Search results for "algorithms"
showing 10 items of 1716 documents
Identification of transcribed protein coding sequence remnants within lincRNAs
2018
Abstract Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences. Importantly, such elements are known to be tissue-specifically expressed and to play a widespread role in gene regulation across thousands of genomic loci. However, very little is known of the mechanisms for the evolutionary biogenesis of these RNA elements, especially given their poor conservation across species. It has been proposed that lincRNAs might arise from pseudogenes. To test this systematically, we developed a novel method that searches for remnants of protein-coding sequences within lincRNA transcripts; the hypothesis is that we can t…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster
2016
AbstractAbout two-thirds of the vital genes in the Drosophila genome are involved in eye development, making the fly eye an excellent genetic system to study cellular function and development, neurodevelopment/degeneration, and complex diseases such as cancer and diabetes. We developed a novel computational method, implemented as Flynotyper software (http://flynotyper.sourceforge.net), to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phen…
Algorithm for the management of patients at low, high and very high risk of osteoporotic fractures
2019
Summary Guidance is provided in an international setting on the assessment and specific treatment of postmenopausal women at low, high and very high risk of fragility fractures. Introduction The International Osteoporosis Foundation and European Society for Clinical and Economic Aspects of Osteoporosis and Osteoarthritis published guidance for the diagnosis and management of osteoporosis in 2019. This manuscript seeks to apply this in an international setting, taking additional account of further categorisation of increased risk of fracture, which may inform choice of therapeutic approach. Methods Clinical perspective and updated literature search. Results The following areas are reviewed: …
A practical algorithmic approach to mature aggressive B cell lymphoma diagnosis in the double/triple hit era. Selecting cases, matching clinical bene…
2019
An accurate diagnosis of clinically distinct subgroups of aggressive mature B cell lymphomas is crucial for the choice of proper treatment. Presently, precise recognition of these disorders relies on the combination of morphological, immunophenotypical, and cytogenetic/molecular features. The diagnostic workup in such situations implies the application of costly and time-consuming analyses, which are not always required, since an intensified treatment option is reasonably reserved to fit patients. The Italian Group of Haematopathology proposes herein a practical algorithm for the diagnosis of aggressive mature B cell lymphomas based on a stepwise approach, aimed to select cases deserving mo…
Fundamentals and implementation of Microbiological Diagnostic Stewardship Programs.
2021
Microbiological diagnostic stewardship programs promote coordinated measures aimed at optimizing the use of diagnostic techniques, thus favouring the adoption of adequate and cost-effective therapeutic, clinical and preventive decisions. The implementation of microbiological diagnostic stewardship relies upon the creation of multidisciplinary committees led by clinical microbiologists for the design of diagnostic algorithms, the adequacy of the laboratory computer system to monitor the relevance of the requested diagnostic tests, the implementation of a quality control system, the design and performance of studies of cost-effectiveness, the training of the petitioner and the technical and n…
Automatic detection and measurement of nuchal translucency.
2017
In this paper we propose a new methodology to support the physician both to identify automatically the nuchal region and to obtain a correct thickness measurement of the nuchal translucency. The thickness of the nuchal translucency is one of the main markers for screening of chromosomal defects such as trisomy 13, 18 and 21. Its measurement is performed during ultrasound scanning in the first trimester of pregnancy. The proposed methodology is mainly based on wavelet and multi resolution analysis. The performance of our method was analysed on 382 random frames, representing mid-sagittal sections, uniformly extracted from real clinical ultrasound videos of 12 patients. According to the groun…
Morphokinetic analysis and embryonic prediction for blastocyst formation through an integrated time-lapse system.
2015
Objective To describe the events associated with the blastocyst formation and implantation that occur in embryos during preimplantation development based on the largest sample size ever described with time-lapse monitoring. Design Observational, retrospective, single-center clinical study. Setting University-affiliated private IVF center. Patient(s) A total of 7,483 zygotes from 990 first treatments of intracytoplasmic sperm injection (ICSI; 627 of oocyte donor vs. 363 autologous oocyte cycles), of which 832 blastocysts were transferred. Intervention(s) No patient intervention. Embryos were cultured in a time-lapse monitoring system, and the embryos were transferred on day 5 after ICSI. Emb…
DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
2019
Abstract Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gai…
Measuring trunk orientation with a CMOS camera: feasibility and accuracy.
2007
International audience; The purpose of this study was to develop and validate a new tool to objectively quantify trunk orientation at the bedside, especially dedicated to the measurement of the lateropulsion in acute and subacute stroke patients. We developed software to analyze 2D movement with a CMOS camera (Logitech Quickcam Pro 4000) and to calculate the orientation of a segment defined by two color markers. First, the accuracy, reproducibility and noise when measuring segment orientations were evaluated with the CMOS camera placed in different positions, and second trunk orientation was measured in static and in dynamic conditions both with a CMOS camera and with a gold standard 3D vid…