bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilot program on patient dosimetry in pediatric interventional cardiology in Chile
Authors: Ubeda Carlos , Vano Eliseo , Miranda Patricia , Leyton Fernando 
Published: April 2012

Purpose:The aim of this study was to present the results of a pilot program on patient dosimetry carried out in Chile during the last 5 yr, using a biplane x‐ray angiography system settled for pediatrics. This research was conducted in Latin America under the auspices of the International Atomic Energy Agency (IAEA) supporting programs on radiological protection (RP) of patients.Methods:Patient age, gender, weight, height, number of cine series, total number of cine frames, fluoroscopy time, and two dosimetric quantities [air kerma‐area product (Pka) and cumulative dose (CD) at the patient entrance reference point] were recorded for each procedure.Results:The study includes 544 patients grouped into four age groups. The distributions by age group were 150 for <1 yr; 203 for 1 to <5 yr; 97 for 5 to <10 yr; and 94 for 10 to <16 yr. Median values of Pka and CD for the four age groups were 0.94, 1.46, 2.13, and 5.03 Gy cm2 and 23.9, 26.8, 33.5, and 51.6 mGy, respectively. No significant statistical differences were found between diagnostic and therapeutic procedures. A moderate correlation (r = 0.64) was seen between Pka and patient weight.Conclusions:The dose values reported in this paper were lower than those published in the previous work for the same age groups as a result of the optimization actions carried out by cardiologists and medical physicists with the support of the IAEA. Methodology and results will be used as a starting point for a wider survey in Chile and Latin America with the goal to obtain regional diagnostic reference levels as recently recommended by the International Commission on Radiological Protection for interventional procedures.
In Silico
Identification of Epitopes in Mycobacterium avium subsp.
paratuberculosis
Proteins That Were Upregulated under Stress Conditions
Authors: Gurung Ratna B. , Purdie Auriol C. , Begg Douglas J. , Whittington Richard J. 
Published: April 2012

ABSTRACT

Johne's disease in ruminants is caused by
Mycobacterium avium
subsp.
paratuberculosis
. Diagnosis of
M. avium
subsp.
paratuberculosis
infection is difficult, especially in the early stages. To date, ideal antigen candidates are not available for efficient immunization or immunodiagnosis. This study reports the
in silico
selection and subsequent analysis of epitopes of
M. avium
subsp.
paratuberculosis
proteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins when
M. avium
subsp.
paratuberculosis
is exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-five
M. avium
subsp.
paratuberculosis
proteins that were previously identified as being upregulated under
in vitro
stress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artificial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded by
desA2
], MAP2312c [encoded by
fadE19
], MAP3651c [encoded by
fadE3_2
], MAP2872c [encoded by
fabG5_2
], MAP3523c [encoded by
oxcA
], MAP0187c [encoded by
sodA
], and the hypothetical proteins MAP3567 and MAP1168c) were identified as potential candidates for study of antibody- and cell-mediated immune responses within infected hosts.
Evaluation of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems for Identification of Nonfermenting Gram-Negative Bacilli Isolated from Cultures from Cystic Fibrosis Patients
Authors: Marko Daniel C. , Saffert Ryan T. , Cunningham Scott A. , Hyman Jay , Walsh John , Arbefeville Sophie , Howard Wanita , Pruessner Jon , Safwat Nedal , Cockerill Franklin R. , Bossler Aaron D. , Patel Robin , Richter Sandra S. 
Published: April 2012

