bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lower-Sensitivity and Avidity Modifications of the Vitros Anti-HIV 1+2 Assay for Detection of Recent HIV Infections and Incidence Estimation
Authors: Keating Sheila M. , Hanson Debra , Lebedeva Mila , Laeyendecker Oliver , Ali-Napo N′ko L. , Owen S. Michele , Stramer Susan L. , Moore Richard D. , Norris Philip J. , Busch Michael P. 
Published: October 2012

ABSTRACT

Recent-infection testing assays/algorithms (RITAs) have been developed to exploit the titer and avidity of HIV antibody evolution following seroconversion for incidence estimation. The Vitros Anti-HIV 1+2 assay (Ortho-Clinical Diagnostics) was approved by the FDA to detect HIV-1 and HIV-2 infections. We developed a less-sensitive (LS) and an avidity-modified version of this assay to detect recent HIV infection. Seroconversion panels (80 subjects, 416 samples) were tested to calculate the mean duration of recent infection (MDR) for these assays. A panel from known long-term (2+ years) HIV-infected subjects on highly active antiretroviral therapy (HAART) (
n
= 134) and subjects with low CD4 counts (AIDS patients [
n
= 140]) was used to measure the false-recent rate (FRR) of the assays. Using a signal-to-cutoff ratio of 20 and the LS-Vitros assay gave a RITA MDR of 215 days (95% confidence interval [95% CI], ±65 days) and using an avidity index (AI) of 0.6 gave an MDR of 170 days (±44 days), while a combination of the two assays yielded a MDR of 146 days (±38.6) and an FRR of 8%. Misclassifying subjects with known long-term infection as recently infected occurred in 14% of AIDS patients and 29% (95% CI, 22, 38) of HAART subjects and 3% (95% CI, 0.8, 7.2) and 42% (95% CI, 33, 51), respectively, for the LS- and avidity-modified Vitros assays, with a misclassification rate of 15% (95% CI, 11, 20) overall using a dual-assay algorithm. Both modified Vitros assays can be used to estimate the length of time since seroconversion and in calculations for HIV incidence. Like other RITAs, they are subject to high FRR in subjects on HAART or with AIDS.
Recovery of Bordetella pertussis from PCR-Positive Nasopharyngeal Samples Is Dependent on Bacterial Load
Authors: Vestrheim Didrik F. , Steinbakk Martin , Bjørnstad Martha L. , Moghaddam Amir , Reinton Nils , Dahl Mette L. , Grude Nils , Sandven Per 
Published: October 2012

ABSTRACT

Viable
Bordetella pertussis
isolates are essential for surveillance purposes. We performed culture of 223 PCR-positive nasopharyngeal samples.
B. pertussis
was recovered from 45 (20.2%) of the samples. Growth was associated with a high bacterial load, as determined by PCR. Culture from PCR-positive samples is a feasible approach to recover
B. pertussis
isolates, and culture can be limited to samples with a high bacterial load.
Carriage of Neisseria lactamica in 1- to 29-Year-Old People in Burkina Faso: Epidemiology and Molecular Characterization
Authors: Kristiansen Paul A. , Diomandé Fabien , Ouédraogo Rasmata , Sanou Idrissa , Sangaré Lassana , Ouédraogo Abdoul-Salam , Ba Absatou Ky , Kandolo Denis , Dolan Thomas Jennifer , Clark Thomas A. , Préziosi Marie-Pierre , LaForce F. Marc , Caugant Dominique A. 
Published: October 2012

ABSTRACT

Neisseria lactamica
is a true commensal bacterium occupying the same ecological niche as the pathogenic
Neisseria meningitidis
, which is responsible for outbreaks and large epidemics, especially in sub-Saharan Africa. To better understand the epidemiology of
N. lactamica
in Africa and its relationship to
N. meningitidis
, we studied
N. lactamica
carriage in 1- to 29-year-old people living in three districts of Burkina Faso from 2009 to 2011.
N. lactamica
was detected in 18.2% of 45,847 oropharyngeal samples. Carriage prevalence was highest among the 2-year-olds (40.1%) and decreased with age. Overall prevalence was higher for males (19.1%) than females (17.5%) (odds ratio [OR], 1.11; 95% confidence interval [CI], 1.04 to 1.18), while among the 18- to 29-year-olds, carriage prevalence was significantly higher in women (9.1%) than in men (3.9%) (OR, 2.49; 95% CI, 1.94 to 3.19). Carriage prevalence of
N. lactamica
was remarkably homogeneous in the three districts of Burkina Faso and stable over time, in comparison with carriage of
N. meningitidis
(P. A. Kristiansen et al., Clin. Vaccine Immunol. 18:435–443, 2011). There was no significant seasonal variation of
N. lactamica
carriage and no significant change in carriage prevalence after introduction of the serogroup A meningococcal conjugate vaccine, MenAfriVac. Multilocus sequence typing was performed on a selection of 142 isolates. The genetic diversity was high, as we identified 62 different genotypes, of which 56 were new. The epidemiology of
N. lactamica
carriage and the molecular characteristics of carried isolates were similar to those reported from industrialized countries, in contrast to the particularities of
N. meningitidis
carriage and disease epidemiology in Burkina Faso.
First Isolation of Dietzia cinnamea from a Dog Bite Wound in an Adult Patient
Authors: Hirvonen Jari J. , Lepistö Inari , Mero Sointu , Kaukoranta Suvi-Sirkku 
Published: October 2012

