bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Sensitive Loop-Mediated Isothermal Amplification Assay That Provides Specimen-to-Result Diagnosis of Respiratory Syncytial Virus Infection in 30 Minutes
Authors: Mahony James , Chong Sylvia , Bulir David , Ruyter Alexandra , Mwawasi Ken , Waltho Daniel 
Published: June 2013

ABSTRACT

Rapid isothermal amplification methods have recently been introduced, and some of these methods offer significant advantages over PCR. The objective of this study was to develop a rapid and sensitive multiplex loop-mediated isothermal amplification (M-LAMP) assay for the detection of respiratory syncytial virus subgroups A and B (RSV A and B). We designed six primers each for the matrix gene of RSV A and the polymerase gene of RSV B and developed an M-LAMP assay by using a commercially available master mix and a real-time fluorometer (Genie II; Optigene, United Kingdom) that displays real-time amplification, time to positivity, and amplicon annealing temperature (

T
m

). The M-LAMP was evaluated against PCR by testing 275 nasopharyngeal (NP) specimens. The final optimized M-LAMP assay had a mean amplification time of 14.2 min (compared with 90 to 120 min for PCR) and had an analytical sensitivity of 1 genome equivalent (ge) for both RSV A and B. Using PCR as a comparator, M-LAMP had a sensitivity of 100% (81/81) and specificity of 100% (194/194). We also evaluated a 3- to 10-min specimen processing method involving vortexing with glass beads and heating to 98°C in M-swab medium (Copan Italia, Brescia, Italy) and found that this rapid processing method allowed detection of 37/41 (90.2%) of positives when we used extracted nucleic acid. In summary, the M-LAMP assay had excellent sensitivity and specificity for detecting RSV A and B in NP specimens and, when coupled with a rapid specimen preparation method, could provide a specimen-to-result diagnosis time of 30 min.
RECall for Automated Genotypic Tropism Testing
Authors: Pou Christian , Bellido Rocío , Casadellà Maria , Puig Teresa , Clotet Bonaventura , Harrigan Richard , Paredes Roger 
Published: June 2013

ABSTRACT
Standardization of sequence chromatogram analysis is required for consistent genotypic tropism determination across laboratories. A freely available, fast, and automated chromatogram analysis tool (RECall) provided tropism interpretations equivalent to those of manual sequence editing of 521 V3 loop HIV-1 population sequences, suggesting that RECall can be useful in standardizing genotypic tropism testing across laboratories.
Multiplex Real-Time PCR for Detection of Campylobacter, Salmonella, and Shigella
Authors: Barletta F. , Mercado E. H. , Lluque A. , Ruiz J. , Cleary T. G. , Ochoa T. J. 
Published: June 2013

ABSTRACT

Infectious diarrhea can be classified based on its clinical presentation as noninflammatory or inflammatory disease. In developing countries, among inflammatory diarrhea cases,
Shigella
is the most common cause, followed by
Campylobacter
and
Salmonella
. Because the time frame in which treatment choices must be made is short and conventional stool cultures lack good sensitivity, there is a need for a rapid, sensitive, and inexpensive detection technique. The purpose of our study was to develop a multiplex real-time PCR procedure to simultaneously identify
Campylobacter
spp.,
Salmonella
spp., and
Shigella
spp. Primers were designed to amplify the
invA
,
ipaH
, and 16S rRNA genes simultaneously in a single reaction to detect
Salmonella
,
Shigella
, and
Campylobacter
, respectively. Using this approach, we correctly identified 102 of 103 strains of the targeted enteropathogens and 34 of 34 other pathogens. The melting temperatures were 82.96 ± 0.05°C for
invA
, 85.56 ± 0.28°C for
ipaH
, and 89.21 ± 0.24°C for 16S rRNA. The limit of accurate quantification for the assay in stool samples was 10
4
CFU g
−1
; however, the limit of detection was 10
3
CFU g
−1
. This assay is a simple, rapid, inexpensive, and reliable system for the practical detection of these three enteropathogens in clinical specimens.
Frog Virus 3 Open Reading Frame 97R Localizes to the Endoplasmic Reticulum and Induces Nuclear Invaginations
Authors: Ring Brooke A. , Ferreira Lacerda Andressa , Drummond Dylan J. , Wangen Christina , Eaton Heather E. , Brunetti Craig R. 
Published: June 2013

