bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a Single-Platform, Volumetric, CD45-Assisted PanLeucogating Auto40 Flow Cytometer To Determine the Absolute Number and Percentages of CD4 T Cells in Resource-Constrained Settings Using Cameroonian Patients' Samples
Authors: Mbopi-Kéou François-Xavier , Mion Stefano , Sagnia Bertrand , Bélec Laurent 
Published: February 2012

ABSTRACTThe study evaluated the single-platform, volumetric, CD45-assisted PanLeucogating Auto40 flow cytometer (Apogee Flow Systems Ltd., Hemel Hempstead, United Kingdom) for CD4 T cell numeration, compared to the reference FACSCalibur flow cytometer. Results of absolute counts and percentages of CD4 T cells by Auto40 and FACSCalibur of 234 tripotassium EDTA (K3-EDTA)-blood samples from 146 adults and 88 children (aged from 18 months to 5 years), living in Yaoundé, Cameroon, were highly correlated (r2= 0.97 andr2= 0.98, respectively). The mean absolute bias and relative bias between Apogee Auto40 and FACSCalibur absolute CD4 T cell counts were +9.6 cells/μl, with limits of agreement from −251 to 270 cells/μl, and +4.1%, with limits of agreement from −16.1 to 24.4%, respectively. The mean absolute bias and relative bias between Apogee Auto40 and FACSCalibur CD4 T cell results expressed as percentages were +0.05% CD4 (95% confidence interval [CI], −0.03 to 0.41), with limits of agreement from −6.0 to 5.9% CD4, and +1.0%, with limits of agreement from −32.3 to 34.4%, respectively. The Auto40 counting allowed identification of the majority of adults with CD4 T cell counts below 200 cells/μl (sensitivity, 87%; specificity, 98%) or below 350 cells/μl (sensitivity, 92%; specificity, 98%) and of children with CD4 T cell counts below 750 cells/μl (sensitivity, 82%; specificity, 98%) or below 25% CD4+(sensitivity, 96%; specificity, 99%). The Auto40 analyzer is a reliable alternative flow cytometer for CD4 T lymphocyte enumeration to be used in routine immunological monitoring according to the WHO recommendations for HIV-infected adults as well as children living in resource-constrained settings.
Concurrent Occurrence of
bla
ampC
Families and
bla
CTX-M
Genogroups and Association with Mobile Genetic Elements IS
Ecp1
, IS
26
, IS
CR1
, and
sul1
-Type Class 1 Integrons in Escherichia coli and Klebsiella pneumoniae Isolates Originating from India
Authors: Shahid Mohammed , Sobia Farrukh , Singh Anuradha , Khan Haris M. 
Published: February 2012

ABSTRACT

Cefoxitin-resistant
Escherichia coli
(
n
= 109) and
Klebsiella pneumoniae
(
n
= 16) isolates collected from patients in India in 2009 to 2010 were screened for
bla
ampC
families and mobilizing elements (
ISE
cp1,
IS
26,
IS
CR1, and
sul
-1-type class 1 integrons) and their association with
bla
ampC
and for the occurrence of class A beta-lactamases (BLs) (CTX-M, TEM, and SHV). The concurrent occurrences of two distinct AmpC families (
bla
CIT
and
bla
EBC
) and of class A with class C beta-lactamase were observed. All but one of the isolates harboring CTX-M extended-spectrum BLs (ESBLs) were carrying
bla
CTX-M
genogroup 1; the remaining isolate carried
bla
CTX-M
genogroup 9. The mobilizing elements occurred in different combinations in the study isolates.
Cutaneous Infection Caused by Gordonia amicalis after a Traumatic Injury
Authors: Lai Chih-Cheng , Hsieh Jung-Hsien , Tsai Hsih-Yeh , Liao Chun-Hsing , Hsueh Po-Ren 
Published: February 2012

ABSTRACT

Gordonia amicalis
infection has never been reported in humans. We report here the first case of
G. amicalis
-related cutaneous infection after a traumatic injury. The isolate was confirmed by 16S rRNA sequencing analysis, and the patient responded well to repeated debridement and antibiotic treatment.
Analysis of Pathogen and Host Factors Related to Clinical Outcomes in Patients with Hospital-Acquired Pneumonia Due to Methicillin-Resistant Staphylococcus aureus
Authors: Haque Nadia Z. , Arshad Samia , Peyrani Paula , Ford Kimbal D. , Perri Mary B. , Jacobsen Gordon , Reyes Katherine , Scerpella Ernesto G. , Ramirez Julio A. , Zervos Marcus J. 
Published: February 2012

