bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Antibodies Secreted from CirculatingMycobacterium tuberculosis-Specific Plasma Cells in the Diagnosis of Pediatric Tuberculosis
Authors: Raqib Rubhana , Mondal Dinesh , Karim M. Anwarul , Chowdhury Fahima , Ahmed Sultan , Luby Stephen , Cravioto Alejandro , Andersson Jan , Sack David 
Published: February 2009

ABSTRACTDiagnosis of tuberculosis (TB) in children is difficult because symptoms are often nonspecific or absent in infected children, diagnostic specimens are difficult to obtain from younger children, and >50% have negative TB cultures. Thus, there is an urgent need for improved diagnosis of pediatric TB. This study aimed to evaluate the diagnostic value of a new serological method, the ALS (antibodies in lymphocyte supernatant) assay, for the diagnosis of active TB in children with clinically identified TB. The ALS test is based on the concept that antigen-specific plasma cells are present in the circulation only at times of acute infection and not in latency. A cross-sectional study of pediatric patients (age range, 11 to 167 months) who were clinically identified as TB (n= 58) or non-TB (n= 16) patients was conducted, and they were monitored for 6 months. Healthy children (n= 58) were enrolled as controls. Spontaneous release of TB antigen-specific antibodies by in vitro-cultured, unstimulated peripheral blood mononuclear cells was assessed by an enzyme-linked immunosorbent assay usingMycobacterium bovisbacillus Calmette-Guérin (BCG) as the detecting antigen. Of the patients clinically diagnosed with TB, 15% had culture-confirmed TB, 64% were positive for TB by clinically established scoring charts (K. Edwards, P. N. G. Med. J. 30: 169-178, 1987; G. Stegen, K. Jones, and P. Kaplan, Pediatrics 43: 260-263, 1969; and stop TB Partnership, Childhood TB subgroup, World Health Organization, Int. J. Tuberc. Lung Dis. 10: 1091-1097, 2006), and 91% were TB positive by the ALS method. All TB patients had significantly higher BCG-specific ALS titers at enrollment (optical density [OD], 1.06 ± 0.32) than healthy-control children (OD, 0.18 ± 0.06) and non-TB children (OD, 0.21 ± 0.10) (P= 0.001). The ALS titers declined in children with active disease from enrollment through 6 months following anti-TB therapy (P= 0.001). The ALS assay is a novel diagnostic method with potential applications in the diagnosis of pediatric TB and in subsequent monitoring of treatment effectiveness.
Novel Method for Determination of Substance P Levels in Unextracted Human Plasma by Using Acidification
Authors: Campbell Donald E. , Bruckner Paula , Tustin Nancy B. , Tustin Richard , Douglas Steven D. 
Published: February 2009

ABSTRACT
Substance P (SP) is a member of the tachykinin family and has an important role in immune responses. SP is detectable in plasma in a free and bound state. Simple modification of a commercially available SP enzyme-linked immunosorbent assay allows the dissociation and capture of plasma SP without solid-phase extraction.
Application of the Dengue Virus NS1 Antigen Rapid Test for On-Site Detection of Imported Dengue Cases at Airports
Authors: Shu Pei-Yun , Yang Cheng-Fen , Kao Jeng-Fong , Su Chien-Ling , Chang Shu-Fen , Lin Chien-Chou , Yang Wen-Chih , Shih Hsiu , Yang Shih-Yan , Wu Ping-Fuai , Wu Ho-Sheng , Huang Jyh-Hsiung 
Published: February 2009

ABSTRACT
We used the dengue virus NS1 antigen (Ag) rapid test for on-site detection of imported dengue cases at airports. Among 22 positive cases of dengue identified from 850 patients with a fever suspected to have dengue, 17 were NS1 Ag test positive. These findings demonstrate the usefulness of the NS1 Ag rapid test in screening imported dengue cases at airports.
Use of Spoligotyping and Large Sequence Polymorphisms To Study the Population Structure of the
Mycobacterium tuberculosis
Complex in a Cohort Study of Consecutive Smear-Positive Tuberculosis Cases in The Gambia
Authors: de Jong Bouke C. , Antonio Martin , Awine Timothy , Ogungbemi Kunle , de Jong Ype P. , Gagneux Sebastien , DeRiemer Kathryn , Zozio Thierry , Rastogi Nalin , Borgdorff Martien , Hill Philip C. , Adegbola Richard A. 
Published: February 2009

