bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal Expression Patterns and Antibody Reactivity of Taeniidae Endophilin B1
Authors: Ahn Chun-Seob , Bae Young-An , Kim Seon-Hee , Kim Jeong-Geun , Yu Jae-Ran , Yang Hyun-Jong , Eom Keeseon S. , Wang Hu , Kang Insug , Yang Yichao , Kong Yoon 
Published: August 2016

ABSTRACT

Larval Taeniidae, such as metacestodes of
Taenia solium
,
Echinococcus granulosus
, and
Echinococcus multilocularis
, produce chronic and fatal helminthic diseases. Proper identification of these zoonotic cestodiases is often challenging and is hampered in some clinical settings. Endophilin B1 plays critical roles in the maintenance of membrane contours and endocytosis. We isolated proteins homologous to endophilin B1 from
T. solium
,
Taenia saginata
, and
Taenia asiatica
. The three Taeniidae endophilin B1 proteins shared 92.9 to 96.6% sequence identity. They harbored a Bin1/amphiphysin/Rvs (BAR) domain and residues for a dimeric interface but lacked a SRC homology 3 (SH3) domain. Endophilin B1 showed a unique immunological profile and was abundantly expressed in the tegumental syncytium of Taeniidae metacestodes and adults. Bacterially expressed recombinant
T. solium
endophilin B1 (rTsMEndoB1) demonstrated a sensitivity of 79.7% (345/433 cases) for serodiagnosis of larval Taeniidae infections. The protein showed strong immune recognition patterns against sera from patients with chronic neurocysticercosis, cystic echinococcosis, or advanced-stage alveolar echinococcosis. Adult Taeniidae infections exhibited moderate degrees of positive antibody responses (65.7% [23/35 samples]). rTsMEndoB1 showed some cross-reactivity with sera from patients infected with Diphyllobothriidae (23.6% [25/106 samples]) but not with sera from patients with other parasitic diseases or normal controls. The specificity was 91.7% (256/301 samples). The positive and negative predictive values were 93.6% and 73.4%, respectively. Our results demonstrate that Taeniidae endophilin B1 may be involved in the control of membrane dynamics, thus contributing to shaping and maintaining the tegumental curvature. rTsMEndoB1 may be useful for large-scale screening, as well as for individual diagnosis and follow-up surveillance of Taeniidae infections.
Characterization of Vibrio cholerae Strains Isolated from the Nigerian Cholera Outbreak in 2010
Authors: Dupke Susann , Akinsinde Kehinde A. , Grunow Roland , Iwalokun Bamidele A. , Olukoya Daniel K. , Oluwadun Afolabi , Velavan Thirumalaisamy P. , Jacob Daniela 
Published: August 2016

ABSTRACT

We examined clinical samples from Nigerian patients with acute watery diarrhea for
Vibrio cholerae
during the 2010 cholera outbreak. A total of 109 suspected isolates were characterized, but only 57
V. cholerae
strains could be confirmed using multiplex real-time PCR as well as
rpoB
sequencing and typed as
V. cholerae
O:1 Ogawa biotype El Tor. This finding highlighted the need for accurate diagnosis of cholera in epidemic countries to implement life-saving interventions.
Human Choline Kinase-α Promotes Hepatitis C Virus RNA Replication through Modulation of Membranous Viral Replication Complex Formation
Authors: Wong Mun-Teng , Chen Steve S. 
Published: August 2016

ABSTRACT
Hepatitis C virus (HCV) infection reorganizes cellular membranes to create an active viral replication site named the membranous web (MW). The role that human choline kinase-α (hCKα) plays in HCV replication remains elusive. Here, we first showed that hCKα activity, not the CDP-choline pathway, promoted viral RNA replication. Confocal microscopy and subcellular fractionation of HCV-infected cells revealed that a small fraction of hCKα colocalized with the viral replication complex (RC) on the endoplasmic reticulum (ER) and that HCV infection increased hCKα localization to the ER. In the pTM-NS3-NS5B model, NS3-NS5B expression increased the localization of the wild-type, not the inactive D288A mutant, hCKα on the ER, and hCKα activity was required for effective trafficking of hCKα and NS5A to the ER. Coimmunoprecipitation showed that hCKα was recruited onto the viral RC presumably through its binding to NS5A domain 1 (D1). hCKα silencing or treatment with CK37, an hCKα activity inhibitor, abolished HCV-induced MW formation. In addition, hCKα depletion hindered NS5A localization on the ER, interfered with NS5A and NS5B colocalization, and mitigated NS5A-NS5B interactions but had no apparent effect on NS5A-NS4B and NS4B-NS5B interactions. Nevertheless, hCKα activity was not essential for the binding of NS5A to hCKα or NS5B. These findings demonstrate that hCKα forms a complex with NS5A and that hCKα activity enhances the targeting of the complex to the ER, where hCKα protein, not activity, mediates NS5A binding to NS5B, thereby promoting functional membranous viral RC assembly and viral RNA replication.

