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1. Lift the Veil of Breast Cancers Using 4 or Fewer Critical Genes

   https://doi.org/10.1177/11769351221076360  

   Zhang, Zhengjun ( January 2022 , Cancer Informatics)

   Known genes in the breast cancer study literature could not be confirmed whether they are vital to breast cancer formations due to lack of convincing accuracy, although they may be biologically directly related to breast cancer based on present biological knowledge. It is hoped vital genes can be identified with the highest possible accuracy, for example, 100% accuracy and convincing causal patterns beyond what has been known in breast cancer. One hope is that finding gene-gene interaction signatures and functional effects may solve the puzzle. This research uses a recently developed competing linear factor analysis method in differentially expressed gene detection to advance the study of breast cancer formation. Surprisingly, 3 genes are detected to be differentially expressed in TNBC and non-TNBC (Her2, Luminal A, Luminal B) samples with 100% sensitivity and 100% specificity in 1 study of triple-negative breast cancers (TNBC, with 54 675 genes and 265 samples). These 3 genes show a clear signature pattern of how TNBC patients can be grouped. For another TNBC study (with 54 673 genes and 66 samples), 4 genes bring the same accuracy of 100% sensitivity and 100% specificity. Four genes are found to have the same accuracy of 100% sensitivity and 100% specificity in 1 breast cancer study (with 54 675 genes and 121 samples), and the same 4 genes bring an accuracy of 100% sensitivity and 96.5% specificity in the fourth breast cancer study (with 60 483 genes and 1217 samples). These results show the 4-gene-based classifiers are robust and accurate. The detected genes naturally classify patients into subtypes, for example, 7 subtypes. These findings demonstrate the clearest gene-gene interaction patterns and functional effects with the smallest numbers of genes and the highest accuracy compared with findings reported in the literature. The 4 genes are considered to be essential for breast cancer studies and practice. They can provide focused, targeted researches and precision medicine for each subtype of breast cancer. New breast cancer disease types may be detected using the classified subtypes, and hence new effective therapies can be developed. 

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2. Invention of 3Mint for feature grouping and scoring in multi-omics

   https://doi.org/10.3389/fgene.2023.1093326  

   Unlu Yazici, Miray ; Marron, J. S. ; Bakir-Gungor, Burcu ; Zou, Fei ; Yousef, Malik ( March 2023 , Frontiers in Genetics)

   Advanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense studies with immense amounts of biological information have boosted the discovery of molecular biomarkers. Cancer is one of the leading causes of death around the world in recent years. Elucidation of genomic and epigenetic factors in Breast Cancer (BRCA) can provide a roadmap to uncover the disease mechanisms. Accordingly, unraveling the possible systematic connections between-omics data types and their contribution to BRCA tumor progression is crucial. In this study, we have developed a novel machine learning (ML) based integrative approach for multi-omics data analysis. This integrative approach combines information from gene expression (mRNA), microRNA (miRNA) and methylation data. Due to the complexity of cancer, this integrated data is expected to improve the prediction, diagnosis and treatment of disease through patterns only available from the 3-way interactions between these 3-omics datasets. In addition, the proposed method bridges the interpretation gap between the disease mechanisms that drive onset and progression. Our fundamental contribution is the 3 Multi-omics integrative tool (3Mint). This tool aims to perform grouping and scoring of groups using biological knowledge. Another major goal is improved gene selection via detection of novel groups of cross-omics biomarkers. Performance of 3Mint is assessed using different metrics. Our computational performance evaluations showed that the 3Mint classifies the BRCA molecular subtypes with lower number of genes when compared to the miRcorrNet tool which uses miRNA and mRNA gene expression profiles in terms of similar performance metrics (95% Accuracy). The incorporation of methylation data in 3Mint yields a much more focused analysis. The 3Mint tool and all other supplementary files are available at https://github.com/malikyousef/3Mint/ . 

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3. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform

   https://doi.org/10.1186/s40537-021-00423-z  

   Villanustre, Flavio ; Chala, Arjuna ; Dev, Roger ; Xu, Lili ; LexisNexis, Jesse Shaw ; Furht, Borko ; Khoshgoftaar, Taghi ( December 2021 , Journal of Big Data)