ABSTRACT

We report the first case of deep-wound colonization by
Dietzia cinnamea
in a patient who had been bitten by a dog.
Swab Protocol for Rapid Laboratory Diagnosis of Cutaneous Anthrax
Authors: Dauphin Leslie A. , Marston Chung K. , Bhullar Vinod , Baker Daniel , Rahman Mahmudur , Hossain M. Jahangir , Chakraborty Apurba , Khan Salah Uddin , Hoffmaster Alex R. 
Published: October 2012

ABSTRACT

The clinical laboratory diagnosis of cutaneous anthrax is generally established by conventional microbiological methods, such as culture and directly straining smears of clinical specimens. However, these methods rely on recovery of viable
Bacillus anthracis
cells from swabs of cutaneous lesions and often yield negative results. This study developed a rapid protocol for detection of
B. anthracis
on clinical swabs. Three types of swabs, flocked-nylon, rayon, and polyester, were evaluated by 3 extraction methods, the swab extraction tube system (SETS), sonication, and vortex. Swabs were spiked with virulent
B. anthracis
cells, and the methods were compared for their efficiency over time by culture and real-time PCR. Viability testing indicated that the SETS yielded greater recovery of
B. anthracis
from 1-day-old swabs; however, reduced viability was consistent for the 3 extraction methods after 7 days and nonviability was consistent by 28 days. Real-time PCR analysis showed that the PCR amplification was not impacted by time for any swab extraction method and that the SETS method provided the lowest limit of detection. When evaluated using lesion swabs from cutaneous anthrax outbreaks, the SETS yielded culture-negative, PCR-positive results. This study demonstrated that swab extraction methods differ in their efficiency of recovery of viable
B. anthracis
cells. Furthermore, the results indicated that culture is not reliable for isolation of
B. anthracis
from swabs at ≥7 days. Thus, we recommend the use of the SETS method with subsequent testing by culture and real-time PCR for diagnosis of cutaneous anthrax from clinical swabs of cutaneous lesions.
Similarity and Divergence of Phylogenies, Antimicrobial Susceptibilities, and Virulence Factor Profiles of Escherichia coli Isolates Causing Recurrent Urinary Tract Infections That Persist or Result from Reinfection
Authors: Luo Yanping , Ma Yanning , Zhao Qiang , Wang Leili , Guo Ling , Ye Liyan , Zhang Youjiang , Yang Jiyong 
Published: October 2012

ABSTRACT

In order to obtain a better molecular understanding of recurrent urinary tract infection (RUTI), we collected 75 cases with repeatedly occurring uncomplicated UTI. The genetic relationships among uropathogenic
Escherichia coli
(UPEC) isolates were analyzed by pulsed-field gel electrophoresis. While 39 (52%) of the RUTI cases were defined as “persistence” of the same strain as the primary infecting strain, 36 (48%) were characterized by “reinfection” with a new strain that is different from the primary strain. We then examined the antimicrobial susceptibilities and phylogenetic backgrounds of 39 persistence and 86 reinfection UPEC isolates, and screened 44 virulence factor (VF) genes. We found that isolates had significant differences in the following: placement in phylogenetic group B2 (41% versus 21%;
P
= 0.0193) and the presence of adhesin genes
iha
(49% versus 28%;
P
= 0.0233) and
papG
allele
I
′ (51% versus 24%;
P
= 0.003), iron uptake genes
fyuA
(85% versus 58%;
P
= 0.0037),
irp-2
(87% versus 65%;
P
= 0.0109), and
iutA
(87% versus 58%;
P
= 0.0014), and an aggregate VF score (median, 11 versus 9;
P
= 0.0030). In addition, 41% of persistence strains harbored three adhesin genes simultaneously, whereas 22% of reinfection isolates did (
P
= 0.0289). Moreover, 59% versus 29% (
P
= 0.0014) of persistence and reinfection isolates contained seven types of iron uptake genes. Taken together, the antimicrobial susceptibilities of UPEC isolates had little effect on the RUTI. Compared with reinfection strains, persistence UPEC isolates exhibited higher VF scores and carried more VF genes than may be involved in the development and progression of RUTI.
Use of Clustered Regularly Interspaced Short Palindromic Repeat Sequence Polymorphisms for Specific Detection of Enterohemorrhagic Escherichia coli Strains of Serotypes O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 by Real-Time PCR
Authors: Delannoy Sabine , Beutin Lothar , Fach Patrick 
Published: October 2012

