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1.
Read Writ ; 33(4): 1037-1073, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32831478

RESUMO

As readers struggle to coordinate various reading- and language-related skills during oral reading fluency (ORF), miscues can emerge, especially when processing complex texts. Following a miscue, students often self-correct as a strategy to potentially restore ORF and online linguistic comprehension. Executive functions (EF) are hypothesized to play an interactive role during ORF. Yet, the role of EF in self-corrections while reading complex texts remains elusive. To this end, we evaluated the relation between students' probability of self-correcting miscues-or P(SC)-and their EF profile in a cohort of 143 participants (aged 9-15) who represented a diverse spectrum of reading abilities. Moreover, we used experimentally-manipulated passages (decoding, vocabulary, syntax, and cohesion) and employed a fully cross-classified mixed-effects multilevel regression strategy to evaluate the interplay between components of ORF, EF, and text complexity. Our results revealed that, after controlling for reading and language abilities, increased production of miscues across different passage conditions was explained by worse EF. We also found that students with better EF exhibited greater P(SC) when reading complex texts. While text complexity taxes students' EF and influences their production of miscues, findings suggest that EF may be interactively recruited to restore ORF via self-correcting oral reading errors. Overall, our results suggest that domain-general processes (e.g., EF) are associated with production of miscues and may underlie students' behavior of self-corrections, especially when reading complex texts. Further understanding of the relation between different components of ORF and cognitive processes may inform intervention strategies to improve reading proficiency and overall academic performance.

2.
Artigo em Inglês | MEDLINE | ID: mdl-32663319

RESUMO

Disentangling the dimensionality in environmental adversity offers nuanced insights at both theoretical and practical levels, such as the ways that disadvantaged socioeconomic circumstances during childhood development may contribute to adolescent psychopathology. Miller and colleagues (2020) provide evidence into how early deprivation and threat may exacerbate later psychopathology. Yet, how certain factors in this early environment differentially facilitate children's cognitive and socioemotional growth may modulate the severity of later psychopathology. In this commentary, we reflect on the promising evidence offered by Miller and colleagues and extend additional considerations regarding academic growth, cognitive abilities, and protective environmental factors.

3.
Life Sci Alliance ; 3(7)2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32487689

RESUMO

Despite the importance of mitochondrial fatty acid oxidation (FAO) in cancer metabolism, the biological mechanisms responsible for the FAO in cancer and therapeutic intervention based on catabolic metabolism are not well defined. In this study, we observe that Snail (SNAI1), a key transcriptional repressor of epithelial-mesenchymal transition, enhances catabolic FAO, allowing pro-survival of breast cancer cells in a starved environment. Mechanistically, Snail suppresses mitochondrial ACC2 (ACACB) by binding to a series of E-boxes located in its proximal promoter, resulting in decreased malonyl-CoA level. Malonyl-CoA being a well-known endogenous inhibitor of fatty acid transporter carnitine palmitoyltransferase 1 (CPT1), the suppression of ACC2 by Snail activates CPT1-dependent FAO, generating ATP and decreasing NADPH consumption. Importantly, combinatorial pharmacologic inhibition of pentose phosphate pathway and FAO with clinically available drugs efficiently reverts Snail-mediated metabolic reprogramming and suppresses in vivo metastatic progression of breast cancer cells. Our observations provide not only a mechanistic link between epithelial-mesenchymal transition and catabolic rewiring but also a novel catabolism-based therapeutic approach for inhibition of cancer progression.

