bluuebunny/crossref_metadata_2025_split huggingface dataset:
EUS GUIDED FNA FOR MEDIASTINAL TUMORS (LUNG CANCER AND LYMPH NODES)
Authors: Vilmann Peter , Larsen Søren S. , Krasnik Mark 
Published: October 2004

Trans‐esophageal endoscopic ultrasound‐guided fine needle aspiration biopsy (EUS‐FNA) has proven to be a safe and minimally invasive tissue‐sampling method which can be used to obtain a cytological diagnosis from mediastinal lesions. The aims of EUS‐FNA in the mediastinum are either to diagnose a lesion of unknown origin, to stage mediastinal lymph nodes in lung cancer patients or to diagnose other diseases involving lymph nodes of the mediastinum. In patients with non‐small cell lung cancer (NSCLC), surgery may be regarded as futile in up to 45% of patients operated, apparently because the stage of the disease is more advanced than expected preoperatively. This, combined with a stage‐dependent multimodality treatment, underlines the importance of exact staging of the disease. Conventional imaging and tissue sampling methods all have variable sensitivities.Twenty‐two studies concerning EUS‐FNA and mediastinal staging of lung cancer have been published with a total number of 1245 patients. The reported sensitivity for mediastinal malignancy range from 0.61–1.00 (median 0.90), and with specificities of 0.71–1.00 (median 1.00). The majority of the studies are retrospective and present the results of EUS‐FNA performed in lung cancer patients selected by computer tomography (CT). Recent data suggests that EUS‐FNA in addition can diagnose advanced mediastinal disease in 22–42% of NSCLC patients with normal sized lymph nodes (< 1 cm) on chest CT. EUS‐FNA may also be used as a re‐staging procedure after induction chemotherapy and it seems that EUS‐FNA is more accurate for mediastinal staging of NSCLC compared to positron emission tomography (PET). However, further studies are necessary before final conclusions can be made. At present, mediastinoscopy is still considered complementary to EUS‐FNA because EUS‐FNA cannot visualize structures anterior to the air‐filled trachea and main bronchi. Endoscopic trans‐bronchial real‐time ultrasound guided biopsy (EBUS‐TBNA) performed via the trachea and main bronchi seems to be an obvious solution. Preliminary experience with a prototype EBUS‐TBNA bronchoscope (Olympus, XBF‐UC40P, Tokyo, Japan) in 214 patients has shown promising results. Hopefully the combination of EUS‐FNA and EBUS‐TBNA will be able to replace more invasive and risky staging methods and improve the N‐staging accuracy of the mediastinum and lung hilar regions in the near future.
In situ analysis of p16/INK4 promoter hypermethylation in esophageal carcinoma and gastric carcinoma
Authors: ZHANG Fan , WANG Li , WU Ping Ping , YAN Zhao Wen , ZHENG Lin , YU Ying Yan , JIANG Xu Cheng 
Published: October 2004

OBJECTIVE:  Inactivation of the tumor suppressor gene by CpG hypermethylation is a common event in a variety of tumors. The present study was designed to be a comprehensive analysis of p16/INK4 methylation in carcinomas of the upper digestive tract.METHODS:  Series of esophageal carcinomas (34 cases) and gastric carcinomas (25 cases) were examined for CpG methylation in p16/INK4 using methylation‐specific PCR (MSP). The tissue sections underwent MSP in situ and were then examined microscopically. Immunohistochemical detection of the expression of p16 in the tumor specimens was also performed.RESULTS:  Immunohistochemistry detected positive p16 expression in 8 cases of esophageal squamous cell carcinoma and 15 cases of gastric carcinoma. In esophageal carcinoma, hypermethylation of the p16/INK4 promoter region was detected in 5 cases without statistical correlation with its loss of expression, whereas in the gastric carcinomas, p16 expression was positively correlated with the T‐classification (r = 0.488, P = 0.01); p16/INK4 methylation was identified in 8 cases. In addition, p16 expression was lower in the methylated samples than in the non‐methylated samples (25% vs 76.47%, P = 0.03). Analysis of the MSP‐in‐situ sections showed that the distribution of methylated cells in esophageal carcinoma differed from that in gastric carcinoma.CONCLUSION:  The role of DNA methylation in the silence of p16/INK4 may different between these two types of upper digestive tract tumor.
Clinical relevance of iceA and babA2 genotypes of Helicobacter pylori in a Shanghai population
Authors: HAN Yue Hua , LIU Wen Zhong , ZHU Hong Yin , XIAO Shu Dong 
Published: October 2004

