: Schommartz Tim , Tang Jiajia , Brost Rebekka , Brune Wolfram 
Published: June 2017

ABSTRACT
The UL112-113 gene is one of the few alternatively spliced genes of human cytomegalovirus (HCMV). It codes for four phosphoproteins, p34, p43, p50, and p84, all of which are expressed with early kinetics and accumulate at sites of viral DNA replication within the host cell nucleus. Although these proteins are known to play important, possibly essential, roles in the viral replication cycle, little is known about the contribution of individual UL112-113 protein products. Here we used splice site mutagenesis, intron deletion and substitution, and nonsense mutagenesis to prevent the individual expression of each UL112-113 protein isoform and to investigate the importance of each isoform for viral replication. We show that HCMV mutants lacking p34 or p50 expression replicated to high titers in human fibroblasts and endothelial cells, indicating that these proteins are nonessential for viral replication, while mutant viruses carrying a stop mutation within the p84 coding sequence were severely growth impaired. Viral replication could not be detected upon the inactivation of p43 expression, indicating that this UL112-113 protein is essential for viral replication. We also analyzed the ability of UL112-113 proteins to recruit other viral proteins to intranuclear prereplication compartments. While UL112-113 expression was sufficient to recruit the UL44-encoded viral DNA polymerase processivity factor, it was not sufficient for the recruitment of the viral UL84 and UL117 proteins. Remarkably, both the p43 and p84 isoforms were required for the efficient recruitment of pUL44, which is consistent with their critical role in the viral life cycle.

IMPORTANCE
Human cytomegalovirus requires gene products from 11 genetic loci for the lytic replication of its genome. One of these loci, UL112-113, encodes four proteins with common N termini by alternative splicing. In this study, we inactivated the expression of each of the four UL112-113 proteins individually and determined their requirement for HCMV replication. We found that two of the UL112-113 gene products were dispensable for viral replication in human fibroblasts and endothelial cells. In contrast, viral replication was severely reduced or absent when one of the other two gene products was inactivated, indicating that they are of crucial importance for the viral replication cycle. We further showed that the latter two gene products are involved in the recruitment of pUL44, an essential cofactor of the viral DNA polymerase, to specific sites within the cell nucleus that are thought to serve as starting points for viral DNA replication.
Identification of an Intermediate in Hepatitis B Virus Covalently Closed Circular (CCC) DNA Formation and Sensitive and Selective CCC DNA Detection
Authors: Luo Jun , Cui Xiuji , Gao Lu , Hu Jianming 
Published: June 2017

ABSTRACT
Hepatitis B virus (HBV) covalently closed circular (CCC) DNA functions as the only viral template capable of coding for all the viral RNA species and is thus essential to initiate and sustain viral replication. CCC DNA is converted, in a multistep and ill-understood process, from a relaxed circular (RC) DNA, in which neither of the two DNA strands is covalently closed. To detect putative intermediates during RC DNA to CCC DNA conversion, two 3′ exonucleases, exonuclease I (Exo I) and Exo III, were used in combination to degrade all DNA strands with a free 3′ end, which would nevertheless preserve closed circular DNA in either single-stranded (SS) or double-stranded (DS) form. Indeed, an RC DNA species with a covalently closed minus strand but an open plus strand (closed minus-strand RC DNA [cM-RC DNA]) was detected by this approach. Further analyses indicated that at least some of the plus strands in such a putative intermediate likely still retained the RNA primer that is attached to the 5′ end of the plus strand in RC DNA, suggesting that minus-strand closing can occur before plus-strand processing. Furthermore, the same nuclease treatment proved to be useful for sensitive and specific detection of CCC DNA by removing all DNA species other than closed circular DNA. Application of these and similar approaches may allow the identification of additional intermediates during CCC DNA formation and facilitate specific and sensitive detection of CCC DNA, which should help elucidate the pathways of CCC DNA formation and the factors involved.

