bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outsourcing, offshoring and productivity measurement in United States manufacturing
Authors: HOUSEMAN Susan 
Published: December 2007

Abstract:Productivity growth in a sector or economy is the economic basis for improvements in workers' wages. Recent growth of domestic and foreign outsourcing in developed economies greatly complicates the measurement and interpretation of this key economic indicator and may result in inflated and misleading increases in productivity statistics. In the context of United States manufacturing, this article points to several pieces of evidence that suggest these effects of outsourcing and offshoring on productivity measures are significant. These factors may help explain why wage growth for most United States workers has been relatively low in spite of high measured productivity growth.
Preparation of Bacterial DNA Template by Boiling and Effect of Immunoglobulin G as an Inhibitor in Real-Time PCR for Serum Samples from Patients with Brucellosis
Authors: Queipo-Ortuño Maria Isabel , De Dios Colmenero Juan , Macias Manuel , Bravo Maria Jose , Morata Pilar 
Published: December 2007

ABSTRACT
Real-time PCR is a widely used tool for the diagnosis of many infectious diseases. However, little information exists about the influences of the different factors involved in PCR on the amplification efficiency. The aim of this study was to analyze the effect of boiling as the DNA preparation method on the efficiency of the amplification process of real-time PCR for the diagnosis of human brucellosis with serum samples. Serum samples from 10 brucellosis patients were analyzed by a SYBR green I LightCycler-based real-time PCR and by using boiling to obtain the DNA. DNA prepared by boiling lysis of the bacteria isolated from serum did not prevent the presence of inhibitors, such as immunoglobulin G (IgG), which were extracted with the template DNA. To identify and confirm the presence of IgG, serum was precipitated to separate and concentrate the IgG and was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. The use of serum volumes above 0.6 ml completely inhibited the amplification process. The inhibitory effect of IgG in serum samples was not concentration dependent, and it could be eliminated by diluting the samples 1/10 and 1/20 in water. Despite the lack of the complete elimination of the IgG from the template DNA, boiling does not require any special equipment and it provides a rapid, reproducible, and cost-effective method for the preparation of DNA from serum samples for the diagnosis of brucellosis.
Impact of Protein Shedding on Detection of
Mycobacterium avium
subsp.
paratuberculosis
by a Whole-Cell Immunoassay Incorporating Surface-Enhanced Raman Scattering
Authors: Yakes Betsy Jean , Lipert Robert J. , Bannantine John P. , Porter Marc D. 
Published: December 2007

ABSTRACT

The etiological agent of Johne's disease is
Mycobacterium avium
subsp.
paratuberculosis
. Controlling the spread of this disease is hindered by the lack of sensitive, selective, and rapid detection methods for
M. avium
subsp.
paratuberculosis
. By using a recently optimized sandwich immunoassay (B. J. Yakes, R. J. Lipert, J. P. Bannantine, and M. D. Porter, Clin. Vaccine Immunol. 15:227-234, 2008), which incorporates a new monoclonal antibody for the selective capture and labeling of
M. avium
subsp.
paratuberculosis
and surface-enhanced Raman scattering for sensitive readout, detection limits of ∼630 and ∼740
M. avium
subsp.
paratuberculosis
cells/ml are achieved in phosphate-buffered saline and whole milk samples, respectively, after spiking with heat-treated
M. avium
subsp.
paratuberculosis
. Surprisingly, these detection limits are 3 orders of magnitude lower than expected based on theoretical predictions. Experiments designed to determine the origin of the improvement revealed that the major membrane protein targeted by the monoclonal antibody was present in the sample suspensions as shed protein. This finding indicates that the capture and labeling of shed protein function as a facile amplification strategy for lowering the limit of detection for
M. avium
subsp.
paratuberculosis
that may also be applicable to the design of a wide range of highly sensitive assays for other cells and viruses.
Efficient Identification of Clinically Relevant
Candida
Yeast Species by Use of an Assay Combining Panfungal Loop-Mediated Isothermal DNA Amplification with Hybridization to Species-Specific Oligonucleotide Probes
Authors: Inácio João , Flores Orfeu , Spencer-Martins Isabel 
Published: December 2007

