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  1. Article: Gene Screening for Prognosis of Non-Muscle-Invasive Bladder Carcinoma under Competing Risks Endpoints.

    Ke, Chenlu / Bandyopadhyay, Dipankar / Sarkar, Devanand

    Cancers

    2023  Volume 15, Issue 2

    Abstract: Background: Discovering clinically useful molecular markers for predicting the survival of patients diagnosed with non−muscle-invasive bladder cancer can provide insights into cancer dynamics and improve treatment outcomes. However, the presence of ... ...

    Abstract Background: Discovering clinically useful molecular markers for predicting the survival of patients diagnosed with non−muscle-invasive bladder cancer can provide insights into cancer dynamics and improve treatment outcomes. However, the presence of competing risks (CR) endpoints complicates the estimation and inferential framework. There is also a lack of statistical analysis tools and software for coping with the high-throughput nature of these data, in terms of marker screening and selection. Aims: To propose a gene screening procedure for proportional subdistribution hazards regression under a CR framework, and illustrate its application in using molecular profiling to predict survival for non-muscle invasive bladder carcinoma. Methods: Tumors from 300 patients diagnosed with bladder cancer were analyzed for genomic abnormalities while controlling for clinically important covariates. Genes with expression patterns that were associated with survival were identified through a screening procedure based on proportional subdistribution hazards regression. A molecular predictor of risk was constructed and examined for prediction accuracy. Results: A six-gene signature was found to be a significant predictor associated with survival of non−muscle-invasive bladder cancer, subject to competing risks after adjusting for age, gender, reevaluated WHO grade, stage and BCG/MMC treatment (p-value < 0.001). Conclusion: The proposed gene screening procedure can be used to discover molecular determinants of survival for non−muscle-invasive bladder cancer and in general facilitate high-throughput competing risks data analysis with easy implementation.
    Language English
    Publishing date 2023-01-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15020379
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Partial sufficient variable screening with categorical controls

    Ke, Chenlu / Yang, Wei / Yuan, Qingcong / Li, Lu

    Computational Statistics and Data Analysis. 2023 Nov., v. 187 p.107784-

    2023  

    Abstract: Variable screening as a fast and effective dimension reduction tool plays an important role in analyzing ultrahigh dimensional data. While a very large number of actual datasets contain both continuous and categorical variables, existing methods are ... ...

    Abstract Variable screening as a fast and effective dimension reduction tool plays an important role in analyzing ultrahigh dimensional data. While a very large number of actual datasets contain both continuous and categorical variables, existing methods are mostly designed for continuous data. Partial sufficient variable screening, which aims to reduce the predictive set of primary interest without loss of regression information in the presence of some control variables, is proposed with theoretical guarantees. Specifically, for regression analyses involving mixed types of predictors, variable screening is approached under the notion of sufficiency by constraining the reduction of the continuous variables through the subpopulations identified by the categorical variables. The effectiveness of the proposed method is demonstrated through simulation studies encompassing a variety of regression and classification models, and an application in prognostic gene screening for diffuse large-B-cell lymphoma.
    Keywords data analysis ; data collection ; genes ; lymphoma ; statistics ; Categorical data ; Conditional independence ; Sufficient dimension reduction ; Sure screening ; Ultrahigh dimensional data analysis
    Language English
    Dates of publication 2023-11
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 1478763-5
    ISSN 0167-9473
    ISSN 0167-9473
    DOI 10.1016/j.csda.2023.107784
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Gene Screening in High-Throughput Right-Censored Lung Cancer Data.

    Ke, Chenlu / Bandyopadhyay, Dipankar / Acunzo, Mario / Winn, Robert

    Onco

    2022  Volume 2, Issue 4, Page(s) 305–318

    Abstract: Background: Advances in sequencing technologies have allowed collection of massive genome-wide information that substantially advances lung cancer diagnosis and prognosis. Identifying influential markers for clinical endpoints of interest has been an ... ...

