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Causal discovery from medical textual data.

Mani, S.; Cooper, G. F.
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: Artigo de Revista Científica
Publicado em //2000 EN
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Medical records usually incorporate investigative reports, historical notes, patient encounters or discharge summaries as textual data. This study focused on learning causal relationships from intensive care unit (ICU) discharge summaries of 1611 patients. Identification of the causal factors of clinical conditions and outcomes can help us formulate better management, prevention and control strategies for the improvement of health care. For causal discovery we applied the Local Causal Discovery (LCD) algorithm, which uses the framework of causal Bayesian Networks to represent causal relationships among model variables. LCD takes as input a dataset and outputs causes of the form variable Y causally influences variable Z. Using the words that occur in the discharge summaries as attributes for input, LCD output 8 purported causal relationships. The relationships ranked as most probable subjectively appear to be most causally plausible.

MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 17/03/2008 EN
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35.87%
The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL) and S5 domains that together constitute a catalytically active ATPase module. We identify the prokaryotic MORCs and establish that the MORC family belongs to a larger radiation of several families of GHKL proteins (paraMORCs) in prokaryotes. Using contextual information from conserved gene neighborhoods we show that these proteins primarily function in restriction-modification systems, in conjunction with diverse superfamily II DNA helicases and endonucleases. The common ancestor of these GHKL proteins, MutL and topoisomerase ATPase modules appears to have catalyzed structural reorganization of protein complexes and concomitant DNA-superstructure manipulations along with fused or standalone nuclease domains. Furthermore, contextual associations of the prokaryotic MORCs and their relatives suggest that their eukaryotic counterparts are likely to carry out chromatin remodeling by DNA superstructure manipulation in response to epigenetic signals such as histone and DNA methylation.

Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea

Daniels, Jan-Peter; Kelly, Steven; Wickstead, Bill; Gull, Keith
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 29/07/2009 EN
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The transcription machineries of Archaea and eukaryotes are similar in many aspects, but little is understood about archaeal chromatin and its role in transcription. Here, we describe the identification in hyperthermophilic Crenarchaeota and a Korarchaeon of an orthologue of the eukaryotic transcription elongation factor Elf1, which has been shown to function in chromatin structure maintenance of actively transcribed templates. Our discovery has implications for the relationship of chromatin and transcription in Archaea and the evolution of these processes in eukaryotes.

Tmod: toolbox of motif discovery

Sun, Hanchang; Yuan, Yuan; Wu, Yibo; Liu, Hui; Liu, Jun S.; Xie, Hongwei
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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Summary: Motif discovery is an important topic in computational transcriptional regulation studies. In the past decade, many researchers have contributed to the field and many de novo motif-finding tools have been developed, each may have a different strength. However, most of these tools do not have a user-friendly interface and their results are not easily comparable. We present a software called Toolbox of Motif Discovery (Tmod) for Windows operating systems. The current version of Tmod integrates 12 widely used motif discovery programs: MDscan, BioProspector, AlignACE, Gibbs Motif Sampler, MEME, CONSENSUS, MotifRegressor, GLAM, MotifSampler, SeSiMCMC, Weeder and YMF. Tmod provides a unified interface to ease the use of these programs and help users to understand the tuning parameters. It allows plug-in motif-finding programs to run either separately or in a batch mode with predetermined parameters, and provides a summary comprising of outputs from multiple programs. Tmod is developed in C++ with the support of Microsoft Foundation Classes and Cygwin. Tmod can also be easily expanded to include future algorithms.

Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index

Paredes, Sur Herrera; Melgar, Michael F.; Sethupathy, Praveen
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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35.87%
Motivation: It has been known for more than 2 decades that after RNA polymerase II (RNAPII) initiates transcription, it can enter into a paused or stalled state immediately downstream of the transcription start site before productive elongation. Recent advances in high-throughput genomic technologies facilitated the discovery that RNAPII pausing at promoters is a widespread physiologically regulated phenomenon. The molecular underpinnings of pausing are incompletely understood. The CCCTC-factor (CTCF) is a ubiquitous nuclear factor that has diverse regulatory functions, including a recently discovered role in promoting RNAPII pausing at splice sites.