ABSTRACTThe Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) instruments were evaluated for the identification of nonfermenting Gram-negative bacilli (NFGNB) by a blinded comparison to conventional biochemical or molecular methods. Two hundred NFGNB that were recovered from cultures from cystic fibrosis patients in the University of Iowa Health Care (UIHC) Microbiology Laboratory between 1 January 2006 and 31 October 2010 were sent to Mayo Clinic for analysis with the Bruker Biotyper (software version 3.0) and to bioMérieux for testing with Vitek MS (SARAMIS database version 3.62). If two attempts at direct colony testing failed to provide an acceptable MALDI-TOF identification, an extraction procedure was performed. The MS identifications from both of these systems were provided to UIHC for comparison to the biochemical or molecular identification that had been reported in the patient record. Isolates with discordant results were analyzed by 16S rRNA gene sequencing at UIHC. After discrepancy testing, the Bruker Biotyper result agreed with the biochemical or molecular method, with 72.5% of isolates to the species level, 5.5% to the complex level, and 19% to the genus level (3% not identified). The level of agreement for Vitek MS was 80% species, 3.5% complex, 6% genus, and 3.5% family (7% not identified). Both MS systems provided rapid (≤3 min per isolate) and reliable identifications. The agreement of combined species/complex/genus-level identification with the reference method was higher for the Bruker Biotyper (97% versus 89.5%,P= 0.004) but required an extraction step more often. Species-level agreement with the reference method was similar for both MS systems (72.5% and 80%,P= 0.099).
Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Chlamydia felis Genotyping: Comparison with Multilocus Sequence Typing
Authors: Laroucau Karine , Di Francesco Antonietta , Vorimore Fabien , Thierry Simon , Pingret Jean Luc , Bertin Claire , Willems Hermann , Bölske Goran , Harley Ross 
Published: April 2012

ABSTRACT

Chlamydia felis
is an important ocular pathogen in cats worldwide. A multilocus variable-number tandem-repeat analysis (MLVA) system for the detection of tandem repeats across the whole genome of
C. felis
strain Fe/C-56 was developed. Nine selected genetic loci were tested by MLVA in 17
C. felis
isolates, including the
C. felis
Baker vaccine strain, and 122 clinical samples from different geographic origins. Analysis of the results identified 25 distinct
C. felis
MLVA patterns. In parallel, a recently described multilocus sequence typing scheme for the typing of
Chlamydia
was applied to 13 clinical samples with 12 different
C. felis
MLVA patterns. Rare sequence differences were observed. Thus, the newly developed MLVA system provides a highly sensitive high-resolution test for the differentiation of
C. felis
isolates from different origins that is suitable for molecular epidemiological studies.
Clinical and Microbiological Characteristics of Bacteremia Caused by Eggerthella, Paraeggerthella, and Eubacterium Species at a University Hospital in Taiwan from 2001 to 2010
Authors: Lee Meng-Rui , Huang Yu-Tsung , Liao Chun-Hsing , Chuang Tzu-Yi , Wang Wei-Jie , Lee Shih-Wei , Lee Li-Na , Hsueh Po-Ren 
Published: April 2012

ABSTRACT

We describe 16 patients with bacteremia caused by
Eggerthella lenta
(
n
= 7),
Paraeggerthella hongkongensis
(
n
= 3),
Eubacterium limosum
(
n
= 4),
Eubacterium callanderi
(
n
= 1), and concomitant
Eubacterium limosum
/
Eggerthella lenta
(
n
= 1). Nine (56%) patients had polymicrobial bacteremia. The overall 60-day mortality rate was 19%, and all deaths occurred in patients with
E. lenta
bacteremia.
Genotyping Reveals the Presence of a Predominant Genotype of Coxiella burnetii in Consumer Milk Products
Authors: Tilburg Jeroen J. H. C. , Roest Hendrik Jan I. J. , Nabuurs-Franssen Marrigje H. , Horrevorts Alphons M. , Klaassen Corné H. W. 
Published: April 2012

ABSTRACT

Real-time PCR shows the widespread presence of
Coxiella burnetii
DNA in a broad range of commercially available milk and milk products. MLVA genotyping shows that this is the result of the presence of a predominant
C. burnetii
genotype in the dairy cattle population.
Genetic Analysis of Cytomegalovirus in Malignant Gliomas
Authors: Bhattacharjee Bornali , Renzette Nicholas , Kowalik Timothy F. 
Published: April 2012

