bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection of Human Cytomegalovirus UL97 and UL54 Mutations Directly from Patient Samples
Authors: Hall Sedlak Ruth , Castor Jared , Butler-Wu Susan M. , Chan Elaine , Cook Linda , Limaye Ajit P. , Jerome Keith R. 
Published: May 2013

ABSTRACT
Human cytomegalovirus (CMV) is a significant contributor to morbidity and mortality in immunocompromised patients, particularly in the transplant setting. The availability of anti-CMV drugs has improved treatment, but drug resistance is an emerging problem. Here, we describe an improved, rapid, sequencing-based assay for the two genes in CMV where drug resistance occurs, the UL97 and UL54 genes. This assay is performed in 96-well format with a single master mix and provides clinical results within 2 days. It sequences codons 440 to 645 in the UL97 gene and codons 255 to 1028 in the UL54 gene with a limit of detection of 240 IU/ml. With this assay, we tested 43 specimens that had previously been tested for UL97 drug resistance and identified 3 with UL54 mutations. One of these patients had no concurrent UL97 mutation, pointing toward the need for an assay that facilitates dual UL97/UL54 gene testing for complete resistance profiling.
Comparative Evaluation of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization–Time Of Flight (MALDI-TOF) Mass Spectrometry Systems for Identification of Yeasts of Medical Importance
Authors: Mancini Nicasio , De Carolis Elena , Infurnari Laura , Vella Antonietta , Clementi Nicola , Vaccaro Luisa , Ruggeri Alberto , Posteraro Brunella , Burioni Roberto , Clementi Massimo , Sanguinetti Maurizio 
Published: May 2013

ABSTRACT

We report the first comparative evaluation between the Bruker Biotyper MS (BMS) and the Vitek MS (VMS) for the identification of yeasts. The rate of correct identifications at the species level was comparable using the commercial databases (89.8% versus 84.3%;
P
= 0.712), but higher for BMS using an in-house-extended database (100% versus 84.3%;
P
= 0.245). Importantly, the rate of misidentification was significantly higher for VMS (1% versus 12.1%;
P
< 0.0001), including the rate of major errors (0% versus 4.5%;
P
= 0.0036).
Intraventricular Hemorrhage and Multiple Intracranial Cysts Associated with Congenital Cytomegalovirus Infection
Authors: Suksumek Nithipun , Scott James N. , Chadha Rati , Yusuf Kamran 
Published: May 2013

ABSTRACT
Intraventricular hemorrhage with congenital cytomegalovirus (CMV) infection is rare and has been reported only in extremely premature infants or in association with thrombocytopenia. We report the first case of a full-term male infant with congenital CMV infection and intraventricular hemorrhage with a normal platelet count and coagulation profile. The infant also had a left subependymal cyst and bilateral occipital cysts without any other manifestations of CMV infection.
Prevalence of Porcine Noroviruses, Molecular Characterization of Emerging Porcine Sapoviruses from Finisher Swine in the United States, and Unified Classification Scheme for Sapoviruses
Authors: Scheuer Kelly A. , Oka Tomoichiro , Hoet Armando E. , Gebreyes Wondwossen A. , Molla Bayleyegn Z. , Saif Linda J. , Wang Qiuhong 
Published: May 2013