BioPlat: a software for human cancer biomarker discovery

Butti, Matias D.; Chanfreau, Hernan; Martinez, Diego; García, Diego; Lacunza, Ezequiel; Abba, Martin C.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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35.87%
Summary: Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data.

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

Leung, Alvin; Bader, Gary D.; Reimand, Jüri
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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35.87%
Summary: Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks.

Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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35.87%
Summary: We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of protein candidates determined by a set of machine learning algorithms. Vacceed has the potential to save time and money by reducing the number of false candidates allocated for laboratory validation. Vacceed, if required, can also predict protein sequences from the pathogen’s genome.

Population-based structural variation discovery with Hydra-Multi

Lindberg, Michael R.; Hall, Ira M.; Quinlan, Aaron R.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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35.87%
Summary: Current strategies for SNP and INDEL discovery incorporate sequence alignments from multiple individuals to maximize sensitivity and specificity. It is widely accepted that this approach also improves structural variant (SV) detection. However, multisample SV analysis has been stymied by the fundamental difficulties of SV calling, e.g. library insert size variability, SV alignment signal integration and detecting long-range genomic rearrangements involving disjoint loci. Extant tools suffer from poor scalability, which limits the number of genomes that can be co-analyzed and complicates analysis workflows. We have developed an approach that enables multisample SV analysis in hundreds to thousands of human genomes using commodity hardware. Here, we describe Hydra-Multi and measure its accuracy, speed and scalability using publicly available datasets provided by The 1000 Genomes Project and by The Cancer Genome Atlas (TCGA).

A new family of hybrid virophages from an animal gut metagenome

Yutin, Natalya; Kapitonov, Vladimir V; Koonin, Eugene V
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 25/04/2015 EN
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35.87%
Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, with terminal inverted repeats. Thus, the RVP seem to represent virophage-Polinton hybrids that are likely capable of formation of infectious virions. Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen.

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE

Najafabadi, Hamed S.; Albu, Mihai; Hughes, Timothy R.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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25.94%
Summary: Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys2His2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail.

The Discovery of New Spain in 1518. By Juan De Grijalva. A translation of the original texts with an introduction and notes by Henry R. Wagner. Documents and Narratives concerning the Discovery and Conquest of Latin America, new series, No. 2

Jacobsen, Jerome V.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica Formato: text/html
EN
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The Australian colonies : together with notes of a voyage from Australia to Panama in the "Golden Age", descriptions of Tahiti and other islands in the Pacific and a tour through some of the States of America in 1854 / by H. Hussey

Hussey, Henry, 1825-1903.
Fonte: London : Blackburn & Burt ; Adelaide : E.S. Wigg, [1855] Publicador: London : Blackburn & Burt ; Adelaide : E.S. Wigg, [1855]
Tipo: Livro Formato: 430260 bytes; application/pdf
Publicado em //1855 EN
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35.87%
Notes of a voyage from Australia to Panama in the "Golden Age", descriptions of Tahiti and other islands in this Pacific and a tour through some of the States of America in 1854 Voyage from Australia to Panama in the "Golden Age", descriptions of Tahiti and other islands in this Pacific and a tour through some of the States of America in 1854; Scanned from the original held in Rare Books & Special Collections, Barr Smith Library.