    Abstract Background: Advances in sequencing technologies have allowed collection of massive genome-wide information that substantially advances lung cancer diagnosis and prognosis. Identifying influential markers for clinical endpoints of interest has been an indispensable and critical component of the statistical analysis pipeline. However, classical variable selection methods are not feasible or reliable for high-throughput genetic data. Our objective is to propose a model-free gene screening procedure for high-throughput right-censored data, and to develop a predictive gene signature for lung squamous cell carcinoma (LUSC) with the proposed procedure.
    Methods: A gene screening procedure was developed based on a recently proposed independence measure. The Cancer Genome Atlas (TCGA) data on LUSC was then studied. The screening procedure was conducted to narrow down the set of influential genes to 378 candidates. A penalized Cox model was then fitted to the reduced set, which further identified a 6-gene signature for LUSC prognosis. The 6-gene signature was validated on datasets from the Gene Expression Omnibus.
    Results: Both model-fitting and validation results reveal that our method selected influential genes that lead to biologically sensible findings as well as better predictive performance, compared to existing alternatives. According to our multivariable Cox regression analysis, the 6-gene signature was indeed a significant prognostic factor (
    Conclusions: Gene screening as a fast dimension reduction technique plays an important role in analyzing high-throughput data. The main contribution of this paper is to introduce a fundamental yet pragmatic model-free gene screening approach that aids statistical analysis of right-censored cancer data, and provide a lateral comparison with other available methods in the context of LUSC.
    Language English
    Publishing date 2022-10-17
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7523
    ISSN (online) 2673-7523
    DOI 10.3390/onco2040017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Independence index sufficient variable screening for categorical responses

    Yuan, Qingcong / Chen, Xianyan / Ke, Chenlu / Yin, Xiangrong

    Computational statistics & data analysis. 2022 Oct., v. 174

    2022  

    Abstract: Variable screening is very popular in modern data analysis and is particularly useful for large p small n data. In this paper, a novel two-stage sufficient variable screening procedure, especially when the response is categorical is proposed. This ... ...

    Abstract Variable screening is very popular in modern data analysis and is particularly useful for large p small n data. In this paper, a novel two-stage sufficient variable screening procedure, especially when the response is categorical is proposed. This procedure is very general and model-free, thus is robust against model mis-specification. In addition, the proposed procedure always improves existing screening approach in literature which only uses marginal relation. Asymptotic results and sure screening properties of the proposed methods are proved. Numerical studies and real data analysis are provided to demonstrate the advantages of the proposed method.
    Keywords data analysis ; models ; screening ; statistics
    Language English
    Dates of publication 2022-10
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1478763-5
    ISSN 0167-9473
    ISSN 0167-9473
    DOI 10.1016/j.csda.2022.107530
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Prescribing patterns of opioid analgesics in a dental setting: 2013-2018.

    Miller, Craig S / Ke, Chenlu / Witty, Jeffrey T / Nagarajan, Radha

    Oral surgery, oral medicine, oral pathology and oral radiology

    2020  Volume 130, Issue 4, Page(s) 402–410

    Abstract: Objective: Analgesic prescribing patterns are influenced by internal and external factors. Understanding these factors could help improve prescribing practices.: Study design: We conducted a retrospective analysis of electronic health records with ... ...

    Abstract Objective: Analgesic prescribing patterns are influenced by internal and external factors. Understanding these factors could help improve prescribing practices.
    Study design: We conducted a retrospective analysis of electronic health records with regard to analgesic prescriptions written from 2013 through 2018 at the University of Kentucky College of Dentistry. Deidentified information (age, gender, dental procedures, analgesic drug, quantity, and refills) were recorded and studied with respect to national guidelines and recent state legislation using the χ
    Results: Opioids comprised 74.9% of the 17,099 analgesic prescriptions written. Extractions were most commonly associated with opioid prescriptions. Multivariate analysis showed that (1) older patients were more likely to receive an opioid prescription (P < .01) but with fewer pills (P < .01); (2) surgical extractions were associated with a lower opioid prescription rate (P < .01) but more opioid pills per prescription compared with nonsurgical extractions (P < .01); and (3) the odds of receiving an opioid prescription and the number of opioid pills prescribed decreased over year after release of the national guideline (P < .01) and after enactment of state legislation (P < .01).
    Conclusions: Regulations and guidelines were associated with reduction in opioid prescriptions.
    MeSH term(s) Analgesics, Opioid/therapeutic use ; Electronic Health Records ; Humans ; Practice Patterns, Dentists' ; Practice Patterns, Physicians' ; Retrospective Studies
    Chemical Substances Analgesics, Opioid
    Language English
    Publishing date 2020-06-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2650843-6
    ISSN 2212-4411 ; 2212-4403
    ISSN (online) 2212-4411
    ISSN 2212-4403
    DOI 10.1016/j.oooo.2020.06.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ul III Zs.121: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  6. Article ; Online: Adipose-Derived Inflammatory and Coagulant Mediators in Patients With Sepsis.

    Zwischenberger, Brittany A / Balasuriya, Beverly K / Harris, Dwight D / Nataraj, Nisha / Owen, Allison M / Bruno, Maria E C / Mukherjee, Sujata / Ortiz-Soriano, Victor / O'Connor, William / Ke, Chenlu / Stromberg, Arnold J / Chang, Phillip K / Neyra, Javier A / Saito, Hiroshi / Starr, Marlene E

    Shock (Augusta, Ga.)

