bluuebunny/crossref_metadata_2025_split huggingface dataset:
Presentation ofToxoplasma gondiiAntigens via the Endogenous Major Histocompatibility Complex Class I Pathway in Nonprofessional and Professional Antigen-Presenting Cells
Authors: Dzierszinski Florence , Pepper Marion , Stumhofer Jason S. , LaRosa David F. , Wilson Emma H. , Turka Laurence A. , Halonen Sandra K. , Hunter Christopher A. , Roos David S. 
Published: September 2007

ABSTRACTChallenge with the intracellular protozoan parasiteToxoplasma gondiiinduces a potent CD8+T-cell response that is required for resistance to infection, but many questions remain about the factors that regulate the presentation of major histocompatibility complex class I (MHC-I)-restricted parasite antigens and about the role of professional and nonprofessional accessory cells. In order to address these issues, transgenic parasites expressing ovalbumin (OVA), reagents that track OVA/MHC-I presentation, and OVA-specific CD8+T cells were exploited to compare the abilities of different infected cell types to stimulate CD8+T cells and to define the factors that contribute to antigen processing. These studies reveal that a variety of infected cell types, including hematopoietic and nonhematopoietic cells, are capable of activating an OVA-specific CD8+T-cell hybridoma, and that this phenomenon is dependent on the transporter associated with antigen processing and requires liveT. gondii. Several experimental approaches indicate that T-cell activation is a consequence of direct presentation by infected host cells rather than cross-presentation. Surprisingly, nonprofessional antigen-presenting cells (APCs) were at least as efficient as dendritic cells at activating this MHC-I-restricted response. Studies to assess whether these cells are involved in initiation of the CD8+T-cell response toT. gondiiin vivo show that chimeric mice expressing MHC-I only in nonhematopoietic compartments are able to activate OVA-specific CD8+T cells upon challenge. These findings associate nonprofessional APCs with the initial activation of CD8+T cells during toxoplasmosis.
Regional Characterization of Pasture Changes through Time and Space in Rondônia, Brazil
Authors: Numata Izaya , Roberts Dar A. , Sawada Yoshito , Chadwick Oliver A. , Schimel Joshua P. , Soares João V. 
Published: September 2007

Abstract
Although pasture degradation has been a regional concern in Amazonian ecosystems, our ability to characterize and monitor pasture degradation under different environmental and human-related conditions is still limited. Regional analysis of pasture dynamic patterns was conducted using high-frequency temporal satellite data and ancillary data to better understand pasture degradation under varied soil, environmental, and pasture management conditions in the state of Rondônia, Brazil. The 10-day normalized difference vegetation index (NDVI) composite derived from Moderate Resolution Imaging Spectroradiometer (MODIS) 250-m resolution was used to characterize different grass phenological patterns for 32 counties in Rondônia between 2001 and 2003. Six pasture greenness classes showed that high greenness pasture classes dominated in young pastures, while low greenness pasture classes were least common. As pastures aged, the proportion of high greenness pasture classes decreased and the proportion of low greenness pastures increased, indicating a decrease in forage productivity over time in Rondônia. The magnitude of productivity decline depended on environmental constraints and land use systems. To refine this analysis, trajectories of pasture change were determined using spectral mixture analysis applied to Landsat time series data from 1988 to 2001 with the focus on two counties that show contrasting patterns of potential of grass production: Pimenteira, representing the “degraded” pasture category, and Governador Jorge Teixeira, as the “productive” pasture category. The results revealed a clear pasture degradation pattern in Pimenteira, related to low soil fertility and dry climate conditions, while Governador Jorge Teixeira, with better soil fertility and intermediate precipitation, did not show signs of pasture degradation through time.
A Displacement-Based Error Measure Applied in a Regional Ensemble Forecasting System
Authors: Keil Christian , Craig George C. 
Published: September 2007

Abstract
Errors in regional forecasts often take the form of phase errors, where a forecasted weather system is displaced in space or time. For such errors, a direct measure of the displacement is likely to be more valuable than traditional measures. A novel forecast quality measure is proposed that is based on a comparison of observed and forecast satellite imagery from the Meteosat-7 geostationary satellite. The measure combines the magnitude of a displacement vector calculated with a pyramid matching algorithm and the local squared difference of observed and morphed forecast brightness temperature fields. Following the description of the method and its application for a simplified case, the measure is applied to regional ensemble forecasts for an episode of prefrontal summertime convection in Bavaria. It is shown that this new method provides a plausible measure of forecast error, which is consistent with a subjective ranking of ensemble members for a sample forecast. The measure is then applied to hourly images over a 36-h forecast period and compared with the bias and equitable threat score. The two conventional measures fail to provide any systematic distinction between different ensemble members, while the new measure identifies ensemble members of differing skill levels with a strong degree of temporal consistency. Using the displacement-based error measure, individual ensemble members are found to compare better with observations than either a short-term deterministic forecast or the ensemble mean throughout the convective period.
The Implications of Implementing a `Flexible' Syllabus for ESL Policy in the Sultanate of Oman
Authors: Al-Issa Ali S.M. 
Published: September 2007