ABSTRACT

Human cytomegalovirus (HCMV) has been found in malignant gliomas at variable frequencies with efforts to date focused on characterizing the role(s) of single gene products in disease. Here, we reexamined the HCMV prevalence in malignant gliomas using different methods and began to dissect the genetics of HCMV in tumors. HCMV DNA was found in 16/17 (94%) tumor specimens. Viral DNA copy numbers were found to be low and variable, ranging from 10
2
to 10
6
copies/500 ng of total DNA. The tumor tissues had incongruences between viral DNA copy numbers and protein levels. However, nonlatent protein expression was detected in many tumors. The viral
UL83
gene, encoding pp65, was found to segregate into five cancer-associated genotypes with a bias for amino acid changes in glioblastoma multiforme (GBM) in comparison to the low-grade tumors. Deep sequencing of a GBM-associated viral population resulted in 81,224 bp of genome coverage. Sequence analysis revealed the presence of intact open reading frames and higher numbers of high-frequency variations within the repeat long region compared to the unique long region, which harbors many core genes, and the unique short region (
P
= 0.001). This observation was in congruence with phylogenetic analyses across replication-competent viral strains in databases. The tumor-associated viral population was less variable (π = 0.1% and π
AA
= 0.08%) than that observed in other clinical infections. Moreover, 42/46 (91.3%) viral genes analyzed had
dN/dS
scores of <1, which is indicative of high amino acid sequence conservation. Taken together, these findings raise the possibility that replication-competent HCMV may exist in malignant gliomas.
Simultaneous Treatment of Human Bronchial Epithelial Cells with Serine and Cysteine Protease Inhibitors Prevents Severe Acute Respiratory Syndrome Coronavirus Entry
Authors: Kawase Miyuki , Shirato Kazuya , van der Hoek Lia , Taguchi Fumihiro , Matsuyama Shutoku 
Published: April 2012

ABSTRACTThe type II transmembrane protease TMPRSS2 activates the spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) on the cell surface following receptor binding during viral entry into cells. In the absence of TMPRSS2, SARS-CoV achieves cell entry via an endosomal pathway in which cathepsin L may play an important role, i.e., the activation of spike protein fusogenicity. This study shows that a commercial serine protease inhibitor (camostat) partially blocked infection by SARS-CoV and human coronavirus NL63 (HCoV-NL63) in HeLa cells expressing the receptor angiotensin-converting enzyme 2 (ACE2) and TMPRSS2. Simultaneous treatment of the cells with camostat and EST [(23,25)trans-epoxysuccinyl-l-leucylamindo-3-methylbutane ethyl ester], a cathepsin inhibitor, efficiently prevented both cell entry and the multistep growth of SARS-CoV in human Calu-3 airway epithelial cells. This efficient inhibition could be attributed to the dual blockade of entry from the cell surface and through the endosomal pathway. These observations suggest camostat as a candidate antiviral drug to prevent or depress TMPRSS2-dependent infection by SARS-CoV.
Murine Cytomegalovirus Targets Transcription Factor ATF4 To Exploit the Unfolded-Protein Response
Authors: Qian Zhikang , Xuan Baoqin , Chapa Travis J. , Gualberto Nathaniel , Yu Dong 
Published: April 2012

