Descriptive Data in the EDIT Platform for Cybertaxonomy

This paper describes the integration of structured descriptive data in the EDIT platform for Cybertaxonomy. The platform is composed of several software modules supporting the taxonomic workflow from data capture and storage to publication. Descriptive data play an important role within the taxonomic work process. The integration of these data via import/export modules to and from the platform and the publication as natural language output or as keys are explained

Toward a service-based workflow for automated information extraction from herbarium specimens

Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses. The evolving system presently covers the generation of optical character recognition (OCR) from specimen images, the identification of regions of interest in images and the extraction of meaningful information items from OCR. These implementations were developed as part of the Deutsche Forschungsgemeinschaft-funded a standardised and optimised process for data acquisition from digital images of herbarium specimens (StanDAP-Herb) Project

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.

BACKGROUND: Genetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups. RESULTS: A small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P < 0.001); large regions that differed were found on chromosomes 2 and 6. Haplotype blocks inferred from pairwise linkage disequilibrium (LD) statistics (Haploview) as well as by expectation-maximization haplotype phase inference (HAP) showed a greater number of haplotype blocks in AJ compared to CEU by Haploview (50,397 vs. 44,169) or by HAP (59,269 vs. 54,457). Average haplotype blocks were smaller in AJ compared to CEU (e.g., 36.8 kb vs. 40.5 kb HAP). Analysis of global patterns of local LD decay for closely-spaced SNPs in CEU demonstrated more LD, while for SNPs further apart, LD was slightly greater in the AJ. A likelihood ratio approach showed that runs of homozygous SNPs were approximately 20% longer in AJ. A principal components analysis was sufficient to completely resolve the CEU from the AJ. CONCLUSION: LD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure

Service-based information extraction from herbarium specimens

On herbarium sheets, data elements such as plant name, collection site, collector, barcode and accession number are found mostly on labels glued to the sheet. The data are thus visible on specimen images. With continuously improving technologies for collection mass-digitisation it has become easier and easier to produce high quality images of herbarium sheets and in the last few years herbarium collections worldwide have started to digitize specimens on an industrial scale (Tegelberg et al. 2014). To use the label data contained in these massive numbers of images, they have to be captured and databased. Currently, manual data entry prevails and forms the principal cost and time limitation in the digitization process. The StanDAP-Herb Project has developed a standard process for (semi-) automatic detection of data on herbarium sheets. This is a formal extensible workflow integrating a wide range of automated specimen image analysis services, used to replace time-consuming manual data input as far as possible. We have created web-services for OCR (Optical Character Recognition); for identifying regions of interest in specimen images and for the context-sensitive extraction of information from text recognized by OCR. We implemented the workflow as an extension of the OpenRefine platform (Verborgh and De Wilde 2013)

Clinical practice recommendations for the diagnosis and management of X-linked hypophosphataemia

X-linked hypophosphataemia (XLH) is the most common cause of inherited phosphate wasting and is associated with severe complications such as rickets, lower limb deformities, pain, poor mineralization of the teeth and disproportionate short stature in children as well as hyperparathyroidism, osteomalacia, enthesopathies, osteoarthritis and pseudofractures in adults. The characteristics and severity of XLH vary between patients. Because of its rarity, the diagnosis and specific treatment of XLH are frequently delayed, which has a detrimental effect on patient outcomes. In this Evidence-Based Guideline, we recommend that the diagnosis of XLH is based on signs of rickets and/or osteomalacia in association with hypophosphataemia and renal phosphate wasting in the absence of vitamin D or calcium deficiency. Whenever possible, the diagnosis should be confirmed by molecular genetic analysis or measurement of levels of fibroblast growth factor 23 (FGF23) before treatment. Owing to the multisystemic nature of the disease, patients should be seen regularly by multidisciplinary teams organized by a metabolic bone disease expert. In this article, we summarize the current evidence and provide recommendations on features of the disease, including new treatment modalities, to improve knowledge and provide guidance for diagnosis and multidisciplinary care.status: publishe

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.

BackgroundGenetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups.ResultsA small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P &lt; 0.001); large regions that differed were found on chromosomes 2 and 6. Haplotype blocks inferred from pairwise linkage disequilibrium (LD) statistics (Haploview) as well as by expectation-maximization haplotype phase inference (HAP) showed a greater number of haplotype blocks in AJ compared to CEU by Haploview (50,397 vs. 44,169) or by HAP (59,269 vs. 54,457). Average haplotype blocks were smaller in AJ compared to CEU (e.g., 36.8 kb vs. 40.5 kb HAP). Analysis of global patterns of local LD decay for closely-spaced SNPs in CEU demonstrated more LD, while for SNPs further apart, LD was slightly greater in the AJ. A likelihood ratio approach showed that runs of homozygous SNPs were approximately 20% longer in AJ. A principal components analysis was sufficient to completely resolve the CEU from the AJ.ConclusionLD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure

Educational and occupational outcomes of childhood cancer survivors 30 ă years after diagnosis: a French cohort study

International audienceBackground: Although survival from childhood cancer has increased, ă little is known on the long-term impact of treatment late effects on ă occupational attainment or work ability. ă Methods: A total of 3512 five-year survivors treated before the age of ă 19 years in 10 French cancer centres between 1948 and 2000 were ă identified. Educational level, employment status and occupational class ă of survivors were assessed by a self-reported questionnaire. These ă outcome measures were compared with sex-age rates recorded in the French ă population, using indirect standardisation. Paternal occupational class ă was also considered to control for the role of survivors' socioeconomic ă background on their achievement. Multivariable analyses were conducted ă to explore clinical characteristics associated with the outcomes. ă Results: A total of 2406 survivors responded to the questionnaire and ă survivors aged below 25 years were included in the current analysis. ă Compared with national statistics adjusted on age and sex, male ă survivors were more likely to be college graduates (39.2% vs 30.9% ă expected; P<0.001). This higher achievement was not observed either for ă leukaemia or central nervous system (CNS) tumour survivors. ă Health-related unemployment was higher for survivors of CNS tumour ă (28.1% vs 4.3%; P<0.001) but not for survivors of other diagnoses. ă Survivors of non-CNS childhood cancer had a similar or a higher ă occupational class than expected. ă Conclusions: Survivors treated for CNS tumour or leukaemia, especially ă when treatment included cranial irradiation, might need support ă throughout their lifespan

Susceptibility Loci Associated with Specific and Shared Subtypes of Lymphoid Malignancies

<div><p>The genetics of lymphoma susceptibility reflect the marked heterogeneity of diseases that comprise this broad phenotype. However, multiple subtypes of lymphoma are observed in some families, suggesting shared pathways of genetic predisposition to these pathologically distinct entities. Using a two-stage GWAS, we tested 530,583 SNPs in 944 cases of lymphoma, including 282 familial cases, and 4,044 public shared controls, followed by genotyping of 50 SNPs in 1,245 cases and 2,596 controls. A novel region on 11q12.1 showed association with combined lymphoma (LYM) subtypes. SNPs in this region included rs12289961 near <em>LPXN</em>, (P_LYM = 3.89×10⁻⁸, OR = 1.29) and rs948562 (P_LYM = 5.85×10⁻⁷, OR = 1.29). A SNP in a novel non-HLA region on 6p23 (rs707824, P_NHL = 5.72×10⁻⁷) was suggestive of an association conferring susceptibility to lymphoma. Four SNPs, all in a previously reported HLA region, 6p21.32, showed genome-wide significant associations with follicular lymphoma. The most significant association with follicular lymphoma was for rs4530903 (P_FL = 2.69×10⁻¹², OR = 1.93). Three novel SNPs near the HLA locus, rs9268853, rs2647046, and rs2621416, demonstrated additional variation contributing toward genetic susceptibility to FL associated with this region. Genes implicated by GWAS were also found to be cis-eQTLs in lymphoblastoid cell lines; candidate genes in these regions have been implicated in hematopoiesis and immune function. These results, showing novel susceptibility regions and allelic heterogeneity, point to the existence of pathways of susceptibility to both shared as well as specific subtypes of lymphoid malignancy.</p> </div