The education system in general and ELT in particular are rigidly controlled in the Sultanate of Oman, which gives teachers little room to supplement the mandated textbook. This article, hence, discusses ideologies about the `flexible' ELT syllabus and the role of the teacher's professionalism in the syllabus implementation process. One of the powerful `ideologies' that govern ELT in the Sultanate of Oman is thus the `neocolonial/communicative'. Another powerful ideology is the `professional', which is exclusively concerned with the teacher's professionalism. These two ideologies complement each other and are present in the various statements made by different agents involved in the Omani ELT system, the pertinent literature and the Philosophy and Guidelines for the Omani English Language School Curriculum (Nunan et al. 1987), herewith referred to as the National English Language Policy/ Plan (NELP). However, these seem to conflict with the `colonialist/culturalist' ideologies incorporated in the content of the materials produced locally by the Ministry of Education— Our World through English (OWTE) and its suggested means of implementation. This is considered to negatively impact `Omanization'. This research paper, therefore, critically examines and discusses this state of ideological conflict via triangulating data from semi-structured interviews conducted with different agents involved in the implementation of ELT in Oman, pertinent literature and policy texts and NELP. Such examination and discussion have their implications for second language policy implementation.
Improving the efficiency of estimation in randomized trials of adaptive treatment strategies
Authors: Lavori Philip W , Dawson Ree 
Published: September 2007

Background Given the history of treatments to date, and the responses of the patient, what is the best treatment to try next? An ensemble of sequential, multistage rules guiding such adaptive decision making can be described as an `adaptive treatment strategy (ATS)'. Robins' G-computation can be used for estimation of the mean outcome of an ATS from a `sequential multiple assignment randomized (SMAR)' trial. Purpose To develop a variance estimate for the G-computation formula, based on a sequential analysis of the states and treatments observed in the trial, and compare its properties with those of the `marginal mean' method described by Murphy, which is based on an estimating equation. Methods We use both mathematical calculation and simulation studies to demonstrate the properties of the G-computation and its sequential variance estimate, including finite-sample bias and coverage. Results The sequential method is unbiased and more efficient when the variation in intervening states contributes substantially to the variation in final outcome, and when the study can be designed to guarantee full observation of the ATS under study. The method extends to the comparison of two or more ATS. Limitations If full observation cannot be guaranteed, the method may have poor finite-sample properties. Conclusions When the states used to adapt treatment contribute substantially to the outcome, and good design technique can be applied, the sequential method provides more efficient estimation. Clinical Trials 2007; 4: 297—308. http://ctj.sagepub.com
Noncompliance in cancer screening trials
Authors: Gareen Ilana F. 
Published: September 2007

Background Randomized trials evaluating new cancer screening technologies may underestimate the efficacy of screening to reduce cancer mortality if study participants are noncompliant. Participants may fail to comply with the screening itself or fail to obtain appropriate diagnostic follow-up and treatment. Noncompliance with screening has drawn wide attention, but little attention has been paid to noncompliance with diagnostic follow-up and treatment. Purpose To examine the importance of noncompliance with screening, follow-up, and treatment in cancer screening trials. Methods The unique problems associated with noncompliance in screening trials are described and provide an example illustrating the potential impact of noncompliance in a screening trial. I discuss issues that arise with measurement of follow-up and therapeutic noncompliance, and the benefit of collecting information on health system and participant characteristics associated with noncompliance. Results The estimate of the efficacy of a screening program on cancer mortality can be adjusted for screening, follow-up, and treatment noncompliance. Noncompliance needs to be measured in a rigorous, systematic manner across all arms of the trial. Information on health system and participant characteristics associated with compliance may also be incorporated into statistical models to estimate screening effects with full compliance, plan interventions to increase compliance, and extrapolate results of screening trials from one population to another. Limitations Measuring compliance with follow-up and treatment can be difficult when these occur outside the trial, and when there is variation among providers in follow-up and treatment practices. Conclusions Noncompliance may alter the estimate of a screening effect on cancer mortality in clinical trials. It is possible to adjust screening efficacy estimates for noncompliance using existing statistical techniques. It is important that data describing compliance with screening, follow-up, and treatment are collected as part of standard data collection in cancer screening trials. Clinical Trials 2007; 4: 341—349. http://ctj.sagepub.com
A novel approach to detect hot-spots in large-scale multivariate data
Authors: Wu Jianhua , Kendrick Keith M , Feng Jianfeng 
Published: September 2007

Abstract

Background
Progressive advances in the measurement of complex multifactorial components of biological processes involving both spatial and temporal domains have made it difficult to identify the variables (genes, proteins, neurons etc.) significantly changed activities in response to a stimulus within large data sets using conventional statistical approaches. The set of all changed variables is termed hot-spots. The detection of such hot spots is considered to be an NP hard problem, but by first establishing its theoretical foundation we have been able to develop an algorithm that provides a solution.

