bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cross‐Sectional Study of Hepatitis E Virus Infection in Healthy People Directly Exposed and Unexposed to Pigs in a Rural Community in Northern Thailand
Authors: Hinjoy S. , Nelson K. E. , Gibbons R. V. , Jarman R. G. , Mongkolsirichaikul D. , Smithsuwan P. , Fernandez S. , Labrique A. B. , Patchanee P. 
Published: December 2012

SummaryA cross‐sectional study of the association between occupational pig exposure and hepatitis E virus (HEV) infection in adult pig farmers and the general population who were not directly exposed to pigs was conducted in Nan Province, Thailand, from November 2010 to April 2011. All participants were interviewed to provide information on their job history, eating habits and other potential confounders. The prevalence of anti‐HEV immunoglobulin G antibodies (IgG) among 513 subjects was 23.0%. Hand washing with water and soap was associated with a lower seroprevalence of HEV infection, whereas living in an area with frequent flooding (OR 1.64, 95% CI: 1.00–2.68) and consuming internal pig organs more than twice per week (OR 3.23, 95%CI: 1.15–9.01) were both associated with a higher seroprevalence of anti‐HEV IgG. There was no association between HEV seroprevalence and frequent, direct occupational pig contact.
Massively parallelizable list‐mode reconstruction using a Monte Carlo‐based elliptical Gaussian model
Authors: Sportelli G. , Ortuño J. E. , Vaquero J. J. , Desco M. , Santos A. 
Published: December 2012

Purpose:A fully three‐dimensional (3D) massively parallelizable list‐mode ordered‐subsets expectation‐maximization (LM‐OSEM) reconstruction algorithm has been developed for high‐resolution PET cameras. System response probabilities are calculated online from a set of parameters derived from Monte Carlo simulations. The shape of a system response for a given line of response (LOR) has been shown to be asymmetrical around the LOR. This work has been focused on the development of efficient region‐search techniques to sample the system response probabilities, which are suitable for asymmetric kernel models, including elliptical Gaussian models that allow for high accuracy and high parallelization efficiency. The novel region‐search scheme using variable kernel models is applied in the proposed PET reconstruction algorithm.Methods:A novel region‐search technique has been used to sample the probability density function in correspondence with a small dynamic subset of the field of view that constitutes the region of response (ROR). The ROR is identified around the LOR by searching for any voxel within a dynamically calculated contour. The contour condition is currently defined as a fixed threshold over the posterior probability, and arbitrary kernel models can be applied using a numerical approach. The processing of the LORs is distributed in batches among the available computing devices, then, individual LORs are processed within different processing units. In this way, both multicore and multiple many‐core processing units can be efficiently exploited. Tests have been conducted with probability models that take into account the noncolinearity, positron range, and crystal penetration effects, that produced tubes of response with varying elliptical sections whose axes were a function of the crystal's thickness and angle of incidence of the given LOR. The algorithm treats the probability model as a 3D scalar field defined within a reference system aligned with the ideal LOR.Results:This new technique provides superior image quality in terms of signal‐to‐noise ratio as compared with the histogram‐mode method based on precomputed system matrices available for a commercial small animal scanner. Reconstruction times can be kept low with the use of multicore, many‐core architectures, including multiple graphic processing units.Conclusions: A highly parallelizable LM reconstruction method has been proposed based on Monte Carlo simulations and new parallelization techniques aimed at improving the reconstruction speed and the image signal‐to‐noise of a given OSEM algorithm. The method has been validated using simulated and real phantoms. A special advantage of the new method is the possibility of defining dynamically the cut‐off threshold over the calculated probabilities thus allowing for a direct control on the trade‐off between speed and quality during the reconstruction.
Distribution of Pilus Islands in Streptococcus agalactiae That Cause Human Infections: Insights into Evolution and Implication for Vaccine Development
Authors: Martins E. R. , Andreu A. , Melo-Cristino J. , Ramirez M. 
Published: December 2012

ABSTRACT

At least one pilus island, PI-1 (70%), PI-2a (79%), or PI-2b (21%), was found among 898
Streptococcus agalactiae
(group B streptococcus [GBS]) isolates recovered from humans, supporting the use of pilus proteins in vaccines. The stability and dominance of PI-1 and PI-2a in multiple serotypes and founder multilocus sequence types disseminated worldwide suggest it could be the PI combination present in ancestral GBS human pathogens.
Adhesion Protein ApfA of Actinobacillus pleuropneumoniae Is Required for Pathogenesis and Is a Potential Target for Vaccine Development
Authors: Zhou Yang , Li Lu , Chen Zhaohui , Yuan Hong , Chen Huanchun , Zhou Rui 
Published: December 2012