ABSTRACT

We explored the genetic diversity of the clustered regularly interspaced short palindromic repeat (CRISPR) regions of enterohemorrhagic
Escherichia coli
(EHEC) to design simplex real-time PCR assays for each of the seven most important EHEC serotypes worldwide. A panel of 958
E. coli
strains investigated for their CRISPR loci by high-throughput real-time PCR showed that CRISPR polymorphisms in
E. coli
strongly correlated with both O:H serotypes and the presence of EHEC virulence factors (
stx
and
eae
genes). The CRISPR sequences chosen for simplex real-time PCR amplification of EHEC strains belonging to the top 7 EHEC serogroups differentiated clearly between EHEC and non-EHEC strains. Specificity estimates for the CRISPR PCR assays varied from 97.5% to 100%. Sensitivity estimates for the assays ranged from 95.7% to 100%. The assays targeting EHEC O145:H28, O103:H2, and O45:H2 displayed 100% sensitivity. The combined usage of two simplex PCR assays targeting different sequences of the O26 CRISPR locus allowed detection of EHEC O26:H11 with 100% sensitivity. By combining two simplex PCR assays targeting different sequences of the EHEC O157 CRISPR locus, EHEC O157:H7 was detected with 99.56% sensitivity. EHEC O111:H8 and EHEC O121:H19 were detected with 95.9% and 95.7% sensitivity, respectively. This study demonstrates that the identification of EHEC serotype-specific CRISPR sequences is more specific than the mere identification of O-antigen gene sequences, as is used in current PCR protocols for detection of EHEC strains.
Atypical H-Type Bovine Spongiform Encephalopathy in a Cow Born after the Reinforced Feed Ban on Meat-and-Bone Meal in Europe
Authors: Guldimann Claudia , Gsponer Michaela , Drögemüller Cord , Oevermann Anna , Seuberlich Torsten 
Published: October 2012

ABSTRACTThe significance of atypical bovine spongiform encephalopathies (BSE) in cattle for controlling the BSE epidemic is poorly understood. Here we report a case of atypical H-type BSE in a cow born after the implementation of the reinforced feed ban in Europe. This supports an etiology of H-type BSE unrelated to that of classical BSE.
Utilisation of primary total knee joint replacements across socioeconomic status in the Barwon Statistical Division, Australia, 2006–2007: a cross-sectional study
Authors: Brennan Sharon Lee , Stanford Tyman , Wluka Anita E , Page Richard S , Graves Stephen E , Kotowicz Mark A , Nicholson Geoffrey C , Pasco Julie A 
Published: October 2012

ObjectivesThere are few Australian data that examine the association between total knee joint replacement (TKR) utilisation and socioeconomic status (SES). This study examined TKR surgeries with a diagnosis of osteoarthritis (OA) performed for residents of Barwon Statistical Division (BSD) for 2006–2007.DesignCross-sectional.SettingBSD, South-eastern Victoria, AustraliaParticipantsAll patients who underwent a TKR for OA, 2006–2007, and whose residential postcode was identified as within the BSD of Australia, and for whom SES data were available, were eligible for inclusion.Primary outcome measurePrimary TKR data ascertained from the Australian Orthopaedic Association National Joint Replacement Registry. Residential addresses were matched with the Australian Bureau of Statistics census data, and the Index of Relative Socioeconomic Disadvantage was used to determine SES, categorised into quintiles whereby quintile 1 indicated the most disadvantaged and quintile 5 the least disadvantaged. Age-specific and sex-specific rates of TKR utilisation per 1000 person-years were reported for 10-year age bands.ResultsFemales accounted for 62.7% of the 691 primary TKR surgeries performed during 2006–2007. The greatest utilisation rates of TKR in males was 7.6 observed in those aged >79 years, and in 10.2 in females observed in those aged 70–79 years. An increase in TKR was observed for males in SES quintile four compared to quintile 1 in which the lowest utilisation which was observed (p=0.04). No differences were observed in females across SES quintiles.ConclusionsFurther investigation is warranted on a larger scale to examine the role that SES may play in TKR utilisation, and to determine whether any social disparities in TKR utilisation reflect health system biases or geographic differences.
Prediction of Rice Production in the Philippines Using Seasonal Climate Forecasts
Authors: Koide Naohisa , Robertson Andrew W. , Ines Amor V. M. , Qian Jian-Hua , DeWitt David G. , Lucero Anthony 
Published: October 2012

