Search results for "alignment"
showing 10 items of 627 documents
HOWERD: A Hidden Markov Model for Automatic OWL-ERD Alignment
2016
The HOWERD model for estimating the most likely alignment between an OWL ontology and an Entity Relation Diagram (ERD) is presented. Automatic alignment between relational schema and ontology represents a big challenge in Semantic Web research due to the different expressiveness of these representations. A relational schema is less expressive than the ontology; this is a non trivial problem when accessing data via an ontology and for ontology storing by means of a relational schema. Existent alignment methodologies fail in loosing some contents of the involved representations because the ontology captures more semantic information, and several elements are left unaligned. HOWERD relies on a…
Nonlinear Time-Series Adaptation for Land Cover Classification
2017
Automatic land cover classification from satellite image time series is of paramount relevance to assess vegetation and crop status, with important implications in agriculture, biofuels, and food. However, due to the high cost and human resources needed to characterize and classify land cover through field campaigns, a recurrent limiting factor is the lack of available labeled data. On top of this, the biophysical–geophysical variables exhibit particular temporal structures that need to be exploited. Land cover classification based on image time series is very complex because of the data manifold distortions through time. We propose the use of the kernel manifold alignment (KEMA) method for…
Type II keratin cDNAs from the rainbow trout: implications for keratin evolution.
2002
From a teleost fish, the rainbow trout Oncorhynchus mykiss, we have cloned and sequenced cDNAs encoding five different type II keratins. The corresponding protein spots, as separated by 2D-PAGE of trout cytoskeletal preparations, have been identified by peptide mass mapping using MALDI mass spectrometry. Three of the sequenced keratins are expressed in the epidermis (subtype IIe), and two in simple epithelia and mesenchymal cells (subtype IIs). The IIs keratins are both orthologs of human K8. This leaves unsequenced only the trace component S3 of the biochemically established trout keratin catalog. A phylogenetic tree has been constructed from a multiple alignment of the rod domains of the …
Possible Editing of Alu Transcripts in Blood Cells of Sporadic Creutzfeldt–Jakob Disease (sCJD)
2011
Editing of RNA molecules gained major interest when coding mRNA was analyzed. A small, noncoding, Alu DNA element transcript that may act as regulatory RNA in cells was examined in this study. Alu DNA element transcription was determined in buffy coat from healthy humans and human sporadic Creutzfeldt-Jakob disease (sCJD) cases. In addition, non-sCJD controls, mostly dementia cases and Alzheimer's disease (AD) cases, were included. The Alu cDNA sequences were aligned to genomic Alu DNA elements by database search. A comparison of best aligned Alu DNA sequences with our RNA/cDNA clones revealed editing by deamination by ADAR (adenosine deaminase acting on RNA) and APOBEC (apolipoprotein B ed…
A mutation in the second intracellular loop of the pituitary adenylate cyclase activating polypeptide type I receptor confers constitutive receptor a…
2000
AbstractThe pituitary adenylate cyclase activating polypeptide (PACAP) type I receptor belongs to the glucagon/secretin/vasoactive intestinal polypeptide (VIP) receptor family. We mutated and deleted an amino acid residue (E261) which is located within the second intracellular loop of the rat PACAP type I receptor and which is highly conserved among the receptor family. The wild-type receptor and the mutant receptors were efficiently expressed at the surface of COS-7 cells at nearly the same level and revealed the same high affinity for the agonist PACAP-27. The cAMP contents of COS cells transfected with the E261A, E261Q, and the deletion mutant receptor were 4.6-, 5.7-, and 6.7-fold highe…
Aligned microcontact printing of biomolecules on microelectronic device surfaces
2001
Microcontact printing (/spl mu/CP) of extracellular matrix proteins is a fascinating approach to control cell positioning and outgrowth, which is essential in the development of applications ranging from cellular biosensors to tissue engineering. Microelectronic devices can be used to detect the activity from a large number of recording sites over the long term. However, signals from cells can only be recorded at small sensitive spots. Here, the authors present an innovative setup to perform aligned /spl mu/CP of extracellular matrix proteins on microelectronic devices in order to guide the growth of electrogenic cells specifically to these sensitive spots. The authors' system is based on t…
A Framework to Support Business-IT Alignment in Enterprise Architecture Decision Making
2008
First published in the proceedings of the EBRF 2007 conference ”Research Forum to Understand Business in Knowledge Society”, September 25-27, Jyväskylä, Finland Business-IT alignment is one of the key concerns of general management and chief information officers. It is commonly recognized as an important instrument for realizing organizational effectiveness. Achieving business-IT alignment requires often change in the way managers regard IT and it demands co-operation between general and IT management. The challenge of aligning business- and IT-related concerns and requirements in architecture decision making situations is the focus of this study. As one possible solution, we present a fram…
CUDA-BLASTP: Accelerating BLASTP on CUDA-enabled graphics hardware
2011
Scanning protein sequence database is an often repeated task in computational biology and bioinformatics. However, scanning large protein databases, such as GenBank, with popular tools such as BLASTP requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper, we demonstrate how GPUs, powered by the Compute Unified Device Architecture (CUDA), can be used as an efficient computational platform to accelerate the BLASTP algorithm. In order to exploit the GPU's capabilities for accelerating BLASTP, we have used a compressed deterministic finite state automaton for hit detection as wel…
easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
2012
Video abstract A video abstract by the authors of this paper is available. video-abstract8870.mov
Initialization of the JYFLTRAP system
2013
The IGISOL facility has been moved into a new location at the acceleration laboratory of the University of Jyväskylä. The superconducting magnet that is part of the JYFLTRAP system has been re-energized. In this thesis a commissioning of the Penning trap apparatus JYFLTRAP is described. This involves a precise alignment of the structure of the trap along field lines of strong solenoid field. The alignment was completed successfully with a special alignment device. In addition, some improvements were done for the Penning traps and transfer line from RFQ cooler, and a buncher to the injection of Penning traps was built during this project. Jyväskylän yliopiston IGISOL-ryhmän laboratorio on mu…