the rare bone disorders use case

Background Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possibility of multiple communities building, in parallel, conceptualisations of the same domain, and thus providing slightly different perspectives on the same knowledge. The individual nature of this effort leads to the need of a mechanism to enable us to create an overarching and comprehensive overview of the different perspectives on the domain knowledge. Results We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource. To accurately track the original knowledge statements, we record the provenance at very granular levels. We exemplify the approach in the rare bone disorders domain by proposing the Rare Bone Disorders Ontology (RBDO). Using RBDO, researchers are able to answer queries, such as: “What phenotypes describe a particular disorder and are common to all sources?” or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources

Analysis of continuous neuronal activity evoked by natural speech with computational corpus linguistics methods

In the field of neurobiology of language, neuroimaging studies are generally based on stimulation paradigms consisting of at least two different conditions. Designing those paradigms can be very time-consuming and this traditional approach is necessarily data-limited. In contrast, in computational and corpus linguistics, analyses are often based on large text corpora, which allow a vast variety of hypotheses to be tested by repeatedly re-evaluating the data set. Furthermore, text corpora also allow exploratory data analysis in order to generate new hypotheses. By drawing on the advantages of both fields, neuroimaging and computational corpus linguistics, we here present a unified approach combining continuous natural speech and MEG to generate a corpus of speech-evoked neuronal activity

Evolutionary Comparison Provides Evidence for Pathogenicity of RMRP Mutations

Cartilage-hair hypoplasia (CHH) is a pleiotropic disease caused by recessive mutations in the RMRP gene that result in a wide spectrum of manifestations including short stature, sparse hair, metaphyseal dysplasia, anemia, immune deficiency, and increased incidence of cancer. Molecular diagnosis of CHH has implications for management, prognosis, follow-up, and genetic counseling of affected patients and their families. We report 20 novel mutations in 36 patients with CHH and describe the associated phenotypic spectrum. Given the high mutational heterogeneity (62 mutations reported to date), the high frequency of variations in the region (eight single nucleotide polymorphisms in and around RMRP), and the fact that RMRP is not translated into protein, prediction of mutation pathogenicity is difficult. We addressed this issue by a comparative genomic approach and aligned the genomic sequences of RMRP gene in the entire class of mammals. We found that putative pathogenic mutations are located in highly conserved nucleotides, whereas polymorphisms are located in non-conserved positions. We conclude that the abundance of variations in this small gene is remarkable and at odds with its high conservation through species; it is unclear whether these variations are caused by a high local mutation rate, a failure of repair mechanisms, or a relaxed selective pressure. The marked diversity of mutations in RMRP and the low homozygosity rate in our patient population indicate that CHH is more common than previously estimated, but may go unrecognized because of its variable clinical presentation. Thus, RMRP molecular testing may be indicated in individuals with isolated metaphyseal dysplasia, anemia, or immune dysregulation

Building in China - Study trip of the faculty of Civil Engineering of the HTWG Konstanz 2008

Im März 2008 führte die Fakultät Bauingenieurwesen der HTWG Konstanz eine studentische Exkursion nach China durch. Auf dem Programm standen interessante Baustellen Shanghai, Nanjing, Zhenjiang und Beijing sowie der Besuch von Hochschulen. Der Exkursionsbericht beschreibt die besuchten Bauvorhaben und gibt persönliche Eindrücke der Exkursionsteilnehmer wieder.In March 2008 the faculty of civil engineering of the University of Applied Sciences Konstanz, Germany, conducted a study trip for students of civil engineering to China. Construction sites and universities in Shanghai, Nanjing, Zhenjiang and Beijing have been visited. The report describes the places seen and reflects the personal impressions of the participants

TRPV4 related skeletal dysplasias: a phenotypic spectrum highlighted byclinical, radiographic, and molecular studies in 21 new families