4.
Ultrasound Med Biol ; 46(9): 2493-2504, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32595057

RESUMO

Non-invasive assessment is preferred for monitoring arteriovenous dialysis fistulas (AVFs). Vector concentration assesses flow complexity, which may correlate with stenosis severity. We determined whether vector concentration could assess stenosis severity in dysfunctional AVFs. Vector concentration was estimated in four stenotic phantoms at different pulse repetition frequencies. Spectral Doppler peak velocity and vector concentration were measured in 12 patients with dysfunctional AVFs. Additionally, 5 patients underwent digital subtraction angiography (DSA). In phantoms, vector concentration exhibited an inverse relationship with stenosis severity and was less affected by aliasing in severe stenoses. In nine stenoses of 5 patients undergoing DSA, vector concentration correlated strongly with stenosis severity (first stenosis: r = -0.73, p = 0.04; other stenoses; r = -0.69, p = 0.02) and mid-stenotic diameter (first stenosis: r = 0.87, p = 0.006; other stenoses: r = 0.70, p = 0.02) as opposed to peak velocities (p > 0.05). Vector concentration is less affected by aliasing in severe stenoses and correlates with DSA in patients with dysfunctional AVF.

5.
Anal Chem ; 92(11): 7382-7387, 2020 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-32392040

RESUMO

AMP-activated protein kinase (AMPK in human and AAK in C. elegans) is a master regulator of metabolism. It has many isotypes, but its isotype-dependent functions are largely unknown. By developing real-time in-organism NMR metabolomics for C. elegans, we were able to study different roles of the isotypic catalytic subunits of AAK/AMPK, AAK-1, and AAK-2 in live worms at the whole organism level. The aak-1 knockout animals exhibited enhanced glucose production under starvation, strikingly opposite to aak-2 knockout animals. Unusually high compensatory expression of the reciprocal isotypes in each KO strain and the results for the double KO animals suggested an unconventional phenotype-genotype relationship and the dominance of aak-2 in glucose production. The gene expression patterns showed that the differential phenotypes of aak-1 KO strain are due to reduced TCA and glycolysis and enhanced gluconeogenesis compared to the aak-2 KO strain. Subsequent 13C-isotope incorporation experiment showed that the glucose production in aak-1 KO occurs through the activation of fatty acid oxidation and glyoxylate shunt. Revealing differential roles of the isotypes of AAK/AMPK, our convenient approach is readily applicable to many C. elegans models for human metabolic diseases.

6.
J Vasc Surg ; 2020 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-32447038

RESUMO

OBJECTIVE: The purpose of this study was to report our results of patients' characteristics, procedural complications, and long-term patency in treatment of isolated infrarenal aortic stenosis (IIAS). METHODS: Forty symptomatic patients (28 female, 12 male; median age, 60 years [54.8-68 years]) with IIAS who underwent endovascular intervention between 2001 and 2017 were retrospectively analyzed. Patient, lesion, procedure, and balloon/stent characteristics were assessed. Follow-up included clinical status evaluation and color Doppler ultrasound examination. RESULTS: The cause of IIAS was atherosclerosis in all patients. Twenty percent of the patients were younger than 50 years; 85% had hypertension, 80% were smokers, 38% had hyperlipidemia, 23% had diabetes mellitus, 15% were obese (body mass index ≥30 kg/m2), and 8% had chronic kidney disease. The median stenosis grade was 80% (70%-80%), and the median lesion length was 19.9 mm (13-29.4 mm). Severe calcification was present in 8% of the patients. Percutaneous transluminal angioplasty was performed in four cases (10%), whereas stenting was performed in 36 (90%). One complication, an aortic rupture requiring surgical repair, occurred. The median follow-up was 61 months (17-101 months). The primary patency rate was 100% at 6 months, 97% at 12 and 24 months, and 88% at 60 and 96 months. Restenosis developed in three patients (8%); reintervention was carried out in two cases (5%). CONCLUSIONS: Endovascular therapy for IIAS provides a safe and effective long-term treatment strategy.