ABSTRACT

Actinobacillus pleuropneumoniae
is the etiologic agent of porcine pleuropneumonia, which causes serious economic losses in the pig farming industry worldwide. Due to a lack of knowledge of its virulence factors and a lack of effective vaccines able to confer cross-serotype protection, it is difficult to place this disease under control. By analyzing its genome sequences, we found that type IV fimbrial subunit protein ApfA is highly conserved among different serotypes of
A. pleuropneumoniae
. Our study shows that ApfA is an adhesin since its expression was greatly upregulated (135-fold) upon contact with host cells, while its deletion mutant attenuated its capability of adhesion. The inactivation of
apfA
dramatically reduced the ability of
A. pleuropneumoniae
to colonize mouse lung, suggesting that
apfA
is a virulence factor. Purified recombinant ApfA elicited an elevated humoral immune response and conferred robust protection against challenges with
A. pleuropneumoniae
serovar 1 strain 4074 and serovar 7 strain WF83 in mice. Importantly, the anti-ApfA serum conferred significant protection against both serovar 1 and serovar 7 in mice. These studies indicate that ApfA promotes virulence through attachment to host cells, and its immunogenicity renders it a promising novel subunit vaccine candidate against infection with
A. pleuropneumoniae
.
Comparing Pulsed-Field Gel Electrophoresis with Multilocus Sequence Typing,
spa
Typing, Staphylococcal Cassette Chromosome
mec
(SCC
mec
) Typing, and PCR for Panton-Valentine Leukocidin,
arcA
, and
opp3
in Methicillin-Resistant Staphylococcus aureus Isolates at a U.S. Medical Center
Authors: David Michael Z. , Taylor Alexis , Lynfield Ruth , Boxrud Dave J. , Short Ginette , Zychowski Diana , Boyle-Vavra Susan , Daum Robert S. 
Published: December 2012

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) has become a common cause of skin infections and invasive infections in community dwellers in the United States since the late 1990s. Isolates characterized as USA300 by pulsed-field gel electrophoresis (PFGE) are the predominant strain type in these infections. USA100 and USA500 strains commonly cause health care-associated infections. We compared PFGE with a number of other methods of genotyping in a sample of 149 clinical MRSA isolates from the University of Chicago Medical Center. The 5 USA500 isolates yielded 3
spa
types and 2 multilocus sequence types (MLSTs). Among the 24 USA100 isolates, 21 (88%) were of
spa
type t002, 19 (79%) were of ST5, 2 carried
arcA
and
opp3
, and 1 was Panton-Valentine leukocidin positive (PVL
+
). Among the 102 USA300 isolates, 96 (94%) were of ST8 and 94 (92%) were of
spa
type t008. The combination of traits that provided the best sensitivity (98%), specificity (97%), positive predictive value (PPV) (99%), and negative predictive value (NPV) (95%) for identifying USA300 isolates were the presence of the
arcA
gene and the presence of the PVL genes (area under the curve, 0.980; 95% confidence interval [CI], 0.955 to 1.0). PFGE did not delineate a homogeneous group of MRSA genetic backgrounds, as documented for other typing methods, particularly for USA500 and USA100 pulsotypes. Documenting the presence of
arcA
and PVL genes by PCR was an efficient and accurate means of identifying USA300 in a collection of MRSA isolates in which USA300 is common. None of the tested genotyping methods provided an accurate means of identifying the next most common PFGE-based backgrounds, USA100 and USA500.
Longitudinal Analyses of Gut Mucosal Microbiotas in Ulcerative Colitis in Relation to Patient Age and Disease Severity and Duration
Authors: Fite Alemu , Macfarlane Sandra , Furrie Elizabeth , Bahrami Bahram , Cummings John H. , Steinke Douglas T. , Macfarlane George T. 
Published: December 2012