ABSTRACT

Noroviruses (NoVs) and sapoviruses (SaVs) are important human pathogens. Although the involvement of porcine NoVs in disease in pigs is unclear, they are genetically and antigenically closely related to human NoVs. Human NoV-like strains have been detected in pigs, raising public health concerns of potential interspecies transmission. Porcine SaVs are highly diverse and emerging in swine populations. Recently, at least three new genogroups of porcine SaVs have been proposed. In this study, we tested 413 pooled fecal samples collected from apparently healthy finisher pigs in North Carolina swine farms during 2009. Reverse transcription (RT)-PCR coupled hybridization assays were performed to detect known porcine NoVs. The overall prevalence of porcine NoVs determined was 18.9% based on this method. Samples were then tested by RT-PCR targeting the 5′ end of the capsid region for genogroup II (GII) NoVs, a group which includes human NoVs, followed by sequence analysis. All NoVs identified belonged to typical porcine NoV genotypes, and no human NoV-like strains were detected in specimens from these pigs. Porcine NoV-negative samples (
n
= 335) were subsequently screened using universal calicivirus primers, and 17 SaV strains were confirmed by sequencing. Based on the partial RNA-dependent RNA polymerase (RdRp) region, they clustered with GIII, GVII, and GVIII and with currently unclassified SaVs. According to analysis of the complete capsid sequences, 7 representative strains clustered with GVII, GVIII, and GIX? SaVs. We tentatively classified SaVs into 14 genogroups based on the complete capsid protein VP1. In summary, porcine NoVs and highly divergent SaVs were present in North Carolina finisher pigs.
Easily Modified Factors Contribute to Delays in Diagnosis of Clostridium difficile Infection: a Cohort Study and Intervention
Authors: Kundrapu Sirisha , Jury Lucy A. , Sitzlar Brett , Sunkesula Venkata C. K. , Sethi Ajay K. , Donskey Curtis J. 
Published: May 2013

ABSTRACT

Although rapid laboratory tests are available for diagnosis of
Clostridium difficile
infection (CDI), delays in completion of CDI testing are common in clinical practice. We conducted a cohort study of 242 inpatients tested for CDI to determine the timing of different steps involved in diagnostic testing and to identify modifiable factors contributing to delays in diagnosis. The average time from test order to test result was 1.8 days (range, 0.2 to 10.6), with time from order to stool collection accounting for most of the delay (mean, 1.0 day; range, 0 to 10). Several modifiable factors contributed to delays, including not providing stool collection supplies to patients in a timely fashion, rejection of specimens due to incorrect labeling or leaking from the container, and holding samples in the laboratory for batch processing. Delays in testing contributed to delays in initiation of treatment for patients diagnosed with CDI and to frequent prescription of empirical CDI therapy for patients with mild to moderate symptoms whose testing was ultimately negative. An intervention that addressed several easily modified factors contributing to delays resulted in a significant decrease in the time required to complete CDI testing. These findings suggest that health care facilities may benefit from a review of their processes for CDI testing to identify and address modifiable factors that contribute to delays in diagnosis and treatment of CDI.
Sequence Analysis of
In Vivo
Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus
Authors: Saira Kazima , Lin Xudong , DePasse Jay V. , Halpin Rebecca , Twaddle Alan , Stockwell Timothy , Angus Brian , Cozzi-Lepri Alessandro , Delfino Marina , Dugan Vivien , Dwyer Dominic E. , Freiberg Matthew , Horban Andrzej , Losso Marcelo , Lynfield Ruth , Wentworth Deborah N. , Holmes Edward C. , Davey Richard , Wentworth David E. , Ghedin Elodie 
Published: May 2013

ABSTRACT

Influenza virus defective interfering (DI) particles are naturally occurring noninfectious virions typically generated during
in vitro
serial passages in cell culture of the virus at a high multiplicity of infection. DI particles are recognized for the role they play in inhibiting viral replication and for the impact they have on the production of infectious virions. To date, influenza virus DI particles have been reported primarily as a phenomenon of cell culture and in experimentally infected embryonated chicken eggs. They have also been isolated from a respiratory infection of chickens. Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. The distribution of these
in vivo
-derived DI-like RNAs was similar to that of
in vitro
DIs, with the majority of the defective RNAs generated from the PB2 (segment 1) of the polymerase complex, followed by PB1 and PA. The lengths of the
in vivo
-derived DI-like segments also are similar to those of known
in vitro
DIs, and the
in vivo
-derived DI-like segments share internal deletions of the same segments. The presence of identical DI-like RNAs in patients linked by direct contact is compatible with transmission between them. The functional role of DI-like RNAs in natural infections remains to be established.
New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata
Authors: Thézé Julien , Takatsuka Jun , Li Zhen , Gallais Julie , Doucet Daniel , Arif Basil , Nakai Madoka , Herniou Elisabeth A. 
Published: May 2013

