Search results for "Election"
showing 10 items of 2159 documents
Differential geometric LARS via cyclic coordinate descent method
2012
We address the problem of how to compute the coefficient path implicitly defined by the differential geometric LARS (dgLARS) method in a high-dimensional setting. Although the geometrical theory developed to define the dgLARS method does not need of the definition of a penalty function, we show that it is possible to develop a cyclic coordinate descent algorithm to compute the solution curve in a high-dimensional setting. Simulation studies show that the proposed algorithm is significantly faster than the prediction-corrector algorithm originally developed to compute the dgLARS solution curve.
[Pharmacogenomics of antiretrovirals].
2008
HIV infection is a serious but treatable disease, yet current treatment is limited by development of resistance and high rates of adverse drug reactions. Antiretroviral therapy is especially suitable for pharmacogenomic investigation as both drug exposure and treatment response can be reliably measured. Increasing knowledge about genes implicated in pharmacokinetics, mode of action, efficacy, and toxicity of drugs has already provided relevant results for clinical practice, for example: The strong association of the abacavir hypersensitivity reaction with HLA-B*5701 permits testing patients for the allele, and if present avoiding the drug and therefore preventing the reaction. Persons with …
Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe
2021
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA…
DBSCAN Algorithm for Document Clustering
2019
Abstract Document clustering is a problem of automatically grouping similar document into categories based on some similarity metrics. Almost all available data, usually on the web, are unclassified so we need powerful clustering algorithms that work with these types of data. All common search engines return a list of pages relevant to the user query. This list needs to be generated fast and as correct as possible. For this type of problems, because the web pages are unclassified, we need powerful clustering algorithms. In this paper we present a clustering algorithm called DBSCAN – Density-Based Spatial Clustering of Applications with Noise – and its limitations on documents (or web pages)…
Codominance of Lactobacillus plantarum and obligate heterofermentative lactic acid bacteria during sourdough fermentation
2015
Fifteen sourdoughs produced in western Sicily (southern Italy) were analysed by classical methods for their chemico-physical characteristics and the levels of lactic acid bacteria (LAB). pH and total titratable acidity (TTA) were mostly in the range commonly reported for similar products produced in Italy, but the fermentation quotient (FQ) of the majority of samples was above 4.0, due to the low concentration of acetic acid estimated by high performance liquid chromatography (HPLC). Specific counts of LAB showed levels higher than 10(8) CFU g(-1) for many samples. The colonies representing various morphologies were isolated and, after the differentiation based on phenotypic characteristics…
Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition.
2014
ABSTRACT The Mycobacterium tuberculosis genome includes the large family of pe_pgrs genes, whose functions are unknown. Because of precedents in other pathogens in which gene families showing high sequence variation are involved in antigenic variation, a similar role has been proposed for the pe_pgrs genes. However, the impact of immune selection on pe_pgrs genes has not been examined. Here, we sequenced 27 pe_pgrs genes in 94 clinical strains from five phylogenetic lineages of the M. tuberculosis complex (MTBC). We found that pe_pgrs genes were overall more diverse than the remainder of the MTBC genome, but individual members of the family varied widely in their nucleotide diversity and in…
Fitness drift of an atrazine-degrading population under atrazine selection pressure.
2008
International audience; Pseudomonas sp. ADP harbouring the atrazine catabolic plasmid ADP1 was subcultured in liquid medium containing atrazine as sole source of nitrogen. After approximately 320 generations, a new population evolved which replaced the initial population. This newly evolved population grew faster and degraded atrazine more rapidly than the initial population. Plasmid profiles and Southern blot analyses revealed that the evolved strain, unlike the ancestral strain, presented a tandem duplication of the atzB gene encoding the second enzyme of the atrazine catabolic pathway responsible for the transformation of hydroxyatrazine to N-isopropylammelide. This duplication resulted …
Social transmission in the wild can reduce predation pressure on novel prey signals
2021
Funder: Suomen Kulttuurirahasto (Finnish Cultural Foundation); doi: https://doi.org/10.13039/501100003125
UVPAR: fast detection of functional shifts in duplicate genes.
2006
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…
Context matters-consensus molecular subtypes of colorectal cancer as biomarkers for clinical trials
2019
Abstract The Colorectal Cancer Subtyping Consortium identified four gene expression consensus molecular subtypes, CMS1 (immune), CMS2 (canonical), CMS3 (metabolic), and CMS4 (mesenchymal), using multiple microarray or RNA-sequencing datasets of primary tumor samples mainly from early stage colon cancer patients. Consequently, rectal tumors and stage IV tumors (possibly reflective of more aggressive disease) were underrepresented, and no chemo- and/or radiotherapy pretreated samples or metastatic lesions were included. In view of their possible effect on gene expression and consequently subtype classification, sample source and treatments received by the patients before collection must be ca…