Completeness and validity in a national clinical thyroid cancer database: DATHYRCA

BackgroundAlthough a prospective national clinical thyroid cancer database (DATHYRCA) has been active in Denmark since January 1, 1996, no assessment of data quality has been performed. The purpose of the study was to evaluate completeness and data validity in the Danish national clinical thyroid cancer database: DATHYRCA.Study design and settingNational prospective cohort. Denmark; population 5.5 million. Completeness of case ascertainment was estimated by the independent case ascertainment method using three governmental registries as a reference. The reabstracted record method was used to appraise the validity. For validity assessment 100 cases were randomly selected from the DATHYRCA database; medical records were used as a reference.ResultThe database held 1934 cases of thyroid carcinoma and completeness of case ascertainment was estimated to 90.9%. Completeness of registration was around or above 90% in most instances. Perfect agreement on the diagnosis of thyroid carcinoma was found, both inter- and intra-observer, and κ values of selected variables showed overall good to excellent agreement.ConclusionIn a setup with public health insurance, personal identity numbers and extended governmental databases, it is possible to establish national clinical cancer databases with a satisfactory completeness and validity. The DATHYRCA database is considered reliable in terms of describing thyroid carcinoma at a national level.     

Fish Karyome: A karyological information network database of Indian Fishes

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.     

Construction and use of a computerized DNA fingerprint database for lactic acid bacteria from silage

Efficient selection of new silage inoculant strains from a collection of over 10,000 isolates of lactic acid bacteria (LAB) requires excellent strain discrimination. Toward that end, we constructed a GelCompar II database of DNA fingerprint patterns of ethidium bromide-stained EcoRI fragments of total LAB DNA separated by conventional agarose gel electrophoresis. We found that the total DNA patterns were strain-specific; 56/60 American Type Culture Collection strains of 33 species of LAB could be distinguished. Enterococcus faecium strains ATCC19434 and ATCC35667 had identical total DNA patterns and RiboPrints. Lactobacillus rhamnosus strains ATCC7469 and ATCC27773 also had identical total DNA patterns, but different RiboPrints. EcoRI RiboPrint patterns could distinguish only about 9/23 Lactobacillus plantarum strains and about 6/10 Lactobacillus buchneri strains, whereas all 33 strains could be distinguished by EcoRI total DNA patterns. Despite gel-to-gel variation, new DNA patterns can be readily grouped with existing patterns using GelCompar II. The database contains large homogenous clusters of L. plantarum, E. faecium, L. buchneri, Lactobacillus brevis and Pediococcus species that can be used for tentative taxonomic assignment. We routinely use the DNA fingerprint database to identify and characterize new strains, eliminate duplicate isolates and for quality control of inoculant product strains. The GelCompar II database has been in continuous use for 7 years and contains more than 3600 patterns representing approximately 700 unique patterns from over 300 gels and is the largest computerized DNA fingerprint database for LAB yet reported.     

NABIC marker database: A molecular markers information network of agricultural crops

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers.

Availability

The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/     

The establishment and maintenance of a small culture collection in Egypt with a computerized database

A major constraint for expanding biotechnology in developing countries is the tack of appropriate microbial strains and microbial genetic resources. The recently established Microbial Strain Data Network (MSDN) offers the opportunity of, at least partially, llfting these constraints, since even a small institutional culture collection with limited to moderate facilities can act as an active two-way node in the network. We describe the establlshment of a nucleus for culture collection in the biotechnology laboratory, selecting methodologies as compatible as possible with those of the Cairo MIRCEN, and in assembling a database on the collected strains using a format that lends itself to participation in the MSDN.

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Résumé Une des limitations majeures à l'expansion de la biotechnologie dans les pays en développement est l'absence de souches microblennes appropriées et de ressources génétiques microbiennes. Le réseau de données de souches microbiennes (MSDN), récemment constitué, offre cette possibillité ou, tout au moins, lève en partie cette limitation, car même une petite collection de cultures institutionnelle avec des facilités limitées à modérées peut prendre une part interactive binodlale dans ce réseau. Nous décrivons la mise sur pied d'un noyau pour la collection de cultures dans le laboratoire de biotechnologie, sélectif de méthodologies aussi compatibies que possible avec celle du MIRCEN du Caire, et assembiant une banque de données sur les souches réunies en utilisant un formulaire qui se prête à la participation au MSDN.

