Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.

The comprehensiveness of the ESHRE/ESGE classification of female genital tract congenital anomalies: a systematic review of cases not classified by the AFS system.

STUDY QUESTION How comprehensive is the recently published European Society of Human Reproduction and Embryology (ESHRE)/European Society for Gynaecological Endoscopy (ESGE) classification system of female genital anomalies? SUMMARY ANSWER The ESHRE/ESGE classification provides a comprehensive description and categorization of almost all of the currently known anomalies that could not be classified properly with the American Fertility Society (AFS) system. WHAT IS KNOWN ALREADY Until now, the more accepted classification system, namely that of the AFS, is associated with serious limitations in effective categorization of female genital anomalies. Many cases published in the literature could not be properly classified using the AFS system, yet a clear and accurate classification is a prerequisite for treatment. STUDY DESIGN, SIZE AND DURATION The CONUTA (CONgenital UTerine Anomalies) ESHRE/ESGE group conducted a systematic review of the literature to examine if those types of anomalies that could not be properly classified with the AFS system could be effectively classified with the use of the new ESHRE/ESGE system. An electronic literature search through Medline, Embase and Cochrane library was carried out from January 1988 to January 2014. Three participants independently screened, selected articles of potential interest and finally extracted data from all the included studies. Any disagreement was discussed and resolved after consultation with a fourth reviewer and the results were assessed independently and approved by all members of the CONUTA group. PARTICIPANTS/MATERIALS, SETTING, METHODS Among the 143 articles assessed in detail, 120 were finally selected reporting 140 cases that could not properly fit into a specific class of the AFS system. Those 140 cases were clustered in 39 different types of anomalies. MAIN RESULTS AND THE ROLE OF CHANCE The congenital anomaly involved a single organ in 12 (30.8%) out of the 39 types of anomalies, while multiple organs and/or segments of Müllerian ducts (complex anomaly) were involved in 27 (69.2%) types. Uterus was the organ most frequently involved (30/39: 76.9%), followed by cervix (26/39: 66.7%) and vagina (23/39: 59%). In all 39 types, the ESHRE/ESGE classification system provided a comprehensive description of each single or complex anomaly. A precise categorization was reached in 38 out of 39 types studied. Only one case of a bizarre uterine anomaly, with no clear embryological defect, could not be categorized and thus was placed in Class 6 (un-classified) of the ESHRE/ESGE system. LIMITATIONS, REASONS FOR CAUTION The review of the literature was thorough but we cannot rule out the possibility that other defects exist which will also require testing in the new ESHRE/ESGE system. These anomalies, however, must be rare. WIDER IMPLICATIONS OF THE FINDINGS The comprehensiveness of the ESHRE/ESGE classification adds objective scientific validity to its use. This may, therefore, promote its further dissemination and acceptance, which will have a positive outcome in clinical care and research. STUDY FUNDING/COMPETING INTERESTS None.

An analysis of two methods for the classification of stage of readiness to obtain repeat mammography screening

Background and purpose: Breast cancer continues to be a health problem for women, representing 28 percent of all female cancers and remaining one of the leading causes of death for women. Breast cancer incidence rates become substantial before the age of 50. After menopause, breast cancer incidence rates continue to increase with age creating a long-lasting source of concern (Harris et al., 1992). Mammography, a technique for the detection of breast tumors in their nonpalpable stage when they are most curable, has taken on considerable importance as a public health measure. The lifetime risk of breast cancer is approximately 1 in 9 and occurs over many decades. Recommendations are that screening be periodic in order to detect cancer at early stages. These recommendations, largely, are not followed. Not only are most women not getting regular mammograms, but this circumstance is particularly the case among older women where regular mammography has been proven to reduce mortality by approximately 30 percent. The purpose of this project was to increase our understanding of factors that are associated with stage of readiness to obtain subsequent mammograms. A secondary purpose of this research was to suggest further conceptual considerations toward the extension of the Transtheoretical Model (TTM) of behavior change to repeat screening mammography. ^ Methods. A sample (n = 1,222) of women 50 years and older in a large multi-specialty clinic in Houston, Texas was surveyed by mail questionnaire regarding their previous screening experience and stage of readiness to obtain repeat screening. A computerized database, maintained on all women who undergo mammography at the clinic, was used to identify women who are eligible for the project. The major statistical technique employed to select the significant variables and to examine the man and interaction effects of independent variables on dependent variables was polychotomous stepwise, logistic regression. A prediction model for each stage of readiness definition was estimated. The expected probabilities for stage of readiness were calculated to assess the magnitude and direction of significant predictors. ^ Results. Analysis showed that both ways of defining stage of readiness for obtaining a screening mammogram were associated with specific constructs, including decisional balance and processes of the change. ^ Conclusions. The results of the present study demonstrate that the TTM appears to translate to repeat mammography screening. Findings in the current study also support finding of previous studies that suggest that stage of readiness is associated with respondent decisional balance and the processes of change. ^