ABSTRACT

Frog virus 3 (FV3) is the type species of the genus
Ranavirus
, family
Iridoviridae
. The genome of FV3 is 105,903 bases in length and encodes 97 open reading frames (ORFs). The FV3 ORF 97R contains a B-cell lymphoma 2 (Bcl-2) homology 1 (BH1) domain and has sequence similarity to the myeloid cell leukemia-1 (Mcl-1) protein, suggesting a potential role in apoptosis. To begin to understand the role of 97R, we characterized 97R through immunofluorescence and mutagenesis. Here we demonstrated that 97R localized to the endoplasmic reticulum (ER) at 24 h posttransfection. However, at 35 h posttransfection, 97R localized to the ER but also began to form concentrated pockets continuous with the nuclear membrane. After 48 h posttransfection, 97R was still localized to the ER, but we began to observe the ER and the outer nuclear membrane invaginating into the nucleus. To further explore 97R targeting to the ER, we created a series of C-terminal transmembrane domain deletion mutants. We found that deletion of 29 amino acids from the C terminus of 97R abolished localization to the ER. In contrast, deletion of 12 amino acids from the C terminus of 97R did not affect 97R localization to the ER. In addition, a hybrid protein containing the 97R C-terminal 33 amino acids was similarly targeted to the ER. These data indicate that the C-terminal 33 amino acids of 97R are necessary and sufficient for ER targeting.
NS1′ Colocalizes with NS1 and Can Substitute for NS1 in West Nile Virus Replication
Authors: Young Lucy B. , Balmori Melian Ezequiel , Khromykh Alexander A. 
Published: June 2013

ABSTRACT
NS1′ is a C-terminally extended form of the NS1 protein produced only by encephalitic flaviviruses from the Japanese encephalitis virus serogroup. Here we show that West Nile virus (WNV) NS1′ and NS1 localize to the same cellular compartments when expressed from plasmid DNAs and also colocalize to viral RNA replication sites in infected cells. Using complementation analysis with NS1-deleted WNV cDNA, we demonstrated that NS1′ is able to substitute for the crucial function of NS1 in virus replication.
The effect of field condition and shoe type on lower extremity injuries in American Football
Authors: Iacovelli Jaclyn Nicole , Yang Jingzhen , Thomas Geb , Wu Hongqian , Schiltz Trisha , Foster Danny T 
Published: June 2013

Background/aimConsiderable improvement has been made in football field surfaces and types of shoe, yet relatively few epidemiological studies have investigated their roles in the risk of football injuries. This study examined the effects of field surface, surface condition and shoe type on the likelihood of lower extremity football injuries.MethodsDeidentified data from 188 players from one division I university football team during the 2007–2010 seasons were analysed. Lower extremity injury rate and rate ratio, along with 95% confidence limits, were calculated by football activity, playing surface condition and shoe type.ResultsA total of 130 lower extremity injuries were sustained, with an overall lower extremity injury rate of 33.5/10 000 athlete-sessions. The lower extremity injury rate was 2.61 times higher when the surface condition was abnormal compared with when the surface condition was normal. During games, the risk for lower extremity injury was 3.34 times higher (95% CI 1.70 to 6.56) on artificial turf compared with natural grass. However, this trend was not statistically significant in practice sessions. Furthermore, neither the number of shoe cleats nor the height of the shoe top was statistically associated with risk of lower extremity injuries.ConclusionsFootball players who played on artificial turf or when the surface condition was abnormal were susceptible to lower extremity injuries. Evidence from this study suggests that further research into playing surfaces and shoe types may provide fruitful opportunities to reduce injuries to collegiate football players.
The Nordic Football Injury Audit: higher injury rates for professional football clubs with third-generation artificial turf at their home venue
Authors: Kristenson Karolina , Bjørneboe John , Waldén Markus , Andersen Thor Einar , Ekstrand Jan , Hägglund Martin 
Published: June 2013