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) is a major cause of nosocomial pneumonia. To characterize pathogen-derived and host-related factors in intensive care unit (ICU) patients with MRSA pneumonia, we evaluated the Improving Medicine through Pathway Assessment of Critical Therapy in Hospital-Acquired Pneumonia (IMPACT-HAP) database. We performed multivariate regression analyses of 28-day mortality and clinical response using univariate analysis variables at a
P
level of <0.25. In isolates from 251 patients, the most common molecular characteristics were USA100 (55.0%) and USA300 (23.9%), SCC
mec
types II (64.1%) and IV (33.1%), and
agr
I (36.7%) and II (61.8%). Panton-Valentine leukocidin (PVL) was present in 21.9%, and vancomycin heteroresistance was present in 15.9%. Mortality occurred in 37.1% of patients; factors in the univariate analysis were age, APACHE II score, AIDS, cardiac disease, vascular disease, diabetes, SCC
mec
type II, PVL negativity, and higher vancomycin MIC (all
P
values were <0.05). In multivariate analysis, independent predictors were APACHE II score (odds ratio [OR], 1.090; 95% confidence interval [CI], 1.041 to 1.141;
P
< 0.001) and age (OR, 1.024; 95% CI, 1.003 to 1.046;
P
= 0.02). Clinical failure occurred in 36.8% of 201 evaluable patients; the only independent predictor was APACHE II score (OR, 1.082; 95% CI, 1.031 to 1.136;
P
= 0.002). In summary, APACHE II score (mortality, clinical failure) and age (mortality) were the only independent predictors, which is consistent with severity of illness in ICU patients with MRSA pneumonia. Interestingly, our univariate findings suggest that both pathogen and host factors influence outcomes. As the epidemiology of MRSA pneumonia continues to evolve, both pathogen- and host-related factors should be considered when describing epidemiological trends and outcomes of therapeutic interventions.
Real-Time Multiplex PCR for Detecting Shiga Toxin 2-Producing Escherichia coli O104:H4 in Human Stools
Authors: Zhang Wenlan , Bielaszewska Martina , Bauwens Andreas , Fruth Angelika , Mellmann Alexander , Karch Helge 
Published: February 2012

ABSTRACT

A real-time multiplex PCR targeting
stx
2
,
wzy
O104
, and
fliC
H4
of enterohemorrhagic
Escherichia coli
(EHEC) O104:H4 correctly determined the presence or absence of these genes in 253 EHEC isolates and enrichment cultures of stool samples from 132 patients. It is a rapid, sensitive, and specific tool for detecting EHEC O104:H4 in human stools.
Tracking Viral Evolution during a Disease Outbreak: the Rapid and Complete Selective Sweep of a Circovirus in the Endangered Echo Parakeet
Authors: Kundu Samit , Faulkes Christopher G. , Greenwood Andrew G. , Jones Carl G. , Kaiser Pete , Lyne Owen D. , Black Simon A. , Chowrimootoo Aurelie , Groombridge Jim J. 
Published: February 2012

ABSTRACTCircoviruses are among the smallest and simplest of all viruses, but they are relatively poorly characterized. Here, we intensively sampled two sympatric parrot populations from Mauritius over a period of 11 years and screened for the circovirusBeak and feather disease virus(BFDV). During the sampling period, a severe outbreak of psittacine beak and feather disease, which is caused by BFDV, occurred in Echo parakeets. Consequently, this data set presents an ideal system for studying the evolution of a pathogen in a natural population and to understand the adaptive changes that cause outbreaks. Unexpectedly, we discovered that the outbreak was most likely caused by changes in functionally important regions of the normally conservedreplication-associated proteingene and not the immunogeniccapsid. Moreover, these mutations were completely fixed in the Echo parakeet host population very shortly after the outbreak. Severalcapsidalleles were linked to thereplication-associated proteinoutbreak allele, suggesting that whereas the key changes occurred in the latter, the scope of the outbreak and the selective sweep may have been influenced by positive selection in the capsid. We found evidence for viral transmission between the two host populations though evidence for the invasive species as the source of the outbreak was equivocal. Finally, the high evolutionary rate that we estimated shows how rapidly new variation can arise in BFDV and is consistent with recent results from other small single-stranded DNA viruses.
The PI3K/Akt Pathway Contributes to Arenavirus Budding
Authors: Urata Shuzo , Ngo Nhi , de la Torre Juan Carlos 
Published: February 2012

