Search results for " alignment"

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…

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…

The fnr Gene of Bacillus licheniformis and the Cysteine Ligands of the C-Terminal FeS Cluster

1998

Many of the O2-responsive gene regulators of bacteria are members of the fumarate nitrate reductase-cyclic AMP receptor protein family of transcriptional regulators (12, 13, 15, 17) with predicted structures similar to those of the cyclic AMP receptor protein (11). The Fnr (stands for fumarate nitrate reductase regulator) protein from Escherichia coli (FnrEc) controls the expression of a variety of genes, mainly of anaerobic respiration and metabolism (5, 13). It contains a N-terminal cluster of three essential cysteine residues which are supposed to bind together with Cys122 a [4Fe 4S]2+ cluster which is required for O2 sensing (4, 7, 8, 10, 16). A wide variety of gram-negative bacteria co…

Action-Depicting Gestures and Morphosyntax: The Function of Gesture-Speech Alignment in the Conversational Turn

2021

The current study examines the role of action-depicting gestures in conversational turns by focusing on their semantic characteristics and temporal position in relation to their verbal affiliates (action verbs or more complex verb phrases). The data are video recordings of naturally occurring interactions in multilingual construction sites in Norway. The analysis distinguishes two modes of action depiction: generic depictions, which represent the action as a general type, and contextualized depictions, which in addition include deictic references to the spatio-material environment or iconic representations of the specific manner of action performance. These two modes typically occupy differ…

Immunoaffinity purification and characterization of mitochondrial membrane-bound D-3-hydroxybutyrate dehydrogenase from Jaculus orientalis.

2008

Abstract Background The interconversion of two important energy metabolites, 3-hydroxybutyrate and acetoacetate (the major ketone bodies), is catalyzed by D-3-hydroxybutyrate dehydrogenase (BDH1: EC 1.1.1.30), a NAD+-dependent enzyme. The eukaryotic enzyme is bound to the mitochondrial inner membrane and harbors a unique lecithin-dependent activity. Here, we report an advanced purification method of the mammalian BDH applied to the liver enzyme from jerboa (Jaculus orientalis), a hibernating rodent adapted to extreme diet and environmental conditions. Results Purifying BDH from jerboa liver overcomes its low specific activity in mitochondria for further biochemical characterization of the e…

Alignment and leadership in ICT strategies of private and public organizations

2015

Designing a graphics processing unit accelerated petaflop capable lattice Boltzmann solver: Read aligned data layouts and asynchronous communication

2017

The lattice Boltzmann method is a well-established numerical approach for complex fluid flow simulations. Recently, general-purpose graphics processing units (GPUs) have become available as high-performance computing resources at large scale. We report on designing and implementing a lattice Boltzmann solver for multi-GPU systems that achieves 1.79 PFLOPS performance on 16,384 GPUs. To achieve this performance, we introduce a GPU compatible version of the so-called bundle data layout and eliminate the halo sites in order to improve data access alignment. Furthermore, we make use of the possibility to overlap data transfer between the host central processing unit and the device GPU with comp…

Euclid preparation. XII. Optimizing the photometric sample of the Euclid survey for galaxy clustering and galaxy-galaxy lensing analyses

2021

Pocino, A., et al. (Euclid Collaboration)