Objective To study the incidence, natural history and ated with bacteriuria after urodynamic studies (P= 0.05). Menopausal status, past history of urinary tract symptomatic eCects of bacteriuria after urodynamic studies in women.infection, number of urethral instrumentations required, order number in a session, peak urinary flow Patients and methods In a prospective study in the urogynaecology clinic of a large District General rate and urodynamic diagnosis were not associated variables. Hospital, 214 women (mean age 52.3 years, range 23-81) underwent urodynamic studies. BacteriuriaConclusions In a large series of women presenting to a urogynaecology clinic, urodynamic investigations was detected by semiquantitative culture at 2 and 7 days after the test. Women completed a 7-day diary were associated with a high incidence of transient irritative symptoms but a low incidence of bacteriuria of symptoms and events. Results The incidence of bacteriuria after urodynamic (8%). Infection was asymptomatic in most patients, but its natural history was unpredictable. Transient, studies was 7.9%. Bacteriuria was transient in four of 17 women but persisted in nine and developed late in persistent and late cases of bacteriuria all occurred. In this population, urodynamic studies are associated four; only one of 17 infections gave rise to symptoms. Irritative bladder symptoms after the test occurred in with a low level of morbidity.
Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i) do not fully exploit available parallel computing power and (ii) they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.
Motivation Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects. Results To overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project). Availability and implementation The software is freely available at: https://github.com/pinellolab/CRISPRitzhttps://github.com/InfOmics/CRISPRitz. Supplementary information Supplementary data are available at Bioinformatics online.
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