ABSTRACT

Bacteria belonging to the normal colonic microbiota are associated with the etiology of ulcerative colitis (UC). Although several mucosal species have been implicated in the disease process, the organisms and mechanisms involved are unknown. The aim of this investigation was to characterize mucosal biofilm communities over time and to determine the relationship of these bacteria to patient age and disease severity and duration. Multiple rectal biopsy specimens were taken from 33 patients with active UC over a period of 1 year. Real-time PCR was used to quantify mucosal bacteria in UC patients compared to 18 noninflammatory bowel disease controls, and the relationship between indicators of disease severity and bacterial colonization was evaluated by linear regression analysis. Significant differences were detected in bacterial populations on the UC mucosa and in the control group, which varied over the study period. High clinical activity indices (CAI) and sigmoidoscopy scores (SS) were associated with enterobacteria, desulfovibrios, type E
Clostridium perfringens
, and
Enterococcus faecalis
, whereas the reverse was true for
Clostridium butyricum
,
Ruminococcus albus
, and
Eubacterium rectale
. Lactobacillus and bifidobacterium numbers were linked with low CAI. Only
E. rectale
and
Clostridium clostridioforme
had a high age dependence. These findings demonstrated that longitudinal variations in mucosal bacterial populations occur in UC and that bacterial community structure is related to disease severity.
Evaluation of the Chromogenic Agar chromID C. difficile
Authors: Eckert Catherine , Burghoffer Béatrice , Lalande Valérie , Barbut Frederic 
Published: December 2012

ABSTRACT

Three selective media (chromID C. difficile agar, taurocholate cycloserine cefoxitin agar [TCCA; homemade], and CLO medium) were compared from 406 stool samples of patients suspected of having
Clostridium difficile
infection. The sensitivities of chromID C. difficile agar at 24 h and 48 h, CLO medium, and TCCA were 74.1%, 87%, 85.2%, and 70.4%, respectively.
Development of a Clinically Comprehensive Database and a Simple Procedure for Identification of Molds from Solid Media by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Lau Anna F. , Drake Steven K. , Calhoun Leslie B. , Henderson Christina M. , Zelazny Adrian M. 
Published: December 2012

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the rapid and highly accurate identification of clinical pathogens but has not been utilized extensively in clinical mycology due to challenges in developing an effective protein extraction method and the limited databases available. Here, we developed an alternate extraction procedure and constructed a highly stringent database comprising 294 individual isolates representing 76 genera and 152 species. To our knowledge, this is the most comprehensive clinically relevant mold database developed to date. When challenged with 421 blinded clinical isolates from our institution, by use of the BioTyper software, accurate species-level (score of ≥2.0) and genus-level (score of ≥1.7) identifications were obtained for 370 (88.9%) and 18 (4.3%) isolates, respectively. No isolates were misidentified. Of the 33 isolates (7.8%) for which there was no identification (score of <1.7), 25 were basidiomycetes not associated with clinical disease and 8 were
Penicillium
species that were not represented in the database. Our library clearly outperformed the manufacturer's database that was obtained with the instrument, which identified only 3 (0.7%) and 26 (6.2%) isolates at species and genus levels, respectively. Identification was not affected by different culture conditions. Implementation into our routine workflow has revolutionized our mycology laboratory efficiency, with improved accuracy and decreased time for mold identification, eliminating reliance on traditional phenotypic features.
Molecular Characterization of High-Level Mupirocin Resistance in Staphylococcus pseudintermedius
Authors: Matanović Krešimir , Pérez-Roth Eduardo , Pintarić Selma , Šeol Martinec Branka 
Published: December 2012

ABSTRACT

The genetic analysis of high-level mupirocin resistance (Hi-Mup
r
) in a
Staphylococcus pseudintermedius
isolate from a dog is presented. The Hi-Mup
r
ileS2
gene flanked by a novel rearrangement of directly repeated insertion sequence IS
257
elements was located, together with the aminoglycoside resistance
aacA-aphD
determinant, on a conjugative plasmid related to the pSK41/pGO1 family plasmids.
Performance of Clostridium difficile Toxin Enzyme Immunoassay and Nucleic Acid Amplification Tests Stratified by Patient Disease Severity
Authors: Humphries Romney M. , Uslan Daniel Z. , Rubin Zachary 
Published: December 2012

