Search results for "Reference"
showing 10 items of 2491 documents
Offspring performance is linked to parental identity and male breeding ornamentation in whitefish
2009
The ‘good genes’ hypothesis predicts that males advertise their quality with different sexual ornaments and that females are able to recognize the genetic quality of males by evaluating these characteristics. In the present study, we investigated the parental effects on offspring performance (feeding and swimming ability of newly-hatched larvae) and examined whether male ornamentation indicates offspring success in performance trials of whitefish (Coregonus lavaretus Linnaeus). Offspring first-feeding success had a strong paternal effect and it was also positively correlated with the size of male breeding tubercles, indicating that breeding ornamentation of males can function as an honest i…
Comparative Cytogenetics Allows the Reconstruction of Human Chromosome History: The Case of Human Chromosome 13
2019
Comparative cytogenetics permits the identification of human chromosomal homologies and rearrangements between species, allowing the reconstruction of the history of each human chromosome. The aim of this work is to review evolutionary aspects regarding human chromosome 13. Classic and molecular cytogenetics using comparative banding, chromosome painting, and bacterial artificial chromosome (BAC) mapping can help us formulate hypotheses about chromosome ancestral forms; more recently, sequence data have been integrated as well. Although it has been previously shown to be conserved when compared to the ancestral primate chromosome, it shows a degree of rearrangements in some primate taxa; fu…
MetaCache-GPU: Ultra-Fast Metagenomic Classification
2021
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is commonly facilitated by constructing index data structures which allow for efficient querying of substrings. Recent metagenomic classification pipelines annotate reads with taxonomic labels by analyzing their $k$-mer histograms with respect to a reference genome database. CPU-based index construction is often performed in a preprocessing phase due to the relatively high cost of building irregular data structures such as hash maps. However, the rapidly growi…
Comparing DNA sequence collections by direct comparison of compressed text indexes
2012
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have h…
MHC class II genes influence the susceptibility to chronic active hepatitis C
1997
Chronic hepatitis C develops in more than 70% of hepatitis C virus infected subjects. Viral factors influence the disease course, but little is known about the importance of host factors.Frequencies of major histocompatibility complex (MHC) class I and class II antigens were analyzed in two groups of patients with chronic hepatitis C virus infection and in control subjects. MHC class I typing was done by standard microlymphocytotoxicity assays. DRB1 and DQA1 genotyping was done by PCR based typing methods.DRB1*0301 was found in 26 of 75 patients with chronic hepatitis C virus infection (34.7%) and in 12 of 101 control subjects (11.9%) (relative risk 3.9; p0.001). Homozygosity for this allel…
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm
2014
Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation…
Digital Zenith Cameras Results and Its Use in DFHRS v.4.3 Software for Quasi-Geoid Determination
2017
The design of digital zenith camera was started in 2010 by Institute of Geodesy and Geoinformatics. Since then the prototype of digital zenith camera has been developed. Now, after improvements of design and manufacturing of the second version, it has reached operational status. This paper describes the construction of zenith camera and features of its control software. The results of vertical deflections' measurements are discussed. At the moment measurements are done in Riga region and are used in DFHRS v.4.3 software in order to check and improve local quasigeoid model. It is a new method of quasigeoid model determination and has not been used in Latvia before. DFHRS (Digital Finite Elem…
Direct and fast determination of polychlorinated biphenyls in contaminated soils and sediments by thermal desorption-gas chromatography-tandem mass s…
2019
Abstract A direct procedure based on thermal desorption-gas chromatography-tandem mass spectrometry (TD–GC–MS–MS) was developed for the fast extraction of seven polychlorinated biphenyls (PCBs) from sediments and soils. PCBs were directly extracted, from 20 to 75 mg of sample, without any chemical pre-treatment or use of organic solvents, after the addition of 10 µL internal standard (PCB 195) in acetone. Sample treatment was totally automated. PCBs were extracted at 250 °C for 20 min, using a helium flow and the PCBs were trapped in a cryogenic Tenax trap at −10 °C. After that, analytes were directly desorbed at 270 °C and introduced to the GC–MS–MS system. Recoveries were established usin…
The determination of certain major and minor elements in geological samples by inductively coupled plasma atomic emission spectrometry. Some interfer…
2000
Direct ICP-AES measurements of the digested geological standard reference material samples yielded the wrong information about their composition. The differences between certified and measured concentrations of the samples were due to the complicated sample matrix. The measured concentrations can be successfully corrected by using a multiple linear regression technique. The correction is based on the multiple regression line calculated from the analytical results at synthetic mixtures of matrix elements, where concentrations varied on five levels. There were no significant (P = 0.05) differences between certified and measured concentrations in standard reference materials after the correcti…
LKS-92 Coordinates Transformation to ITRF2000
2014
LKS-92 is Latvian geodetic coordinate system used as an EUREF89 realization in Latvia. LKS-92 is official coordinate system for procuring of essential geospatial data. For aeronautical and other purposes ITRF2000 is used in publication of geospatial data. Research is done to obtain transformation parameters from LKS-92 realization epoch 1992.75 through LatPos to ITRF2000 epoch 2000.00. Valuation of two different coordinate adjustment strategies and accuracy of parameters is done. Results of research could be used for transformation from LKS-92 to ITRF2000 for all kind of geospatial data.