ABSTRACT

Poxviruses are nucleocytoplasmic large DNA viruses encompassing two subfamilies, the
Chordopoxvirinae
and the
Entomopoxvirinae
, infecting vertebrates and insects, respectively. While chordopoxvirus genomics have been widely studied, only two entomopoxvirus (EPV) genomes have been entirely sequenced. We report the genome sequences of four EPVs of the
Betaentomopoxvirus
genus infecting the Lepidoptera:
Adoxophyes honmai
EPV (AHEV),
Choristoneura biennis
EPV (CBEV),
Choristoneura rosaceana
EPV (CREV), and
Mythimna separata
EPV (MySEV). The genomes are 80% AT rich, are 228 to 307 kbp long, and contain 247 to 334 open reading frames (ORFs). Most genes are homologous to those of
Amsacta moorei
entomopoxvirus and encode several protein families repeated in tandem in terminal regions. Some genomes also encode proteins of unknown functions with similarity to those of other insect viruses. Comparative genomic analyses highlight a high colinearity among the lepidopteran EPV genomes and little gene order conservation with other poxvirus genomes. As with previously sequenced EPVs, the genomes include a relatively conserved central region flanked by inverted terminal repeats. Protein clustering identified 104 core EPV genes. Among betaentomopoxviruses, 148 core genes were found in relatively high synteny, pointing to low genomic diversity. Whole-genome and spheroidin gene phylogenetic analyses showed that the lepidopteran EPVs group closely in a monophyletic lineage, corroborating their affiliation with the
Betaentomopoxvirus
genus as well as a clear division of the EPVs according to the orders of insect hosts (Lepidoptera, Coleoptera, and Orthoptera). This suggests an ancient coevolution of EPVs with their insect hosts and the need to revise the current EPV taxonomy to separate orthopteran EPVs from the lepidopteran-specific betaentomopoxviruses so as to form a new genus.
Activation of the B Cell Antigen Receptor Triggers Reactivation of Latent Kaposi's Sarcoma-Associated Herpesvirus in B Cells
Authors: Kati Semra , Tsao Edward H. , Günther Thomas , Weidner-Glunde Magdalena , Rothämel Thomas , Grundhoff Adam , Kellam Paul , Schulz Thomas F. 
Published: May 2013

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic herpesvirus and the cause of Kaposi's sarcoma, primary effusion lymphoma (PEL) and multicentric Castleman's disease. Latently infected B cells are the main reservoir of this virus
in vivo
, but the nature of the stimuli that lead to its reactivation in B cells is only partially understood. We established stable BJAB cell lines harboring latent KSHV by cell-free infection with recombinant virus carrying a puromycin resistance marker. Our latently infected B cell lines, termed BrK.219, can be reactivated by triggering the B cell receptor (BCR) with antibodies to surface IgM, a stimulus imitating antigen recognition. Using this B cell model system we studied the mechanisms that mediate the reactivation of KSHV in B cells following the stimulation of the BCR and could identify phosphatidylinositol 3-kinase (PI3K) and X-box binding protein 1 (XBP-1) as proteins that play an important role in the BCR-mediated reactivation of latent KSHV.
The B-Cell-Specific Transcription Factor and Master Regulator Pax5 Promotes Epstein-Barr Virus Latency by Negatively Regulating the Viral Immediate Early Protein BZLF1
Authors: Raver Ryan M. , Panfil Amanda R. , Hagemeier Stacy R. , Kenney Shannon C. 
Published: May 2013

