Visual analytics in histopathology diagnostics: a protocol-based approach

Computer-Aided-Diagnosis (CAD) systems supporting the diagnostic process are widespread in radiology. Digital Pathology is still behind in the introduction of such solutions. Several studies investigated pathologists' behavior but only a few aimed to improve the diagnostic and report process with novel applications. In this work we designed and implemented a first protocol-based CAD viewer supported by visual analytics. The system targets the optimization of the diagnostic workflow in breast cancer diagnosis by means of three image analysis features that belong to the standard grading system (Nottingham Histologic Grade). A pathologist's routine was tracked during the examination of breast cancer tissue slides and diagnostic traces were analyzed from a qualitative perspective. Accordingly, a set of generic requirements was elicited to define the design and the implementation of the CAD-Viewer. A first qualitative evaluation conducted with five pathologists shows that the interface suffices the diagnostic workflow and diminishes the manual effort. We present promising evidence of the usefulness of our CAD-viewer and opportunities for its extension and integration in clinical practice. As a conclusion, the findings demonstrate that it is feasibile to optimize the Nottingham Grading workflow and, generally, the histological diagnosis by integrating computational pathology data with visual analytics techniques

Magnetic Helicity, Tilt, and Twist

The final publication is available at Springer via http://dx.doi.org/10.1007/s11214-014-0082-2Since its introduction to astro- and solar physics, the concept of helicity has proven to be useful in providing critical insights into physics of various processes from astrophysical dynamos, to magnetic reconnection and eruptive phenomena. Signature of helicity was also detected in many solar features, including orientation of solar active regions, or Joy’s law. Here we provide a summary of both solar phenomena and consider mutual relationship and its importance for the evolution of solar magnetic fields.European Union (European Social Fund—ESF)Greek national fundsScience and Technology Facilities Council (STFC)Hungarian Research grantsNAS

Generalized Drinfeld-Sokolov Reductions and KdV Type Hierarchies

Generalized Drinfeld-Sokolov (DS) hierarchies are constructed through local reductions of Hamiltonian flows generated by monodromy invariants on the dual of a loop algebra. Following earlier work of De Groot et al, reductions based upon graded regular elements of arbitrary Heisenberg subalgebras are considered. We show that, in the case of the nontwisted loop algebra $\ell(gl_n)$, graded regular elements exist only in those Heisenberg subalgebras which correspond either to the partitions of $n$ into the sum of equal numbers $n=pr$ or to equal numbers plus one $n=pr+1$. We prove that the reduction belonging to the grade $1$ regular elements in the case $n=pr$ yields the $p\times p$ matrix version of the Gelfand-Dickey $r$-KdV hierarchy, generalizing the scalar case $p=1$ considered by DS. The methods of DS are utilized throughout the analysis, but formulating the reduction entirely within the Hamiltonian framework provided by the classical r-matrix approach leads to some simplifications even for $p=1$.Comment: 43 page

A Comparison of Solar Cycle Variations in the Equatorial Rotation Rates of the Sun's Subsurface, Surface, Corona, and Sunspot Groups

Using the Solar Optical Observing Network (SOON) sunspot-group data for the period 1985-2010, the variations in the annual mean equatorial-rotation rates of the sunspot groups are determined and compared with the known variations in the solar equatorial-rotation rates determined from the following data: i) the plasma rotation rates at 0.94Rsun, 0.95Rsun,...,1.0Rsun measured by Global Oscillation Network Group (GONG) during the period 1995-2010, ii) the data on the soft X-ray corona determined from Yohkoh/SXT full disk images for the years 1992-2001, iii) the data on small bright coronal structures (SBCS) which were traced in Solar and Heliospheric Observatory (SOHO)/EIT images during the period 1998-2006, and iv) the Mount Wilson Doppler-velocity measurements during the period 1986-2007. A large portion (up to approximate 30 deg latitude) of the mean differential-rotation profile of the sunspot groups lies between those of the internal differential-rotation rates at 0.94Rsun and 0.98Rsun.The variation in the yearly mean equatorial-rotation rate of the sunspot groups seems to be lagging that of the equatorial-rotation rate determined from the GONG measurements by one to two years.The amplitude of the latter is very small.The solar-cycle variation in the equatorial-rotation rate of the solar corona closely matches that determined from the sunspot-group data.The variation in the equatorial-rotation rate determined from the Mount Wilson Doppler-velocity data closely resembles the corresponding variation in the equatorial-rotation rate determined from the sunspot-group data that included the values of the abnormal angular motions (> 3 deg per day) of the sunspot groups. Implications of these results are pointed out.Comment: 22 pages, 10 figures, accepted by Solar Physic

Systematic review of measurement properties of questionnaires measuring somatization in primary care patients

Objective The aim of this review is to critically appraise the evidence on measurement properties of self-report questionnaires measuring somatization in adult primary care patients and to provide recommendations about which questionnaires are most useful for this purpose. Methods We assessed the methodological quality of included studies using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklist. To draw overall conclusions about the quality of the questionnaires, we conducted an evidence synthesis using predefined criteria for judging the measurement properties. Results We found 24 articles on 9 questionnaires. Studies on the Patient Health Questionnaire-15 (PHQ-15) and the Four-Dimensional Symptom Questionnaire (4DSQ) somatization subscale prevailed and covered the broadest range of measurement properties. These questionnaires had the best internal consistency, test-retest reliability, structural validity, and construct validity. The PHQ-15 also had good criterion validity, whereas the 4DSQ somatization subscale was validated in several languages. The Bodily Distress Syndrome (BDS) checklist had good internal consistency and structural validity. Some evidence was found for good construct validity and criterion validity of the Physical Symptom Checklist (PSC-51) and good construct validity of the Symptom Check-List (SCL-90-R) somatization subscale. However, these three questionnaires were only studied in a small number of primary care studies. Conclusion Based on our findings, we recommend the use of either the PHQ-15 or 4DSQ somatization subscale for somatization in primary care. Other questionnaires, such as the BDS checklist, PSC-51 and the SCL-90-R somatization subscale show promising results but have not been studied extensively in primary care. © 2017 Elsevier Inc

