Search results for "CoDi"
showing 10 items of 1391 documents
The Engineering of a Compression Boosting Library: Theory vs Practice in BWT Compression
2006
Data Compression is one of the most challenging arenas both for algorithm design and engineering. This is particularly true for Burrows and Wheeler Compression a technique that is important in itself and for the design of compressed indexes. There has been considerable debate on how to design and engineer compression algorithms based on the BWT paradigm. In particular, Move-to-Front Encoding is generally believed to be an "inefficient " part of the Burrows-Wheeler compression process. However, only recently two theoretically superior alternatives to Move-to-Front have been proposed, namely Compression Boosting and Wavelet Trees. The main contribution of this paper is to provide the first ex…
From First Principles to the Burrows and Wheeler Transform and Beyond, via Combinatorial Optimization
2007
AbstractWe introduce a combinatorial optimization framework that naturally induces a class of optimal word permutations with respect to a suitably defined cost function taking into account various measures of relatedness between words. The Burrows and Wheeler transform (bwt) (cf. [M. Burrows, D. Wheeler, A block sorting lossless data compression algorithm, Technical Report 124, Digital Equipment Corporation, 1994]), and its analog for labelled trees (cf. [P. Ferragina, F. Luccio, G. Manzini, S. Muthukrishnan, Structuring labeled trees for optimal succinctness, and beyond, in: Proc. of the 45th Annual IEEE Symposium on Foundations of Computer Science, 2005, pp. 198–207]), are special cases i…
Statistical Modeling of Huffman Tables Coding
2005
An innovative algorithm for automatic generation of Huffman coding tables for semantic classes of digital images is presented. Collecting statistics over a large dataset of corresponding images, we generated Huffman tables for three images classes: landscape, portrait and document. Comparisons between the new tables and the JPEG standard coding tables, using also different quality settings, have shown the effectiveness of the proposed strategy in terms of final bit size (e.g. compression ratio).
Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms
2003
The Burrows-Wheeler transform [1] is one of the mainstays of lossless data compression. In most cases, its output is fed to Move to Front or other variations of symbol ranking compression. One of the main open problems [2] is to establish whether Move to Front, or more in general symbol ranking compression, is an essential part of the compression process. We settle this question positively by providing a new class of Burrows-Wheeler algorithms that use optimal partitions of strings, rather than symbol ranking, for the additional step. Our technique is a quite surprising specialization to strings of partitioning techniques devised by Buchsbaum et al. [3] for two-dimensional table compression…
Exposing the structure of an Arctic food web
2015
15 pages; International audience; How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) a…
Detection of a synthetic sex steroid in the American crocodile (Crocodylus acutus): Evidence for a novel environmental androgen
2017
Endocrine-disrupting contaminants (EDC's) are well known to alter sexual differentiation among vertebrates via estrogenic effects during development, particularly in organisms characterized by temperature-dependent sex determination. However, substances producing androgenic effects typically lack potency when tested in laboratory settings and are virtually unstudied in field settings. Here, we assay levels of a synthetic androgen, 17a-methyltestosterone (MT), in a heavily male-biased population of American crocodiles in the Tempisque River Basin of Costa Rica based on the recent hypothesis that this chemical is an EDC in developing crocodilian embryos. The presence of MT was documented in a…
Low-Frequency Repetitive Transcranial Magnetic Stimulation of the Right Dorsolateral Prefrontal Cortex Enhances Recognition Memory in Alzheimer’s Dis…
2019
Background: The lack of effective pharmacological or behavioral interventions for memory impairments associated with Alzheimer’s disease (AD) emphasizes the need for the investigation of approaches based on neuromodulation. Objective: This study examined the effects of inhibitory repetitive transcranial magnetic stimulation (rTMS) of prefrontal cortex on recognition memory in AD patients. Methods: In a first experiment, 24 mild AD patients received sham and real 1Hz rTMS over the left and right dorsolateral prefrontal cortex (DLPFC), in different sessions, between encoding and retrieval phases of a non-verbal recognition memory task. In a second experiment, another group of 14 AD patients u…
Genome-wide association study identifies novel susceptibility loci for KIT D816V positive mastocytosis
2021
Mastocytosis is a rare myeloid neoplasm characterized by uncontrolled expansion of mast cells, driven in >80% of affected individuals by acquisition of the KIT D816V mutation. To explore the hypothesis that inherited variation predisposes to mastocytosis, we performed a two-stage genome-wide association study, analyzing 1,035 individuals with KIT D816V positive disease and 17,960 healthy control individuals from five European populations. After quality control, we tested 592,007 SNPs at stage 1 and 75 SNPs at stage 2 for association by using logistic regression and performed a fixed effects meta-analysis to combine evidence across the two stages. From the meta-analysis, we identified three …
NeuPAT: an intranet database supporting translational research in neuroblastic tumors.
2013
Translational research in oncology is directed mainly towards establishing a better risk stratification and searching for appropriate therapeutic targets. This research generates a tremendous amount of complex clinical and biological data needing speedy and effective management. The authors describe the design, implementation and early experiences of a computer-aided system for the integration and management of data for neuroblastoma patients. NeuPAT facilitates clinical and translational research, minimizes the workload in consolidating the information, reduces errors and increases correlation of data through extensive coding. This design can also be applied to other tumor types.
The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments.
2011
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their assoc…