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David Haro Alonso, Miles N Wernick, Yongyi Yang, Guido Germano, Daniel S Berman, Piotr Slomka
BACKGROUND: We developed machine-learning (ML) models to estimate a patient's risk of cardiac death based on adenosine myocardial perfusion SPECT (MPS) and associated clinical data, and compared their performance to baseline logistic regression (LR). We demonstrated an approach to visually convey the reasoning behind a patient's risk to provide insight to clinicians beyond that of a "black box." METHODS: We trained multiple models using 122 potential clinical predictors (features) for 8321 patients, including 551 cases of subsequent cardiac death...
March 14, 2018: Journal of Nuclear Cardiology: Official Publication of the American Society of Nuclear Cardiology
Cristina Di Poto, Shisi He, Rency S Varghese, Yi Zhao, Alessia Ferrarini, Shan Su, Abdullah Karabala, Mesfin Redi, Hassen Mamo, Amol S Rangnekar, Thomas M Fishbein, Alexander H Kroemer, Mahlet G Tadesse, Rabindra Roy, Zaki A Sherif, Deepak Kumar, Habtom W Ressom
Disparities in hepatocellular carcinoma (HCC) incidence and survival have been observed between ethnic groups including African-Americans (AA) and European-Americans (EA). The evaluation of the changes in the levels of metabolites in samples stratified by race could provide a snapshot of ethnically diverse disease related pathways and identify reliable biomarkers. In this study, we considered AA and EA to investigate metabolites that may be associated with HCC in a race-specific manner. The levels of 46 metabolites in plasma samples, collected from patients recruited at MedStar Georgetown University Hospital, were analyzed by Agilent GC-qMS in selected ion monitoring (SIM) mode...
2018: PloS One
Maria C Mora-Pinzon, Amy Trentham-Dietz, Ronald E Gangnon, Scott V Adams, John M Hampton, Elizabeth Burnside, Martin M Shafer, Polly A Newcomb
PURPOSE: Heavy metals and other elements may act as breast carcinogens due to estrogenic activity. We investigated associations between urine concentrations of a panel of elements and breast density. METHODS: Mammographic density categories were abstracted from radiology reports of 725 women aged 40-65 yr in the Avon Army of Women. A panel of 27 elements was quantified in urine using high resolution magnetic sector inductively coupled plasma mass spectrometry. We applied LASSO (least absolute shrinkage and selection operator) logistic regression to the 27 elements and calculated odds ratios (OR) and 95% confidence intervals (CI) for dense vs...
March 14, 2018: Nutrition and Cancer
Jonathan Preszler, David K Marcus, John F Edens, Barbara E McDermott
The question of which features represent the most central components of psychopathy remains unresolved and is the subject of considerable debate. Network analysis, which is a relatively new way to conceptualize mental disorders that emphasizes complex causal systems, provides a means to graphically and quantitatively describe the centrality of the various symptoms of a disorder. We applied association and adaptive LASSO networks on two samples of forensic patients. The first sample included forensic inpatients (N = 277) who were administered the Psychopathy Checklist-Revised (Hare, 2003), and the second sample included patients who previously had been civilly committed (N = 1136), who were administered the Psychopathy Checklist: Screening Version (Hart, Cox, & Hare, 1995)...
February 2018: Journal of Abnormal Psychology
Yiming Li, Zenghui Qian, Kaibin Xu, Kai Wang, Xing Fan, Shaowu Li, Tao Jiang, Xing Liu, Yinyan Wang
Background: P53 mutation status is a pivotal biomarker for gliomas. Here, we developed a machine-learning model to predict p53 status in lower-grade gliomas based on radiomic features extracted from conventional magnetic resonance (MR) images. Methods: Preoperative MR images were retrospectively obtained from 272 patients with primary grade II/III gliomas. The patients were randomly allocated in a 2:1 ratio to a training ( n  = 180) or validation ( n  = 92) set...
2018: NeuroImage: Clinical
Qian Du, Chi Zhang, Xiaofeng Zhu, Xiaoying Liang, Chi Zhang, Vivek Verma, Kenneth Follet, Shuo Wang, Qiyong Fan, Rongtao Ma, Sumin Zhou, Dandan Zheng
OBJECTIVES: To apply advanced statistical and computational methodology in evaluating the impact of anatomical and technical variables on normal tissue dosimetry of trigeminal neuralgia (TN) stereotactic radiosurgery (SRS). METHODS: Forty patients treated with LINAC-based TN SRS with 90 Gy maximum dose were randomly selected for the study. Parameters extracted from the treatment plans for the study included three dosimetric output variables: the maximum dose to the brainstem (BSmax), the volume of brainstem that received at least 10 Gy (V10BS), and the volume of normal brain that received at least 12 Gy (V12)...