IMPORTANCE
The hepatitis B virus (HBV) covalently closed circular (CCC) DNA, by serving as the viral transcriptional template, is the molecular basis of viral persistence. CCC DNA is converted, in a multistep and ill-understood process, from relaxed circular (RC) DNA. Little is currently understood about the pathways or factors involved in CCC DNA formation. We have now detected a likely intermediate during the conversion of RC DNA to CCC DNA, thus providing important clues to the pathways of CCC DNA formation. Furthermore, the same experimental approach that led to the detection of the intermediate could also facilitate specific and sensitive detection of CCC DNA, which has remained challenging. This and similar approaches will help identify additional intermediates during CCC DNA formation and elucidate the pathways and factors involved.
High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia
Authors: Shi Mang , Neville Peter , Nicholson Jay , Eden John-Sebastian , Imrie Allison , Holmes Edward C. 
Published: June 2017

ABSTRACT

Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the
Aedes
genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the
Culex
genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three
Culex
species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.

IMPORTANCE
Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with
Culex
species harboring more viruses at higher abundance than those from
Aedes
mosquitoes.
Seasonal H3N2 and 2009 Pandemic H1N1 Influenza A Viruses Reassort Efficiently but Produce Attenuated Progeny
Authors: Phipps Kara L. , Marshall Nicolle , Tao Hui , Danzy Shamika , Onuoha Nina , Steel John , Lowen Anice C. 
Published: June 2017

ABSTRACT
Reassortment of gene segments between coinfecting influenza A viruses (IAVs) facilitates viral diversification and has a significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have cocirculated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous coinfections with pH1N1 and H3N2 viruses were compared to those obtained following coinfection with homologous, genetically tagged, pH1N1 viruses as a control. High genotype diversity was observed among progeny of both coinfections; however, diversity was more limited following heterologous coinfection. Pairwise analysis of genotype patterns revealed that homologous reassortment was random while heterologous reassortment was characterized by specific biases. pH1N1/H3N2 reassortant genotypes produced under single-cycle coinfection conditions showed a strong preference for homologous PB2-PA combinations and general preferences for the H3N2 NA, pH1N1 M, and H3N2 PB2 except when paired with the pH1N1 PA or NP. Multicycle coinfection results corroborated these findings and revealed an additional preference for the H3N2 HA. Segment compatibility was further investigated by measuring chimeric polymerase activity and growth of selected reassortants in human tracheobronchial epithelial cells. In guinea pigs inoculated with a mixture of viruses, parental H3N2 viruses dominated but reassortants also infected and transmitted to cage mates. Taken together, our results indicate that strong intrinsic barriers to reassortment between seasonal H3N2 and pH1N1 viruses are few but that the reassortants formed are attenuated relative to parental strains.

IMPORTANCE
The genome of IAV is relatively simple, comprising eight RNA segments, each of which typically encodes one or two proteins. Each viral protein carries out multiple functions in coordination with other viral components and the machinery of the cell. When two IAVs coinfect a cell, they can exchange genes through reassortment. The resultant progeny viruses often suffer fitness defects due to suboptimal interactions among divergent viral components. The genetic diversity generated through reassortment can facilitate the emergence of novel outbreak strains. Thus, it is important to understand the efficiency of reassortment and the factors that limit its potential. The research described here offers new tools for studying reassortment between two strains of interest and applies those tools to viruses of the 2009 pandemic H1N1 and seasonal H3N2 lineages, which currently cocirculate in humans and therefore have the potential to give rise to novel epidemic strains.
Red blood cell distribution width as a risk factor for inhospital mortality in obstetric patients admitted to an intensive care unit: a single centre retrospective cohort study
Authors: Chu Yufeng , Yuan Zhongshang , Meng Mei , Zhou Haiyan , Wang Chunting , Yang Gong , Ren Hongsheng 
Published: June 2017