The Effect of Deleting Anchor on the Classification of Examinees

The presence of outlying anchor items is an issue faced by many testing agencies. This study examines the effect of removing or retaining one aberrant anchor item. The degree of aberrancy was manipulated as well as the ability distribution of examinees, and four IRT scaling methods were investigated (Mean-sigma, mean-mean, Stocking & Lord, and Haebara). The results indicate that the percent of correctly classified students was not affected by either retaining or removing the aberrant item, although the over- and under- classification of examinees was. There was no difference among the methods.

Classification of cellular malignancy associated changes in cervical cancer

Cervical cancer is the leading cause of death and disease from malignant neoplasms among women in developing countries. Even though the Pap smear has significantly decreased the number of deaths from cervical cancer in the past years, it has its limitations. Researchers have developed an automated screening machine which can potentially detect abnormal cases that are overlooked by conventional screening. The goal of quantitative cytology is to classify the patient's tissue sample based on quantitative measurements of the individual cells. It is also much cheaper and potentially can take less time. One of the major challenges of collecting cells with a cytobrush is the possibility of not sampling any existing dysplastic cells on the cervix. Being able to correctly classify patients who have disease without the presence of dysplastic cells could improve the accuracy of quantitative cytology algorithms. Subtle morphologic changes in normal-appearing tissues adjacent to or distant from malignant tumors have been shown to exist, but a comparison of various statistical methods, including many recent advances in the statistical learning field, has not previously been done. The objective of this thesis is to use different classification methods applied to quantitative cytology data for the detection of malignancy associated changes (MACs). In this thesis, Elastic Net is the best algorithm. When we applied the Elastic Net algorithm to the test set, we combined the training set and validation set as "training" set and used 5-fold cross validation to choose the parameter for Elastic Net. It has a sensitivity of 47% at 80% specificity, an AUC 0.52, and a partial AUC 0.10 (95% CI 0.09-0.11).^

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

International Collection of JGOFS (Joint Global Ocean Flux Study), Volume 2: Integrated Data Sets (1989-2003)

The JGOFS International Collection Volume 2: Integrated Data Sets CD is a coherent, organised compilation of existing data sets produced by member countries which participated in JGOFS. In most cases, the data were gathered from the JGOFS International Collection, Volume 1: Discrete Datasets DVD. To produce Vol. 1 data were taken from the original sources and copied "as is" on the DVD. For Vol. 2 data and metadata have been harmonized using the conversion software PanTool and the import routine of PANGAEA checking for completeness of metadata and defining the relations between data and metadata. Prior to the import, data had performed a technical quality control, i.e. format and readability of the file, availability and combination of parameters and units, range of values.

Contextual classification of full waveform lidar data in the Wadden Sea

The classification of airborne lidar data is a relevant task in different disciplines. The information about the geometry and the full waveform can be used in order to classify the 3D point cloud. In Wadden Sea areas the classification of lidar data is of main interest for the scientific monitoring of coastal morphology and habitats, but it becomes a challenging task due to flat areas with hardly any discriminative objects. For the classification we combine a Conditional Random Fields framework with a Random Forests approach. By classifying in this way, we benefit from the consideration of context on the one hand and from the opportunity to utilise a high number of classification features on the other hand. We investigate the relevance of different features for the lidar points in coastal areas as well as for the interaction of neighbouring points.