7.
Sci Rep ; 10(1): 4188, 2020 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-32144346

RESUMO

With the explosion of high-throughput data, effective integrative analyses are needed to decipher the knowledge accumulated in biological databases. Existing meta-analysis approaches in systems biology often focus on hypothesis testing and neglect real expression changes, i.e. effect sizes, across independent studies. In addition, most integrative tools completely ignore the topological order of gene regulatory networks that hold key characteristics in understanding biological processes. Here we introduce a novel meta-analysis framework, Network-Based Integrative Analysis (NBIA), that transforms the challenging meta-analysis problem into a set of standard pathway analysis problems that have been solved efficiently. NBIA utilizes techniques from classical and modern meta-analysis, as well as a network-based analysis, in order to identify patterns of genes and networks that are consistently impacted across multiple studies. We assess the performance of NBIA by comparing it with nine meta-analysis approaches: Impact Analysis, GSA, and GSEA combined with classical meta-analysis methods (Fisher's and the additive method), plus the three MetaPath approaches that employ multiple datasets. The 10 approaches have been tested on 1,737 samples from 27 expression datasets related to Alzheimer's disease, acute myeloid leukemia (AML), and influenza. For all of the three diseases, NBIA consistently identifies biological pathways relevant to the underlying diseases while the other 9 methods fail to capture the key phenomena. The identified AML signature is also validated on a completely independent cohort of 167 AML patients. In this independent cohort, the proposed signature identifies two groups of patients that have significantly different survival profiles (Cox p-value 2 × 10-6). The NBIA framework will be included in the next release of BLMA Bioconductor package (http://bioconductor.org/packages/release/bioc/html/BLMA.html).

8.
Bioinformatics ; 36(2): 487-495, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31329248

RESUMO

MOTIVATION: Recent advances in biomedical research have made massive amount of transcriptomic data available in public repositories from different sources. Due to the heterogeneity present in the individual experiments, identifying reproducible biomarkers for a given disease from multiple independent studies has become a major challenge. The widely used meta-analysis approaches, such as Fisher's method, Stouffer's method, minP and maxP, have at least two major limitations: (i) they are sensitive to outliers, and (ii) they perform only one statistical test for each individual study, and hence do not fully utilize the potential sample size to gain statistical power. RESULTS: Here, we propose a gene-level meta-analysis framework that overcomes these limitations and identifies a gene signature that is reliable and reproducible across multiple independent studies of a given disease. The approach provides a comprehensive global signature that can be used to understand the underlying biological phenomena, and a smaller test signature that can be used to classify future samples of a given disease. We demonstrate the utility of the framework by constructing disease signatures for influenza and Alzheimer's disease using nine datasets including 1108 individuals. These signatures are then validated on 12 independent datasets including 912 individuals. The results indicate that the proposed approach performs better than the majority of the existing meta-analysis approaches in terms of both sensitivity as well as specificity. The proposed signatures could be further used in diagnosis, prognosis and identification of therapeutic targets. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

9.
Pac Symp Biocomput ; 25: 551-562, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31797627

RESUMO

Vast repositories of heterogeneous data from existing sources present unique opportunities. Taken individually, each of the datasets offers solutions to important domain and source-specific questions. Collectively, they represent complementary views of related data entities with an aggregate information value often well exceeding the sum of its parts. Integration of heterogeneous data is therefore paramount to i) obtain a more unified picture and comprehensive view of the relations, ii) achieve more robust results, iii) improve the accuracy and integrity, and iv) illuminate the complex interactions among data features. In this paper, we have proposed a data integration methodology to identify subtypes of cancer using multiple data types (mRNA, methylation, microRNA and somatic variants) and different data scales that come from different platforms (microarray, sequencing, etc.). The Cancer Genome Atlas (TCGA) dataset is used to build the data integration and cancer subtyping framework. The proposed data integration and disease subtyping approach accurately identifies novel subgroups of patients with significantly different survival profiles. With current availability of vast genomics, and variant data for cancer, the proposed data integration system will better differentiate cancer and patient subtypes for risk and outcome prediction and targeted treatment planning without additional cost and precious lost time.