March 9, 2018: Medical Physics
Alexander P Christensen, Yoed N Kenett, Tomaso Aste, Paul J Silvia, Thomas R Kwapil
Schizotypy is a multidimensional construct that provides a useful framework for understanding the etiology, development, and risk for schizophrenia-spectrum disorders. Past research has applied traditional methods, such as factor analysis, to uncovering common dimensions of schizotypy. In the present study, we aimed to advance the construct of schizotypy, measured by the Wisconsin Schizotypy Scales-Short Forms (WSS-SF), beyond this general scope by applying two different psychometric network filtering approaches-the state-of-the-art approach (lasso), which has been employed in previous studies, and an alternative approach (information-filtering networks; IFNs)...
March 8, 2018: Behavior Research Methods
Deepthi P Varikuti, Sarah Genon, Aristeidis Sotiras, Holger Schwender, Felix Hoffstaedter, Kaustubh R Patil, Christiane Jockwitz, Svenja Caspers, Susanne Moebus, Katrin Amunts, Christos Davatzikos, Simon B Eickhoff
The relationship between grey matter volume (GMV) patterns and age can be captured by multivariate pattern analysis, allowing prediction of individuals' age based on structural imaging. Raw data, voxel-wise GMV and non-sparse factorization (with Principal Component Analysis, PCA) show good performance but do not promote relatively localized brain components for post-hoc examinations. Here we evaluated a non-negative matrix factorization (NNMF) approach to provide a reduced, but also interpretable representation of GMV data in age prediction frameworks in healthy and clinical populations...
March 5, 2018: NeuroImage
Lauren P Grant, Chris Gennings, Edmond P Wickham, Derek Chapman, Shumei Sun, David C Wheeler
In public health research, it has been well established that geographic location plays an important role in influencing health outcomes. In recent years, there has been an increased emphasis on the impact of neighborhood or contextual factors as potential risk factors for childhood obesity. Some neighborhood factors relevant to childhood obesity include access to food sources, access to recreational facilities, neighborhood safety, and socioeconomic status (SES) variables. It is common for neighborhood or area-level variables to be available at multiple spatial scales (SS) or geographic units, such as the census block group and census tract, and selection of the spatial scale for area-level variables can be considered as a model selection problem...
March 8, 2018: International Journal of Environmental Research and Public Health
Hangcheng Fu, Yu Zhu, Yiwei Wang, Zheng Liu, Junyu Zhang, Huyang Xie, Qiang Fu, Bo Dai, Dingwei Ye, Jiejie Xu
PURPOSE: This study aims to construct the stromal immunotype which could improve prediction of postsurgical survival and adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer (MIBC). PATIENTS AND METHODS: A total of 118 MIBC patients from Shanghai Cancer Center, 140 MIBC patients from Zhongshan hospital and 287 MIBC patients from TCGA cohort were included in the study. Immune cell infiltration was evaluated by immunohistochemical staining or CIBERSORT method...
March 7, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Tonje G Lien, Ørnulf Borgan, Sjur Reppe, Kaare Gautvik, Ingrid Kristine Glad
BACKGROUND: Using high-dimensional penalized regression we studied genome-wide DNA-methylation in bone biopsies of 80 postmenopausal women in relation to their bone mineral density (BMD). The women showed BMD varying from severely osteoporotic to normal. Global gene expression data from the same individuals was available, and since DNA-methylation often affects gene expression, the overall aim of this paper was to include both of these omics data sets into an integrated analysis. METHODS: The classical penalized regression uses one penalty, but we incorporated individual penalties for each of the DNA-methylation sites...
March 7, 2018: BMC Medical Genomics
Baptiste Maille, Moloy Das, Ahmed Hussein, Matthew Shaw, Vivek Chaturvedi, Maureen Morgan, Christina Ronayne, Richard L Snowdon, Dhiraj Gupta
INTRODUCTION: The ConfiDENSE™ module (Carto3 v4) allows rapid annotation of endocardial electrograms acquired by multi-electrode (ME) mapping. However, its accuracy in assessing atrial voltages is unknown. METHODS AND RESULTS: Two ConfiDENSE™ left atrial voltage maps were created during continuous pacing in 20 patients undergoing catheter ablation for persistent AF using a ME lasso catheter and a Contact Force (CF) sensing ablation catheter. The automated Tissue Proximity indicator (TPI) filter was then applied to the ME map to yield a TPI map...
March 5, 2018: Journal of Cardiovascular Electrophysiology
Yirong Chen, Collins Wenhan Chu, Mark I C Chen, Alex R Cook
INTRODUCTION: Accurate and timely prediction for endemic infectious diseases is vital for public health agencies to plan and carry out any control methods at an early stage of disease outbreaks. Climatic variables has been identified as important predictors in models for infectious disease forecast. Various approaches has been proposed in literature trying to produce accurate and timely predictions and potentially improve public health response. METHODS: We assessed how the machine learning LASSO method may be useful in providing useful forecasts for different pathogens in countries with different climates...