ABSTRACT
Several arenaviruses, chiefly Lassa virus (LASV), cause hemorrhagic fever (HF) disease in humans and pose a significant public health concern in regions where they are endemic. On the other hand, evidence indicates that the globally distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen. The phosphatidylinositol 3-kinase (PI3K)/Akt pathway participates in many cellular processes, including cell survival and differentiation, and also has been shown to play important roles in different steps of the life cycles of a variety of viruses. Here we report that the inhibition of the PI3K/Akt pathway inhibited budding and to a lesser extent RNA synthesis, but not cell entry, of LCMV. Accordingly, BEZ-235, a PI3K inhibitor currently in cancer clinical trials, inhibited LCMV multiplication in cultured cells. These findings, together with those previously reported for Junin virus (JUNV), indicate that targeting the PI3K/Akt pathway could represent a novel antiviral strategy to combat human-pathogenic arenaviruses.
Host Acyl Coenzyme A Binding Protein Regulates Replication Complex Assembly and Activity of a Positive-Strand RNA Virus
Authors: Zhang Jiantao , Diaz Arturo , Mao Lan , Ahlquist Paul , Wang Xiaofeng 
Published: February 2012

ABSTRACT
All positive-strand RNA viruses reorganize host intracellular membranes to assemble their replication complexes. Similarly, brome mosaic virus (BMV) induces two alternate forms of membrane-bound RNA replication complexes: vesicular spherules and stacks of appressed double-membrane layers. The mechanisms by which these membrane rearrangements are induced, however, remain unclear. We report here that host ACB1-encoded acyl coenzyme A (acyl-CoA) binding protein (ACBP) is required for the assembly and activity of both BMV RNA replication complexes. ACBP is highly conserved among eukaryotes, specifically binds to long-chain fatty acyl-CoA, and promotes general lipid synthesis. Deleting ACB1 inhibited BMV RNA replication up to 30-fold and resulted in formation of spherules that were ∼50% smaller but ∼4-fold more abundant than those in wild-type (wt) cells, consistent with the idea that BMV 1a invaginates and maintains viral spherules by coating the inner spherule membrane. Furthermore, smaller and more frequent spherules were preferentially formed under conditions that induce layer formation in wt cells. Conversely, cellular karmella structures, which are arrays of endoplasmic reticulum (ER) membranes formed upon overexpression of certain cellular ER membrane proteins, were formed normally, indicating a selective inhibition of 1a-induced membrane rearrangements. Restoring altered lipid composition largely complemented the BMV RNA replication defect, suggesting that ACBP was required for maintaining lipid homeostasis. Smaller and more frequent spherules are also induced by 1a mutants with specific substitutions in a membrane-anchoring amphipathic α-helix, implying that the 1a-lipid interactions play critical roles in viral replication complex assembly.
Receptor-Binding Profiles of H7 Subtype Influenza Viruses in Different Host Species
Authors: Gambaryan Alexandra S. , Matrosovich Tatyana Y. , Philipp Jennifer , Munster Vincent J. , Fouchier Ron A. M. , Cattoli Giovanni , Capua Ilaria , Krauss Scott L. , Webster Robert G. , Banks Jill , Bovin Nicolai V. , Klenk Hans-Dieter , Matrosovich Mikhail N. 
Published: February 2012