10.
Sci Rep ; 9(1): 17947, 2019 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-31784600

RESUMO

This study aimed to determine the role of magnetic resonance imaging (MRI) in diagnosing and describing the characteristics of fistula-in-ano, and the agreement between MRI and operative findings. We conducted a retrospective study in 367 patients with fistula-in-ano who were diagnosed and had an operation at the University Medical Center between January 2016 and January 2018. MRI findings were evaluated and compared with surgical findings using the kappa coefficient (k) method. 367 patients (327 male and 40 female, mean age 39.3 ± 12.4 years). A total of 411 primary fistulas were found during surgery. There was a strong agreement between MRI and surgery for classifying primary tracts (k = 0.89) and detecting secondary tracts (k = 0.94). While the sensitivity and specificity of MRI for detecting internal openings were 99% and 85.2% respectively; these rates were 100% for abscesses. Both T2-weighted turbo spin-echo (T2W TSE) and postcontrast fat-saturated T1-weighted turbo spin-echo (FS T1W TSE) sequences showed high sensitivity (96.6% and 98.4% respectively) and specificity (92.6% and 81.5% respectively) for depicting internal openings and secondary tracts. Post-contrast FS T1W TSE sequence was very effective in detecting abscesses with an accuracy of 100%. In conclusion, MRI can be considered an accurate tool for the preoperative evaluation of fistula-in-ano, which is a major determinant of the surgical outcome. Both T2W TSE and post-contrast FS T1W TSE sequences are highly accurate in depicting the features of fistula-in-ano. If there are no contraindications, contrast administration is recommended to differentiate abscesses from active inflammation.

11.
Genome Biol ; 20(1): 234, 2019 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-31718689

RESUMO

Following publication of the original paper [1], the authors reported the following update to the competing interests declaration.

12.
BMC Public Health ; 19(1): 1355, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31647001

RESUMO

BACKGROUND: The low diagnosis rate and poor access to clinical care among people with CHB is a major barrier to reducing HBV-related morbidity and mortality in Australia. One explanation for this is a lack of disease-specific knowledge among people living with CHB. Health literacy has been shown to be important for maximising engagement with medical care and adherence to recommended management. The 'teach-back' communication strategy has been shown to improve patient understanding in other clinical areas. This study aims to assess disease-specific knowledge; and evaluate the efficacy of the teach-back strategy for improving HBV knowledge, compared to a standard medical consultation. METHOD: A randomized pilot study was conducted between February and June 2017. Participants were recruited from the liver clinic at an inner-city tertiary hospital. English-speaking patients aged ≥18 years and diagnosed with CHB were eligible for the study. Participants were randomised to a control group (medical specialist appointment) and intervention group (teach-back). Knowledge was assessed at baseline, immediately post-intervention and at one month using a validated questionnaire. Participants in the intervention group received a one-on-one teach-back session about CHB. The main outcome measure was a combined knowledge score of the domains assessed - transmission, natural history, epidemiology and prevention and clinical management. RESULTS: Seventy participants were recruited (control n = 32, teach-back n = 38). Mean baseline knowledge score was 19.1 out of 23 with 55 (79%) participants scoring ≥17.3 (defined as high knowledge) (7). Sub-analysis of CHB knowledge domains identified focal deficits concerning transmission and whether HBV is curable. Knowledge scores were found to be positively associated with English proficiency and antiviral treatment experience (p < 0.05). Teach-back was associated with a significant increase in CHB knowledge at early recall (22.5 vs 18.7, p < 0.001) and at 1-month follow-up (21.9 vs 18.7, p < 0.001); there was no improvement in CHB knowledge associated with standard clinical consultant (early recall: 19.6 vs 19.4, p = 0.49, one-month follow-up: 19.5 vs 19.4, p = 0.94). CONCLUSION: In a tertiary hospital liver clinic population, baseline knowledge about CHB was good, but there were focal deficits concerning transmission and potential for cure. Teach-back was associated with improvement in CHB knowledge and it is a simple communication tool suitable for incorporation into a standard medical consultation.