BackgroundPreviously, no difference in acute injury rate has been found when playing football on artificial turf (AT) compared with natural grass (NG).AimTo compare acute injury rates in professional football played on AT and NG at the individual player level; and to compare, at club level, acute and overuse injury rates between clubs that have AT at their home venue (AT clubs) and clubs that have NG (NG clubs).Methods32 clubs (AT, n=11; NG, n=21) in the male Swedish and Norwegian premier leagues were followed prospectively during the 2010 and 2011 seasons. Injury rate was expressed as the number of time loss injuries/1000 h and compared with rate ratio (RR) and 99% CI.ResultsNo statistically significant differences were found in acute injury rates on AT compared with NG during match play (RR 0.98, 99% CI 0.79 to 1.22) or training (RR 1.14, 99% CI 0.86 to 1.50) when analysing at the individual player level. When analysing at the club level, however, AT clubs had a significantly higher acute training injury rate (RR 1.31, 99% CI 1.04 to 1.63) and overuse injury rate (RR 1.38, 99% CI 1.14 to 1.65) compared with NG clubs.ConclusionsAt the individual player level, no significant differences were found in acute injury rates when playing on AT compared with NG. However, clubs with AT at their home venue had higher rates of acute training injuries and overuse injuries compared with clubs that played home matches on NG.
Economic determinants of diet in older adults: systematic review
Authors: Conklin Annalijn I , Maguire Eva R , Monsivais Pablo 
Published: June 2013

Background and aimsMany economic factors are associated with diet, yet the evidence is generally cross-sectional. Older people are considered especially vulnerable to poor diets from negative changes to varied economic factors. This review extends current knowledge on known correlates to decipher actual economic determinants of diet in older adults.MethodsEight bibliometric databases were searched between May and December 2012, supplemented by hand-searches, with no restrictions on publication date or country. Longitudinal studies, or reviews, were eligible when examining diet as a function of change in an economic factor in non-institutionalised adults ≥60 years. Data were extracted using a standardised evidence table and quality assessed before narrative synthesis.ResultsWe found nine original studies for inclusion, of which eight examined change from work to retirement and one evaluated a food price intervention. Designs were generally pre-post without controls and varying in follow-up. Studies reported mixed impact on food spending and/or food intake. Retirement was shown to both reduce and have no impact on food spending and to have either positive and negative, or positive and no impact on food intake. Subgroup differences were observed, especially between men and women.ConclusionsDespite ample research on economic correlates of older adults' diets, little is still known about actual economic determinants of diet in this population. Studies of retirement suggest divergent effects in some but not all older people. Robust high-quality longitudinal studies to decipher economic drivers of diet must be prioritised in research and policy as firm conclusions remain elusive.
Improvement of working memory after stenting for cervicocerebral artery stenosis
Authors: He Zi-Jun , Qin Bin , Cui Zhuang , Liu Fang , Qi Peng , Lu Jun , Liu Jia-Chun , Wang Li-Jun , Zeng Ping , Wang Da-Ming 
Published: June 2013

ObjectiveTo investigate the working memory of patients with cervicocerebral artery stenosis and its change after stenting.Methods35 patients with cervicocerebral artery stenosis (≥50% with related symptoms of cerebral ischemia, or ≥70% with or without related symptoms of cerebral ischemia) underwent endovascular stenting. Working memory of all 35 patients before and within 3 weeks of stenting was evaluated by memory quotient (MQ) scores. Change in regional cerebral blood flow (rCBF) was assessed by single photon emission CT (SPECT) for 13 of the patients. MQ scores were compared according to location and degree of stenosis for all patients, as well as changes in rCBF for the 13 patients.ResultsMean MQ scores were significantly lower than normal for patients with carotid artery stenosis alone and for patients with carotid stenosis in addition to vertebrobasilar and/or subclavical stenosis, but not for patients with vertebrobasilar and/or subclavical stenosis. MQ scores were significantly increased after stenting for all patients, especially those with carotid stenosis. There was no significant difference between patients with moderate stenosis and those with severe (>70%) stenosis in MQ increments pre- and post-stenting (p=0.085). Nine of the 13 patients who received SPECT showed an improvement in rCBF after stenting, and their MQ increments were significantly higher than those without an improvement in rCBF (p=0.020).ConclusionsWorking memory impairment can be observed in patients with cervicocerebral artery stenosis, especially those with carotid stenosis. Endovascular stenting of stenosis might improve the impairment by alleviating cerebral perfusion deficit.
Association of genital human papillomavirus infection with HIV acquisition: a systematic review and meta-analysis
Authors: Lissouba Pascale , Van de Perre Philippe , Auvert Bertran 
Published: June 2013