IMPORTANCE
HCV infection reorganizes the cellular membrane to create an active viral replication site named the membranous web (MW). Here, we report that human choline kinase-α (hCKα) acts as an essential host factor for HCV RNA replication. A fraction of hCKα colocalizes with the viral replication complex (RC) on the endoplasmic reticulum (ER) in HCV-infected cells. NS3-NS5B expression increases ER localization of wild-type, but not D288A mutant, hCKα, and hCKα activity facilitates the transport of itself and NS5A to the ER. Silencing or inactivation of hCKα abrogates MW formation. Moreover, hCKα is recruited by NS5A independent of hCKα activity, presumably through binding to NS5A D1. hCKα activity then mediates the ER targeting of the hCKα-NS5A complex. On the ER membrane, hCKα protein,
per se
, induces NS5A binding to NS5B, thereby promoting membranous RC formation and viral RNA replication. Our study may benefit the development of hCKα-targeted anti-HCV therapeutics.
Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis
Authors: Mojardín Laura , Salas Margarita 
Published: August 2016

ABSTRACT

The study of phage-host relationships is essential to understanding the dynamic of microbial systems. Here, we analyze genome-wide interactions of
Bacillus subtilis
and its lytic phage ϕ29 during the early stage of infection. Simultaneous high-resolution analysis of virus and host transcriptomes by deep RNA sequencing allowed us to identify differentially expressed bacterial genes. Phage ϕ29 induces significant transcriptional changes in about 0.9% (38/4,242) and 1.8% (76/4,242) of the host protein-coding genes after 8 and 16 min of infection, respectively. Gene ontology enrichment analysis clustered upregulated genes into several functional categories, such as nucleic acid metabolism (including DNA replication) and protein metabolism (including translation). Surprisingly, most of the transcriptional repressed genes were involved in the utilization of specific carbon sources such as ribose and inositol, and many contained promoter binding-sites for the catabolite control protein A (CcpA). Another interesting finding is the presence of previously uncharacterized antisense transcripts complementary to the well-known phage ϕ29 messenger RNAs that adds an additional layer to the viral transcriptome complexity.

IMPORTANCE
The specific virus-host interactions that allow phages to redirect cellular machineries and energy resources to support the viral progeny production are poorly understood. This study provides, for the first time, an insight into the genome-wide transcriptional response of the Gram-positive model
Bacillus subtilis
to phage ϕ29 infection.
Infectious Progression of Canine Distemper Virus from Circulating Cerebrospinal Fluid into the Central Nervous System
Authors: Takenaka Akiko , Sato Hiroki , Ikeda Fusako , Yoneda Misako , Kai Chieko 
Published: August 2016

ABSTRACT

In the current study, we generated recombinant chimeric canine distemper viruses (CDVs) by replacing the hemagglutinin (H) and/or phosphoprotein (P) gene in an avirulent strain expressing enhanced green fluorescent protein (EGFP) with those of a mouse-adapted neurovirulent strain. An
in vitro
experimental infection indicated that the chimeric CDVs possessing the H gene derived from the mouse-adapted CDV acquired infectivity for neural cells. These cells lack the CDV receptors that have been identified to date (SLAM and nectin-4), indicating that the H protein defines infectivity in various cell lines. The recombinant viruses were administered intracerebrally to 1-week-old mice. Fatal neurological signs of disease were observed only with a recombinant CDV that possessed both the H and P genes of the mouse-adapted strain, similar to the parental mouse-adapted strain, suggesting that both genes are important to drive virulence of CDV in mice. Using this recombinant CDV, we traced the intracerebral propagation of CDV by detecting EGFP. Widespread infection was observed in the cerebral hemispheres and brainstems of the infected mice. In addition, EGFP fluorescence in the brain slices demonstrated a sequential infectious progression in the central nervous system: CDV primarily infected the neuroependymal cells lining the ventricular wall and the neurons of the hippocampus and cortex adjacent to the ventricle, and it then progressed to an extensive infection of the brain surface, followed by the parenchyma and cortex. In the hippocampal formation, CDV spread in a unidirectional retrograde pattern along neuronal processes in the hippocampal formation from the CA1 region to the CA3 region and the dentate gyrus. Our mouse model demonstrated that the main target cells of CDV are neurons in the acute phase and that the virus spreads via neuronal transmission pathways in the hippocampal formation.