ABSTRACT

Mycobacterium africanum
, first described in Senegal in 1968, causes up to half of the smear-positive pulmonary tuberculosis cases in West Africa, but it has not been found in other geographical areas except among recent West African migrants. The reasons for the geographic restriction of
M. africanum
are unknown. We used molecular tools to determine the population structure of the
Mycobacterium tuberculosis
complex in a cohort study of consecutive smear-positive tuberculosis cases in The Gambia. We collected and genotyped 386 clinical isolates using spoligotype analysis and PCRs for large sequence polymorphisms (LSPs) and compared the genotype patterns to the patterns in an international database. The results of spoligotyping and LSP analysis for the study population were also compared to determine the correlation between them. The main lineages within the
Mycobacterium tuberculosis
complex identified in The Gambia included
M. africanum
type I (38.4%), characterized by an LSP in region of difference 702 (RD702; West African type 2). Among the
M. tuberculosis
sensu stricto isolates, lineages characterized by RD182 and by RD174 were the most common. We also detected a gradient in the prevalence of
M. africanum
that extended from neighboring Guinea-Bissau. The genotypic diversity of the spoligotype patterns was greater among the isolates of
M. africanum
than among the isolates of
M. tuberculosis
. We postulate that
M. africanum
became endemic in West Africa first, before the introduction of different lineages within
M. tuberculosis
sensu stricto.
Predominance and Circulation of Enteric Viruses in the Region of Greater Cairo, Egypt
Authors: Kamel Aziza H. , Ali Mohamed A. , El-Nady Hala G. , de Rougemont Alexis , Pothier Pierre , Belliot Gaël 
Published: February 2009

ABSTRACT
The circulation of enteric viruses among the population of Cairo, Egypt, between March 2006 and February 2007 was studied. At least one virus was detected in 50% of fecal samples, 57.4% of which were positive for rotavirus, 26% for norovirus, 10.4% for adenovirus, and 1.7% for astrovirus. Over 10% of infections were mixed infections. Rotavirus typing showed that G1P[8] and G2P[4] were predominant but that the unusual G12P[4] and G12P[6] reassortants were also present. Among the noroviruses, half belonged to the predominant GGII.4 cluster. The phylogenetic analysis of the capsid gene suggested that GGII.4 strains from Cairo were similar to those circulating elsewhere. It also showed the emergence of new GGII.4 variants that were not associated with any previously known GGII.4 isolate. Further studies are required to assess the disease burden of enteric viruses in Egypt and the impact of atypical strains.
Nucleic Acid Amplification Tests for Diagnosis of
Neisseria gonorrhoeae
Oropharyngeal Infections
Authors: Bachmann Laura H. , Johnson Robert E. , Cheng Hong , Markowitz Lauri E. , Papp John R. , Hook Edward W. 
Published: February 2009

ABSTRACT

The optimal methods for the diagnosis of pharyngeal
Neisseria gonorrhoeae
infection are uncertain. The objective of this study was to define the performance of culture and nucleic acid amplification tests (NAATs) for the diagnosis of pharyngeal
N. gonorrhoeae
. In this cross-sectional study, males and females >15 years old who acknowledged performing fellatio or cunnilingus (in the previous 2 months) were recruited from three clinics (two human immunodeficiency virus clinics and one sexually transmitted diseases clinic) located in Birmingham, AL. The test performance of culture for
N. gonorrhoeae
, the Gen-Probe Aptima Combo 2 transcription-mediated amplification assay (TMA), the BD ProbeTec ET amplified DNA strand displacement assay (SDA), and the Roche Cobas Amplicor PCR was defined by using a rotating “gold standard” of any positive results by two or three of the three tests that excluded the test being evaluated. A total of 961 evaluable test sets were collected. On the basis of a rotating gold standard of positive results by two of three comparator tests, the sensitivity and the specificity were as follows: culture for
N. gonorrhoeae
, 50.0% and 99.4%, respectively; PCR, 80.3% and 73.0%, respectively; TMA, 83.6% and 98.6%, respectively; and SDA, 93.2% and 96.3%, respectively. On the basis of a rotating gold standard of positive results by three of three comparator tests, the sensitivity and specificity were as follows: culture for
N. gonorrhoeae
, 65.4% and 99.0%, respectively; PCR, 91.9% and 71.8%, respectively; TMA, 100% and 96.2%, respectively; and SDA, 97.1% and 94.2%, respectively. In conclusion, currently available NAATs are more sensitive than culture for the detection of pharyngeal gonorrhea in at-risk patients. PCR is substantially less specific than culture, TMA, or SDA and should not be used for the detection of pharyngeal gonorrhea.
Human Bocavirus in an Immunocompromised Child Presenting with Severe Diarrhea
Authors: de Vries Jutte J. C. , Bredius Robbert G. M. , van Rheenen Patrick F. , Smiers Frans J. W. , Schölvinck Elisabeth H. , Vossen Ann C. T. M. , Claas Eric C. J. , Niesters Hubert G. M. 
Published: February 2009