ABSTRACT

The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus
Candida
remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.
Prevalence and Characterization of Multidrug-Resistant (Type ACSSuT)
Salmonella enterica
Serovar Typhimurium Strains in Isolates from Four Gosling Farms and a Hatchery Farm
Authors: Yu Chang-You , Chou Shih-Jen , Yeh Chia-Ming , Chao Maw-Rong , Huang Kwo-Ching , Chang Yung-Fu , Chiou Chien-Shun , Weill Francois-Xavier , Chiu Cheng-Hsun , Chu Chi-Hong , Chu Chishih 
Published: December 2007

ABSTRACT

Salmonella enterica
serovar Typhimurium strains of phage types DT104 and U302 are often resistant to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (the ACSSuT resistance type) and are major zoonotic pathogens. Increased consumption of goose meat may enhance the risk of transferring
S. enterica
serovar Typhimurium and other enteric pathogens from geese to human due to the consumption of meats from infected geese or improper preparation of meats. Therefore, we characterized
S. enterica
serovar Typhimurium strains isolated from four goose farms (farms A, B, C, and D) and one hatchery farm (farm E) to determine the epidemic and genetic differences among them. Antibiotic susceptibility tests and multiplex PCR confirmed that 77.6% (52/67) of strains were ACSSuT strains isolated from farms A, C, and E. Antibiotic-susceptible strains were isolated mostly from farm B, and no strain was observed in farm D. All ACSSuT strains harbored a 94.7-kb virulence plasmid and contained one 1.1-kb conserved segment identical to that of
Salmonella
genomic island 1. Four genotypes were determined among these
S. enterica
serovar Typhimurium isolates by pulsed-field gel electrophoresis analysis of XbaI-digested DNA fragments. Most isolates (85.29%; 29/34) of major genotype Ib were ACSSuT strains isolated mainly from goslings of farm C and egg membranes of farm E, a hatchery farm, suggesting that
S. enterica
serovar Typhimurium strains in isolates from goslings might originate from its hatchery, from the egg membranes to the gosling fluff after hatching. Multiple phage types, types 8, 12, U283, DT104, and U302, were identified. In conclusion, geese were a reservoir of diverse multidrug-resistant (type ACSSuT)
S. enterica
serovar Typhimurium strains, and each farm was colonized with genetically closely related
S. enterica
serovar Typhimurium strains.
Health Care-Associated Endocarditis Caused by
Staphylococcus aureus
with Reduced Susceptibility to Vancomycin
Authors: Chi Chia-Yu , Lauderdale Tsai-Ling , Wang Shih-Min , Wu Jing-Ming , Yang Yu-Jen , Liu Ching-Chuan 
Published: December 2007

ABSTRACT

Infective endocarditis (IE) caused by methicillin-resistant
Staphylococcus aureus
with reduced vancomycin susceptibility (SARV) has been reported worldwide. We report the successful treatment of a pediatric patient with SARV IE and characterization of the infecting strain. The MIC of vancomycin rose from 1.5 to 2 μg/ml, and the SARV was confirmed by population analysis.
Early Infant Human Immunodeficiency Virus Type 1 Detection Suitable for Resource-Limited Settings with Multiple Circulating Subtypes by Use of Nested Three-Monoplex DNA PCR and Dried Blood Spots
Authors: Zhang Qi , Wang Linhong , Jiang Yan , Fang Liwen , Pan Pinliang , Gong Shuangyan , Yao Jun , Tang Yi-Wei , Vermund Sten H. , Jia Yujiang 
Published: December 2007