Results
Our results show that a first-order phase transition is observable whose critical point separates the hot-spot set from the remaining variables. Its application is also found to be more successful than existing approaches in identifying statistically significant hot-spots both with simulated data sets and in real large-scale multivariate data sets from gene arrays, electrophysiological recording and functional magnetic resonance imaging experiments.

Conclusion
In summary, this new statistical algorithm should provide a powerful new analytical tool to extract the maximum information from complex biological multivariate data.
How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
Authors: Barriot Roland , Sherman David J , Dutour Isabelle 
Published: September 2007

Abstract

Background
The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlations amongst heterogeneous data such as Gene Ontology annotations, gene expression data and genome location of genes. Despite the rapid growth of available data, very little has been proposed in terms of formalization and optimization. Additionally, current methods mainly ignore the structure of the data which causes results redundancy. For example, when searching for enrichment in GO terms, genes can be annotated with multiple GO terms and should be propagated to the more general terms in the Gene Ontology. Consequently, the gene sets often overlap partially or totally, and this causes the reported enriched GO terms to be both numerous and redundant, hence, overwhelming the researcher with non-pertinent information. This situation is not unique, it arises whenever some hierarchical clustering is performed (e.g. based on the gene expression profiles), the extreme case being when genes that are neighbors on the chromosomes are considered.

Results
We present a generic framework to efficiently identify the most pertinent over-represented features in a set of genes. We propose a formal representation of gene sets based on the theory of partially ordered sets (posets), and give a formal definition of target set pertinence. Algorithms and compact representations of target sets are provided for the generation and the evaluation of the pertinent target sets. The relevance of our method is illustrated through the search for enriched GO annotations in the proteins involved in a multiprotein complex. The results obtained demonstrate the gain in terms of pertinence (up to 64% redundancy removed), space requirements (up to 73% less storage) and efficiency (up to 98% less comparisons).

Conclusion
The generic framework presented in this article provides a formal approach to adequately represent available data and efficiently search for pertinent over-represented features in a set of genes or proteins. The formalism and the pertinence definition can be directly used by most of the methods and tools currently available for feature enrichment analysis.
Comparison of Bayesian and frequentist approaches in modelling risk of preterm birth near the Sydney Tar Ponds, Nova Scotia, Canada
Authors: Ismaila Afisi S , Canty Angelo , Thabane Lehana 
Published: September 2007

AbstractBackgroundThis study compares the Bayesian and frequentist (non-Bayesian) approaches in the modelling of the association between the risk of preterm birth and maternal proximity to hazardous waste and pollution from the Sydney Tar Pond site in Nova Scotia, Canada.MethodsThe data includes 1604 observed cases of preterm birth out of a total population of 17559 at risk of preterm birth from 144 enumeration districts in the Cape Breton Regional Municipality. Other covariates include the distance from the Tar Pond; the rate of unemployment to population; the proportion of persons who are separated, divorced or widowed; the proportion of persons who have no high school diploma; the proportion of persons living alone; the proportion of single parent families and average income. Bayesian hierarchical Poisson regression, quasi-likelihood Poisson regression and weighted linear regression models were fitted to the data.ResultsThe results of the analyses were compared together with their limitations.ConclusionThe results of the weighted linear regression and the quasi-likelihood Poisson regression agrees with the result from the Bayesian hierarchical modelling which incorporates the spatial effects.
Staphylococcus aureus intestinal colonization is associated with increased frequency of S. aureuson skin of hospitalized patients
Authors: Bhalla Anita , Aron David C , Donskey Curtis J 
Published: September 2007

Abstract

Background
Intestinal colonization by Staphylococcus aureus among hospitalized patients has been associated with increased risk of staphylococcal infection and could potentially contribute to transmission. We hypothesized that S. aureus intestinal colonization is associated with increased frequency of S. aureus on patients' skin and nearby environmental surfaces.

Methods
Selected inpatients were cultured weekly for S. aureus from stool, nares, skin (groin and axilla), and environmental surfaces (bed rail and bedside table). Investigator's hands were cultured after contacting the patients' skin and the environmental surfaces.