     

GBIF information is not enough: national database improves the inventory completeness of Amazonian epiphytes

Distribution data sharing in global databases (e.g. GBIF) allowed the knowledge synthesis in several biodiversity areas. However, their Wallacean shortfalls still reduce our capacity to understand distribution patterns. Including exclusive records from other databases, such as national ones (e.g. SpeciesLink), could mitigate these shortfall problems, but it remains not evaluated. Therefore, we assessed whether (i) the inventory completeness, (ii) taxonomic contribution and (iii) spatial biases could be improved when integrating both global and national biodiversity databases. Using Amazonian epiphytes as a model, we compared the available taxonomic information spatially between GBIF and SpeciesLink databases using a species contribution index. We obtained the inventory completeness from sources using species accumulation curves and assessed their spatial biases by constructing spatial autoregressive models. We found that both databases have a high amount of exclusive records (GBIF: 36.7%; SpeciesLink: 21.7%) and species (17.8%). Amazonia had a small epiphyte inventory completeness, but it was improved when we analyzed both databases together. Individually, both database records were biased to sites with higher altitude, population and herbarium density. Together, river density appeared as a new predictor, probably due to the higher species contribution of SpeciesLink along them. Our findings provide strong evidence that using both global and national databases increase the overall biodiversity knowledge and reduce inventory gaps, but spatial biases may persist. Therefore, we highlight the importance of aggregating more than one database to understand biodiversity patterns, to address conservation decisions and direct shortfalls more efficiently in future studies.

     

Validation of endogenous peptide identifications using a database of tandem mass spectra

The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pl, precursor protein and potential post-translational modifications. Here, we have improved and extended the SwePep database with tandem mass spectra, by adding a locally curated version of the global proteome machine database (GPMDB). In peptidomic experiment practice, many peptide sequences contain multiple tandem mass spectra with different quality. The new tandem mass spectra database in SwePep enables validation of low quality spectra using high quality tandem mass spectra. The validation is performed by comparing the fragmentation patterns of the two spectra using algorithms for calculating the correlation coefficient between the spectra. The present study is the first step in developing a tandem spectrum database for endogenous peptides that can be used for spectrum-to-spectrum identifications instead of peptide identifications using traditional protein sequence database searches.     

Validation of protein models by a neural network approach

Background  

The development and improvement of reliable computational methods designed to evaluate the quality of protein models is relevant in the context of protein structure refinement, which has been recently identified as one of the bottlenecks limiting the quality and usefulness of protein structure prediction.     

The current knowledge on centipedes (Chilopoda) in Slovenia: faunistic and ecological records from a national database

In spite of Slovenia’s very high biodiversity, it has only a few animal groups that have been significantly investigated and are well known in this area. Slovenian researchers have studied only about half of the species known to be living in the country (Mršić 1997), but among well investigated species are centipedes. All available data about centipedes in Slovenia collected from 1921 to 2014 have been consolidated and constitute a general electronic database called “CHILOBIO”, which was created to provide an easy overview of the Slovenian centipede fauna and to allow entry and interpretation of new data collected in future research. The level of investigation has been studied with this database, in conjunction with a geographic information system (GIS). In the study period, 109 species were identified from 350 localities in 109 of the 236 UTM 10 × 10 km quadrants which cover the study area. The south-central part of the country has been the subject of the best investigations, whereas there is an absence of data from the south-eastern, eastern and north-eastern regions The highest number of species (52) has been recorded near the Iška valley (Central Slovenia, quadrant VL68). In 48% of the UTM quadrants investigated fewer than 10 species were recorded and just 5 species were found in one locality. Seventeen species were reported only in the Dinaric region, 4 in the Prealpine-subpannonian region and 7 in the Primorska-submediterranean region.     

Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information

1.33 Mb of sequence from the human Y chromosome was searched for tri- to hexanucleotide microsatellites. Twenty loci containing a stretch of eight or more repeat units with complete repeat sequence homogeneity were found, 18 of which were novel. Six loci (one tri-, four tetra- and one pentanucleotide) were assembled into a single multiplex reaction and their degree of polymorphism was investigated in a sample of 278 males from Pakistan. Diversities of the individual loci ranged from 0.064 to 0.727 in Pakistan, while the haplotype diversity was 0.971. One population, the Hazara, showed particularly low diversity, with predominantly two haplotypes. As the sequence builds up in the databases, direct methods such as this will replace more biased and technically demanding indirect methods for the isolation of microsatellites.     

Acquiring new information in a neuronal network: from Hebb's concept to homeostatic plasticity

Synaptic plasticity is the cellular mechanism underlying the phenomena of learning and memory. Much of the research on synaptic plasticity is based on the postulate of Hebb (1949) who proposed that, when a neuron repeatedly takes part in the activation of another neuron, the efficacy of the connections between these neurons is increased. Plasticity has been extensively studied, and often demonstrated through the processes of LTP (Long Term Potentiation) and LTD (Long Term Depression), which represent an increase and a decrease of the efficacy of long-term synaptic transmission. This review summarizes current knowledge concerning the cellular mechanisms of LTP and LTD, whether at the level of excitatory synapses, which have been the most studied, or at the level of inhibitory synapses. However, if we consider neuronal networks rather than the individual synapses, the consequences of synaptic plasticity need to be considered on a large scale to determine if the activity of networks are changed or not. Homeostatic plasticity takes into account the mechanisms which control the efficacy of synaptic transmission for all the synaptic inputs of a neuron. Consequently, this new concept deals with the coordinated activity of excitatory and inhibitory networks afferent to a neuron which maintain a controlled level of excitability during the acquisition of new information related to the potentiation or to the depression of synaptic efficacy. We propose that the protocols of stimulation used to induce plasticity at the synaptic level set up a "homeostatic potentiation" or a "homeostatic depression" of excitation and inhibition at the level of the neuronal networks. The coordination between excitatory and inhibitory circuits allows the neuronal networks to preserve a level of stable activity, thus avoiding episodes of hyper- or hypo-activity during the learning and memory phases.     

Validation of radiocarpal joint contact models based on images from a clinical MRI scanner

This study was undertaken to assess magnetic resonance imaging (MRI)-based radiocarpal surface contact models of functional loading in a clinical MRI scanner for future in vivo studies, by comparison with experimental measures from three cadaver forearm specimens. Experimental data were acquired using a Tekscan sensor during simulated light grasp. Magnetic resonance (MR) images were used to obtain model geometry and kinematics (image registration). Peak contact pressures (PPs) and average contact pressures (APs), contact forces and contact areas were determined in the radiolunate and radioscaphoid joints. Contact area was also measured directly from MR images acquired with load and compared with model data. Based on the validation criteria (within 25% of experimental data), out of the six articulations (three specimens with two articulations each), two met the criterion for AP (0%, 14%); one for peak pressure (20%); one for contact force (5%); four for contact area with respect to experiment (8%, 13%, 19% and 23%), and three contact areas met the criterion with respect to direct measurements (14%, 21% and 21%). Absolute differences between model and experimental PPs were reasonably low (within 2.5 MPa). Overall, the results indicate that MRI-based models generated from 3T clinical MR scanner appear sufficient to obtain clinically relevant data.     

Mycoplasmoses of ruminants in France: recent data from the national surveillance network

Background  

Ruminant mycoplasmoses are important diseases worldwide and several are listed by the World Organization for Animal Health to be of major economic significance. In France the distribution of mycoplasmal species isolated from clinical samples collected from diseased animals upon veterinary request, is monitored by a network known as VIGIMYC (for VIGIlance to MYCoplasmoses of ruminants). The veterinary diagnostic laboratories collaborating with VIGIMYC are responsible for isolating the mycoplasmas while identification of the isolates is centralized by the French Food Safety Agency (AFSSA) in Lyon. The VIGIMYC framework can also be used for specific surveys and one example, on the prevalence of M. bovis in bovine respiratory diseases, is presented here.     

Validation of the diagnostic potential of mtDNA copy number derived from whole genome sequencing

正Diagnosis of mitochondrial DNA(mt DNA)disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions(Bai and Wong,2005).For example,reduced mt DNA copy number could be a result of defective mt DNA biosynthesis or mt DNA replication and is associated