IMPORTANCE
CDV is the etiological agent of distemper in dogs and other carnivores, and in many respects, the pathogenesis of CDV infection in animals resembles that of measles virus infection in humans. We successfully generated a recombinant CDV containing the H and P genes from a mouse-adapted neurovirulent strain and expressing EGFP. The recombinant CDV exhibited severe neurovirulence with high mortality, comparable to the parental mouse-adapted strain. The mouse-infectious model could become a useful tool for analyzing CDV infection of the central nervous system subsequent to passing through the blood-cerebrospinal fluid barrier and infectious progression in the target cells in acute disease.
Interleukin-1β and tumour necrosis factor-α levels in conjunctiva of diabetic patients with symptomatic moderate dry eye: case–control study
Authors: Zhang Chen , Xi Lei , Zhao Shaozhen , Wei Ruihua , Huang Yue , Yang Ruibo , Su Long , Liu Xun 
Published: August 2016

ObjectivesTo compare expression of interleukin (IL)-1β and tumour necrosis factor (TNF)-α in the conjunctiva of diabetic and non-diabetic patients with symptomatic moderate dry eye.Setting and participantsNineteen diabetic patients with dry eye, 15 non-diabetic patients with dry eye and 14 diabetic patients without dry eye were recruited. The relative expression of IL-1β and TNF-α in conjunctival impression cytology (CIC) specimens was evaluated using immunofluorescent staining and in conjunctival biopsy specimens using immunohistochemical staining.ResultsThe diabetic dry eye group showed significantly higher grades of metaplasia than the non-diabetic dry eye and diabetic without dry eye groups (both p<0.05). There was no significant difference in the concentration of IL-1β and TNF-α in CIC specimens between the three groups (p=0.504 and p=0.310, respectively). The mean levels of IL-1β and TNF-α in conjunctival biopsy specimens from the diabetic dry eye group was significantly increased compared with the non-diabetic dry eye and diabetic without dry eye groups (p=0.002, p<0.001; p=0.001, p<0.001, respectively). Interestingly, IL-1β- and TNF-α-positive cells were mainly located in the basal layer of the conjunctival epithelium, and rarely seen in the apical conjunctival epithelium in the three groups. The levels of both IL-1β and TNF-α did not correlate with conjunctival squamous metaplasia grades.ConclusionsLevels of IL-1β and TNF-α in conjunctival biopsy specimens were increased in diabetic patients with dry eye, while levels of IL-1β and TNF-α in apical conjunctival epithelium were similar in the CIC specimens. These findings suggest that the inflammatory response is not limited to the surface of conjunctival epithelial cells, and is more serious in the basal layer of the epithelium, which may play an important role in the pathogenesis of dry eye in diabetic patients.
Bibliometric analysis of scientific publications in transplantation journals from Mainland China, Japan, South Korea and Taiwan between 2006 and 2015
Authors: Pu Qiang-Hong , Lyu Qiu-Ju , Su Huai-Yu 
Published: August 2016

ObjectivesThe aim of this study is to compare the quantity and quality of scientific publications in transplantation fields that were written by researchers from Mainland China, Japan, South Korea and Taiwan in the East Asia region.SettingsEast Asia.Participants and outcome measuresArticles except editorials, conference abstracts, letters, news and corrections published in 25 transplantation journals from 2006 to 2015 were screened with the Web of Science database. The number of total and annual articles, article types (study design and transplantation site), impact factor, citations and articles in the high-impact journals was determined to assess the quantity and quality of transplantation research from East Asia. The correlation of socioeconomic factors and annual publications was also analysed.ResultsFrom 2006 to 2015, there were 47 141 articles published in transplantation journals, of which researchers from Japan published 3694 articles, followed by Mainland China, South Korea and Taiwan with 2778, 1643 and 951 articles, respectively. Similar trends were observed in accumulated impact factor, accumulated citations, articles in the high-impact journals and articles on transplantation site. Publications from Japan had the highest average impact factor and citation, while those from Mainland China had the lowest. Additionally, in terms of study design, authors from Mainland China contributed to most clinical trials and randomised controlled trials, but authors from Japan contributed to most case reports. The annual numbers of articles from Mainland China and South Korea increased linearly (p<0.05), but those from Japan and Taiwan remained stable for the period studied. The annual numbers of articles from Mainland China and South Korea were positively correlated with gross domestic product (p<0.05).ConclusionsTransplantation research productivity in East Asia is highly skewed, with gross domestic product having a significant positive correlation. Mainland China still lags far behind Japan in most bibliometric indicators; thus, there is vast room for improvement.
Live cumulative network meta-analysis: protocol for second-line treatments in advanced non-small-cell lung cancer with wild-type or unknown status for epidermal growth factor receptor
Authors: Créquit Perrine , Trinquart Ludovic , Ravaud Philippe 
Published: August 2016