AbstractPredictive skills of retrospective seasonal climate forecasts (hindcasts) tailored to Philippine rice production data at national, regional, and provincial levels are investigated using precipitation hindcasts from one uncoupled general circulation model (GCM) and two coupled GCMs, as well as using antecedent observations of tropical Pacific sea surface temperatures, warm water volumes (WWV), and zonal winds (ZW). Contrasting cross-validated predictive skills are found between the “dry” January–June and “rainy” July–December crop-production seasons. For the dry season, both irrigated and rain-fed rice production are shown to depend strongly on rainfall in the previous October–December. Furthermore, rice-crop hindcasts based on the two coupled GCMs, or on the observed WWV and ZW, are each able to account for more than half of the total variance of the dry-season national detrended rice production with about a 6-month lead time prior to the beginning of the harvest season. At regional and provincial levels, predictive skills are generally low. The relationships are found to be more complex for rainy-season rice production. Area harvested correlates positively with rainfall during the preceding dry season, whereas the yield has positive and negative correlations with rainfall in June–September and in October–December of the harvested year, respectively. Tropical cyclone activity is also shown to be a contributing factor in the latter 3-month season. Hindcasts based on the WWV and ZW are able to account for almost half of the variance of the detrended rice production data in Luzon with a few months’ lead time prior to the beginning of the rainy season.
Impact of Surface Parameter Uncertainties within the Canadian Regional Ensemble Prediction System
Authors: Lavaysse Christophe , Carrera Marco , Bélair Stéphane , Gagnon Normand , Frenette Ronald , Charron Martin , Yau M. K. 
Published: October 2012

Abstract
The aim of this study is to assess the impact of uncertainties in surface parameter and initial conditions on numerical prediction with the Canadian Regional Ensemble Prediction System (REPS). As part of this study, the Canadian version of the Interactions between Soil–Biosphere–Atmosphere (ISBA) land surface scheme has been coupled to Environment Canada’s numerical weather prediction model within the REPS. For 20 summer periods in 2009, stochastic perturbations of surface parameters have been generated in several experiments. Each experiment corresponds to 20 simulations differing by the perturbations at the initial time of one or several surface parameters or prognostic variables. The sensitivity to these perturbations is quantified especially for 2-m temperature, 10-m wind speed, cloud fraction, and precipitation up to 48-h lead time. Spatial variability of these sensitivities over the North American continent shows that soil moisture, albedo, leaf area index, and SST have the largest impacts on the screen-level variables. The temporal evolution of these sensitivities appears to be closely linked to the diurnal cycle of the boundary layer. The surface perturbations are shown to increase the ensemble spread of the REPS for all screen-level variables especially for 2-m temperature and 10-m wind speed during daytime. A preliminary study of the impact on the ensemble forecast has shown that the inclusion of the surface perturbations tends to significantly increase the 2-m temperature and 10-m wind speed skill.
Design of a Basic System of Indicators for Monitoring and Evaluating Spanish Cooperation’s Culture and Development Strategy
Authors: Coll-Serrano Vicente , Carrasco-Arroyo Salvador , Blasco-Blasco Olga , Vila-Lladosa Luis 
Published: October 2012

Objective: This article describes the process implemented in order to define and build up a Basic Monitoring and Evaluation System for Spanish Cooperation’s Culture and Development Strategy (CD-S). Research Design: Delphi techniques were used to assess a wide catalogue of indicators for each of the strategic areas included in the CD-S. Afterward, those indicators considered most suitable for monitoring and evaluating purposes were selected based on the assessments provided by a panel of experts. Results: As a consequence, the resulting system, made up by a total of 80 indicators, was designed to be a practical, manageable, and targeted tool for its potential users, who include managers and technical officers who map out strategy together with stakeholders involved in its implementation, and specifically with staff at cultural centers abroad and in technical aid offices.
A retrospective review of antiemetic use for chemotherapy-induced nausea and vomiting in pediatric oncology patients at a tertiary care center
Authors: Aseeri Mohammed , Mukhtar Amnah , Khansa Sara Al , Elimam Nagla , Jastaniah Wasil 
Published: October 2012