Assuntos
Comunicação , Conhecimentos, Atitudes e Prática em Saúde , Hepatite B Crônica/epidemiologia , Educação de Pacientes como Assunto/métodos , Adulto , Austrália/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Projetos Piloto , Inquéritos e Questionários
13.
Genome Biol ; 20(1): 203, 2019 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-31597578

RESUMO

BACKGROUND: Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the importance of this type of analysis, more than 70 pathway analysis methods have been proposed so far. These can be categorized into two main categories: non-topology-based (non-TB) and topology-based (TB). Although some review papers discuss this topic from different aspects, there is no systematic, large-scale assessment of such methods. Furthermore, the majority of the pathway analysis approaches rely on the assumption of uniformity of p values under the null hypothesis, which is often not true. RESULTS: This article presents the most comprehensive comparative study on pathway analysis methods available to date. We compare the actual performance of 13 widely used pathway analysis methods in over 1085 analyses. These comparisons were performed using 2601 samples from 75 human disease data sets and 121 samples from 11 knockout mouse data sets. In addition, we investigate the extent to which each method is biased under the null hypothesis. Together, these data and results constitute a reliable benchmark against which future pathway analysis methods could and should be tested. CONCLUSION: Overall, the result shows that no method is perfect. In general, TB methods appear to perform better than non-TB methods. This is somewhat expected since the TB methods take into consideration the structure of the pathway which is meant to describe the underlying phenomena. We also discover that most, if not all, listed approaches are biased and can produce skewed results under the null.


Assuntos
Genômica/métodos , Animais , Humanos , Estatística como Assunto
14.
Nat Commun ; 10(1): 2674, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31209238

RESUMO

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Biologia Computacional/métodos , Neoplasias/tratamento farmacológico , Farmacogenética/métodos , Proteína ADAM17/antagonistas & inibidores , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Benchmarking , Biomarcadores Tumorais/genética , Linhagem Celular Tumoral , Biologia Computacional/normas , Conjuntos de Dados como Assunto , Antagonismo de Drogas , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/genética , Sinergismo Farmacológico , Genômica/métodos , Humanos , Terapia de Alvo Molecular/métodos , Mutação , Neoplasias/genética , Farmacogenética/normas , Fosfatidilinositol 3-Quinases/genética , Inibidores de Fosfoinositídeo-3 Quinase , Resultado do Tratamento
15.
Curr Protoc Bioinformatics ; 66(1): e76, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31125519

RESUMO

The three-dimensional (3D) interactions of chromatin regulate cell-type-specific gene expression, recombination, X-chromosome inactivation, and many other genomic processes. High-throughput chromatin conformation capture (Hi-C) technologies capture the structure of the chromatin on a global scale by measuring all-vs.-all interactions and can provide new insights into genomic regulation. The workflow presented here describes how to analyze and interpret a comparative Hi-C experiment. We describe the process of obtaining Hi-C data from public repositories and give suggestions for pre-processing pipelines for users who intend to analyze their own raw data. We then describe the data normalization and comparative analysis process. We present three protocols describing the use of the multiHiCcompare, diffHic, and FIND R packages, respectively, to perform a comparative analysis of Hi-C experiments. Finally, visualization of the results and downstream interpretation of the differentially interacting regions are discussed. The bulk of this tutorial uses the R programming environment, and the processes described can be performed with most operating systems and a single computer. © 2019 by John Wiley & Sons, Inc.


Assuntos
Cromatina/metabolismo , Bases de Dados de Ácidos Nucleicos , Software , Sítios de Ligação , Perfilação da Expressão Gênica , Simulação de Dinâmica Molecular
16.
Front Genet ; 10: 159, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30941158

RESUMO

Although massive amounts of condition-specific molecular profiles are being accumulated in public repositories every day, meaningful interpretation of these data remains a major challenge. In an effort to identify the biomarkers that describe the key biological phenomena for a given condition, several approaches have been developed over the past few years. However, the majority of these approaches either (i) do not consider the known intermolecular interactions, or (ii) do not integrate molecular data of multiple types (e.g., genomics, transcriptomics, proteomics, epigenomics, etc.), and thus potentially fail to capture the true biological changes responsible for complex diseases (e.g., cancer). In addition, these approaches often ignore the heterogeneity and study bias present in independent molecular cohorts. In this manuscript, we propose a novel multi-cohort and multi-omics meta-analysis framework that overcomes all three limitations mentioned above in order to identify robust molecular subnetworks that capture the key dynamic nature of a given biological condition. Our framework integrates multiple independent gene expression studies, unmatched DNA methylation studies, and protein-protein interactions to identify methylation-driven subnetworks. We demonstrate the proposed framework by constructing subnetworks related to two complex diseases: glioblastoma and low-grade gliomas. We validate the identified subnetworks by showing their ability to predict patients' clinical outcome on multiple independent validation cohorts.