February 26, 2018: Journal of Biomedical Informatics
Qipeng Feng, Feiran Yang, Jun Yang
A time-domain sound field reproduction (SFR) method based on the group Lasso (GL) is presented. The proposed method optimizes the positions and the number of active loudspeakers in the time domain by iteratively solving a mixed-norm constrained optimization problem. Simulation results demonstrate that the proposed method achieves accurate broadband SFR using a small number of active loudspeakers and significantly outperforms the least-squares method when the desired sound field is under-sampled. Moreover, the GL algorithm can also be used to optimize the loudspeaker placement for sound field control systems...
February 2018: Journal of the Acoustical Society of America
Sara Carvalho, Ralph T H Leijenaar, Esther G C Troost, Janna E van Timmeren, Cary Oberije, Wouter van Elmpt, Lioe-Fee de Geus-Oei, Johan Bussink, Philippe Lambin
BACKGROUND: Lymph node stage prior to treatment is strongly related to disease progression and poor prognosis in non-small cell lung cancer (NSCLC). However, few studies have investigated metabolic imaging features derived from pre-radiotherapy 18F-fluorodeoxyglucose (FDG) positron-emission tomography (PET) of metastatic hilar/mediastinal lymph nodes (LNs). We hypothesized that these would provide complementary prognostic information to FDG-PET descriptors to only the primary tumor (tumor)...
2018: PloS One
Lin Chen, Yihui Wen, Jingwei Zhang, Wei Sun, Vivian W Y Lui, Yi Wei, Fenghong Chen, Weiping Wen
Radiotherapy is unlikely to benefit all patients with head and neck squamous cell carcinoma (HNSCC). Therefore, novel method is warranted to predict the radiotherapy response. Our study aimed to construct a microRNA (miRNA)-based nomogram to predict clinical outcomes of patients with HNSCC receiving radiotherapy. We screened out 56 differential miRNAs by analyzing 44 paired tumor and adjacent normal samples miRNA expression profiles from The Cancer Genome Atlas (TCGA). A total of 307 patients with HNSCC receiving adjuvant radiotherapy were randomly divided into a training set (n = 154) and a validation set (n = 153)...
February 23, 2018: Cancer Medicine
Long-Biao Cui, Lin Liu, Hua-Ning Wang, Liu-Xian Wang, Fan Guo, Yi-Bin Xi, Ting-Ting Liu, Chen Li, Ping Tian, Kang Liu, Wen-Jun Wu, Yi-Huan Chen, Wei Qin, Hong Yin
Specific biomarker reflecting neurobiological substrates of schizophrenia (SZ) is required for its diagnosis and treatment selection of SZ. Evidence from neuroimaging has implicated disrupted functional connectivity in the pathophysiology. We aimed to develop and validate a method of disease definition for SZ by resting-state functional connectivity using radiomics strategy. This study included 2 data sets collected with different scanners. A total of 108 first-episode SZ patients and 121 healthy controls (HCs) participated in the current study, among which 80% patients and HCs (n = 183) and 20% (n = 46) were selected for training and testing in intra-data set validation and 1 of the 2 data sets was selected for training and the other for testing in inter-data set validation, respectively...
February 17, 2018: Schizophrenia Bulletin
Firdaus Hafidz, Tim Ensor, Sandy Tubeuf
Total health care costs have dramatically increased in Indonesia, and health facilities consume the largest share of health resources. This study aims to provide a better understanding of the characteristics of the best-performing health facilities. We use 4 national Indonesian datasets for 2011 and analysed 200 hospitals and 95 health centres. We first apply the Pabón-Lasso model to assess the relative performance of health facilities in terms of bed occupancy rate and the number of admissions per bed; the model gathers together health facilities into 4 sectors representing different levels of productivity...
February 21, 2018: International Journal of Health Planning and Management
Andrew C Kidd, Michael McGettrick, Selina Tsim, Daniel L Halligan, Max Bylesjo, Kevin G Blyth
Introduction: Accurate prognostication is difficult in malignant pleural mesothelioma (MPM). We developed a set of robust computational models to quantify the prognostic value of routinely available clinical data, which form the basis of published MPM prognostic models. Methods: Data regarding 269 patients with MPM were allocated to balanced training (n=169) and validation sets (n=100). Prognostic signatures (minimal length best performing multivariate trained models) were generated by least absolute shrinkage and selection operator regression for overall survival (OS), OS <6 months and OS <12 months...
2018: BMJ Open Respiratory Research
Konstantinos Ioannidis, Matthias S Treder, Samuel R Chamberlain, Franz Kiraly, Sarah A Redden, Dan J Stein, Christine Lochner, Jon E Grant
BACKGROUND AND AIMS: Problematic internet use (PIU; otherwise known as Internet Addiction) is a growing problem in modern societies. There is scarce knowledge of the demographic variables and specific internet activities associated with PIU and a limited understanding of how PIU should be conceptualized. Our aim was to identify specific internet activities associated with PIU and explore the moderating role of age and gender in those associations. METHODS: We recruited 1749 participants aged 18 and above via media advertisements in an Internet-based survey at two sites, one in the US, and one in South Africa; we utilized Lasso regression for the analysis...
February 12, 2018: Addictive Behaviors
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