ABSTRACTInfluenza viruses of gallinaceous poultry and wild aquatic birds usually have distinguishable receptor-binding properties. Here we used a panel of synthetic sialylglycopolymers and solid-phase receptor-binding assays to characterize receptor-binding profiles of about 70 H7 influenza viruses isolated from aquatic birds, land-based poultry, and horses in Eurasia and America. Unlike typical duck influenza viruses with non-H7 hemagglutinin (HA), all avian H7 influenza viruses, irrespective of the host species, displayed a poultry-virus-like binding specificity, i.e., preferential binding to sulfated oligosaccharides Neu5Acα2-3Galβ1-4(6-O-HSO3)GlcNAc and Neu5Acα2-3Galβ1-4(Fucα1-3)(6-O-HSO3)GlcNAc. This phenotype correlated with the unique amino acid sequence of the amino acid 185 to 189 loop of H7 HA and seemed to be dependent on ionic interactions between the sulfate group of the receptor and Lys193 and on the lack of sterical clashes between the fucose residue and Gln222. Many North American and Eurasian H7 influenza viruses displayed weak but detectable binding to the human-type receptor moiety Neu5Acα2-6Galβ1-4GlcNAc, highlighting the potential of H7 influenza viruses for avian-to-human transmission. Equine H7 influenza viruses differed from other viruses by preferential binding to the N-glycolyl form of sialic acid. Our data suggest that the receptor-binding site of contemporary H7 influenza viruses in aquatic and terrestrial birds was formed after the introduction of their common precursor from ducks to a new host, presumably, gallinaceous poultry. The uniformity of the receptor-binding profile of H7 influenza viruses in various wild and domestic birds indicates that there is no strong receptor-mediated host range restriction in birds on viruses with this HA subtype. This notion agrees with repeated interspecies transmission of H7 influenza viruses from aquatic birds to poultry.
Susceptibility to Acute Mouse Adenovirus Type 1 Respiratory Infection and Establishment of Protective Immunity in Neonatal Mice
Authors: Procario Megan C. , Levine Rachael E. , McCarthy Mary K. , Kim Eunnie , Zhu Lingqiao , Chang Cheong-Hee , Hershenson Marc B. , Weinberg Jason B. 
Published: February 2012

ABSTRACTThere is an incomplete understanding of the differences between neonatal immune responses that contribute to the increased susceptibility of neonates to some viral infections. We tested the hypothesis that neonates are more susceptible than adults to mouse adenovirus type 1 (MAV-1) respiratory infection and are impaired in the ability to generate a protective immune response against a second infection. Following intranasal infection, lung viral loads were greater in neonates than in adults during the acute phase but the virus was cleared from the lungs of neonates as efficiently as it was from adult lungs. Lung gamma interferon (IFN-γ) responses were blunted and delayed in neonates, and lung viral loads were higher in adult IFN-γ−/−mice than in IFN-γ+/+controls. However, administration of recombinant IFN-γ to neonates had no effect on lung viral loads. Recruitment of inflammatory cells to the airways was impaired in neonates. CD4 and CD8 T cell responses were similar in the lungs of neonates and adults, although a transient increase in regulatory T cells occurred only in the lungs of infected neonates. Infection of neonates led to protection against reinfection later in life that was associated with increased effector memory CD8 T cells in the lungs. We conclude that neonates are more susceptible than adults to acute MAV-1 respiratory infection but are capable of generating protective immune responses.
Impact of Human Adenovirus Type 3 Dodecahedron on Host Cells and Its Potential Role in Viral Infection
Authors: Fender Pascal , Hall Kathryn , Schoehn Guy , Blair G. Eric 
Published: February 2012

ABSTRACT
During human adenovirus type 3 (Ad3) infection, an excess of penton base and fiber proteins are produced which form dodecahedral particles composed of 12 pentamers of penton base and 12 trimers of fiber protein. No biological functions have yet been ascribed to Ad3 dodecahedra. Here, we show that dodecahedra compete with Ad3 virions for binding to the cell surface and trigger cell remodeling, giving new insights into possible biological functions of dodecahedra in the Ad3 infectious cycle.
Biological Characterization and Next-Generation Genome Sequencing of the Unclassified Cotia Virus SPAn232 (Poxviridae)
Authors: Afonso Priscila P. , Silva Patrícia M. , Schnellrath Laila C. , Jesus Desyreé M. , Hu Jianhong , Yang Yajie , Renne Rolf , Attias Marcia , Condit Richard C. , Moussatché Nissin , Damaso Clarissa R. 
Published: February 2012

