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Increasing Sequence Search Sensitivity with Transitive Alignments
Ketil Malde, Tomasz Furmanek
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054422
Abstract: Sequence alignment is an important bioinformatics tool for identifying homology, but searching against the full set of available sequences is likely to result in many hits to poorly annotated sequences providing very little information. Consequently, we often want alignments against a specific subset of sequences: for instance, we are looking for sequences from a particular species, sequences that have known 3d-structures, sequences that have a reliable (curated) function annotation, and so on. Although such subset databases are readily available, they only represent a small fraction of all sequences. Thus, the likelihood of finding close homologs for query sequences is smaller, and the alignments will in general have lower scores. This makes it difficult to distinguish hits to homologous sequences from random hits to unrelated sequences. Here, we propose a method that addresses this problem by first aligning query sequences against a large database representing the corpus of known sequences, and then constructing indirect (or transitive) alignments by combining the results with alignments from the large database against the desired target database. We compare the results to direct pairwise alignments, and show that our method gives us higher sensitivity alignments against the target database.
Enterovesical Fistulae: Aetiology, Imaging, and Management
Tomasz Golabek,Anna Szymanska,Tomasz Szopinski,Jakub Bukowczan,Mariusz Furmanek,Jan Powroznik,Piotr Chlosta
Gastroenterology Research and Practice , 2013, DOI: 10.1155/2013/617967
Abstract: Background and Study Objectives. Enterovesical fistula (EVF) is a devastating complication of a variety of inflammatory and neoplastic diseases. Radiological imaging plays a vital role in the diagnosis of EVF and is indispensable to gastroenterologists and surgeons for choosing the correct therapeutic option. This paper provides an overview of the diagnosis of enterovesical fistulae. The treatment of fistulae is also briefly discussed. Material and Methods. We performed a literature review by searching the Medline database for articles published from its inception until September 2013 based on clinical relevance. Electronic searches were limited to the keywords: “enterovesical fistula,” “colovesical fistula” (CVF), “pelvic fistula”, and “urinary fistula”. Results. EVF is a rare pathology. Diverticulitis is the commonest aetiology. Over two-thirds of affected patients describe pathognomonic features of pneumaturia, fecaluria, and recurrent urinary tract infections. Computed tomography is the modality of choice for the diagnosis of enterovesical fistulae as not only does it detect a fistula, but it also provides information about the surrounding anatomical structures. Conclusions. In the vast majority of cases, this condition is diagnosed because of unremitting urinary symptoms after gastroenterologist follow-up procedures for a diverticulitis or bowel inflammatory disease. Computed tomography is the most sensitive test for enterovesical fistula. 1. Introduction Enterovesical fistula (EVF) represents an abnormal communication between the intestine and the bladder. Although EVF are uncommon, they cause significant morbidity and may markedly affect patient’s quality of life. Enterovesical fistulae most frequently occur as a consequence of advanced-stage disease or due to traumatic or iatrogenic injuries. The diagnosis of EVF can be challenging and is often delayed for several months after symptoms begin. Radiological imaging plays a vital role in establishing the site, course, and complexity of fistulae and in identifying an aetiological factor. This paper describes the imaging appearances of enterovesical fistulae and the option for their management. 2. Material and Methods A comprehensive search strategy was applied for Medline/PubMed electronic database from its inception until September 2013. We selected all human research articles published in English, not classified as case report, editorial, comment, letter, or news. The search strategy included the following terms: “enterovesical fistula,” “colovesical fistula”, “pelvic fistula” and “urinary
Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development
Teshome T Bizuayehu, Carlos FC Lanes, Tomasz Furmanek, B?rd O Karlsen, Jorge MO Fernandes, Steinar D Johansen, Igor Babiak
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-11
Abstract: miRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.Developmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.Atlantic halibut, Hippoglossus hippoglossus L., the largest flatfish of Atlantic Ocean, is a species of commercial interest to the aquaculture industry. Halibut's early developmental stages are prolonged and morphologically defined [1,2]. The critical developmental stages, when dramatic changes in signaling, physiology and morphology occur, include: (i) maternal to zygote transition (MZT), when maternally stocked transcripts are degraded and zygote transcripts take control over the development; (ii) organogenesis, when the germ layers are formed; (iii) hatching, when the embryo becomes a free-swimming larva; (iv) first feeding, when active movement, visualization, recognition of prey, and exogenous feeding begin; and (v) metamorphosis, the most dramatic morphological and behavioral change in a flatfish during the transition from a symmetric post-larval to an asymmetric juvenile stage, when migration of one eye towards the other one occurs across the skull [1].MiRNAs are small (18 - 26 nucleotides) non-coding RNAs
The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males
Fernando Ayllon?,Erik Kj?rner-Semb?,Tomasz Furmanek,Vidar Wennevik?,Monica F. Solberg?,Geir Dahle?,Geir Lasse Taranger?,Kevin A. Glover?,Markus S?llman Almén?,Carl J Rubin
PLOS Genetics , 2015, DOI: 10.1371/journal.pgen.1005628
Abstract: Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1–5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33–36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates.