Extent: 8p.Background: The TRPV4 gene encodes a calcium-permeable ion-channel that is widely expressed, responds to many different stimuli and participates in an extraordinarily wide range of physiologic processes. Autosomal dominant brachyolmia, spondylometaphyseal dysplasia Kozlowski type (SMDK) and metatropic dysplasia (MD) are currently considered three distinct skeletal dysplasias with some shared clinical features, including short stature, platyspondyly, and progressive scoliosis. Recently, TRPV4 mutations have been found in patients diagnosed with these skeletal phenotypes. Methods and Results: We critically analysed the clinical and radiographic data on 26 subjects from 21 families, all of whom had a clinical diagnosis of one of the conditions described above: 15 with MD; 9 with SMDK; and 2 with brachyolmia. We sequenced TRPV4 and identified 9 different mutations in 22 patients, 4 previously described, and 5 novel. There were 4 mutation-negative cases: one with MD and one with SMDK, both displaying atypical clinical and radiographic features for these diagnoses; and two with brachyolmia, who had isolated spine changes and no metaphyseal involvement. Conclusions: Our data suggest the TRPV4 skeletal dysplasias represent a continuum of severity with areas of phenotypic overlap, even within the same family. We propose that AD brachyolmia lies at the mildest end of this spectrum and, since all cases described with this diagnosis and TRPV4 mutations display metaphyseal changes, we suggest that it is not a distinct entity but represents the mildest phenotypic expression of SMDK.Elena Andreucci, Salim Aftimos, Melanie Alcausin, Eric Haan, Warwick Hunter, Peter Kannu, Bronwyn Kerr, George McGillivray, RJ McKinlay Gardner, Maria G Patricelli, David Sillence, Elizabeth Thompson, Margaret Zacharin, Andreas Zankl, Shireen R Lamandé and Ravi Savariraya

Accuracy Bounds and Measurements of a Contactless Permittivity Sensor for Gases Using Synchronized Low-Cost mm-Wave Frequency Modulated Continuous Wave Radar Transceivers

A primary concern in a multitude of industrial processes is the precise monitoring of gaseous substances to ensure proper operating conditions. However, many traditional technologies are not suitable for operation under harsh environmental conditions. Radar-based time-of-flight permittivity measurements have been proposed as alternative but suffer from high cost and limited accuracy in highly cluttered industrial plants. This paper examines the performance limits of low-cost frequency-modulated continuous-wave (FMCW) radar sensors for permittivity measurements. First, the accuracy limits are investigated theoretically and the Cramér-Rao lower bounds for time-of-flight based permittivity and concentration measurements are derived. In addition, Monte-Carlo simulations are carried out to validate the analytical solutions. The capabilities of the measurement concept are then demonstrated with different binary gas mixtures of Helium and Carbon Dioxide in air. A low-cost time-of-flight sensor based on two synchronized fully-integrated millimeter-wave (MMW) radar transceivers is developed and evaluated. A method to compensate systematic deviations caused by the measurement setup is proposed and implemented. The theoretical discussion underlines the necessity of exploiting the information contained in the signal phase to achieve the desired accuracy. Results of various permittivity and gas concentration measurements are in good accordance to reference sensors and measurements with a commercial vector network analyzer (VNA). In conclusion, the proposed radar-based low-cost sensor solution shows promising performance for the intended use in demanding industrial applications

Multicentric Carpotarsal Osteolysis Is Caused by Mutations Clustering in the Amino-Terminal Transcriptional Activation Domain of MAFB

(The American Journal of Human Genetics, 90, 494–501; March 9, 2012)\ud In the published version of this article, the amino acid alteration caused by c.161C>T should have been notated as\ud p.Ser54Leu and not p.Pro54Leu. The wild-type amino acid is incorrectly notated in the main text, in Table 2, and in\ud Figure 4. The authors regret this error. Additionally, The Journal regrets that this erratum, originally requested in 2012,\ud was not published in a timely fashion

Pseudoachondroplasia and Multiple Epiphyseal Dysplasia: A 7-Year Comprehensive Analysis of the Known Disease Genes Identify Novel and Recurrent Mutations and Provides an Accurate Assessment of Their Relative Contribution

Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are relatively common skeletal dysplasias resulting in short-limbed dwarfism, joint pain, and stiffness. PSACH and the largest proportion of autosomal dominant MED (AD-MED) results from mutations in cartilage oligomeric matrix protein (COMP); however, AD-MED is genetically heterogenous and can also result from mutations in matrilin-3 (MATN3) and type IX collagen (COL9A1, COL9A2, and COL9A3). In contrast, autosomal recessive MED (rMED) appears to result exclusively from mutations in sulphate transporter solute carrier family 26 (SLC26A2). The diagnosis of PSACH and MED can be difficult for the nonexpert due to various complications and similarities with other related diseases and often mutation analysis is requested to either confirm or exclude the diagnosis. Since 2003, the European Skeletal Dysplasia Network (ESDN) has used an on-line review system to efficiently diagnose cases referred to the network prior to mutation analysis. In this study, we present the molecular findings in 130 patients referred to ESDN, which includes the identification of novel and recurrent mutations in over 100 patients. Furthermore, this study provides the first indication of the relative contribution of each gene and confirms that they account for the majority of PSACH and MED. Hum Mutat 33:144–157, 2012. © 2011 Wiley Periodicals, Inc