   Abstract This project is funded by the US National Science Foundation (NSF) through their NSF RAPID program under the title “Modeling Corona Spread Using Big Data Analytics.” The project is a joint effort between the Department of Computer & Electrical Engineering and Computer Science at FAU and a research group from LexisNexis Risk Solutions. The novel coronavirus Covid-19 originated in China in early December 2019 and has rapidly spread to many countries around the globe, with the number of confirmed cases increasing every day. Covid-19 is officially a pandemic. It is a novel infection with serious clinical manifestations, including death, and it has reached at least 124 countries and territories. Although the ultimate course and impact of Covid-19 are uncertain, it is not merely possible but likely that the disease will produce enough severe illness to overwhelm the worldwide health care infrastructure. Emerging viral pandemics can place extraordinary and sustained demands on public health and health systems and on providers of essential community services. Modeling the Covid-19 pandemic spread is challenging. But there are data that can be used to project resource demands. Estimates of the reproductive number (R) of SARS-CoV-2 show that at the beginning of the epidemic, each infected person spreads the virus to at least two others, on average (Emanuel et al. in N Engl J Med. 2020, Livingston and Bucher in JAMA 323(14):1335, 2020). A conservatively low estimate is that 5 % of the population could become infected within 3 months. Preliminary data from China and Italy regarding the distribution of case severity and fatality vary widely (Wu and McGoogan in JAMA 323(13):1239–42, 2020). A recent large-scale analysis from China suggests that 80 % of those infected either are asymptomatic or have mild symptoms; a finding that implies that demand for advanced medical services might apply to only 20 % of the total infected. Of patients infected with Covid-19, about 15 % have severe illness and 5 % have critical illness (Emanuel et al. in N Engl J Med. 2020). Overall, mortality ranges from 0.25 % to as high as 3.0 % (Emanuel et al. in N Engl J Med. 2020, Wilson et al. in Emerg Infect Dis 26(6):1339, 2020). Case fatality rates are much higher for vulnerable populations, such as persons over the age of 80 years (> 14 %) and those with coexisting conditions (10 % for those with cardiovascular disease and 7 % for those with diabetes) (Emanuel et al. in N Engl J Med. 2020). Overall, Covid-19 is substantially deadlier than seasonal influenza, which has a mortality of roughly 0.1 %. Public health efforts depend heavily on predicting how diseases such as those caused by Covid-19 spread across the globe. During the early days of a new outbreak, when reliable data are still scarce, researchers turn to mathematical models that can predict where people who could be infected are going and how likely they are to bring the disease with them. These computational methods use known statistical equations that calculate the probability of individuals transmitting the illness. Modern computational power allows these models to quickly incorporate multiple inputs, such as a given disease’s ability to pass from person to person and the movement patterns of potentially infected people traveling by air and land. This process sometimes involves making assumptions about unknown factors, such as an individual’s exact travel pattern. By plugging in different possible versions of each input, however, researchers can update the models as new information becomes available and compare their results to observed patterns for the illness. In this paper we describe the development a model of Corona spread by using innovative big data analytics techniques and tools. We leveraged our experience from research in modeling Ebola spread (Shaw et al. Modeling Ebola Spread and Using HPCC/KEL System. In: Big Data Technologies and Applications 2016 (pp. 347-385). Springer, Cham) to successfully model Corona spread, we will obtain new results, and help in reducing the number of Corona patients. We closely collaborated with LexisNexis, which is a leading US data analytics company and a member of our NSF I/UCRC for Advanced Knowledge Enablement. The lack of a comprehensive view and informative analysis of the status of the pandemic can also cause panic and instability within society. Our work proposes the HPCC Systems Covid-19 tracker, which provides a multi-level view of the pandemic with the informative virus spreading indicators in a timely manner. The system embeds a classical epidemiological model known as SIR and spreading indicators based on causal model. The data solution of the tracker is built on top of the Big Data processing platform HPCC Systems, from ingesting and tracking of various data sources to fast delivery of the data to the public. The HPCC Systems Covid-19 tracker presents the Covid-19 data on a daily, weekly, and cumulative basis up to global-level and down to the county-level. It also provides statistical analysis for each level such as new cases per 100,000 population. The primary analysis such as Contagion Risk and Infection State is based on causal model with a seven-day sliding window. Our work has been released as a publicly available website to the world and attracted a great volume of traffic. The project is open-sourced and available on GitHub. The system was developed on the LexisNexis HPCC Systems, which is briefly described in the paper. 

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4. Development and External Validation of a Machine Learning Tool to Rule Out COVID-19 Among Adults in the Emergency Department Using Routine Blood Tests: A Large, Multicenter, Real-World Study

   https://doi.org/10.2196/24048  

   Plante, Timothy B ; Blau, Aaron M ; Berg, Adrian N ; Weinberg, Aaron S ; Jun, Ik C ; Tapson, Victor F ; Kanigan, Tanya S ; Adib, Artur B ( January 2020 , Journal of Medical Internet Research)

   null (Ed.)