An overview of the MHONGOOSE survey: Observing nearby galaxies with MeerKAT

MHONGOOSE is a deep survey of the neutral hydrogen distribution in a representative sample of 30 nearby disk and dwarf galaxies with HI masses from 10^6 to ~10^{11} M_sun, and luminosities from M_R ~ -12 to M_R ~ -22. The sample is selected to uniformly cover the available range in log(M_HI). Our extremely deep observations, down to HI column density limits of well below 10^{18} cm^{-2} - or a few hundred times fainter than the typical HI disks in galaxies - will directly detect the effects of cold accretion from the intergalactic medium and the links with the cosmic web. These observations will be the first ever to probe the very low-column density neutral gas in galaxies at these high resolutions. Combination with data at other wavelengths, most of it already available, will enable accurate modelling of the properties and evolution of the mass components in these galaxies and link these with the effects of environment, dark matter distribution, and other fundamental properties such as halo mass and angular momentum. MHONGOOSE can already start addressing some of the SKA-1 science goals and will provide a comprehensive inventory of the processes driving the transformation and evolution of galaxies in the nearby universe at high resolution and over 5 orders of magnitude in column density. It will be a Nearby Galaxies Legacy Survey that will be unsurpassed until the advent of the SKA, and can serve as a highly visible, lasting statement of MeerKAT's capabilities

LADUMA: looking at the distant universe with the MeerKAT array

The cosmic evolution of galaxies’ neutral atomic gas content is a major science driver for the Square Kilometre Array (SKA), as well as for its South African (MeerKAT) and Australian (ASKAP) precursors. Among the H I large survey programs (LSPs) planned for ASKAP and MeerKAT, the deepest and narrowest tier of the “wedding cake” will be defined by the combined L-band+UHF-band Looking At the Distant Universe with the MeerKAT Array (LADUMA) survey, which will probe H I in emission within a single “cosmic vuvuzela” that extends to z = 1.4, when the universe was only a third of its present age. Through a combination of individual and stacked detections (the latter relying on extensive multi-wavelength studies of the survey’s target field), LADUMA will study the redshift evolution of the baryonic Tully–Fisher relation and the cosmic H I density, the variation of the H I mass function with redshift and environment, and the connection between H I content and galaxies’ stellar properties (mass, age, etc.). The survey will also build a sample of OH megamaser detections that can be used to trace the cosmic merger history. This proceedings contribution provides a brief introduction to the survey, its scientific aims, and its technical implementation, deferring a more complete discussion for a future article after the implications of a recent review of MeerKAT LSP project plans are fully worked out

Bioinformatics methods for identifying candidate disease genes

Contains fulltext : 36076.pdf (publisher's version ) (Open Access)With the explosion in genomic and functional genomics information, methods for disease gene identification are rapidly evolving. Databases are now essential to the process of selecting candidate disease genes. Combining positional information with disease characteristics and functional information is the usual strategy by which candidate disease genes are selected. Enrichment for candidate disease genes, however, depends on the skills of the operating researcher. Over the past few years, a number of bioinformatics methods that enrich for the most likely candidate disease genes have been developed. Such in silico prioritisation methods may further improve by completion of datasets, by development of standardised ontologies across databases and species and, ultimately, by the integration of different strategies

Bioinformatics strategies for disease gene identification

Contains fulltext : 33210.pdf (publisher's version ) (Open Access)Disease gene identification based on chromosomal localisation is sometimes difficult and often time-consuming. It requires collecting as much information on the disease as possible. Combining positional information with disease characteristics might give hints by which candidate disease genes can be selected. Our hypothesis was that internet databases, which contain gene specific data as well as databases that contain phenotype descriptions, can be utilized systematically for identification of disease genes. We present two bioinformatics strategies that are able to identify human candidate disease genes and classify human disease phenotypes.Phenotype analysis is equally relevant to disease gene identification as it is to the functional annotation of the human genome: Over the course of the coming years major improvements are to be expected with regard to gene identification methods for monogenic, and multifactorial diseases, mutation detection, and various methods for cross-species comparisons. Bioinformatics approaches such as those described here, should be a useful addition to sequence and gene-based analyses. While much remains to be discovered from systematic phenotype-genotype analyses, an essential prerequisite will be the development of a standardized and internationally agreed nomenclature for phenotype definition that is applicable to humans as well as to the major model organisms that are in use today.RU Radboud Universiteit Nijmegen, 28 november 2005Promotores : Vriend, G., Brunner, H.G. Co-promotor : Leunissen, J.A.M.160 p

Bioinformatics methods for identifying candidate disease genes.

With the explosion in genomic and functional genomics information, methods for disease gene identification are rapidly evolving. Databases are now essential to the process of selecting candidate disease genes. Combining positional information with disease characteristics and functional information is the usual strategy by which candidate disease genes are selected. Enrichment for candidate disease genes, however, depends on the skills of the operating researcher. Over the past few years, a number of bioinformatics methods that enrich for the most likely candidate disease genes have been developed. Such in silico prioritisation methods may further improve by completion of datasets, by development of standardised ontologies across databases and species and, ultimately, by the integration of different strategies