OBJECTIVE:  To determine the distribution of the iceA and babA2 genotypes of Helicobacter pylori in patients with various gastroduodenal diseases in Shanghai, and to explore the association between genotype and the clinical outcome of infection.METHODS:  One hundred and forty‐one strains of H. pylori were isolated from gastric biopsies of 43 patients with chronic gastritis, 47 with duodenal ulcer (DU), 30 with gastric ulcer (GU) and 21 with non‐cardia gastric carcinoma. The iceA, babA2, cagA and vacA genotypes were determined by polymerase chain reaction (PCR).RESULTS:  The iceA1, iceA2 and babA2 genotypes were detected in 74.5% (105/141), 15.6% (22/141) and 63.8% (90/141), respectively, of the H. pylori strains studied. Two H. pylori isolates (1.4%) were positive for both iceA alleles and 16 (11.3%) were negative for both. The prevalence of babA2 and its combination with cagA (cagA+/babA2+) in DU patients was significantly higher than that in GU patients (74.5%vs 50.0% for babA2, P = 0.028; 70.2%vs 46.7% for cagA+/babA2+, P = 0.039). There was no significant difference in the prevalence of babA2 among the other disease groups, and no significant association of the iceA genotypes with the different clinical diseases (P > 0.05).CONCLUSIONS:  The most predominant genotype of the H. pylori strains isolated from patients in Shanghai are iceA1+/babA2+, and the babA2 genotype may play a different role in the pathogenesis of DU and GU. An association between iceA status and clinical outcome of H. pylori infection could not be confirmed in the present study.
Modelling Species Diversity Through Species Level Hierarchical Modelling
Authors: Gelfand Alan E. , Schmidt Alexandra M. , Wu Shanshan , Silander John A. , Latimer Andrew , Rebelo Anthony G. 
Published: October 2004

SummaryUnderstanding spatial patterns of species diversity and the distributions of individ-ual species is a consuming problem in biogeography and conservation. The Cape floristic region of South Africa is a global hot spot of diversity and endemism, and the Protea atlas project, with about 60000 site records across the region, provides an extraordinarily rich data set to model patterns of biodiversity. Model development is focused spatially at the scale of 1′ grid cells (about 37000 cells total for the region). We report on results for 23 species of a flowering plant family known as Proteaceae (of about 330 in the Cape floristic region) for a defined subregion. Using a Bayesian framework, we developed a two-stage, spatially explicit, hierarchical logistic regression. Stage 1 models the potential probability of presence or absence for each species at each cell, given species attributes, grid cell (site level) environmental data with species level coefficients, and a spatial random effect. The second level of the hierarchy models the probability of observing each species in each cell given that it is present. Because the atlas data are not evenly distributed across the landscape, grid cells contain variable numbers of sampling localities. Thus this model takes the sampling intensity at each site into account by assuming that the total number of times that a particular species was observed within a site follows a binomial distribution. After assigning prior distributions to all quantities in the model, samples from the posterior distribution were obtained via Markov chain Monte Carlo methods. Results are mapped as the model-estimated probability of presence for each species across the domain. This provides an alternative to customary empirical ‘range-of-occupancy’ displays. Summing yields the predicted richness of species over the region. Summaries of the posterior for each environmental coefficient show which variables are most important in explaining the presence of species. Our initial results describe biogeographical patterns over the modelled region remarkably well. In particular, species local population size and mode of dispersal contribute significantly to predicting patterns, along with annual precipitation, the coefficient of variation in rainfall and elevation.
A Bayesian Ordinal Logistic Regression Model to Correct for Interobserver Measurement Error in a Geographical Oral Health Study
Authors: Mwalili Samuel M. , Lesaffre Emmanuel , Declerck Dominique 
Published: October 2004

