Enhanced Operational Semantics in Systems Biology

We are faced with a great challenge: the cross-fertilization between the fields of formal methods for concurrency, in the computer science domain, and systems biology in the biological realm

Disease management of leek rust : a study at field, farm and regional level

Leek rust, caused by Puccinia allii Rud., is an important disease of leek ( Allium porrum L.) in the Netherlands. The quality decrease of the product associated with a light infestation of leek rust may cause severe economic loss to the grower. The aim of this study is to develop an improved pathosystem management for leek rust at field, farm and regional level with low use of fungicides, through preventive measures and supervised control based on sampling for detection.Basic temporal and spatial characteristics of leek rust epidemics were studied under field conditions and after natural infection. The spatial distribution of diseased plants during three naturally occurring epidemics of leek rust was analysed with the Black-White join-count statistic. The spatial distribution of rust-infected leek plants was different for each of the three epidemics, ranging from random to highly clustered. The growth of leek rust epidemics in time under favourable conditions in three leek cultivars during two years was studied. In both years, the highest disease levels were found on cultivar Albana, followed by Carina and Cortina. A simple model is presented to correct the results for exchange of inoculum between adjacent plots. The results of this model indicate, that the difference in rust infection between the cultivars may be due to a reduced growth of the epidemic in young plants of cultivars Cortina and Carina. In older plants, the ranking in susceptibility was reversed, causing a less pronounced difference in infection between the cultivars. The growth of leek rust epidemics during the early stage of the epidemic in isolated plots was satisfactorily described by an exponential model.Monte Carlo simulation was used to compare simple sampling patterns in their efficiency of detecting diseased plants under a variety of spatial distributions. Row sampling over four rows has been identified as the most effective sampling pattern. The detection level, i.e. the lowest disease level at which the probability to detect the disease is sufficiently large, was studied in relation with temporal and spatial characteristics of the disease. The calculations indicate, that a weekly sample of 50 plants resulted in detection levels, that were low enough to ensure adequate chemical control, indicating the feasibility of sampling for detection of leek rust.A model is presented to simulate the number of fungicide sprays against leek rust under the proposed system of supervised control, including the spread of the disease between fields in one farm and the influx of spores from outside the farm. The possible reduction in fungicide sprays against leek rust due to various preventive measures are estimated with this model. The results of this preliminary model suggest, that supervised control of leek rust can result in a considerable reduction in the number of fungicide sprays, but only if the leek fields in a farm are sufficiently isolated and care is taken that the planting material is free from the disease. if it is not possible to increase the isolation between the fields, overlap between successive crops should be avoided.Based on a simple metapopulation model, it is argued, that the possible effect of certification of planting material on the occurrence of leek rust in a region can be derived from information on the proportion of infected fields ( v ) and the proportion of newly planted fields with infected planting material ( i ) in that region. If v ≤ Vi , certification of planting material will be highly effective and may even cause the complete eradication of leek rust from the region.A differentiated regional policy of leek rust management is proposed, dependent on the intensity of leek cultivation in a region. To validate the proposed strategies on field, farm and regional level, a survey of the actual disease situation in several farms in different regions is necessary. This study indicates the importance of parameters, that are rarely measured in disease surveys, such as the distance between crops in a farm and in a region and the infection level of planting material

Штанги для горизонтально направленного бурения

В статті наведено технічні дані про конструкцію та експлуатаційні вимоги до бурових штанг горизонтально спрямованого буріння свердловин

A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass

<p>Abstract</p> <p>Background</p> <p>Less than 25% of patients with a pelvic mass who are presented to a gynecologist will eventually be diagnosed with epithelial ovarian cancer. Since there is no reliable test to differentiate between different ovarian tumors, accurate classification could facilitate adequate referral to a gynecological oncologist, improving survival. The goal of our study was to assess the potential value of a SELDI-TOF-MS based classifier for discriminating between patients with a pelvic mass.</p> <p>Methods</p> <p>Our study design included a well-defined patient population, stringent protocols and an independent validation cohort. We compared serum samples of 53 ovarian cancer patients, 18 patients with tumors of low malignant potential, and 57 patients with a benign ovarian tumor on different ProteinChip arrays. In addition, from a subset of 84 patients, tumor tissues were collected and microdissection was used to isolate a pure and homogenous cell population.</p> <p>Results</p> <p>Diagonal Linear Discriminant Analysis (DLDA) and Support Vector Machine (SVM) classification on serum samples comparing cancer versus benign tumors, yielded models with a classification accuracy of 71-81% (cross-validation), and 73-81% on the independent validation set. Cancer and benign tissues could be classified with 95-99% accuracy using cross-validation. Tumors of low malignant potential showed protein expression patterns different from both benign and cancer tissues. Remarkably, none of the peaks differentially expressed in serum samples were found to be differentially expressed in the tissue lysates of those same groups.</p> <p>Conclusion</p> <p>Although SELDI-TOF-MS can produce reliable classification results in serum samples of ovarian cancer patients, it will not be applicable in routine patient care. On the other hand, protein profiling of microdissected tumor tissue may lead to a better understanding of oncogenesis and could still be a source of new serum biomarkers leading to novel methods for differentiating between different histological subtypes.</p

Progressive damage on high resolution computed tomography despite stable lung function in cystic fibrosis

For effective clinical management of cystic fibrosis (CF) lung disease it is important to closely monitor the start and progression of lung damage. The aim of this study was to investigate the ability of high-resolution computed tomography (HRCT) scoring systems and pulmonary function tests (PFT) to detect changes in lung disease. CF children (n=48) had two H

Two major QTLs on chr. 2BL and 3BS influence grain yield in durum wheat across a broad range of water regimes

Cellular mechanisms in basic and clinical gastroenterology and hepatolog

Structure, mass and stability of galactic disks

In this review I concentrate on three areas related to structure of disks in spiral galaxies. First I will review the work on structure, kinematics and dynamics of stellar disks. Next I will review the progress in the area of flaring of HI layers. These subjects are relevant for the presence of dark matter and lead to the conclusion that disk are in general not `maximal', have lower M/L ratios than previously suspected and are locally stable w.r.t. Toomre's Q criterion for local stability. I will end with a few words on `truncations' in stellar disks.Comment: Invited review at "Galaxies and their Masks" for Ken Freeman's 70-th birthday, Sossusvlei, Namibia, April 2010. A version with high-res. figures is available at http://www.astro.rug.nl/~vdkruit/jea3/homepage/Namibiachapter.pd