Calorimetric examinations of austempered ductile iron ADI
F. Binczyk,J. Furmanek,A. Smoliński
Archives of Foundry Engineering , 2007,
Abstract: The study presents the results of calorimetric examinations during heating and cooling of austempered ductile iron ADI after austempering at temperatures of 280, 330 and 380oC. The samples for examinations were taken from cast rods of 20 and 60 mm diameter. Examinations were carried out on a differential scanning calorimeter, type Multi HTC S60. During heating, on a DSC curve one strong exothermic effect has been noted to occur (it does not occur in the case of common-grade cast iron), accompanied by two endothermic effects. The exothermic effect occurs within the range of about 20oC. Depending on the temperature of austempering treatment, its beginning falls to the temperatures from 469 to 490oC. The heat of this effect is proportional to the austenite content in ADI matrix after austempering. The endothermic effects are related with decomposition of pearlite (or bainite) and with phase transformation α → γ (ferrite as a constituent of ausferritic matrix.
The effect of cooling rate on the microstructure of nodular cast iron
F. Binczyk,A. Kowalski,J. Furmanek
Archives of Foundry Engineering , 2007,
Abstract: The study gives the results of the investigations concerning an effect of the casting cooling rate ( casting made from nodular iron used as a starting material for austempering to produce ADI) on the morphology of nodular graphite and metallic matrix composition. The features of the microstructure morphology were determined on a LUCIA computer program using castings of 10, 20, 40 and 60 mm diameter. It has been proved that increasing the casting diameter from 10 to 60 mm (i.e. reducing the cooling rate) increases the content of graphite from 10 to 12% and an average area of the precipitations from about 150 to 440 μm2, while it reduces the number of the graphite precipitations in 1 mm2 from about 700 to 260, the mean value of the shape factor from 0,96 to 0,84, and pearlite content in the matrix from about 96% to 84%. The chemical composition seems to have no significant effect, the only exception being Mo whose presence increases in a visible way pearlite content in the matrix at each cooling rate. The obtained results, and specifically the distribution of the frequencies of occurrence of the examined morphological features of graphite, confirm the vast possibilities that the LUCIA computer program of image analysis offers in evaluation of the effect of technological parameters on cast iron microstructure.
Austempering transformation kinetics of austempered ductile iron obtained by M ssbauer Spectroscopy
F. Binczyk,A. Hanc,A. Kowalski,J. Furmanek
Archives of Foundry Engineering , 2008,
Abstract: The composition of metallic matrix in ductile iron as-cast and after austempering at temperatures of 280, 330 and 380oC (ADI) wasexamined. The study presents the results of these examinations obtained by M ssbauer spectroscopy. The specimens were taken from castrods of 60mm diameter. Using calculated values of the parameters of hyperfine interactions (isomeric shift IS, quadrupole splitting QS andhyperfine effective magnetic field H), isolated by deconvolution of the experimental spectrum, the constituents of the metallic matrix were identified in terms of both quantity and quality. The measured values as well as the data compiled in literature indicate that component Z1 (the, so called, Zeeman spectrum sextet) is related with 57Fe atoms present in the structure of ferrite α1 (I stage of o→α1 + st transformation), component Z2 is typical of ferrite α2 (II stage of st→α2 + carbides transformation), while component Z3 has its origin in 57Fe atoms seated in the structure of carbides (Fe3C, Fe2C or Fe2,4C). On the other hand, by analysis of the parameters of hyperfine interactions describing the non-magnetic components (L and Q) it has been proved that they are typical of austenite.
How to Measure in the Near Field and in the Far Field  [PDF]
Tomasz Dlugosz, Hubert Trzaska
Communications and Network (CN) , 2010, DOI: 10.4236/cn.2010.21010
Abstract: A background of the electromagnetic field (EMF) measurements is presented in the work. A special attention is given to the specificity of the measurements performed in the Near Field. Factors, that should be taken into consideration as during the measurements as well during their analysis, are discussed. Without their understanding and considering a comparison of the measurements’ results, meters’ calibration and EMF standards comparison between different centers is impossible.
Rehabilitation of an Existing Office Block  [PDF]
Tomasz Blaszczynski, Jacek Wdowicki
Engineering (ENG) , 2011, DOI: 10.4236/eng.2011.39107
Abstract: A new owner wishes to refurbish the analysed building assembled in 70’s to modern intelligent office block and to develop up to 3000 m2 of a new part. The old office building has been in use until late 80’s. First two floors are made as a monolithic and the rest are prefabricated as RC frame with the shear walls in both directions. All aspects, which came from the coexistence of an old and new part of the office block, will be the scope of an article. The BW for Windows program has been used for computations. In our paper models of shear wall structures in the modernised part as well as the new adjacent part have been shown. The short period of time necessary to obtain the results of the analysis has allowed for a fully interactive structural design. Many analyses have been created to estimate structural space stiffness for existing and new part of the building. Analysis showed, that existing part deflections were 7 times less then permissible one and after concrete grade of a new part has been changed, deflections for both parts were almost the same.
Why Do the Main Sequence Stars Have Similar Chemical Composition?  [PDF]
Stanislaw Halas, Tomasz Durakiewicz
International Journal of Astronomy and Astrophysics (IJAA) , 2012, DOI: 10.4236/ijaa.2012.21006
Abstract: In this short note we have reconsidered the Jeans criterion for gravitational contraction of a gas nebula at different temperatures, from the present-day background radiation temperature (2.8 K) to those which existed at the early stage of the Universe. We demonstrate that the initial mass of quasars cannot be of the order of single galaxy masses, but rather 106 solar mass only. If they have larger masses, it must be the result of subsequent accretion process. Nevertheless quasars, formed prior to the stars, were the immediate source of the elements heavier than helium.
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