SummaryWe present an approach for correcting for interobserver measurement error in an ordinal logistic regression model taking into account also the variability of the estimated correction terms. The different scoring behaviour of the 16 examiners complicated the identification of a geographical trend in a recent study on caries experience in Flemish children (Belgium) who were 7 years old. Since the measurement error is on the response the factor ‘examiner’ could be included in the regression model to correct for its confounding effect. However, controlling for examiner largely removed the geographical east–west trend. Instead, we suggest a (Bayesian) ordinal logistic model which corrects for the scoring error (compared with a gold standard) using a calibration data set. The marginal posterior distribution of the regression parameters of interest is obtained by integrating out the correction terms pertaining to the calibration data set. This is done by processing two Markov chains sequentially, whereby one Markov chain samples the correction terms. The sampled correction term is imputed in the Markov chain pertaining to the regression parameters. The model was fitted to the oral health data of the Signal–Tandmobiel® study. A WinBUGS program was written to perform the analysis.
Nonparametric Estimation of a Change in Defect Intensity
Authors: Denteneer D. , Keane M. S. 
Published: October 2004

SummaryIn an important class of problems involving mixture distributions, interest focuses on the mixture proportions, considering other possible parameters as nuisance parameters. We formulate a new variation on such problems that arose in a study on the link between the number of cells in a charge-coupled detector image sensor that turned defective because of cosmic radiation and the storage conditions of such sensors. In this variation, the component densities are bivariate, there are two classes and only a subset of the mixture proportions is of relevance. We propose a nonparametric method to estimate the relevant subset of the proportions and apply our method to the data in our study.
A Useful Distribution for Fitting Discrete Data: Revival of the Conway–Maxwell–Poisson Distribution
Authors: Shmueli Galit , Minka Thomas P. , Kadane Joseph B. , Borle Sharad , Boatwright Peter 
Published: October 2004

SummaryA useful discrete distribution (the Conway–Maxwell–Poisson distribution) is revived and its statistical and probabilistic properties are introduced and explored. This distribution is a two-parameter extension of the Poisson distribution that generalizes some well-known discrete distributions (Poisson, Bernoulli and geometric). It also leads to the generalization of distributions derived from these discrete distributions (i.e. the binomial and negative binomial distributions). We describe three methods for estimating the parameters of the Conway–Maxwell–Poisson distribution. The first is a fast simple weighted least squares method, which leads to estimates that are sufficiently accurate for practical purposes. The second method, using maximum likelihood, can be used to refine the initial estimates. This method requires iterations and is more computationally intensive. The third estimation method is Bayesian. Using the conjugate prior, the posterior density of the parameters of the Conway–Maxwell–Poisson distribution is easily computed. It is a flexible distribution that can account for overdispersion or underdispersion that is commonly encountered in count data. We also explore two sets of real world data demonstrating the flexibility and elegance of the Conway–Maxwell–Poisson distribution in fitting count data which do not seem to follow the Poisson distribution.
A Modified False Discovery Rate Multiple-Comparisons Procedure for Discrete Data, Applied to Human Immunodeficiency Virus Genetics
Authors: Gilbert Peter B. 
Published: October 2004

SummaryTo help to design vaccines for acquired immune deficiency syndrome that protect broadly against many genetic variants of the human immunodeficiency virus, the mutation rates at 118 positions in HIV amino-acid sequences of subtype C versus those of subtype B were compared. The false discovery rate (FDR) multiple-comparisons procedure can be used to determine statistical significance. When the test statistics have discrete distributions, the FDR procedure can be made more powerful by a simple modification. The paper develops a modified FDR procedure for discrete data and applies it to the human immunodeficiency virus data. The new procedure detects 15 positions with significantly different mutation rates compared with 11 that are detected by the original FDR method. Simulations delineate conditions under which the modified FDR procedure confers large gains in power over the original technique. In general FDR adjustment methods can be improved for discrete data by incorporating the modification proposed.
Bayesian Methods for the Cross-Design Synthesis of Epidemiological and Toxicological Evidence
Authors: Peters Jaime L. , Rushton Lesley , Sutton Alex J. , Jones David R. , Abrams Keith R. , Mugglestone Moira A. 
Published: October 2004