Results
Of 71 subjects, 32 (45.1%) had negative nares and stool cultures, 23 (32.4%) had positive nares and stool cultures, 13 (18.3%) were nares carriers only, and 3 (4.2%) were stool carriers only. Of the 39 patients with S. aureus carriage, 30 (76.9%) had methicillin-resistant isolates. In comparison to nares colonization only, nares and intestinal colonization was associated with increased frequency of positive skin cultures (41% versus 77%; p = 0.001) and trends toward increased environmental contamination (45% versus 62%; p = 0.188) and acquisition on investigator's hands (36% versus 60%; p = 0.057). Patients with negative nares and stool cultures had low frequency of S. aureus on skin and the environment (4.8% and 11.3%, respectively).

Conclusion
We found that hospitalized patients with S. aureus nares and/or stool carriage frequently had S. aureus on their skin and on nearby environmental surfaces. S. aureus intestinal colonization was associated with increased frequency of positive skin cultures, which could potentially facilitate staphylococcal infections and nosocomial transmission.
Appropriate criteria for identification of near-miss maternal morbidity in tertiary care facilities: A cross sectional study
Authors: Souza JP , Cecatti JG , Parpinelli MA , Serruya SJ , Amaral E 
Published: September 2007

Abstract

Background
The study of severe maternal morbidity survivors (near miss) may be an alternative or a complement to the study of maternal death events as a health care indicator. However, there is still controversy regarding the criteria for identification of near-miss maternal morbidity. This study aimed to characterize the near miss maternal morbidity according to different sets of criteria.

Methods
A descriptive study in a tertiary center including 2,929 women who delivered there between July 2003 and June 2004. Possible cases of near miss were daily screened by checking different sets of criteria proposed elsewhere. The main outcome measures were: rate of near miss and its primary determinant factors, criteria for its identification, total hospital stay, ICU stay, and number and kind of special procedures performed.

Results
There were two maternal deaths and 124 cases of near miss were identified, with 102 of them admitted to the ICU (80.9%). Among the 126 special procedures performed, the most frequent were central venous access, echocardiography and invasive mechanical ventilation. The mean hospital stay was 10.3 (± 13.24) days. Hospital stay and the number of special procedures performed were significantly higher when the organ dysfunction based criteria were applied.

Conclusion
The adoption of a two level screening strategy may lead to the development of a consistent severe maternal morbidity surveillance system but further research is needed before worldwide near miss criteria can be assumed.
Association of CTLA-4 gene polymorphisms with sporadic breast cancer in Chinese Han population
Authors: Wang Lihong , Li Dalin , Fu Zhenkun , Li Heng , Jiang Wei , Li Dianjun 
Published: September 2007

AbstractBackgroundThe host immunogenetic background plays an important role in the development of breast cancer. Cytotoxic T-lymphocyte antigen-4 (CTLA-4) is a molecule expressed predominantly on activated T cells and is important during the down-regulation of T-cell activation. To evaluate the potential influences ofCTLA-4gene polymorphisms on breast cancer risk, a case-control study was conducted in Han women of Northeast China.MethodsWe genotypedCTLA-4variants (-1661 G/A, -658 T/C, -318 T/C, +49 G/A and CT60 G/A) to tag all common haplotypes (≥ 1% frequency) in 117 Chinese breast cancer cases and 148 age/sex matched healthy individuals. Genotypes were determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Data was analyzed using the Chi-square test and Haploview software.ResultsThe frequency ofCTLA-4-1661G allele, -318T allele and CT60G allele carriers was significantly higher in patients than in controls (P= 0.0057, OR 1.91, 95% CI 1.21–3.02;P= 0.0031, OR 2.39, 95% CI 1.34–4.27;P= 0.023, OR 1.52, 95% CI 1.06–2.17, respectively). The -658T allele carrier frequency was significantly lower than in controls (P= 0.0000082, OR 0.17, 95% CI 0.08–0.37), whereas the +49A allele was significantly associated with tumor size in patients (P= 0.0033). Two commonCTLA-4haplotypes, ATCGA and ATCAG, were higher in healthy controls than patients (P= 0.0026, OR 0.17, 95% CI 0.05–0.54;P= 0.034, OR 0.12, 95% CI 0.02–0.92, respectively). A strong association was observed between tumor size and the ACCAA, ACCAG and ACCGA haplotypes (P= 0.0032,P= 0.0000031 andP= 0.017).ConclusionThese results suggest that polymorphisms of theCTLA-4gene may modify individual susceptibility to and progression of breast cancer in Chinese Han women.