ObjectivesTo conduct a systematic review and a meta-analysis of epidemiological studies investigating the association of genital human papillomavirus (HPV) infection and HIV acquisition.DesignSystematic review and meta-analysis.Data SourcesScientific databases and conference abstracts were systematically searched to identify all relevant studies published up to 31 January 2012. Search terms included ‘HIV’, ‘HPV’, ‘human papillomavirus’ and ‘papillomaviridae’ as keywords or text, in the title or abstract.MethodsTo be eligible for inclusion, a study had to be conducted among humans, report data on HIV incidence, and assess genital HPV infection. Summary ORs and 95% CIs were estimated from the extracted data using random-effect meta-analysis. Subgroup analyses were conducted for high-risk (HR) and low-risk (LR) HPV oncogenic risk groups. Between-study heterogeneity and publication bias were assessed.ResultsOf 2601 identified abstracts, six observational studies, comprising 6567 participants were retained for the systematic review and the meta-analysis. HIV acquisition was significantly associated with HPV infection (summary OR=1.96; 95% CI 1.55 to 2.49). HIV incident infection was significantly associated with HR-HPV in five of six studies and with LR-HPV in two out of five. The association was significant for HR-HPV (summary OR=1.92; 95% CI 1.49 to 2.46) and borderline for LR-HPV. No between-study heterogeneity was detected. There was a borderline indication of publication bias.ConclusionsFurther research is needed to elucidate the biological mechanisms involved, and assess the effect of HPV vaccination on HIV acquisition, using vaccines with broad coverage of HPV genotypes. Such research could have important public health implications for HIV prevention.
Haplotype Analysis of Norwegian and Swedish Patients with Acute Intermittent Porphyria (AIP): Extreme Haplotype Heterogeneity for the Mutation R116W
Authors: Tjensvoll Kjersti , Bruland Ove , Floderus Ylva , Skadberg Øyvind , Sandberg Sverre , Apold Jaran 
Published: June 2013

Acute intermittent porphyria (AIP), the most common of the acute porphyrias, is caused by mutations in the gene encoding hydroxymethylbilane synthase (HMBS) also called porphobilinogen deaminase (PBGD). The mutation spectrum in the HMBS gene is characterized by a majority of family specific mutations. Among the exceptions are R116W and W198X, with high prevalence in both the Dutch and Swedish populations. These two mutations were also detected in unrelated Norwegian patients. Thus, Norwegian and Swedish patients were haplotyped using closely linked flanking microsatellites and intragenic single nucleotide polymorphisms (SNPs) to see if the high frequency of these two mutations is due to a founder effect. Twelve intragenic SNPs were determined by a method based on fluorescent restriction enzyme fingerprinting single‐strand conformation polymorphism (F‐REF‐SSCP).W198X occurred exclusively on one haplotype in both Norwegian and Swedish patients, showing that it has originated from a common gene source. In contrast, R116W was found on three different haplotypes in three Norwegian families, and in five Swedish families on four or five haplotypes. This extreme haplotype heterogeneity indicates that R116W is a recurrent mutation, maybe explained by the high mutability of CpG dinucleotides. This can also explain why it is the only AIP mutation reported to occur in seven different populations (Norway, Sweden, Finland, Netherlands, France, Spain and South Africa).
Cervical Acid Phosphatase: A Biomarker of Cervical Dysplasia and a Potential Surrogate Endpoint for Colposcopy
Authors: Markovic Olivera , Markovic Nenad 
Published: June 2013

Background: In 2000, cervical acid phosphatase (CAP) has been recently described as a biomarker labeling abnormal squamous cells on Pap smears (USPTO #6,143,512). The enzyme activity is presented as a red, granular deposit on a modified Papanicolaou background. This unique property was utilized for development of MarkPap® technology intended for cervical cancer screening.Material/patients & methods: We conduct a multicenter, random assignment, assessor blinded, 2‐group (test and control), split‐sample designed clinical trial on 1,500 subject/specimens to assess safety and efficacy of the new test, in comparison with the control, for cervical cancer screening in standard Pap test environment. Safety is measured with frequency, severity and relation of adverse events. Efficacy is measured with primary endpoints (portion of positive/abnormal specimens detected, and the false negative rate). At the end of the follow‐up period (two years) when the study will be completed, other efficacy endpoints such as accuracy (sensitivity/specificity) and predictive values will be added to the method evaluation. Here we present in interim analysis.Results: In April 2003, the recruitment was completed and the first twelve hundred cases have been evaluated. There was no serious or related adverse event in both groups. Minor, unrelated adverse events were rare and insignificantly distributed in both groups.Primary endpoints: A: Portion of positive/abnormal specimens detected: Pe (new test) = 0.166, Ps (Pap control): 0.082; Ps’ (ACS reported value for US in year 2000): 0.07. Pe ≥ Ps + δ, for δ; = 0.5Ps. B. False negative rate: Pe = 0.05, Ps’ = 0.10. Confidence intervals: 95% CI: Test [0.148–0.193], Pap control [0.068–0.098]. OR = 2.26. χ2 = 40.69101 is greater than the critical value of 3.841 (P < 0.01).Conclusion: We concluded that CAP had added to visibility of Pap test and has enabled cytoscreeners to significantly improve the detection of positive/abnormal specimens and reduce false negative rate. We discuss this unique property of CAP with emphasis on using it as a surrogate endpoint for colposcopy and eventual removal of a cervical lesion that, if untreated, could progress into cancer.
Utility of Free/Total Prostate Specific Antigen (f/t PSA) Ratio in Diagnosis of Prostate Carcinoma
Authors: Thakur V. , Singh P. P. , Talwar M. , Mukherjee U. 
Published: June 2013