ABSTRACT

The early detection of human immunodeficiency virus type 1 (HIV-1) infection in infants is complicated by the persistence of maternal antibodies and by diverse HIV-1 subtypes. We developed a nested, three-monoplex HIV-1 DNA PCR (N3M-PCR) assay to detect diverse HIV-1 subtypes in infants born to infected mothers. We optimized the test for use with dried blood spot (DBS) samples for ease of storage and transport from rural China to central laboratories. Six pairs of primers were designed that targeted
env, gag
, and
pol
genes, and the test was run in three reactions with an analytical sensitivity of 10 copies DNA per reaction to cover nine HIV-1 subtypes, A, B, C, D, F, G, CRF01-AE, CRF08-BC, and CRF07-BC. The assay performance was evaluated on 347 DBS specimens from 151 exposed infants in four diverse provinces of China in which multiple subtypes were circulating. The results of this test were compared to those of HIV antibody enzyme immunoassay and Western blotting confirmation for the infants at ≥18 months of age or to convincing clinical and epidemiologic data for deceased infants. The sensitivity of the N3M-PCR assay was 30.0% (3/10) for infants at 48 h after birth, 91.7% (11/12) at 1 to 2 months of age, and 93.7% (15/16) at 3 to 6 months of age. The specificity was 100% (94/94) at all three time points. The PCR reproducibility in the three DNA regions was 100% for samples at 48 h after birth, 96.7% at 1 to 2 months, and 100% at 3 to 6 months of age. The HIV-1 DNA N3M-PCR assay on DBSs offers a simple and affordable approach for early infant HIV-1 diagnosis in regions with diverse HIV-1 circulating subtypes.
Development of Multiplex Assay for Rapid Characterization ofMycobacterium tuberculosis
Authors: Bergval I. L. , Vijzelaar R. N. C. P. , Dalla Costa E. R. , Schuitema A. R. J. , Oskam L. , Kritski A. L. , Klatser P. R. , Anthony R. M. 
Published: December 2007

ABSTRACTWe have developed a multiplex assay, based on multiplex ligation-dependent probe amplification (MLPA), that allows simultaneous detection of multiple drug resistance mutations and genotype-specific mutations at any location in theMycobacterium tuberculosisgenome. The assay was validated on a reference panel of well-characterized strains, and the results show thatM. tuberculosiscan be accurately characterized by our assay. Eighteen discriminatory markers identifying drug resistance (rpoB,katG,inhA,embB), members of theM. tuberculosiscomplex (16S rRNA, IS6110, TbD1), the principal genotypic group (katG,gyrA), and Haarlem and Beijing strains (ogt,mutT2,mutT4) were targeted. A sequence specificity of 100% was reached for 16 of the 18 selected genetic targets. In addition, a panel of 47 clinicalM. tuberculosisisolates was tested by MLPA in order to determine the correlation between phenotypic drug resistance and MLPA and between spoligotyping and MLPA. Again, all mutations present in these isolates that were targeted by the 16 functional probes were identified. Resistance-associated mutations were detected by MLPA in 71% of the identified rifampin-resistant strains and in 80% of the phenotypically isoniazid-resistant strains. Furthermore, there was a perfect correlation between MLPA results and spoligotypes. When MLPA is used on confirmedM. tuberculosisclinical specimens, it can be a useful and informative instrument to aid in the detection of drug resistance, especially in laboratories where drug susceptibility testing is not common practice and where the rates of multidrug-resistant and extensively drug resistant tuberculosis are high. The flexibility and specificity of MLPA, along with the ability to simultaneously genotype and detect drug resistance mutations, make MLPA a promising tool for pathogen characterization.
Analysis of Echovirus 30 Isolates from Russia and New Independent States Revealing Frequent Recombination and Reemergence of Ancient Lineages
Authors: Lukashev Alexander N. , Ivanova Olga E. , Eremeeva Tatiana P. , Gmyl Larisa V. 
Published: December 2007

ABSTRACT
We studied two genome regions, VP1 and 3D, of 48 echovirus 30 (E30) isolates from Russia and the new independent states. In VP1, most isolates were similar to European strains reported earlier, and frequent change of circulating subgroups was noticed. We also observed, in 2003-2006, the reemergence of a group of E30 strains with a VP1 region very distant from most modern E30 strains and remotely similar to E30 isolates from the 1960s and the 1970s. A study of the 3D genome region detected multiple recombination events among the studied strains. Recombination presumably occurred every few years, and therefore, the study of a single VP1 genome region cannot accurately describe the phylogenetic history of the virus or predict pathogenetic properties of an isolate. In general, a comparison of the VP1 and 3D genome region phylogenies revealed, in some instances, virtually independent circulation of enterovirus genome fragments on a scale of years.
Heat Shock Perturbs TRIM5α Restriction of Human Immunodeficiency Virus Type 1
Authors: Anderson Jenny L. , Campbell Edward M. , Figueiredo Anna , Hope Thomas J. 
Published: December 2007

