SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Background The cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives

Adherence to Guidelines for Adult (Non-GIST) Soft Tissue Sarcoma in the Netherlands: A Plea for Dedicated Sarcoma Centers

Introduction: Optimal management of soft tissue sarcoma (STS) remains a challenge. A nationwide survey assessed the quality of STS care in the Netherlands, thereby aiming to identify potentialities for improvement through more centralized disease management. Methods: From the Netherlands Cancer Registry (NCR), data were obtained on 3317 adult STS patients (excluding gastrointestinal stromal tumor, GIST) diagnosed in 2006–2011. Logistic regression models were employed to compare outcomes on selected clinical indicators reflecting prevailing STS guidelines between high-volume (≥10 resections annually) and low-volume (<10 resections) hospitals, between academic and general hospitals, and between sarcoma research centers and other hospitals, adjusted for case mix. Analyses were performed on imputed datasets (m = 50), generated through multiple imputations by chained equations. Results: Overall, 89% of patients underwent surgical resection. Resection status remained unknown in 24% (excluding those with metastasized disease), and grade was not documented for one-third of tumors. Microscopic residual disease was detected in 20% with an increased risk for older patients, larger and deeply located tumors, and those located in the (retro)peritoneum or upper extremity. Almost half of patients with an R1 resection re

Analytic models of plausible gravitational lens potentials

Gravitational lenses on galaxy scales are plausibly modelled as having ellipsoidal symmetry and a universal dark matter density profile, with a Sersic profile to describe the distribution of baryonic matter. Predicting all lensing effects requires knowledge of the total lens potential: in this work we give analytic forms for that of the above hybrid model. Emphasising that complex lens potentials can be constructed from simpler components in linear combination, we provide a recipe for attaining elliptical symmetry in either projected mass or lens potential. We also provide analytic formulae for the lens potentials of Sersic profiles for integer and half-integer index. We then present formulae describing the gravitational lensing effects due to smoothly-truncated universal density profiles in cold dark matter model. For our isolated haloes the density profile falls off as radius to the minus fifth or seventh power beyond the tidal radius, functional forms that allow all orders of lens potential derivatives to be calculated analytically, while ensuring a non-divergent total mass. We show how the observables predicted by this profile differ from that of the original infinite-mass NFW profile. Expressions for the gravitational flexion are highlighted. We show how decreasing the tidal radius allows stripped haloes to be modelled, providing a framework for a fuller investigation of dark matter substructure in galaxies and clusters. Finally we remark on the need for finite mass halo profiles when doing cosmological ray-tracing simulations, and the need for readily-calculable higher order derivatives of the lens potential when studying catastrophes in strong lenses.Comment: 24 pages, 10 figures, matches published versio

Indirect search for dark matter: prospects for GLAST

Possible indirect detection of neutralino, through its gamma-ray annihilation product, by the forthcoming GLAST satellite from our galactic halo, M31, M87 and the dwarf galaxies Draco and Sagittarius is studied. Gamma-ray fluxes are evaluated for the two representative energy thresholds, 0.1 GeV and 1.0 GeV, at which the spatial resolution of GLAST varies considerably. Apart from dwarfs which are described either by a modified Plummer profile or by a tidally-truncated King profiles, fluxes are compared for halos with central cusps and cores. It is demonstrated that substructures, irrespective of their profiles, enhance the gamma-ray emission only marginally. The expected gamma-ray intensity above 1 GeV at high galactic latitudes is consistent with the residual emission derived from EGRET data if the density profile has a central core and the neutralino mass is less than 50 GeV, whereas for a central cusp only a substantial enhancement would explain the observations. From M31, the flux can be detected above 0.1 GeV and 1.0 GeV by GLAST only if the neutralino mass is below 300 GeV and if the density profile has a central cusp, case in which a significant boost in the gamma-ray emission is produced by the central black hole. For Sagittarius, the flux above 0.1 GeV is detectable by GLAST provided the neutralino mass is below 50 GeV. From M87 and Draco the fluxes are always below the sensitivity limit of GLAST.Comment: 14 Pages, 7 Figures, 3 Tables, version to appear on Physical Review

Validity of the self-administered comorbidity questionnaire in patients with inflammatory bowel disease

Background: The International Consortium for Health Outcomes Measurement has selected the self-administered comorbidity questionnaire (SCQ) to adjust case-mix when comparing outcomes of inflammatory bowel disease (IBD) treatment between healthcare providers. However, the SCQ has not been validated for use in IBD patients. Objectives: We assessed the validity of the SCQ for measuring comorbidities in IBD patients. Design: Cohort study. Methods: We assessed the criterion validity of the SCQ for IBD patients by comparing patient-reported and clinician-reported comorbidities (as noted in the electronic health record) of the 13 diseases of the SCQ using Cohen’s kappa. Construct validity was assessed using the Spearman correlation coefficient between the SCQ and the Charlson Comorbidity Index (CCI), clinician-reported SCQ, quality of life, IBD-related healthcare and productivity costs, prevalence of disability, and IBD disease activity. We assessed responsiveness by correlating changes in the SCQ with changes in healthcare costs, productivity costs, quality of life, and disease activity after 15 months. Results: We included 613 patients. At least fair agreement (κ &gt; 0.20) was found for most comorbidities, but the agreement was slight (κ &lt; 0.20) for stomach disease [κ = 0.19, 95% CI (−0.03; 0.41)], blood disease [κ = 0.02, 95% CI (−0.06; 0.11)], and back pain [κ = 0.18, 95% CI (0.11; 0.25)]. Correlations were found between the SCQ and the clinician-reported SCQ [ρ = 0.60, 95% CI (0.55; 0.66)], CCI [ρ = 0.39, 95% CI (0.31; 0.45)], the prevalence of disability [ρ = 0.23, 95% CI (0.15; 0.32)], and quality of life [ρ = −0.30, 95% CI (−0.37; −0.22)], but not between the SCQ and healthcare or productivity costs or disease activity (|ρ| ⩽ 0.2). A change in the SCQ after 15 months was not correlated with a change in any of the outcomes.Conclusion: The SCQ is a valid tool for measuring comorbidity in IBD patients, but face and content validity should be improved before being used to correct case-mix differences.</p