ABSTRACT

The latent-to-lytic switch of Epstein-Barr virus (EBV) is mediated by the immediate early protein BZLF1 (Z). However, the cellular factors regulating this process remain incompletely characterized. In this report, we show that the B-cell-specific transcription factor Pax5 helps to promote viral latency in B cells by blocking Z function. Although Z was previously shown to directly interact with Pax5 and inhibit its activity, the effect of Pax5 on Z function has not been investigated. Here, we demonstrate that Pax5 inhibits Z-mediated lytic viral gene expression and the release of infectious viral particles in latently infected epithelial cell lines. Conversely, we found that shRNA-mediated knockdown of endogenous Pax5 in a Burkitt lymphoma B-cell line leads to viral reactivation. Furthermore, we show that Pax5 reduces Z activation of early lytic viral promoters in reporter gene assays and inhibits Z binding to lytic viral promoters
in vivo
. We confirm that Pax5 and Z directly interact and show that this interaction requires the carboxy-terminal DNA-binding/dimerization domain of Z and the amino-terminal DNA-binding domain of Pax5. A Pax5 DNA-binding mutant (V26G/P80R) that interacts with Z retains the ability to inhibit Z function, whereas a Pax5 mutant (Δ106-110) that is deficient for interaction with Z does not inhibit Z-mediated lytic viral reactivation. Since the B-cell-specific transcription factor Oct-2 also directly interacts with Z and inhibits its function, these results suggest that EBV uses multiple redundant mechanisms to establish and maintain viral latency in B cells.
Productive Entry of HIV-1 during Cell-to-Cell Transmission via Dynamin-Dependent Endocytosis
Authors: Sloan Richard D. , Kuhl Björn D. , Mesplède Thibault , Münch Jan , Donahue Daniel A. , Wainberg Mark A. 
Published: May 2013

ABSTRACT

HIV-1 can be transmitted as cell-free virus or via cell-to-cell contacts. Cell-to-cell transmission between CD4
+
T cells is the more efficient mode of transmission and is predominant in lymphoid tissue, where the majority of virus resides. Yet the cellular mechanisms underlying productive cell-to-cell transmission in uninfected target cells are unclear. Although it has been demonstrated that target cells can take up virus via endocytosis, definitive links between this process and productive infection remain undefined, and this route of transmission has been proposed to be nonproductive. Here, we report that productive cell-to-cell transmission can occur via endocytosis in a dynamin-dependent manner and is sensitive to clathrin-associated antagonists. These data were obtained in a number of CD4
+
T-cell lines and in primary CD4
+
T cells, using both CXCR4- and CCR5-tropic virus. However, we also found that HIV-1 demonstrated flexibility in its use of such endocytic pathways as certain allogeneic transmissions were seen to occur in a dynamin-dependent manner but were insensitive to clathrin-associated antagonists. Also, depleting cells of the clathrin accessory protein AP180 led to a viral uptake defect associated with enhanced infection. Collectively, these data demonstrate that endosomal uptake of HIV-1 during cell-to-cell transmission leads to productive infection, but they are also indicative of a flexible model of viral entry during cell-to-cell transmission, in which the virus can alter its entry route according to the pressures that it encounters.
Infection of Mice, Ferrets, and Rhesus Macaques with a Clinical Mumps Virus Isolate
Authors: Xu Pei , Huang Zhixiang , Gao Xiudan , Michel Frank J. , Hirsch Gwen , Hogan Robert J. , Sakamoto Kaori , Ho Wenzhe , Wu Jianguo , He Biao 
Published: May 2013

ABSTRACTIn recent years, many mumps outbreaks have occurred in vaccinated populations worldwide. The reasons for these outbreaks are not clear. Animal models are needed to investigate the causes of outbreaks and to understand the pathogenesis of mumps virus (MuV). In this study, we have examined the infection of three animal models with an isolate of mumps virus from a recent outbreak (MuV-IA). We have found that while both ferrets and mice generated humoral and cellular immune responses to MuV-IA infection, no obvious signs of illness were observed in these animals; rhesus macaques were the most susceptible to MuV-IA infection. Infection of rhesus macaques via both intranasal and intratracheal routes with MuV-IA led to the typical clinical signs of mumps 2 weeks to 4 weeks postinfection. However, none of the infected macaques showed any fever or neurologic signs during the experimental period. Mumps viral antigen was detected in parotid glands by immunohistochemistry (IHC). Rhesus macaques represent the best animal model for the study of mumps virus pathogenesis.
The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria
Authors: Sassi Mohamed , Bebeacua Cecilia , Drancourt Michel , Cambillau Christian 
Published: May 2013