ABSTRACT

Cotia virus (COTV) SPAn232 was isolated in 1961 from sentinel mice at Cotia field station, São Paulo, Brazil. Attempts to classify COTV within a recognized genus of the
Poxviridae
have generated contradictory findings. Studies by different researchers suggested some similarity to myxoma virus and swinepox virus, whereas another investigation characterized COTV SPAn232 as a vaccinia virus strain. Because of the lack of consensus, we have conducted an independent biological and molecular characterization of COTV. Virus growth curves reached maximum yields at approximately 24 to 48 h and were accompanied by virus DNA replication and a characteristic early/late pattern of viral protein synthesis. Interestingly, COTV did not induce detectable cytopathic effects in BSC-40 cells until 4 days postinfection and generated viral plaques only after 8 days. We determined the complete genomic sequence of COTV by using a combination of the next-generation DNA sequencing technologies 454 and Illumina. A unique contiguous sequence of 185,139 bp containing 185 genes, including the 90 genes conserved in all chordopoxviruses, was obtained. COTV has an interesting panel of open reading frames (ORFs) related to the evasion of host defense, including two novel genes encoding C-C chemokine-like proteins, each present in duplicate copies. Phylogenetic analysis revealed the highest amino acid identity scores with
Cervidpoxvirus
,
Capripoxvirus
,
Suipoxvirus
,
Leporipoxvirus
, and
Yatapoxvirus
. However, COTV grouped as an independent branch within this clade, which clearly excluded its classification as an
Orthopoxvirus
. Therefore, our data suggest that COTV could represent a new poxvirus genus.
Feasibility study of geospatial mapping of chronic disease risk to inform public health commissioning
Authors: Noble Douglas , Smith Dianna , Mathur Rohini , Robson John , Greenhalgh Trisha 
Published: February 2012

ObjectiveTo explore the feasibility of producing small-area geospatial maps of chronic disease risk for use by clinical commissioning groups and public health teams.Study designCross-sectional geospatial analysis using routinely collected general practitioner electronic record data.Sample and settingTower Hamlets, an inner-city district of London, UK, characterised by high socioeconomic and ethnic diversity and high prevalence of non-communicable diseases.MethodsThe authors used type 2 diabetes as an example. The data set was drawn from electronic general practice records on all non-diabetic individuals aged 25–79 years in the district (n=163 275). The authors used a validated instrument, QDScore, to calculate 10-year risk of developing type 2 diabetes. Using specialist mapping software (ArcGIS), the authors produced visualisations of how these data varied by lower and middle super output area across the district. The authors enhanced these maps with information on examples of locality-based social determinants of health (population density, fast food outlets and green spaces). Data were piloted as three types of geospatial map (basic, heat and ring). The authors noted practical, technical and information governance challenges involved in producing the maps.ResultsUsable data were obtained on 96.2% of all records. One in 11 adults in our cohort was at ‘high risk’ of developing type 2 diabetes with a 20% or more 10-year risk. Small-area geospatial mapping illustrated ‘hot spots’ where up to 17.3% of all adults were at high risk of developing type 2 diabetes. Ring maps allowed visualisation of high risk for type 2 diabetes by locality alongside putative social determinants in the same locality. The task of downloading, cleaning and mapping data from electronic general practice records posed some technical challenges, and judgement was required to group data at an appropriate geographical level. Information governance issues were time consuming and required local and national consultation and agreement.ConclusionsProducing small-area geospatial maps of diabetes risk calculated from general practice electronic record data across a district-wide population was feasible but not straightforward. Geovisualisation of epidemiological and environmental data, made possible by interdisciplinary links between public health clinicians and human geographers, allows presentation of findings in a way that is both accessible and engaging, hence potentially of value to commissioners and policymakers. Impact studies are needed of how maps of chronic disease risk might be used in public health and urban planning.
HIV testing and care systems focused on sexually transmitted HIV in China
Authors: Tucker Joseph D , Wong Frank Y , Nehl Eric J , Zhang Fujie 
Published: February 2012

BackgroundOver three-quarters of new HIV infections in China during 2009 were estimated to be from sexual transmission. Over half of those living with HIV do not know their serostatus and identifying and treating individuals with sexually transmitted HIV infection has been challenging.ObjectiveThis global assessment explores Chinese systems for detecting and treating those with HIV infection with a particular focus on groups at increased risk of sexually transmitted HIV.MethodsPublished literature, grey sources and non-governmental reports were reviewed to describe HIV testing and care systems in China.ResultsHIV testing and care in China involve several parallel health systems and have been largely successful in reaching large numbers of vulnerable individuals. Provider-initiated testing and counselling has been more effective than voluntary counselling and testing programmes for expanding HIV testing efforts in China. Individuals with sexually transmitted HIV infection are underrepresented in the antiretroviral care system compared with other high-risk groups.ConclusionsComprehensive HIV testing and care bring together a number of Chinese health systems, but there are still gaps and challenges. Research and programmes focused on HIV testing and care for those with increased sexual risk are needed.