ABSTRACT
TRIM5α restriction factors protect target cells from retroviruses by blocking infection prior to the accumulation of viral reverse transcription (RT) products. Here, we demonstrate that heat shock perturbed owl monkey TRIMCyp and rhesus TRIM5α-mediated restriction of human immunodeficiency virus type 1 (HIV-1) late RT products and 2-long terminal repeat circles. Heat shock partially rescued HIV-1 infection from TRIMCyp restriction, and this rescue became more profound when combined with the presence of the proteasome inhibitor MG132. This indicates that viral RT products rescued from restriction by either heat shock treatment or the presence of MG132 are on a productive pathway, supporting a model in which TRIM5α proteins restrict retroviruses in multiple phases that are differentially sensitive to heat shock and proteasome inhibitors.
Intracellular Localization Map of Human Herpesvirus 8 Proteins
Authors: Sander Gaby , Konrad Andreas , Thurau Mathias , Wies Effi , Leubert Rene , Kremmer Elisabeth , Dinkel Holger , Schulz Thomas , Neipel Frank , Stürzl Michael 
Published: December 2007

ABSTRACT
Human herpesvirus 8 (HHV-8) is the etiological agent of Kaposi's sarcoma. We present a localization map of 85 HHV-8-encoded proteins in mammalian cells. Viral open reading frames were cloned with a Myc tag in expression plasmids, confirmed by full-length sequencing, and expressed in HeLa cells. Protein localizations were analyzed by immunofluorescence microscopy. Fifty-one percent of all proteins were localized in the cytoplasm, 22% were in the nucleus, and 27% were found in both compartments. Surprisingly, we detected viral FLIP (v-FLIP) in the nucleus and in the cytoplasm, whereas cellular FLIPs are generally localized exclusively in the cytoplasm. This suggested that v-FLIP may exert additional or alternative functions compared to cellular FLIPs. In addition, it has been shown recently that the K10 protein can bind to at least 15 different HHV-8 proteins. We noticed that K10 and only five of its 15 putative binding factors were localized in the nucleus when the proteins were expressed in HeLa cells individually. Interestingly, in coexpression experiments K10 colocalized with 87% (13 of 15) of its putative binding partners. Colocalization was induced by translocation of either K10 alone or both proteins. These results indicate active intracellular translocation processes in virus-infected cells. Specifically in this framework, the localization map may provide a useful reference to further elucidate the function of HHV-8-encoded genes in human diseases.
The Picornavirus Avian Encephalomyelitis Virus Possesses a Hepatitis C Virus-Like Internal Ribosome Entry Site Element
Authors: Bakhshesh Mehran , Groppelli Elisabetta , Willcocks Margaret M. , Royall Elizabeth , Belsham Graham J. , Roberts Lisa O. 
Published: December 2007

ABSTRACT
Avian encephalomyelitis virus (AEV) is a picornavirus that causes disease in poultry worldwide, and flocks must be vaccinated for protection. AEV is currently classified within the hepatovirus genus, since its proteins are most closely related to those of hepatitis A virus (HAV). We now provide evidence that the 494-nucleotide-long 5′ untranslated region of the AEV genome contains an internal ribosome entry site (IRES) element that functions efficiently in vitro and in mammalian cells. Unlike the HAV IRES, the AEV IRES is relatively short and functions in the presence of cleaved eIF4G and it is also resistant to an inhibitor of eIF4A. These properties are reminiscent of the recently discovered class of IRES elements within certain other picornaviruses, such as porcine teschovirus 1 (PTV-1). Like the PTV-1 IRES, the AEV IRES shows significant similarity to the hepatitis C virus (HCV) IRES in sequence, function, and predicted secondary structure. Furthermore, mutational analysis of the predicted pseudoknot structure at the 3′ end of the AEV IRES lends support to the secondary structure we present. AEV is therefore another example of a picornavirus harboring an HCV-like IRES element within its genome, and thus, its classification within the hepatovirus genus may need to be reassessed in light of these findings.
Rescue of Maturation-Defective Flock House Virus Infectivity with Noninfectious, Mature, Viruslike Particles
Authors: Walukiewicz Hanna E. , Banerjee Manidipa , Schneemann Anette , Johnson John E. 
Published: December 2007