ABSTRACT
Human bocavirus (HBoV) is frequently detected in young children with respiratory symptoms. However, the prevalence and pathogenicity of HBoV in immunocompromised patients are largely unknown. This report describes a case of life-threatening hypovolemic shock due to diarrhea associated with disseminated HBoV infection in an immunocompromised child.
Eight-Plex PCR and Liquid-Array Detection of Bacterial and Viral Pathogens in Cerebrospinal Fluid from Patients with Suspected Meningitis
Authors: Bøving Mette Kusk , Pedersen Lisbeth Nørum , Møller Jens Kjølseth 
Published: February 2009

ABSTRACT

We here report on the development of a novel multiplex PCR with product detection in a Luminex 100 suspension array system. The assay covers the nine most important bacterial and viral pathogens found in Danish meningitis patients. The microorganisms include
Neisseria meningitidis
,
Streptococcus pneumoniae
,
Escherichia coli
,
Staphylococcus aureus
,
Listeria monocytogenes
,
Streptococcus agalactiae
, herpes simplex virus types 1 and 2, and varicella-zoster virus. The study was based on 1,187 samples, of which 55 were found to be positive by PCR. The assay was found to have an excellent sensitivity and an excellent specificity compared to the results of a “gold standard,” defined by routine laboratory tests, for the two most important pathogens,
S. pneumoniae
(95 and 99.1%, respectively) and
N. meningitidis
(100 and 99.7%, respectively). The method provides a valuable supplement to the traditional microscopy and culture of cerebrospinal fluid (CSF) samples in a routine diagnostic setting, and results can be available within 1 workday. The method is suitable for use for the initial screening and identification of nine important microorganisms in CSF samples from patients with suspected meningitis. Compared to microscopy and culture of CSF, this rapid and sensitive method will support physicians with the selection of the appropriate antimicrobial agents and the initiation of timely treatment in the absence of live microorganisms in the CSF.
Correlation between Human Immunodeficiency Virus Type 1 (HIV-1) RNA Measurements Obtained with Dried Blood Spots and Those Obtained with Plasma by Use of Nuclisens EasyQ HIV-1 and Abbott RealTime HIV Load Tests
Authors: Garrido Carolina , Zahonero Natalia , Corral Angélica , Arredondo Miguel , Soriano Vincent , de Mendoza Carmen 
Published: February 2009

ABSTRACTThe plasma human immunodeficiency virus (HIV) RNA load is used in the clinical routine for the monitoring of HIV infection and the patient's response to antiretroviral therapy. Other body fluids or dried blood spots (DBS) can be used, however, to assess the level of viremia. The use of DBS may be especially helpful for the monitoring of HIV-infected patients in resource-poor settings, where access to adequate laboratory facilities is often difficult. However, the correlation between the HIV RNA levels in plasma and those in DBSs has not been well established. Paired plasma and DBS samples obtained from HIV type 1 (HIV-1)-infected patients were tested for HIV RNA copy numbers by using two different commercial assays, the Nuclisens EasyQ HIV-1 (version 1.1) test (the Nuclisens test; Biomerieux) and the m2000rt RealTime HIV test (the m2000rt test; Abbott). Nucleic acid extraction was performed manually by using either the Nuclisens isolation kit (which uses the Boom methodology) or the m2000rt sample preparation kit (an iron particle-based method). A total of 103 paired plasma and DBS samples were tested. Viral load results were obtained for 97 (94.2%) samples with the Nuclisens isolation kit and 81 (78.6%) samples with the m2000rt kit. The overall correlation between the RNA loads in plasma and DBS was good, although better results were obtained by the Nuclisens test (R2= 0.87,P< 0.001) than by the m2000rt test (R2= 0.70,P< 0.001). While the specificities were excellent and similar for both the Nuclisens and the m2000rt tests (97.1% and 100%, respectively), the sensitivity was greater by the Nuclisens test than by the m2000rt test (75.8% and 56.6%, respectively). Overall, the viral loads in DBS tended to be lower than those in plasma, with mean differences of 0.3 log unit (standard deviation, 0.5 log unit) and 0.76 log unit (standard deviation, 0.8 log unit) for the Nuclisens and the m2000rt tests, respectively. The levels of agreement between the measurements in plasma and DBS were assessed by using the Bland-Altman plot for each assay. The Nuclisens test gave results within its defined limits (−0.65 to 1.26) for 95.9% of the samples, while the m2000rt test gave results within its limits (−0.83 to 2.33) for 100% of the samples. In summary, the HIV-1 load can accurately be quantified by testing DBS by either the Nuclisens or the m2000rt test, although the Nuclisens test may outperform the m2000rt test when nucleic acids are extracted manually.
Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay
Authors: Korn Klaus , Weissbrich Benedikt , Henke-Gendo Cornelia , Heim Albert , Jauer Christin Mariel , Taylor Ninon , Eberle Josef 
Published: February 2009