IntroductionMany second-line treatments for advanced non-small-cell lung cancer (NSCLC) have been assessed in randomised controlled trials, but which treatments work the best remains unclear. Novel treatments are being rapidly developed. We need a comprehensive up-to-date evidence synthesis of all these treatments. We present the protocol for a live cumulative network meta-analysis (NMA) to address this need.Methods and analysisWe will consider trials of second-line treatments in patients with advanced NSCLC with wild-type or unknown epidermal growth factor receptor status. We will consider any single agent of cytotoxic chemotherapy, targeted therapy, combination of cytotoxic chemotherapy and targeted therapy and any combination of targeted therapies. The primary outcomes will be overall survival and progression-free survival. The live cumulative NMA will be initiated with a NMA and then iterations will be repeated at regular intervals to keep the NMA up-to-date over time. We have defined the update frequency as 4 months, based on an assessment of the pace of evidence production on this topic. Each iteration will consist of six methodological steps: adaptive search for treatments and trials, screening of reports and selection of trials, data extraction, assessment of risk of bias, update of the network of trials and synthesis, and dissemination. We will set up a research community in lung cancer, with different groups of contributors of different skills. We will distribute tasks through online crowdsourcing. This proof-of-concept study in second-line treatments of advanced NSCLC will allow one for assessing the feasibility of live cumulative NMA and opening the path for this new form of synthesis.Ethics and disseminationEthical approval is not required because our study will not include confidential participant data and interventions. The description of all the steps and the results of this live cumulative NMA will be available online.Trial registration numberCRD42015017592.
Venous thromboembolism in medical patients during hospitalisation and 3 months after hospitalisation: a prospective observational study
Authors: Khalafallah Alhossain A , Kirkby Brooke E , Wong Sophia , Foong Yi Chao , Ranjan Nishant , Luttrell James , Mathew Ronnie , Chilvers Charles M , Mauldon Emily , Sharp Colin , Hannan Terry 
Published: August 2016

ObjectivesThis study was conducted to assess the incidence and risk factors for venous thromboembolism (VTE) in a cohort of medical patients both during the period of hospitalisation and following discharge.DesignThis was a prospective observational study to document the risk profile and incidence of VTE posthospitalisation among all medical patients admitted to our institution during the trial period.SettingsPrimary healthcare. Single tertiary referral centre, Tasmania, Australia.ParticipantsA total of 986 patients admitted to the medical ward between January 2012 and September 2012 were included in the study with male to female ratio of 497:489. The mean age of patients was 68 years (range 17–112, SD 16).ResultsOverall, 54/986 patients (5.5%) had a VTE during the study period. Of these, 40/54 (74.1%) occurred during hospitalisation and 14/54 (25.9%) occurred following discharge. VTE risk factors revealed in multivariate analysis to be associated with a previous diagnosis of VTE (p<0.001, OR=6.63, 95% CI 3.3 to 13.36), the occurrence of surgery within the past 30 days (p<0.001, OR=2.52, 95% CI 1.33 to 4.79) and an admission diagnosis of pulmonary disease (p<0.01, OR 3.61, 95% CI 1.49 to 8.76). Mobility within 24 hours of admission was not associated with an increased risk. There was risk of VTE when the length of stay prolonged (p=0.046, OR=1.01, 95% CI 1.00 to 1.03), however it was not sustained with multivariate modelling. VTE-specific prophylaxis was used in 53% of the studied patients. Anticoagulation including antiplatelet agents were administered in 63% of patients who developed VTE.ConclusionsThis prospective observational study found that 5.5% of the studied patients developed VTE. Among those, 25.9% (14/54) of patients had a detected VTE posthospitalisation with this risk being increased if there was a history of VTE, recent surgery and pulmonary conditions. Thromboprophylaxis may be worth considering in these cohorts. Further study to confirm these findings are warranted.Trial registration numberACTRN12611001255976.
Analysis of safety outcomes for radial versus femoral access for percutaneous coronary intervention from a large clinical registry
Authors: Dobies David R , Barber Kimberly R , Cohoon Amanda L 
Published: August 2016