ABSTRACT

Many clinical laboratories in the United States are transitioning from toxin enzyme immunoassays (EIA) to nucleic acid amplification tests (NAATs) as the primary diagnostic test for
Clostridium difficile
infection (CDI). While it is known that the analytical sensitivity of the toxin EIA is poor, there are limited clinical data on the performance of these assays for patients with mild or severe CDI. Two hundred ninety-six hospital inpatients with diarrhea and clinical suspicion for CDI were tested prospectively by toxin EIA, by
C. difficile
NAAT, and with a reference standard toxigenic culture. Following completion of laboratory testing, retrospective chart reviews were performed to stratify patients into mild and severe disease groups based on clinical criteria using a standard point-based system. One hundred forty-three patients with CDI confirmed by toxigenic culture were evaluated in this study. Among the patients with mild CDI, 49% tested positive by toxin EIA and 98% tested positive by NAAT. Among patients with severe CDI, 58% tested positive by toxin EIA and 98% tested positive by NAAT. Increased CDI disease severity was not associated with an increased sensitivity of EIA (
P
= 0.31). These data demonstrate that toxin EIA performs poorly both for patients with severe CDI and for those with mild CDI and support the routine use of NAAT for the diagnosis of CDI. The presence of stool toxin measured by EIA does not correlate with disease severity.
Education of Phlebotomy Teams Improves Blood Volume in Blood Culture Bottles
Authors: van Ingen Jakko , Hilt Nataliya , Bosboom Ron 
Published: December 2012

ABSTRACT
The volume of blood sampled for blood culture determines its sensitivity. We measured low mean blood volumes in submitted aerobic (8.38 ± 3.88 ml) and anaerobic (7.16 ± 3.83 ml) blood culture bottles. Educational seminars were held for phlebotomy teams, and renewed measurements thereafter revealed significantly higher blood volumes in submitted aerobic (9.77 ± 4.42 ml) and anaerobic (8.30 ± 3.64 ml) bottles. Education of phlebotomy teams improves the blood volume in blood culture bottles and should be part of quality control procedures.
Biological and Phylogenetic Characteristics of Yellow Fever Virus Lineages from West Africa
Authors: Stock Nina K. , Laraway Hewád , Faye Ousmane , Diallo Mawlouth , Niedrig Matthias , Sall Amadou A. 
Published: December 2012

ABSTRACT
The yellow fever virus (YFV), the first proven human-pathogenic virus, although isolated in 1927, is still a major public health problem, especially in West Africa where it causes outbreaks every year. Nevertheless, little is known about its genetic diversity and evolutionary dynamics, mainly due to a limited number of genomic sequences from wild virus isolates. In this study, we analyzed the phylogenetic relationships of 24 full-length genomes from YFV strains isolated between 1973 and 2005 in a sylvatic context of West Africa, including 14 isolates that had previously not been sequenced. By this, we confirmed genetic variability within one genotype by the identification of various YF lineages circulating in West Africa. Further analyses of the biological properties of these lineages revealed differential growth behavior in human liver and insect cells, correlating with the source of isolation and suggesting host adaptation. For one lineage, repeatedly isolated in a context of vertical transmission, specific characteristics in the growth behavior and unique mutations of the viral genome were observed and deserve further investigation to gain insight into mechanisms involved in YFV emergence and maintenance in nature.
Unraveling of a Neutralization Mechanism by Two Human Antibodies against Conserved Epitopes in the Globular Head of H5 Hemagglutinin
Authors: Qian Mengran , Hu Hongxing , Zuo Teng , Wang Guiqin , Zhang Linqi , Zhou Paul 
Published: December 2012

ABSTRACT
The rapid spread of highly pathogenic avian influenza (HPAI) H5N1 virus underscores the importance of effective antiviral treatment. Previously, we developed human monoclonal antibodies 65C6 and 100F4 that neutralize almost all (sub)clades of HPAI H5N1. The conserved 65C6 epitope was mapped to the globular head of HA. However, neither the 100F4 epitope nor the neutralization mechanism by these antibodies was known. In this study, we determined the 100F4 epitope and unraveled a neutralization mechanism by antibodies 65C6 and 100F4.
Herpes Simplex Virus 1 Tropism for Human Sensory Ganglion Neurons in the Severe Combined Immunodeficiency Mouse Model of Neuropathogenesis
Authors: Zerboni Leigh , Che Xibing , Reichelt Mike , Qiao Yanli , Gu Haidong , Arvin Ann 
Published: December 2012