ABSTRACT
The unfolded-protein response (UPR), activated by sensor molecules PERK, ATF6, and IRE1 to resolve endoplasmic reticulum (ER) stress, has emerged as a key target for host cells and viruses to control the infection outcomes. The UPR regulates ER protein folding, controls cell fate upon ER stress, and plays an important role in innate immunity. We and others have shown that human cytomegalovirus (HCMV) modulates the UPR. We show here that murine CMV (MCMV), the widely used CMV model for small animal infection, regulated the UPR in a manner similar to that of HCMV. This modulatory ability was triggered by virion entry and enhanced by viral immediate-early and early gene expression. Thus, while vulnerable at early times, MCMV became resistant to exogenous ER stress at late times of infection. MCMV activated the PERK-ATF4 pathway but only induced a subset of representative ATF4 targets at levels somewhat lower than those by the ER stress inducer tunicamycin. Moreover, MCMV induced ER chaperone Bip but actively blocked IRE1-mediated Xbp1(s) protein accumulation. ATF4 depletion severely attenuated viral growth at a low multiplicity of infection by modestly reducing viral DNA synthesis and more pronouncedly inhibiting late gene transcription. Collectively, we show that the UPR is a conserved target of CMVs and identify ATF4, a key UPR component, as a factor critical for MCMV infection. This work sets the stage for using the MCMV model to explore the role of this stress response in CMV biology, particularly during infection of the host, which is difficult to study in HCMV.
Herpes Simplex Virus Glycoproteins gH/gL and gB Bind Toll-Like Receptor 2, and Soluble gH/gL Is Sufficient To Activate NF-κB
Authors: Leoni Valerio , Gianni Tatiana , Salvioli Stefano , Campadelli-Fiume Gabriella 
Published: April 2012

ABSTRACT

A number of sentinels sense incoming herpes simplex virus (HSV) virions and initiate an immediate innate response. The first line of defense at the cell surface is TLR2 (Toll-like receptor 2), whose signature signaling activity leads to activation of the key transcription factor NF-κB. We report that the HSV pathogen-associated molecular patterns for TLR2 are the virion glycoproteins gH/gL and gB, which constitute the conserved fusion core apparatus across the members of the
Herpesviridae
family. Specifically, virions devoid singly of one of essential fusion glycoproteins (gD, gB, or gH null), able to attach to cells but defective in fusion/entry, were sufficient to elicit the first wave of NF-κB response to HSV. The most effective were the gD-null virions, positive for gH/gL and gB. A soluble form of gB, truncated upstream of the transmembrane sequence (gB
730t-st
), was produced in human cells and purified by means of a
Strep
tag. gH/gL and gB were each able to physically interact with TLR2 in coimmunoprecipitation assays, one independently of the other, yet gH
t-st
/gL, but not gB
730t-st
, elicited an NF-κB response. Thus, whereas both HSV gH/gL and gB are ligands to TLR2, only gH/gL is sufficient to initiate a signaling cascade which leads to NF-κB activation.
Replication-Uncoupled Histone Deposition during Adenovirus DNA Replication
Authors: Komatsu Tetsuro , Nagata Kyosuke 
Published: April 2012

ABSTRACT
In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of histones, does not affect the level of histone H3 bound on viral chromatin, although CAF-1 is accumulated at viral DNA replication foci together with PCNA. Chromatin immunoprecipitation assays using epitope-tagged histone H3 demonstrated that histone variant H3.3, which is deposited onto the cellular genome in a replication-independent manner, is selectively associated with both incoming and newly synthesized viral DNAs. Microscopic analyses indicated that histones but not USF1, a transcription factor that regulates viral late gene expression, are excluded from viral DNA replication foci and that this is achieved by the oligomerization of the DNA binding protein (DBP). Taken together, these results suggest that histone deposition onto newly synthesized viral DNA is most likely uncoupled with viral DNA replication, and a possible role of DBP oligomerization in this replication-uncoupled histone deposition is discussed.
Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA
Authors: Mosley Ralph T. , Edwards Thomas E. , Murakami Eisuke , Lam Angela M. , Grice Rena L. , Du Jinfa , Sofia Michael J. , Furman Philip A. , Otto Michael J. 
Published: April 2012

ABSTRACT

The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory β-hairpin loop from genotype 2a HCV NS5B increases
de novo
RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory β-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.
Deletion of U
L
21 Causes a Delay in the Early Stages of the Herpes Simplex Virus 1 Replication Cycle
Authors: Mbong Ekaette F. , Woodley Lucille , Frost Elizabeth , Baines Joel D. , Duffy Carol 
Published: April 2012