   Background Conventional diagnosis of COVID-19 with reverse transcription polymerase chain reaction (RT-PCR) testing (hereafter, PCR) is associated with prolonged time to diagnosis and significant costs to run the test. The SARS-CoV-2 virus might lead to characteristic patterns in the results of widely available, routine blood tests that could be identified with machine learning methodologies. Machine learning modalities integrating findings from these common laboratory test results might accelerate ruling out COVID-19 in emergency department patients. Objective We sought to develop (ie, train and internally validate with cross-validation techniques) and externally validate a machine learning model to rule out COVID 19 using only routine blood tests among adults in emergency departments. Methods Using clinical data from emergency departments (EDs) from 66 US hospitals before the pandemic (before the end of December 2019) or during the pandemic (March-July 2020), we included patients aged ≥20 years in the study time frame. We excluded those with missing laboratory results. Model training used 2183 PCR-confirmed cases from 43 hospitals during the pandemic; negative controls were 10,000 prepandemic patients from the same hospitals. External validation used 23 hospitals with 1020 PCR-confirmed cases and 171,734 prepandemic negative controls. The main outcome was COVID 19 status predicted using same-day routine laboratory results. Model performance was assessed with area under the receiver operating characteristic (AUROC) curve as well as sensitivity, specificity, and negative predictive value (NPV). Results Of 192,779 patients included in the training, external validation, and sensitivity data sets (median age decile 50 [IQR 30-60] years, 40.5% male [78,249/192,779]), AUROC for training and external validation was 0.91 (95% CI 0.90-0.92). Using a risk score cutoff of 1.0 (out of 100) in the external validation data set, the model achieved sensitivity of 95.9% and specificity of 41.7%; with a cutoff of 2.0, sensitivity was 92.6% and specificity was 59.9%. At the cutoff of 2.0, the NPVs at a prevalence of 1%, 10%, and 20% were 99.9%, 98.6%, and 97%, respectively. Conclusions A machine learning model developed with multicenter clinical data integrating commonly collected ED laboratory data demonstrated high rule-out accuracy for COVID-19 status, and might inform selective use of PCR-based testing. 

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5. Study on U.S. Parents' Divisions of Labor During COVID-19, Waves 1-2

   https://doi.org/10.3886/E183142V2  

   Carlson, Daniel L. ; Petts, Richard J. ( January 2022 , ICPSR - Interuniversity Consortium for Political and Social Research)

   The COVID-19 pandemic has dramatically altered family life in the United States. Over the long duration of the pandemic, parents had to adapt to shifting work conditions, virtual schooling, the closure of daycare facilities, and the stress of not only managing households without domestic and care supports but also worrying that family members may contract the novel coronavirus. Reports early in the pandemic suggest that these burdens have fallen disproportionately on mothers, creating concerns about the long-term implications of the pandemic for gender inequality and mothers’ well-being. Nevertheless, less is known about how parents’ engagement in domestic labor and paid work has changed throughout the pandemic, what factors may be driving these changes, and what the long-term consequences of the pandemic may be for the gendered division of labor and gender inequality more generally.
   
   The Study on U.S. Parents’ Divisions of Labor During COVID-19 (SPDLC) collects longitudinal survey data from partnered U.S. parents that can be used to assess changes in parents’ divisions of domestic labor, divisions of paid labor, and well-being throughout and after the COVID-19 pandemic. The goal of SPDLC is to understand both the short- and long-term impacts of the pandemic for the gendered division of labor, work-family issues, and broader patterns of gender inequality.
   
   Survey data for this study is collected using Prolifc (www.prolific.co), an opt-in online platform designed to facilitate scientific research. The sample is comprised U.S. adults who were residing with a romantic partner and at least one biological child (at the time of entry into the study). In each survey, parents answer questions about both themselves and their partners. Wave 1 of SPDLC was conducted in April 2020, and parents who participated in Wave 1 were asked about their division of labor both prior to (i.e., early March 2020) and one month after the pandemic began. Wave 2 of SPDLC was collected in November 2020. Parents who participated in Wave 1 were invited to participate again in Wave 2, and a new cohort of parents was also recruited to participate in the Wave 2 survey. Wave 3 of SPDLC was collected in October 2021. Parents who participated in either of the first two waves were invited to participate again in Wave 3, and another new cohort of parents was also recruited to participate in the Wave 3 survey. This research design (follow-up survey of panelists and new cross-section of parents at each wave) will continue through 2024, culminating in six waves of data spanning the period from March 2020 through October 2024. An estimated total of approximately 6,500 parents will be surveyed at least once throughout the duration of the study.
   