Summary
Systematic review and synthesis (meta-analysis) methods are now increasingly used in many areas of health care research. We investigate the potential usefulness of these methods for combining human and animal data in human health risk assessment of exposure to environmental chemicals. Currently, risk assessments are often based on narrative review and expert judgment, but systematic review and formal synthesis methods offer a more transparent and rigorous approach. The method is illustrated by using the example of trihalomethane exposure and its possible association with low birth weight. A systematic literature review identified 13 relevant studies (five epidemiological and eight toxicological). Study-specific dose–response slope estimates were obtained for each of the studies and synthesized by using Bayesian meta-analysis models. Sensitivity analyses of the results obtained to the assumptions made suggest that some assumptions are critical. It is concluded that systematic review methods should be used in the synthesis of evidence for environmental standard setting, that meta-analysis will often be a valuable approach in these contexts and that sensitivity analyses are an important component of the approach whether or not formal synthesis methods (such as systematic review and meta-analysis) are used.
A Bayesian Kriged Kalman Model for Short-Term Forecasting of Air Pollution Levels
Authors: Sahu Sujit K. , Mardia Kanti V. 
Published: October 2004

SummaryShort-term forecasts of air pollution levels in big cities are now reported in news-papers and other media outlets. Studies indicate that even short-term exposure to high levels of an air pollutant called atmospheric particulate matter can lead to long-term health effects. Data are typically observed at fixed monitoring stations throughout a study region of interest at different time points. Statistical spatiotemporal models are appropriate for modelling these data. We consider short-term forecasting of these spatiotemporal processes by using a Bayesian kriged Kalman filtering model. The spatial prediction surface of the model is built by using the well-known method of kriging for optimum spatial prediction and the temporal effects are analysed by using the models underlying the Kalman filtering method. The full Bayesian model is implemented by using Markov chain Monte Carlo techniques which enable us to obtain the optimal Bayesian forecasts in time and space. A new cross-validation method based on the Mahalanobis distance between the forecasts and observed data is also developed to assess the forecasting performance of the model implemented.
Disease Resistance Modelled as First-Passage Times of Genetically Dependent Stochastic Processes
Authors: Sæbø S. , Almøy T. , Aastveit A. H. 
Published: October 2004

Summary
Mastitis resistance data on dairy cattle are modelled as first-passage times of stochastic processes. Population heterogeneity is included by expressing process parameters as functions of shared random variables. We show how dependences between individuals, e.g. genetic relationships, can be exploited in the analyses. The method can be extended to handle situations with multiple hidden causes of failure. Markov chain Monte Carlo methods are used for estimation.
Effect of different time intervals on the viscosity of batter and on the sensory qualities of puras (pancakes) prepared using chhana and paneer whey
Authors: JINDAL A R , SHOREE M , SHUKLA F C 
Published: October 2004

The viscosity of pura (pancakes) batter samples prepared with bovine, buffalo and mixed wheys (80 : 20 whey to water) was measured at different time intervals at a temperature of 25 ± 2°C using a Brookfield viscometer (LVT 98534). The viscosity of sweet pura batter samples increased after 1 h, remained constant for another 2 h and then decreased, whereas the viscosity of salty pura batter samples increased from freshly prepared batter to 1 h and then remained constant. Sensory evaluation of both sweet and salty puras at different time intervals from batter preparation was also carried out. The overall acceptability scores for sweet puras prepared using bovine milk chhana whey, buffalo milk paneer whey and mixed milk chhana whey and stored for up to 4 h at 25 ± 2°C and for 24 h at 4–5°C were not significantly different, and the same conclusion applied to salty puras made from bovine milk chhana whey. It was concluded that sweet and salty pura batters can be prepared from any chhana or paneer whey.
Evolution of a crustal‐scale transpressive shear zone in the Albany–Fraser Orogen, SW Australia: 1. P–T conditions of Mesoproterozoic metamorphism in the Coramup Gneiss
Authors: Bodorkos S. , Clark D. J. 
Published: October 2004