Anonimytext: anonimization of unstructured documents

Pérez Laínez, Rebeca; Iglesias, Ana; Pablo-Sánchez, César de
Fonte: INSTICC (Institute for Systems and Technologies of Information, Control and Communication) Publicador: INSTICC (Institute for Systems and Technologies of Information, Control and Communication)
Tipo: info:eu-repo/semantics/acceptedVersion; info:eu-repo/semantics/conferenceObject; info:eu-repo/semantics/conferenceObject; info:eu-repo/semantics/bookPart
Publicado em 06/10/2009 ENG
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26.16%
The anonymization of unstructured texts is nowadays a task of great importance in several text mining applications. Medical records anonymization is needed both to preserve personal health information privacy and enable further data mining efforts. The described ANONYMITEXT system is designed to de identify sensible data from unstructured documents. It has been applied to Spanish clinical notes to recognize sensible concepts that would need to be removed if notes are used beyond their original scope. The system combines several medical knowledge resources with semantic clinical notes induced dictionaries. An evaluation of the semi automatic process has been carried on a subset of the clinical notes on the most frequent attributes.; This work has been partially supported by MAVIR (S 0505/TIC 0267) and by the TIN2007 67407 C03 01 project BRAVO.; Proceedings of: The International Conference on Knowledge Discovery and Information Retrieval, October, 2009 (KDIR 2009). First International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K 2009), Funchal (Madeira, Portugal)

IU Libraries Discovery Layer Implementation Task Force Progress Report and Notes & Recommendations for Future

McDonald, Courtney Greene; Baich, Tina; Charbonneau, Gary; Cohen, Rachael; Lent, Randy; Long, Chris Evin; McFadden, Sue; Skekloff, Susan
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Trabalho em Andamento
EN_US
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In May 2013, the primary public interface for IUCAT transitioned to a new discovery layer interface, powered by the open source web application Blacklight. This document reports on progress and makes recommendations for enabling ongoing system-wide input into the development of the catalog discovery interface through the completion of the upcoming OLE migration project. Appendices include groups’ charges & memberships, and an annotated version of the original selection rubric notating status of product features.This report was prepared for the IU Council of Head Librarians.

Large-scale evaluation of automated clinical note de-identification and its impact on information extraction

Deleger, Louise; Molnar, Katalin; Savova, Guergana; Xia, Fei; Lingren, Todd; Li, Qi; Marsolo, Keith; Jegga, Anil; Kaiser, Megan; Stoutenborough, Laura; Solti, Imre
Fonte: BMJ Group Publicador: BMJ Group
Tipo: Artigo de Revista Científica
EN_US
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25.94%
Objective: (1) To evaluate a state-of-the-art natural language processing (NLP)-based approach to automatically de-identify a large set of diverse clinical notes. (2) To measure the impact of de-identification on the performance of information extraction algorithms on the de-identified documents. Material and methods A cross-sectional study that included 3503 stratified, randomly selected clinical notes (over 22 note types) from five million documents produced at one of the largest US pediatric hospitals. Sensitivity, precision, F value of two automated de-identification systems for removing all 18 HIPAA-defined protected health information elements were computed. Performance was assessed against a manually generated ‘gold standard’. Statistical significance was tested. The automated de-identification performance was also compared with that of two humans on a 10% subsample of the gold standard. The effect of de-identification on the performance of subsequent medication extraction was measured. Results: The gold standard included 30 815 protected health information elements and more than one million tokens. The most accurate NLP method had 91.92% sensitivity (R) and 95.08% precision (P) overall. The performance of the system was indistinguishable from that of human annotators (annotators' performance was 92.15%(R)/93.95%(P) and 94.55%(R)/88.45%(P) overall while the best system obtained 92.91%(R)/95.73%(P) on same text). The impact of automated de-identification was minimal on the utility of the narrative notes for subsequent information extraction as measured by the sensitivity and precision of medication name extraction. Discussion and conclusion NLP-based de-identification shows excellent performance that rivals the performance of human annotators. Furthermore...