    2020  Volume 55, Issue 5, Page(s) 596–606

    Abstract: Abstract: Results from preclinical sepsis studies using rodents are often criticized as not being reproducible in humans. Using a murine model, we previously reported that visceral adipose tissues (VAT) are highly active during the acute inflammatory ... ...

    Abstract Abstract: Results from preclinical sepsis studies using rodents are often criticized as not being reproducible in humans. Using a murine model, we previously reported that visceral adipose tissues (VAT) are highly active during the acute inflammatory response, serving as a major source of inflammatory and coagulant mediators. The purpose of this study was to determine whether these findings are recapitulated in patients with sepsis and to evaluate their clinical significance. VAT and plasma were obtained from patients undergoing intra-abdominal operations with noninflammatory conditions (control), local inflammation, or sepsis. In mesenteric and epiploic VAT, gene expression of pro-inflammatory (TNFα, IL-6, IL-1α, IL-1β) and pro-coagulant (PAI-1, PAI-2, TSP-1, TF) mediators was increased in sepsis compared with control and local inflammation groups. In the omentum, increased expression was limited to IL-1β, PAI-1, and PAI-2, showing a depot-specific regulation. Histological analyses showed little correlation between cellular infiltration and gene expression, indicating a resident source of these mediators. Notably, a strong correlation between PAI-1 expression in VAT and circulating protein levels was observed, both being positively associated with markers of acute kidney injury (AKI). In another cohort of septic patients stratified by incidence of AKI, circulating PAI-1 levels were higher in those with versus without AKI, thus extending these findings beyond intra-abdominal cases. This study is the first to translate upregulation of VAT mediators in sepsis from mouse to human. Collectively, the data suggest that development of AKI in septic patients is associated with high plasma levels of PAI-1, likely derived from resident cells within VAT.
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; Blood Coagulation Factors/physiology ; Female ; Humans ; Inflammation Mediators/physiology ; Intra-Abdominal Fat/immunology ; Male ; Middle Aged ; Sepsis/blood ; Sepsis/immunology
    Chemical Substances Blood Coagulation Factors ; Inflammation Mediators
    Language English
    Publishing date 2020-07-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1185432-7
    ISSN 1540-0514 ; 1073-2322
    ISSN (online) 1540-0514
    ISSN 1073-2322
    DOI 10.1097/SHK.0000000000001579
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3985: Show issues Location:
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  7. Article: Status epilepticus alert reduces time to administration of second-line antiseizure medications.

    Villamar, Mauricio F / Cook, Aaron M / Ke, Chenlu / Xu, Yan / Clay, Jordan L / Dolbec, Katelyn S / Ward-Mitchell, Rachel / Goldstein, Larry B / Bensalem-Owen, Meriem

    Neurology. Clinical practice

    2018  Volume 8, Issue 6, Page(s) 486–491

    Abstract: Background: Status epilepticus (SE) is a neurologic emergency with high morbidity and mortality. Delays in SE treatment are common in clinical practice and can be associated with poorer outcomes. Our goal was to determine whether the implementation of ... ...

    Abstract Background: Status epilepticus (SE) is a neurologic emergency with high morbidity and mortality. Delays in SE treatment are common in clinical practice and can be associated with poorer outcomes. Our goal was to determine whether the implementation of an SE alert protocol improves time to administration of a second-line antiseizure medication (ASM) in hospitalized adults.
    Methods: We developed and implemented an inpatient SE alert system. A quasiexperimental cohort study was performed. We analyzed all patients aged 18-85 years who were managed at the University of Kentucky Medical Center using the SE alert protocol between March 2015 and June 2017 (n = 19). Controls were the first 20 consecutive patients treated for SE over the same time period, but who were managed with usual care (i.e., without SE alert protocol).
    Results: Time to administration of a second-line ASM was shorter with the use of the SE alert system (22.21 ± 3.44 minutes) compared to usual care (58.30 ± 6.72 minutes;
    Conclusion: Implementation of an SE alert system led to a marked improvement in time to administration of a second-line ASM.
    Classification of evidence: This study provides Class III evidence that for adult inpatients treated for SE, implementation of an SE alert protocol reduces time to administration of second-line ASM.
    Language English
    Publishing date 2018-09-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2645818-4
    ISSN 2163-0933 ; 2163-0402
    ISSN (online) 2163-0933
    ISSN 2163-0402
    DOI 10.1212/CPJ.0000000000000544
    Database MEDical Literature Analysis and Retrieval System OnLINE

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