BackgroundRed blood cell distribution width (RDW) has been shown to predict mortality in critically ill patients. To our knowledge, whether or not RDW is associated with clinical outcomes of obstetric patients requiring critical care has not been evaluated.MethodsThis was a single centre, retrospective, observational study of obstetric patients admitted to the intensive care unit (ICU). Patients were excluded from the analysis if they had known haematological diseases or recently underwent blood transfusion. Patients who died or were discharged from the ICU within 24 hours of admission were also excluded. Patient clinical characteristics at ICU admission were retrieved from the medical charts. Multiple logistic regression was used to estimate OR and 95% CI for inhospital mortality associated with RDW. The receiver operating characteristic curve was used to examine the performance of RDW, alone or in combination with the Acute Physiology and Chronic Health Evaluation II score (APACHE II), in predicting inhospital mortality.ResultsA total of 376 patients were included in the study. The hospital mortality rate was 5.32%. A significant association was found between baseline RDW levels and hospital mortality (OR per per cent increase in RDW, 1.31; 95% CI 1.15 to 1.49). Further adjustment for haematocrit and other potential confounders did not appreciably alter the result (p<0.001). The area under the curve (AUC) for inhospital mortality based on RDW was similar to that based on the APACHE II score (0.752 vs 0.766). A combination of these two factors resulted in substantial improvement in risk prediction, with an AUC value of 0.872 (p<0.001).ConclusionsThe study suggests that RDW is an independent predictor for inhospital mortality among ICU admitted obstetric patients. Combining RDW and APACHE II score could significantly improve inhospital prognostic prediction among these critically ill obstetric patients.
Efficacy of long-acting release octreotide for preventing chemotherapy-induced diarrhoea: protocol for a systematic review
Authors: Deng Chao , Deng Bo , Jia Liqun , Tan Huangying 
Published: June 2017

IntroductionDiarrhoea is a common adverse effect induced by chemotherapy that can reduce the dose of chemotherapeutic drugs or interrupt the chemotherapy schedule. The current treatment strategies have various limitations. It has been shown that long-acting release octreotide (octreotide LAR) can decrease the occurrence and severity of diarrhoea, yet the efficacy of octreotide LAR in preventing chemotherapy-induced diarrhoea (CID) remains to be assessed. The main objective of this paper was to draw up a protocol for systematic review to evaluate the protective effects of octreotide LAR on CID.Methods and analysisWe searched Medline, EMBASE, the Cochrane Library, Chinese National Knowledge Infrastructure, Wanfang Data and the VIP Database without language restrictions from inception until 1 September 2016. The references of relevant studies were also manually searched. Two investigators independently accessed the selected studies, extracted data and assessed the reliability of the studies. Any discrepancies were resolved by a third investigator. The effect size of the selected studies was assessed by different measures based on the type of data. The selected studies were descriptively analysed. We then chose a fixed-effect model or a random-effect model based on statistical homogeneity, and pooled data from the studies for meta-analysis, if possible. The primary outcome was the incidence of diarrhoea. The secondary outcomes were the duration of diarrhoea, incidence of diarrhoea-associated symptoms, physical function and quality of life. All statistical analyses were performed by Review Manager V.5.3.Ethics and disseminationThis systematic review did not require ethics approval, because it included aggregated published data, and not individual patient data. The review was published in a peer-reviewed journal.Trial registrationThis systematic review protocol was registered with PROSPERO (registration number: CRD 42016048573).
Tablet computers versus optical aids to support education and learning in children and young people with low vision: protocol for a pilot randomised controlled trial, CREATE (Children Reading with Electronic Assistance To Educate)
Authors: Crossland Michael D , Thomas Rachel , Unwin Hilary , Bharani Seelam , Gothwal Vijaya K , Quartilho Ana , Bunce Catey , Dahlmann-Noor Annegret 
Published: June 2017