17.
Plant J ; 99(5): 1003-1013, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31034103

RESUMO

Post-translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high-resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post-Translational Modifications (FAT-PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large-scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT-PTM database currently supports tools to visualize protein-centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein-centric metabolic pathways and groups of proteins that are co-modified by multiple PTMs. Overall, the FAT-PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

18.
Front Genet ; 10: 155, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30891064

RESUMO

A recent focus of computational biology has been to integrate the complementary information available in molecular profiles as well as in multiple network databases in order to identify connected regions that show significant changes under different conditions. This allows for capturing dynamic and condition-specific mechanisms of the underlying phenomena and disease stages. Here we review 22 such integrative approaches for active module identification published over the last decade. This article only focuses on tools that are currently available for use and are well-maintained. We compare these methods focusing on their primary features, integrative abilities, network structures, mathematical models, and implementations. We also provide real-world scenarios in which these methods have been successfully applied, as well as highlight outstanding challenges in the field that remain to be addressed. The main objective of this review is to help potential users and researchers to choose the best method that is suitable for their data and analysis purpose.

19.
Bioinformatics ; 35(16): 2843-2846, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-30590381

RESUMO

SUMMARY: Since cancer is a heterogeneous disease, tumor subtyping is crucial for improved treatment and prognosis. We have developed a subtype discovery tool, called PINSPlus, that is: (i) robust against noise and unstable quantitative assays, (ii) able to integrate multiple types of omics data in a single analysis and (iii) dramatically superior to established approaches in identifying known subtypes and novel subgroups with significant survival differences. Our validation on 12,158 samples from 44 datasets shows that PINSPlus vastly outperforms other approaches. The software is easy-to-use and can partition hundreds of patients in a few minutes on a personal computer. AVAILABILITY AND IMPLEMENTATION: The package is available at https://cran.r-project.org/package=PINSPlus. Data and R script used in this manuscript are available at https://bioinformatics.cse.unr.edu/software/PINSPlus/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

20.
Asian J Endosc Surg ; 12(4): 408-411, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30430745

RESUMO

INTRODUCTION: The benefit of mechanical bowel preparation (MBP) before open colon surgery has been debated over the last decade. The aim of this randomized controlled trial was to evaluate the effect of MBP on the outcome of patients who underwent elective laparoscopic colectomy. METHODS: Patients who were scheduled to undergo elective laparoscopic colon resection with primary anastomosis were randomly allocated to a preoperative MBP group (either two bottles of sodium phosphate or 2-L polyethylene glycol) or a no-MBP group. Anastomotic leakage and other complications such as surgical-site infection and extra-abdominal complications were recorded postoperatively. RESULTS: In this study, 122 patients were recruited and randomly allocated to the MBP group (n = 62) or the no-MBP group (n = 60). Demographic and clinical characteristics were not significantly different between the two groups. The rate of abdominal complications, including anastomotic leak and surgical-site infection, was 16.2% in the MBP group and 18.3% in the no-MBP group (P = 0.747). Anastomotic leakage occurred in four patients (6.5%) in the MBP group and in two patients (3.3%) in no-MBP group (P = 0.680). About 29% of patients in the MBP group still had either liquid or solid content in the bowel. No significant difference was found between the length of hospital stay in the MBP group and the no-MBP group (9.0 ± 2.9 vs 8.4 ± 1.9 days, P = 0.180). CONCLUSIONS: Elective laparoscopic colectomy without MBP is safe and offers acceptable postoperative morbidity.


Assuntos
Catárticos/administração & dosagem , Colectomia , Laparoscopia , Cuidados Pré-Operatórios/métodos , Anastomose Cirúrgica , Fístula Anastomótica/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fosfatos/administração & dosagem , Polietilenoglicóis/administração & dosagem , Infecção da Ferida Cirúrgica/epidemiologia
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