ObjectiveUsing a multisite, contemporary registry of 58 862 percutaneous coronary intervention (PCI) procedures in a national healthcare system, the present study compared radial access with femoral access on safety and efficacy outcomes.MethodsThis is a real-world, large-scale, retrospective study using clinical data from a 137-hopsital System and reported to a multisite clinical registry. All patients undergoing a cardiac catheterisation procedure were included in this database. The primary end points were major bleeding and radiation exposure. Multivariate logistic regression modelling was used to compare access groups.ResultsFemoral access (n=55 729) accounted for 94.7% and radial access (n=3137) for 5.3%. There were fewer bleeding events in the radial group (n=28, 0.9%) than those in the femoral group (n=1234, 2.2%) in the unadjusted analysis. For patients receiving bivalirudin, bleeding occurred in 337 patients (1.6%), and there was no difference in rates between radial access (n=13, 1.1%) and femoral access (n=327, 1.7%) (OR=0.65, CI 0.40 to 1.22, p=0.19). The radial technique resulted in higher radiation exposure in each case, but particularly for procedures involving prior coronary artery bypass graft history and non-ST-elevated myocardial infarction patients. The mean fluoroscopy time among femoral access procedures was 15.68 min (SD=11.7) versus 19.86 min (SD=13.8) for radial access procedures (p<0.0001).ConclusionsRadial access for PCI is associated with higher fluoroscopy times but not with less major bleeding when bivalirudin is used. Our analysis, combined with other study findings, suggest that the safest route for PCI may be the use of femoral access with bivalirudin.
Get the Diagnosis: an evidence-based medicine collaborative Wiki for diagnostic test accuracy
Authors: Hammer Mark M , Kohlberg Gavriel D 
Published: August 2016

ABSTRACTBackgroundDespite widespread calls for its use, there are challenges to the implementation of evidence-based medicine (EBM) in clinical practice.MethodsIn response to the challenges of finding timely, pertinent information on diagnostic test accuracy, we developed an online, crowd-sourced Wiki on diagnostic test accuracy called Get the Diagnosis (GTD, http://www.getthediagnosis.org).ResultsSince its launch in November 2008 till October 2015, GTD has accumulated information on 300 diagnoses, with 1617 total diagnostic entries. There are a total of 1097 unique diagnostic tests with a mean of 5.4 tests (range 0–38) per diagnosis. 73% of entries (1182 of 1617) have an associated sensitivity and specificity and 89% of entries (1432 of 1617) have associated peer-reviewed literature citations. Altogether, GTD contains 474 unique literature citations. For a sample of three diagnoses, the search precision (percentage of relevant results in the first 30 entries) in GTD was 100% as compared with a range of 13.3%–63.3% for PubMed and between 6.7% and 76.7% for Google Scholar.ConclusionGTD offers a fast, precise and efficient way to look up diagnostic test accuracy. On three selected examples, GTD had a greater precision rate compared with PubMed and Google Scholar in identifying diagnostic test information. GTD is a free resource that complements other currently available resources.
Analyzing Runtime and Size Complexity of Integer Programs
Authors: Brockschmidt Marc , Emmes Fabian , Falke Stephan , Fuhs Carsten , Giesl Jürgen 
Published: August 2016

We present a modular approach to automatic complexity analysis of integer programs. Based on a novel alternation between finding symbolic time bounds for program parts and using these to infer bounds on the absolute values of program variables, we can restrict each analysis step to a small part of the program while maintaining a high level of precision. The bounds computed by our method are polynomial or exponential expressions that depend on the absolute values of input parameters.
We show how to extend our approach to arbitrary cost measures, allowing the use of our technique to find upper bounds for other expended resources, such as network requests or memory consumption. Our contributions are implemented in the open-source tool KoAT, and extensive experiments show the performance and power of our implementation in comparison with other tools.