ABSTRACT

The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ∼3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from
Mycobacterium abscessus
subsp.
bolletii
, a member of the
Mycobacterium abscessus
group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis.
M. abscessus
subsp.
bolletii
was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the
M. abscessus
subsp.
bolletii
prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to
Siphoviridae
and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram
−
) or Gram
+
bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.
Increased Early RNA Replication by Chimeric West Nile Virus W956IC Leads to IPS-1-Mediated Activation of NF-κB and Insufficient Virus-Mediated Counteraction of the Resulting Canonical Type I Interferon Signaling
Authors: Scherbik S. V. , Pulit-Penaloza J. A. , Basu M. , Courtney S. C. , Brinton M. A. 
Published: May 2013

ABSTRACT
Although infections with “natural” West Nile virus (WNV) and the chimeric W956IC WNV infectious clone virus produce comparable peak virus yields in type I interferon (IFN) response-deficient BHK cells, W956IC infection produces higher levels of “unprotected” viral RNA at early times after infection. Analysis of infections with these two viruses in IFN-competent cells showed that W956IC activated NF-κB, induced higher levels of IFN-β, and produced lower virus yields than WNV strain Eg101. IPS-1 was required for both increased induction of IFN-β and decreased yields of W956IC. In Eg101-infected cells, phospho-STAT1/STAT2 nuclear translocation was blocked at all times analyzed, while some phospho-STAT1/STAT2 nuclear translocation was still detected at 8 h after infection in W956IC-infected mouse embryonic fibroblasts (MEFs), and early viral protein levels were lower in these cells. A set of additional chimeras was made by replacing various W956IC gene regions with the Eg101 equivalents. As reported previously, for three of these chimeras, the low early RNA phenotype of Eg101 was restored in BHK cells. Analysis of infections with two of these chimeric viruses in MEFs detected lower early viral RNA levels, higher early viral protein levels, lower early IFN-β levels, and higher virus yields similar to those seen after Eg101 infection. The data suggest that replicase protein interactions directly or indirectly regulate genome switching between replication and translation at early times in favor of translation to minimize NF-κB activation and IFN induction by decreasing the amount of unprotected viral RNA, to produce sufficient viral protein to block canonical type I IFN signaling, and to efficiently remodel cell membranes for exponential genome amplification.
Predictive models to assess risk of type 2 diabetes, hypertension and comorbidity: machine-learning algorithms and validation using national health data from Kuwait—a cohort study
Authors: Farran Bassam , Channanath Arshad Mohamed , Behbehani Kazem , Thanaraj Thangavel Alphonse 
Published: May 2013

ObjectiveWe build classification models and risk assessment tools for diabetes, hypertension and comorbidity using machine-learning algorithms on data from Kuwait. We model the increased proneness in diabetic patients to develop hypertension and vice versa. We ascertain the importance of ethnicity (and natives vs expatriate migrants) and of using regional data in risk assessment.DesignRetrospective cohort study. Four machine-learning techniques were used: logistic regression, k-nearest neighbours (k-NN), multifactor dimensionality reduction and support vector machines. The study uses fivefold cross validation to obtain generalisation accuracies and errors.SettingKuwait Health Network (KHN) that integrates data from primary health centres and hospitals in Kuwait.Participants270 172 hospital visitors (of which, 89 858 are diabetic, 58 745 hypertensive and 30 522 comorbid) comprising Kuwaiti natives, Asian and Arab expatriates.Outcome measuresIncident type 2 diabetes, hypertension and comorbidity.ResultsClassification accuracies of >85% (for diabetes) and >90% (for hypertension) are achieved using only simple non-laboratory-based parameters. Risk assessment tools based on k-NN classification models are able to assign ‘high’ risk to 75% of diabetic patients and to 94% of hypertensive patients. Only 5% of diabetic patients are seen assigned ‘low’ risk. Asian-specific models and assessments perform even better. Pathological conditions of diabetes in the general population or in hypertensive population and those of hypertension are modelled. Two-stage aggregate classification models and risk assessment tools, built combining both the component models on diabetes (or on hypertension), perform better than individual models.ConclusionsData on diabetes, hypertension and comorbidity from the cosmopolitan State of Kuwait are available for the first time. This enabled us to apply four different case–control models to assess risks. These tools aid in the preliminary non-intrusive assessment of the population. Ethnicity is seen significant to the predictive models. Risk assessments need to be developed using regional data as we demonstrate the applicability of the American Diabetes Association online calculator on data from Kuwait.