ABSTRACT

The herpes simplex virus 1 (HSV-1) U
L
21 gene encodes a 62-kDa tegument protein with homologs in the alpha-, beta-, and gammaherpesvirus subfamilies. In the present study, we characterized a novel U
L
21-null virus and its genetic repair to determine whether this protein plays a role in early stages of the HSV-1 replication cycle. Single-step growth analyses, protein synthesis time courses, and mRNA quantifications indicated that the absence of U
L
21 results in a delay early in the HSV-1 replication cycle.
The N Terminus and C Terminus of Herpes Simplex Virus 1 ICP4 Cooperate To Activate Viral Gene Expression
Authors: Wagner Lauren M. , Lester Jonathan T. , Sivrich Frances L. , DeLuca Neal A. 
Published: April 2012

ABSTRACT
Infected cell polypeptide 4 (ICP4) activates transcription from most viral promoters. Two transactivation domains, one N-terminal and one C terminal, are largely responsible for the activation functions of ICP4. A mutant ICP4 molecule lacking the C-terminal activation domain (n208) efficiently activates many early genes, whereas late genes are poorly activated, and virus growth is severely impaired. The regions within the N terminus of ICP4 (amino acids 1 to 210) that contribute to activation were investigated by analysis of deletion mutants in the presence or absence of the C-terminal activation domain. The mutants were assessed for their abilities to support viral replication and to regulate gene expression. Several deletions in regions conserved in other alphaherpesviruses resulted in impaired activation and viral growth, without affecting DNA binding. The single small deletion that had the greatest effect on activation in the absence of the C terminus corresponded to a highly conserved stretch of amino acids between 81 and 96, rendering the molecule nonfunctional. However, when the C terminus was present, the same deletion had a minimal effect on activity. The amino terminus of ICP4 was predicted to be relatively disordered compared to the DNA-binding domain and the C-terminal 500 amino acids. Moreover, the amino terminus appears to be in a relatively extended conformation as determined by the hydrodynamic properties of several mutants. The data support a model where the amino terminus is an extended and possibly flexible region of the protein, allowing it to efficiently interact with multiple transcription factors at a distance from where it is bound to DNA, thereby enabling ICP4 to function as a general activator of polymerase II transcription. The C terminus of ICP4 can compensate for some of the mutations in the N terminus, suggesting that it either specifies redundant interactions or enables the amino terminus to function more efficiently.
The US16 Gene of Human Cytomegalovirus Is Required for Efficient Viral Infection of Endothelial and Epithelial Cells
Authors: Bronzini Matteo , Luganini Anna , Dell'Oste Valentina , De Andrea Marco , Landolfo Santo , Gribaudo Giorgio 
Published: April 2012

ABSTRACT
The human cytomegalovirus (HCMV) US12 gene family comprises a set of 10 contiguous genes (US12 to US21), each encoding a predicted seven-transmembrane protein and whose specific functions have yet to be ascertained. While inactivation of individual US12 family members in laboratory strains of HCMV has not been found to affect viral replication in fibroblasts, inactivation of US16 was reported to increase replication in microvascular endothelial cells. Here, we investigate the properties of US16 further by ascertaining the expression pattern of its product. A recombinant HCMV encoding a tagged version of the US16 protein expressed a 33-kDa polypeptide that accumulated with late kinetics in the cytoplasmic virion assembly compartment. To elucidate the function(s) of pUS16, we generated US16-deficient mutants in the TR clinical strain of HCMV. According to previous studies, inactivation of US16 had no effect on viral replication in fibroblasts. In contrast, the US16-deficient viruses exhibited a major growth defect in both microvascular endothelial cells and retinal pigment epithelial cells. The expression of representative IE, E, and L viral proteins was impaired in endothelial cells infected with a US16 mutant virus, suggesting a defect in the replication cycle that occurs prior to IE gene expression. This defect must be due to an inefficient entry and/or postentry event, since pp65 and viral DNA did not move to the nucleus in US16 mutant-infected cells. Taken together, these data indicate that the US16 gene encodes a novel virus tropism factor that regulates, in a cell-specific manner, a pre-immediate-early phase of the HCMV replication cycle.