ABSTRACT

Systematic sequence analysis of human immunodeficiency virus type 1 (HIV-1) variants with RNA levels underestimated by the Cobas TaqMan HIV-1 assay demonstrated that mutations at a single position of the downstream primer can lead to the underestimation of HIV-1 RNA levels by more than 2 log and to false-negative results in minipool screening of blood donors. Mutations at this position are found in about 2% of all HIV-1 M
gag
sequences.
Comparison of the Abbott RealTime Human Immunodeficiency Virus Type 1 (HIV-1) Assay to the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test: Workflow, Reliability, and Direct Costs
Authors: Sloma Cari R. , Germer Jeffrey J. , Gerads Tara M. , Mandrekar Jayawant N. , Mitchell P. Shawn , Yao Joseph D. C. 
Published: February 2009

ABSTRACT

The Abbott RealTime human immunodeficiency virus type 1 (HIV-1) assay (ART) and the Cobas AmpliPrep/Cobas TaqMan HIV-1 test (CTM) are commercially available assays for quantification of HIV-1 RNA in plasma. We evaluated performance characteristics, workflow, throughput, reliability, and direct costs of these assays. Both assays yielded good correlation of quantitative results (
r
= 0.95) among clinical specimens, with a mean difference of −0.34 log
10
copies/ml. Testing of healthy donor plasma specimens yielded “target not detected” results by ART, with “HIV-1 RNA detected, <40 copies/ml” results for 3.3% (3 of 90 samples) of these specimens by CTM. Both the m2000sp/m2000rt (ART) and docked CAP/CTM96 (CTM) instrument systems were capable of operating with continuous, uninterrupted workflow. When daily maintenance and cleaning were included, ART and CTM run durations (5 h 52 min and 6 h 4 min, respectively) and hands-on times (53 min and 46 min, respectively) were similar for a run batch size of 24. While ART was more flexible in terms of run batch size, CTM required fewer user interventions and consistently produced higher specimen throughput rates at 8, 16, and 24 h. Assay run failure rates were 6.3% (1 of 16 runs) and 4.2% (1 of 24 runs) for ART and CTM, respectively (
P
= 1.000), with invalid specimen result rates of 1.0% (5 of 495 specimens) and 2.8% (11 of 399 specimens), respectively (
P
= 0.073). Direct reagent and consumable costs for each assay were comparable (difference of <10%). In selecting an assay for implementation, laboratories should consider how various assay and instrument features might impact laboratory operation and patient care.
Distribution of Genes Encoding MSCRAMMs and Pili in Clinical and Natural Populations of
Enterococcus faecium
Authors: Sillanpää Jouko , Prakash Vittal P. , Nallapareddy Sreedhar R. , Murray Barbara E. 
Published: February 2009

ABSTRACT

Enterococcus faecium
has recently emerged as an important cause of nosocomial infections. We previously identified 15 predicted surface proteins with characteristics of MSCRAMMs and/or pili and demonstrated that their genes were frequently present in 30 clinical
E. faecium
isolates studied; one of these,
acm
, has been studied in further detail. To determine the prevalence of the other 14 genes among various
E. faecium
populations, we have now assessed 433
E. faecium
isolates, including 264 isolates from human clinical infections, 69 isolates from stools of hospitalized patients, 70 isolates from stools of community volunteers, and 30 isolates from animal-related sources. A variable distribution of the 14 genes was detected, with their presence ranging from 51% to 98% of isolates. While 81% of clinical isolates carried 13 or 14 of the 14 genes tested, none of the community group isolates and only 13% of animal isolates carried 13 or 14 genes. The presence of these genes was most frequent in endocarditis isolates, with 11 genes present in all isolates, followed by isolates from other clinical sources. The number of genes significantly associated with clinical versus fecal or animal origin (
P
= 0.04 to <0.0001) varied from 10 to 13, depending on whether comparisons were made against individual clinical subgroups (endocarditis, blood, and other clinical isolates) or against all clinical isolates combined as one group. The strong association of these genes with clinical isolates raises the possibility that their preservation/acquisition has favored the adaptation of
E. faecium
to nosocomial environments and/or patients.
Identification of
Candida nivariensis
and
Candida bracarensis
in a Large Global Collection of
Candida glabrata
Isolates: Comparison to the Literature
Authors: Lockhart Shawn R. , Messer Shawn A. , Gherna Michael , Bishop Justin A. , Merz William G. , Pfaller Michael A. , Diekema Daniel J. 
Published: February 2009