Researches on Mathematical Relationship of Five Elements of Containing Notes and Fibonacci Sequence Modulo 5

Chen, Zhaoxue
Fonte: Hindawi Publishing Corporation Publicador: Hindawi Publishing Corporation
Tipo: Artigo de Revista Científica
EN
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26.02%
Considering the five periods and six qi's theory in TCM almost shares a common basis of stem-branch system with the five elements of containing notes, studying the principle or mathematical structure behind the five elements of containing notes can surely bring a novel view for the five periods and six qi's researches. By analyzing typical mathematical rules included in He tu, Luo shu, and stem-branch theory in TCM as well as the Fibonacci sequence especially widely existent in the biological world, novel researches are performed on mathematical relationship between the five elements of containing notes and the Fibonacci sequence modulo 5. Enlightened by elementary Yin or Yang number grouping principle of He tu, Luo shu, the 12534 and 31542 key number series of Fibonacci sequence modulo 5 are obtained. And three new arrangements about the five elements of containing notes are then introduced, which have shown close relationship with the two obtained key subsequences of the Fibonacci sequence modulo 5. The novel discovery is quite helpful to recover the scientific secret of the five periods and six qi's theory in TCM as well as that of whole traditional Chinese culture system, but more data is needed to elucidate the TCM theory further.

A Concept-Wide Association Study of Clinical Notes in Search of New Predictors of Kidney Failure

Singh, Karandeep
Fonte: Harvard University Publicador: Harvard University
Tipo: Thesis or Dissertation; text Formato: application/pdf
EN
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26.06%
Importance: Identifying modifiable risk factors for kidney disease progression is critical towards the development of strategies to prevent the onset of kidney failure. Existing epidemiologic approaches are unable to translate unstructured clinical information into knowledge about potential risks. Objective: The objective of this study is to use clinical notes to identify novel risk factors for kidney failure. Design: We conducted a retrospective study consisting of evaluating the end stage renal disease (ESRD) using individual concepts extracted from clinical notes in the year prior to the first outpatient general nephrology visit. We treated death as a competing risk in this analysis and used proportional subdistribution hazards regression. We determined statistical significance in univariate and multivariate models using a 5% threshold for false discovery rate (q-value < 0.05). The multivariate models included the Tangri score, an established predictive score for ESRD. Setting: A tertiary care center. Participants: Patients were included if they were seen by an adult outpatient nephrologist at a Brigham and Women’s Hospital-affiliated clinic between January 1, 2004 and June 18, 2014. Patients were excluded if they had visits only with renal transplant (and not general nephrology)...

Publishing and Discovery of Mobile Web Services in Peer to Peer Networks

Srirama, Satish Narayana
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 18/07/2010
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It is now feasible to host Web Services on a mobile device due to the advances in cellular devices and mobile communication technologies. However, the reliability, usability and responsiveness of the Mobile Hosts depend on various factors including the characteristics of available network, computational resources, and better means of searching the services provided by them. P2P enhances the adoption of Mobile Host in commercial environments. Mobile Hosts in P2P can collaboratively share the resources of individual peers. P2P also enhances the service discovery of huge number of Web Services possible with Mobile Hosts. Advanced features like post filtering with weight of keywords and context-awareness can also be exploited to select the best possible mobile Web Service. This paper proposes the concept of Mobile Hosts in P2P networks and identifies the means of publishing and discovery of Web Services in mobile P2P networks.; Comment: First International Workshop on Mobile Services and Personalized Environments (MSPE'06), November 16-17, 2006, pp. 15-28. Lecture Notes in Informatics, GI

Empirical Discovery in Linguistics

Pericliev, Vladimir
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 26/06/1995
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25.98%
A discovery system for detecting correspondences in data is described, based on the familiar induction methods of J. S. Mill. Given a set of observations, the system induces the ``causally'' related facts in these observations. Its application to empirical linguistic discovery is described.; Comment: 9 pages, LaTeX, in Working Notes of AAAI Spring Symposium Series, Symposium: Systematic Methods of Scientific Discovery, March 27-29, Stanford University