ABSTRACT
The infectivity of flock house virus (FHV) requires autocatalytic maturation cleavage of the capsid protein at residue 363, liberating the C-terminal 44-residue γ peptides, which remain associated with the particle. In vitro studies previously demonstrated that the amphipathic, helical portion (amino acids 364 to 385) of γ is membrane active, suggesting a role for γ in RNA membrane translocation during infection. Here we show that the infectivity of a maturation-defective mutant of FHV can be restored by viruslike particles that lack the genome but undergo maturation cleavage. We propose that the colocalization of the two defective particle types in an entry compartment allows the restoration of infectivity by γ.
Integration of human papillomavirus type-16 and type-18 is a very early event in cervical carcinogenesis
Authors: Huang L-W , Chao S-L , Lee B-H 
Published: December 2007

Aim:Human papillomavirus (HPV) integration is a critical event in cervical carcinogenesis. The aim of this study was to explore the physical status of HPV-16 and HPV-18 during the progression of cervical precancerous lesions.Methods:A series of 101 HPV-16 or HPV-18 positive cervical neoplasms (32 cervical intraepithelial neoplasia (CIN) cases and 69 cervical carcinoma (CC) cases) were evaluated. The physical status of both types of HPV was assessed from paraffin-embedded formaldehyde-fixed surgical specimens by real-time PCR.Results:For HPV-16, integrated DNA was observed in 5 (83.3%) of 6 CIN I cases, 10 (90.9%) of 11 CIN II/III cases, 29 (82.9%) of 35 FIGO (International Federation of Gynecology and Obstetrics) stage I CC cases and 16 (94.1%) of 17 FIGO stages II∼IV CC cases. For HPV-18, integrated DNA was observed in 3 (50%) of 6 CIN I cases, 5 (55.6%) of 9 CIN II/III cases, 9 (64.3%) of 14 FIGO stage I CC cases, and 1 (33.3%) of 3 FIGO stages II∼IV CC cases. The mixed form of HPV DNA was the most prevalent physical state in HPV-16. There was no significant difference between the physical state of HPV-16 and HPV-18 DNA with regard to the various grades of cervical lesions.Conclusions:These data imply that integration of HPV-16 and HPV-18 DNA into the host genome occurs in the very early stage of cervical neoplastic progression. These early events may play an initiating role in the malignant transformation of HPV-16- and HPV-18-related low-grade lesions into high-grade dysplasia and invasive carcinoma.
Omeprazole-associated changes in the gastric mucosa of children
Authors: Drut R , Altamirano E , Rúa E Cueto 
Published: December 2007

Aims:To describe histological findings in gastric mucosa biopsy specimens of children treated with proton-pump inhibitors (PPIs) for different periods of time.Methods:Biopsy specimens from 12 children (aged 8 months to 15 years) treated with PPIs and 8 controls were processed for paraffin embedding and stained with H&E as well as inmmunohistochemically for sialyl-Tn antigen.Results:The main changes were related to parietal cells which showed brisk cytoplasmic eosinophilia, apical cytoplasmic protrusions to dilated glands, cytoplasmic and nuclear hypertrophy, dilated intracytoplasmic canaliculi, binucleation and multinucleation. The intracellular canaliculi surface showed strong immunohistochemical reaction for sialyl-Tn antigen, apparently a marker for this structure. Some of the patients were biopsied after a short period of oral or intravenously administered omeprazole; the changes may therefore occur rapidly.Conclusions:PPIs induce the same changes in the gastric mucosa of children as in adults, but the number of nuclei is increased. These effects have not been reported previously in this age group. It is suggested that the changes result from a combination of effects of PPIs and gastrin release.