ABSTRACT

We analyzed 1,598
Candida glabrata
isolates for the presence of the cryptic species
Candida nivariensis
and
Candida bracarensis
. Both species were very rare in this collection (0.2% prevalence), despite the number of isolates analyzed and the global distribution of the isolates. We saw no associated antifungal resistance in
C. nivariensis
.
O-Linked
N
-Acetylglucosaminylation of Sp1 Inhibits the Human Immunodeficiency Virus Type 1 Promoter
Authors: Jochmann Ramona , Thurau Mathias , Jung Susan , Hofmann Christian , Naschberger Elisabeth , Kremmer Elisabeth , Harrer Thomas , Miller Matthew , Schaft Niels , Stürzl Michael 
Published: February 2009

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) gene expression and replication are regulated by the promoter/enhancer located in the U3 region of the proviral 5′ long terminal repeat (LTR). The binding of cellular transcription factors to specific regulatory sites in the 5′ LTR is a key event in the replication cycle of HIV-1. Since transcriptional activity is regulated by the posttranslational modification of transcription factors with the monosaccharide O-linked
N
-acetyl-
d
-glucosamine (
O
-GlcNAc), we evaluated whether increased
O
-GlcNAcylation affects HIV-1 transcription. In the present study we demonstrate that treatment of HIV-1-infected lymphocytes with the
O
-GlcNAcylation-enhancing agent glucosamine (GlcN) repressed viral transcription in a dose-dependent manner. Overexpression of
O
-GlcNAc transferase (OGT), the sole known enzyme catalyzing the addition of
O
-GlcNAc to proteins, specifically inhibited the activity of the HIV-1 LTR promoter in different T-cell lines and in primary CD4
+
T lymphocytes. Inhibition of HIV-1 LTR activity in infected T cells was most efficient (>95%) when OGT was recombinantly overexpressed prior to infection.
O
-GlcNAcylation of the transcription factor Sp1 and the presence of Sp1-binding sites in the LTR were found to be crucial for this inhibitory effect. From this study, we conclude that
O
-GlcNAcylation of Sp1 inhibits the activity of the HIV-1 LTR promoter. Modulation of Sp1
O
-GlcNAcylation may play a role in the regulation of HIV-1 latency and activation and links viral replication to the glucose metabolism of the host cell. Hence, the establishment of a metabolic treatment might supplement the repertoire of antiretroviral therapies against AIDS.
Human Rhinovirus Type 2 Uncoating at the Plasma Membrane Is Not Affected by a pH Gradient but Is Affected by the Membrane Potential
Authors: Berka Ursula , Khan Abdul , Blaas Dieter , Fuchs Renate 
Published: February 2009

ABSTRACT

The minor receptor group human rhinovirus type 2 enters host cells by endocytosis via members of the low-density-lipoprotein receptor family. In late endosomes, it undergoes a conformational change solely induced by a pH of ≤5.6, resulting in RNA transfer across the endosomal membrane into the cytoplasm. To determine potential driving forces of this process, we investigated whether RNA penetration might depend on the pH gradient and/or the membrane potential between the acidic endosome lumen and the neutral cytoplasm. Since these parameters are difficult to assess in endosomes, we took advantage of the possibility of inducing structural changes, RNA release, and consequently infection from the plasma membrane. To manipulate the pH gradient, cell-bound virus was exposed to membrane-permeant or -impermeant acidic buffers at 4°C, and this was followed by a shift to 34°C in medium containing bafilomycin to prevent RNA release from endosomes. To manipulate the plasma membrane potential, similar experiments were carried out, but these included K
+
diffusion potentials in the presence of the K
+
ionophore valinomycin. We demonstrated that infection does not depend on a pH gradient but is enhanced by plasma membrane hyperpolarization compared to plasma membrane depolarization.