The discovery that PSA exists in serum in both free and complexed forms led to development of immunoassays specific for different PSA forms. This helped in measuring free PSA in the presence of PSA‐ACT (PSA‐α antichymotrypsin), hence it was possible to calculate the percent free PSA or free to total PSA ratio, measurement of which was helpful in reducing the number of unnecessary biopsies significantly, while maintaining a high clinical sensitivity for detection of cancer. The study was performed on 103 consecutive male patients (mean age 68 ± 10.8 years SD) comprising of 90 patients with benign disease (87%) and 13 prostate carcinoma patients (13%), who had histologically proven prostate cancer. Patients with total PSA between 2–25 ng/ml were included in the study. 30 normal healthy males with age 58 ± 10 years, served as control. Serum total PSA and free PSA were analyzed using streptavidin biotin EIA method (M/s Roche Diagnostics, Germany). The mean total PSA in normal healthy control subjects was 1.86 ± 1.07 ng/ml. It was increased significantly in diseased condition. Its mean concentration in carcinoma patients was 12.6 ± 5.3 ng/ml and in benign patients it was 6.3 ± 4.6 ng/ml. The free to total PSA ratio in all the three groups was significantly different (p Combination of this ratio cutoff with other parameters like serum total PSA, DRE and TRUS helped in increasing the sensitivity of the test and this also helped in reducing the number of unnecessary biopsies. In 103 men who were biopsied, 13 (12.6%) prostatic carcinoma were identified. Among these 13 cancer patients, 9 patients had abnormal findings in DRE.7 individuals out of these 9, also had free to total PSA ratio lower than 0.16 and would have been biopsied and diagnosed anyway. If we use only f/t PSA ratio less than 0.16, to decide whom to biopsy, we would have biopsied and diagnosed 11/13 cases i.e. sensitivity of 85% but If we decide to biopsy those patients who had abnormal DRE and those who had low f/t PSA ratio, we could identify 13/13 carcinoma i.e. 100% sensitivity.Combining the f/t PSA ratio with total PSA, DRE and TRUS findings could help in reducing the number of unnecessary biopsies. 37 patients who were negative for malignancy having total PSA in the range of 5–20 ng/ml, normal DRE and TRUS findings, have been biopsied but with combination of total PSA in the range of 5–20 ng/ml, normal findings in digital rectal examination and TRUS and f/t PSA ratio more than 0.16 (cutoff), we could have avoided 16 biopsies which were unnecessary that means there was 43% reduction in unnecessary biopsies.
Two Polymorphisms in the Epithelial Cell‐Derived Neutrophil‐Activating Peptide (ENA‐78) Gene
Authors: Amoli Mahsa M. , Larijani Bagher , Thomson Wendy , Ollier William E. R. , Gonzalez-Gay Miguel A. 
Published: June 2013

Increased expression of epithelial cell‐derived neutrophil‐activating peptide (ENA‐78) has been reported in several immune and inflammatory conditions suggesting its role in inflammatory response. We have identified two single nucleotide polymorphisms in the promoter and exon 2 of the ENA‐78 gene by scanning the full length gene using DHPLC DNA fragment analysis and DNA sequencing.The polymorphism at position +398 (A/G from the first ATG codon) in exon 2 results in a synonymous substitution not resulting in an amino acid change. The promoter polymorphism was found at position −156 (C/G from the first ATG codon). An assay was designed for the detection of the polymorphisms using SNapshot ddNTP primer extension, followed by capillary electrophoresis (ABI 3100).Allele and genotype frequencies for the promoter −156 polymorphism are presented for 107 healthy Spanish and 54 UK Caucasians. Frequencies for the exon 2 polymorphism are also presented for 63 UK Caucasians.