AbstractThe Albany–Fraser Orogen in southwestern Australia preserves an important thermo‐tectonic record of Australo‐Antarctic cratonic assembly during the Mesoproterozoic. New petrologic and thermobarometric data from the Coramup Gneiss (a 10 km wide zone of high strain rocks within the NE‐trending eastern Albany–Fraser Orogen) indicate at least two high‐grade metamorphic events during 1345–1140 Ma convergence and amalgamation of the West Australian and Mawson cratons. The first event (M1) involved c. 1300 Ma granulite facies metamorphism of the Coramup Gneiss (M1a: 800–850 °C, 5–7 kbar), followed by burial and recrystallization under high‐P conditions (M1b: 800–850 °C, c. 10 kbar) prior to high‐T decompression (M1c: 700–800 °C, 7–8 kbar) and the 1290–1280 Ma emplacement of Recherche Granite sills. The second event (M2) entailed high‐T, low‐P metamorphism within dextral D2 shear zones (M2a: 750–800 °C, 5–6 kbar), followed by fluid‐present amphibolite facies M2b retrogression. Subsequent sinistral D3 mylonites and pseudotachylites are considered contemporaneous with similar structures in the adjacent Nornalup Complex that postdate the c. 1140 Ma Esperance Granite. Our petrological and thermobarometric data permit two end‐member P–T‐time relationships between M1 and M2: (1) a single post‐M1b event involving continuous M1b–M1c–M2a–M2b cooling and decompression, and (2) a two‐stage post‐M1b evolution involving M1c metamorphism during the waning stages of an event unrelated causally or temporally to subsequent M2a metamorphism and D2 deformation. In a companion paper, new structural and U–Pb SHRIMP zircon data are presented to support a two‐stage P–T evolution for the Coramup Gneiss, with M1 and M2, respectively, reflecting thermo‐tectonic activity during Stage I (1345–1260 Ma) and Stage II (1215–1140 Ma) of the Albany–Fraser Orogeny.
Evolution of a crustal‐scale transpressive shear zone in the Albany–Fraser Orogen, SW Australia: 2. Tectonic history of the Coramup Gneiss and a kinematic framework for Mesoproterozoic collision of the West Australian and Mawson cratons
Authors: Bodorkos S. , Clark D. J. 
Published: October 2004

AbstractWithin the Albany–Fraser Orogen of southwestern Australia, the Coramup Gneiss is a NE–SW trending zone of high‐strain rocks that preserves a detailed record of orogenesis related to Mesoproterozoic convergence of the West Australian and Mawson cratons. New structural, metamorphic and U–Pb SHRIMP zircon age data establish that the Coramup Gneiss underwent high‐grade tectonism during both Stage I (c. 1290 Ma) and Stage II (c. 1170 Ma) of the Albany–Fraser Orogeny. Stage I commenced with c. 1300 Ma high‐T, low‐P M1a metamorphism during extension, and the formation of small‐scale ptygmatic folds within a subhorizontal S1a gneissosity. High‐P M1b metamorphism at c. 1290 Ma was accompanied by the transposition and shearing of S1a into a composite, shallow SE‐dipping S1b foliation, and the development of tight recumbent F1b folds with S1‐parallel axial surfaces and asymmetries indicating NW‐directed thrusting. The preservation of a similar P–T–time record in the Fraser Complex (NE of the Coramup Gneiss) is consistent with large‐scale, NW‐directed Stage I thrusting of the Mawson Craton margin over the south‐eastern edge of the West Australian Craton. Stage II tectonism in the western Coramup Gneiss involved high‐T, low‐P M2a metamorphism and the formation of subvertical SE‐dipping D2 shear zones, shallow SW‐plunging L2 mineral stretching lineations, and NW‐verging F2 folds with S2‐parallel axial surfaces. A synkinematic pegmatite dyke emplaced into a D2 shear zone yielded a U–Pb SHRIMP zircon age of 1168 ± 12 Ma. Kinematic indicators suggest a combination of pure shear flattening perpendicular to S2, and dextral simple shear. However, contemporaneous structures elsewhere in the Albany–Fraser Orogen are consistent with continued NW–SE convergence at craton‐scale during Stage II, and oblique compression in the Coramup Gneiss is attributed to the arcuate geometry of the orogen‐scale deformation front.