IntroductionLow vision and blindness adversely affect education and independence of children and young people. New ‘assistive’ technologies such as tablet computers can display text in enlarged font, read text out to the user, allow speech input and conversion into typed text, offer document and spreadsheet processing and give access to wide sources of information such as the internet. Research on these devices in low vision has been limited to case series.Methods and analysisWe will carry out a pilot randomised controlled trial (RCT) to assess the feasibility of a full RCT of assistive technologies for children/young people with low vision. We will recruit 40 students age 10–18 years in India and the UK, whom we will randomise 1:1 into two parallel groups. The active intervention will be Apple iPads; the control arm will be the local standard low-vision aid care. Primary outcomes will be acceptance/usage, accessibility of the device and trial feasibility measures (time to recruit children, lost to follow-up). Exploratory outcomes will be validated measures of vision-related quality of life for children/young people as well as validated measures of reading and educational outcomes. In addition, we will carry out semistructured interviews with the participants and their teachers.Ethics and disseminationNRES reference 15/NS/0068; dissemination is planned via healthcare and education sector conferences and publications, as well as via patient support organisations.Trial registration numberNCT02798848; IRAS ID 179658, UCL reference 15/0570.
Knowledge, attitude and practice of healthcare professionals towards infliximab and insulin glargine biosimilars: result of a UK web-based survey
Authors: Chapman Stephen R , Fitzpatrick Raymond W , Aladul Mohammed I 
Published: June 2017

ObjectiveTo investigate healthcare professionals’ knowledge and attitudes towards infliximab and insulin glargine biosimilars and the factors influencing their prescribing. Then, to compare healthcare professionals’ attitudes with the utilisation of these biosimilars in UK hospitals.DesignSelf-administered, one-time web-based survey and drug utilisation analysis.Setting and data sourcesProfessional associations and societies in the field of dermatology, diabetology, gastroenterology and rheumatology in the UK, between 8 August 2016 and 8 January 2017. The volume of utilisation of branded and biosimilar infliximab and insulin glargine in UK hospitals was derived from the DEFINE database, between 2015 and 2016.OutcomesParticipants’ knowledge and awareness of biosimilars and factors influencing their use and corresponding usage of infliximab and insulin glargine biosimilars.ResultsResponses were obtained from 234 healthcare professionals across dermatology, diabetology, gastroenterology and rheumatology specialties. 75% of respondents were aware that biosimilars were available on their local formulary. 77% of respondents considered biosimilars extremely or very important to save costs for the NHS. Gastroenterologists had the highest utilisation of infliximab biosimilars (14%) in 2015 rising to (62%) in 2016. Healthcare professionals had greater concerns about safety and efficacy when switching patients to biosimilars than when starting biosimilars in biological naïve patients. Guidance from National Institute for Health and Care Excellence and robust pharmacovigilance studies on biosimilars were both considered important factors in increasing biosimilars use.ConclusionBritish healthcare professionals are well informed about biosimilars with high level of awareness. Safety and efficacy concerns were higher in switching than in initiating biosimilars among some prescribers. It is probable that personal experience of biologics as well as discipline-specific guidance influenced prescribers’ responses.
Advance care planning in Medicare: an early look at the impact of new reimbursement on billing and clinical practice
Authors: Tsai Gawin , Taylor Donald H 
Published: June 2017

ObjectiveIn this study, we examined the US Medicare programme’s (government-funded social insurance for the elderly or disabled) new reimbursement for advance care planning (ACP) that began on 1 January 2016. This single-centre study addressed whether clinicians who have ACP conversations with patients will use the new reimbursement code and if the new reimbursement is successful at motivating clinicians to have more ACP conversations with patients.MethodsThis is a multimethod study. To gain a general sense of ACP practice and code visibility, we first surveyed 493 clinicians in a large academic medical centre (20% response rate). Then, for more in-depth answers and to illuminate the reasons behind survey findings, we conducted semistructured interviews with 28 physicians.ResultsWe found that while clinicians are open to using the reimbursement codes, organisational barriers such as low visibility and documentation make it difficult for clinicians to bill for ACP. Moreover, structural and professional factors have rendered Medicare’s ACP reimbursement largely ineffective at motivating healthcare providers to perform more ACP conversations during the first 3 months of this policy.ConclusionsIt does not appear that Medicare’s reimbursement of ACP has made a significant, direct impact on ACP billing or practice during the policy’s first 90 days. However, there is a symbolic role that this change can serve, and the policy could have more impact as its existence becomes more widely known. Barriers to ACP that we identify should be addressed directly to expand the use of ACP.