ABSTRACT

The tropism of herpes simplex virus (HSV-1) for human sensory neurons infected
in vivo
was examined using dorsal root ganglion (DRG) xenografts maintained in mice with severe combined immunodeficiency (SCID). In contrast to the HSV-1 lytic infectious cycle
in vitro
, replication of the HSV-1 F strain was restricted in human DRG neurons despite the absence of adaptive immune responses in SCID mice, allowing the establishment of neuronal latency. At 12 days after DRG inoculation, 26.2% of human neurons expressed HSV-1 protein and 13.1% expressed latency-associated transcripts (LAT). Some infected neurons showed cytopathic changes, but HSV-1, unlike varicella-zoster virus (VZV), only rarely infected satellite cells and did not induce fusion of neuronal and satellite cell plasma membranes. Cell-free enveloped HSV-1 virions were observed, indicating productive infection. A recombinant HSV-1-expressing luciferase exhibited less virulence than HSV-1 F in the SCID mouse host, enabling analysis of infection in human DRG xenografts for a 61-day interval. At 12 days after inoculation, 4.2% of neurons expressed HSV-1 proteins; frequencies increased to 32.1% at 33 days but declined to 20.8% by 61 days. Frequencies of LAT-positive neurons were 1.2% at 12 days and increased to 40.2% at 33 days. LAT expression remained at 37% at 61 days, in contrast to the decline in neurons expressing viral proteins. These observations show that the progression of HSV-1 infection is highly restricted in human DRG, and HSV-1 genome silencing occurs in human neurons infected
in vivo
as a consequence of virus-host cell interactions and does not require adaptive immune control.
Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus
Authors: Escaffre Olivier , Le Nouën Cyril , Amelot Michel , Ambroggio Xavier , Ogden Kristen M. , Guionie Olivier , Toquin Didier , Müller Hermann , Islam Mohammed R. , Eterradossi Nicolas 
Published: December 2012

ABSTRACT
Infectious bursal disease virus (IBDV) causes an economically significant disease of chickens worldwide. Very virulent IBDV (vvIBDV) strains have emerged and induce as much as 60% mortality. The molecular basis for vvIBDV pathogenicity is not understood, and the relative contributions of the two genome segments, A and B, to this phenomenon are not known. Isolate 94432 has been shown previously to be genetically related to vvIBDVs but exhibits atypical antigenicity and does not cause mortality. Here the full-length genome of 94432 was determined, and a reverse genetics system was established. The molecular clone was rescued and exhibited the same antigenicity and reduced pathogenicity as isolate 94432. Genetically modified viruses derived from 94432, whose vvIBDV consensus nucleotide sequence was restored in segment A and/or B, were produced, and their pathogenicity was assessed in specific-pathogen-free chickens. We found that a valine (position 321) that modifies the most exposed part of the capsid protein VP2 critically modified the antigenicity and partially reduced the pathogenicity of 94432. However, a threonine (position 276) located in the finger domain of the virus polymerase (VP1) contributed even more significantly to attenuation. This threonine is partially exposed in a hydrophobic groove on the VP1 surface, suggesting possible interactions between VP1 and another, as yet unidentified molecule at this amino acid position. The restored vvIBDV-like pathogenicity was associated with increased replication and lesions in the thymus and spleen. These results demonstrate that both genome segments influence vvIBDV pathogenicity and may provide new targets for the attenuation of vvIBDVs.
The Feline Calicivirus Leader of the Capsid Protein Is Associated with Cytopathic Effect
Authors: Abente Eugenio J. , Sosnovtsev Stanislav V. , Sandoval-Jaime Carlos , Parra Gabriel I. , Bok Karin , Green Kim Y. 
Published: December 2012

ABSTRACT
Open reading frame 2 (ORF2) of the feline calicivirus (FCV) genome encodes a capsid precursor that is posttranslationally processed to release the mature capsid protein (VP1) and a small protein of 124 amino acids, designated the leader of the capsid (LC). To investigate the role of the LC protein in the virus life cycle, mutations and deletions were introduced into the LC coding region of an infectious FCV cDNA clone. Three cysteine residues that are conserved among all vesivirus LC sequences were found to be critical for the recovery of FCV with a characteristic cytopathic effect in feline kidney cells. A cell-rounding phenotype associated with the transient expression of wild-type and mutagenized forms of the LC correlated with the cytopathic and growth properties of the corresponding engineered viruses. The host cellular protein annexin A2 was identified as a binding partner of the LC protein, consistent with a role for the LC in mediating host cell interactions that alter the integrity of the cell and enable virus spread.