Background Chemotherapy-induced nausea and vomiting are the most dreaded and distressing side effects for cancer patients undergoing chemotherapy treatment. These side effects have a significant impact on the patients’ quality of life and can interfere with their ability to receive intensive chemotherapy regimens. With the recent advances in antiemetic pharmacotherapy and supportive care, the current treatments for chemotherapy-induced nausea and vomiting, when used appropriately, have become highly effective in mitigating these adverse effects. Objective The aim of this study was to evaluate the current practice involving antiemetic treatment in newly diagnosed pediatric oncology patients at our center. Methods This was a retrospective cohort study of newly diagnosed pediatric oncology patients who were less than 14 years of age receiving their first cycle of inpatient chemotherapy. The data abstracted included the following: age, gender, type of cancer, chemotherapy regimen, emetogenic risk and level, prescribed prophylactic antiemetic regimen, incidence of breakthrough emesis, and breakthrough antiemetic medications used. Emetogenic risk was classified based on published guidelines into low, moderate, or high emetogenic chemotherapy, and a scoring system to determine the emetogenic level of combined chemotherapy agents was followed to monitor the efficacy of the antiemetic regimens. Clinical effectiveness was assessed based on breakthrough emesis. Results A total of 49 patients were eligible for the study. High emetogenic chemotherapy was administered in 28/49 (57.1%) and moderate emetogenic chemotherapy was administered in 21/49 (42.9%) patients. Only 10/49 (20.4%) received appropriate antiemetic prophylaxis, whereas 39/49 (79.6%) received inadequate antiemetic prophylaxis; 14/49 (28.6%) patients experienced breakthrough emesis. Breakthrough emesis occurred in 11/28 (39.3%) patients receiving high emetogenic chemotherapy and 3/21 (14.3%) patients receiving moderate emetogenic chemotherapy. The use of an inadequate antiemetic regimen was found in 14/14 (100%) patients with breakthrough emesis. Thus, inadequate prophylaxis resulted in a 35.9% (14/39) risk of breakthrough emesis. This risk was higher in patients receiving high emetogenic chemotherapy versus those receiving moderate emetogenic chemotherapy (39.3% versus 14.3%). Conclusion Inadequate antiemetic prophylaxis is associated with a high risk of breakthrough emesis particularly with high emetogenic chemotherapy regimens. Standardizing antiemetic prophylaxis based on emetogenic level could reduce breakthrough emesis and improve the quality of life in pediatric oncology patients.
Is there still a role for mitomycin-based combination chemotherapy in treating patients with nonsmall cell lung cancer? A single institution experience
Authors: Vitale Felice V , Malaponte Emilia , Calì Stefania , Antonelli Giovanna , Panebianco Vincenzo , Blandino Rosario , Ferraù Francesco 
Published: October 2012

Background: Mitomycin and irinotecan are widely used in the treatment of colorectal cancer, furthermore both of these drugs are active agents against nonsmall cell lung cancer and their combination has shown synergism in preclinical studies. The aim of the study was to evaluate the efficacy and safety of mitomycin- and irinotecan-based chemotherapy combination in patients with advanced nonsmall cell lung cancer progressing after previous antineoplastic therapies. Methods: Thirty-one consecutive patients suffering from nonsmall cell lung cancer, who underwent mitomycin- plus irinotecan-based chemotherapy as salvage treatment after failure of at least two previous systemic treatments, were retrospectively identified in our database. Between September 2003 and March 2011, 31 patients with histologically proven stage IIIB or IV nonsmall cell lung cancer, received mitomycin 5 mg/m2 on day 1 followed by irinotecan 150 mg/m2 on day 2. Cycles were repeated at 2-week interval. Results: A total of 164 cycles of treatment were given with a median of five per patient (range 1–10). The objective responses included partial response in 6 patients (19.3%), stable disease in 4 (13%), and progressive disease in 21 (67.7%). Median time to disease progression was 4 months, and median survival was 9+ months. Twelve patients (38%) reached 1-year survival. Grade 3–4 toxicities occurred in seven patients (22.5%), mainly myelosuppression (neutropenia, anemia, and thrombocytopenia), mucositis, and diarrhea. No treatment-related death was recorded. Conclusion: The mitomycin- and irinotecan-based combination chemotherapy seems to be tolerated and active in this subset of heavily pretreated patients with advanced nonsmall cell lung cancer. However, evaluation or recruitment of a larger number of patients would be needed to provide more adequate data on safety and activity of the described combination.