   SPDLC data will be released to the public two years after data is collected; Waves 1 and 2 are currently publicly available. Wave 3 will be publicly available in October 2023, with subsequent waves becoming available yearly. Data will be available to download in both SPSS (.sav) and Stata (.dta) formats, and the following data files will be available: (1) a data file for each individual wave, which contains responses from all participants in that wave of data collection, (2) a longitudinal panel data file, which contains longitudinal follow-up data from all available waves, and (3) a repeated cross-section data file, which contains the repeated cross-section data (from new respondents at each wave) from all available waves. Codebooks for each survey wave and a detailed user guide describing the data are also available. Response Rates: Of the 1,157 parents who participated in Wave 1, 828 (72%) also participated in the Wave 2 study. Presence of Common Scales: The following established scales are included in the survey:
   

   • Self-Efficacy, adapted from Pearlin's mastery scale (Pearlin et al., 1981) and the Rosenberg self-esteem scale (Rosenberg, 2015) and taken from the American Changing Lives Survey
   • Communication with Partner, taken from the Marriage and Relationship Survey (Lichter & Carmalt, 2009)
     
   • Gender Attitudes, taken from the National Survey of Families and Households (Sweet & Bumpass, 1996)
     
   • Depressive Symptoms (CES-D-10)
   • Stress, measured using Cohen's Perceived Stress Scale (Cohen, Kamarck, & Mermelstein, 1983)
     

   Full details about these scales and all other items included in the survey can be found in the user guide and codebook
   The second wave of the SPDLC was fielded in November 2020 in two stages. In the first stage, all parents who participated in W1 of the SPDLC and who continued to reside in the United States were re-contacted and asked to participate in a follow-up survey. The W2 survey was posted on Prolific, and messages were sent via Prolific’s messaging system to all previous participants. Multiple follow-up messages were sent in an attempt to increase response rates to the follow-up survey. Of the 1,157 respondents who completed the W1 survey, 873 at least started the W2 survey. Data quality checks were employed in line with best practices for online surveys (e.g., removing respondents who did not complete most of the survey or who did not pass the attention filters). After data quality checks, 5.2% of respondents were removed from the sample, resulting in a final sample size of 828 parents (a response rate of 72%).
   
   In the second stage, a new sample of parents was recruited. New parents had to meet the same sampling criteria as in W1 (be at least 18 years old, reside in the United States, reside with a romantic partner, and be a parent living with at least one biological child). Also similar to the W1 procedures, we oversampled men, Black individuals, individuals who did not complete college, and individuals who identified as politically conservative to increase sample diversity. A total of 1,207 parents participated in the W2 survey. Data quality checks led to the removal of 5.7% of the respondents, resulting in a final sample size of new respondents at Wave 2 of 1,138 parents.
   
   In both stages, participants were informed that the survey would take approximately 20 minutes to complete. All panelists were provided monetary compensation in line with Prolific’s compensation guidelines, which require that all participants earn above minimum wage for their time participating in studies.
   To be included in SPDLC, respondents had to meet the following sampling criteria at the time they enter the study: (a) be at least 18 years old, (b) reside in the United States, (c) reside with a romantic partner (i.e., be married or cohabiting), and (d) be a parent living with at least one biological child. Follow-up respondents must be at least 18 years old and reside in the United States, but may experience changes in relationship and resident parent statuses. Smallest Geographic Unit: U.S. State

   This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. In accordance with this license, all users of these data must give appropriate credit to the authors in any papers, presentations, books, or other works that use the data. A suggested citation to provide attribution for these data is included below:            
   
   Carlson, Daniel L. and Richard J. Petts. 2022. Study on U.S. Parents’ Divisions of Labor During COVID-19 User Guide: Waves 1-2.  

   To help provide estimates that are more representative of U.S. partnered parents, the SPDLC includes sampling weights. Weights can be included in statistical analyses to make estimates from the SPDLC sample representative of U.S. parents who reside with a romantic partner (married or cohabiting) and a child aged 18 or younger based on age, race/ethnicity, and gender. National estimates for the age, racial/ethnic, and gender profile of U.S. partnered parents were obtained using data from the 2020 Current Population Survey (CPS). Weights were calculated using an iterative raking method, such that the full sample in each data file matches the nationally representative CPS data in regard to the gender, age, and racial/ethnic distributions within the data. This variable is labeled CPSweightW2 in the Wave 2 dataset, and CPSweightLW2 in the longitudinal dataset (which includes Waves 1 and 2). There is not a weight variable included in the W1-W2 repeated cross-section data file.
    

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