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https://www.readbyqxmd.com/read/28549952/drug-target-interaction-prediction-using-ensemble-learning-and-dimensionality-reduction
#1
Ali Ezzat, Min Wu, Xiao-Li Li, Chee-Keong Kwoh
Experimental prediction of drug-target interactions is expensive, time-consuming and tedious. Fortunately, computational methods help narrow down the search space for interaction candidates to be further examined via wet-lab techniques. Nowadays, the number of attributes/features for drugs and targets, as well as the amount of their interactions, are increasing, making these computational methods inefficient or occasionally prohibitive. This motivates us to derive a reduced feature set for prediction. In addition, since ensemble learning techniques are widely used to improve the classification performance, it is also worthwhile to design an ensemble learning framework to enhance the performance for drug-target interaction prediction...
May 23, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28545610/a-case-based-reasoning-system-based-on-weighted-heterogeneous-value-distance-metric-for-breast-cancer-diagnosis
#2
Dongxiao Gu, Changyong Liang, Huimin Zhao
OBJECTIVE: We present the implementation and application of a case-based reasoning (CBR) system for breast cancer related diagnoses. By retrieving similar cases in a breast cancer decision support system, oncologists can obtain powerful information or knowledge, complementing their own experiential knowledge, in their medical decision making. METHODS: We observed two problems in applying standard CBR to this context: the abundance of different types of attributes and the difficulty in eliciting appropriate attribute weights from human experts...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28545393/quantgenius-implementation-of-a-decision-support-system-for-qpcr-based-gene-quantification
#3
Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak, Kristina Gruden
BACKGROUND: Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. RESULTS: We have developed "quantGenius" ( http://quantgenius...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28544060/predictive-factors-upon-discontinuation-of-renal-replacement-therapy-for-long-term-chronic-dialysis-and-death-in-acute-kidney-injury-patients
#4
Tingting Yang, Si Sun, Liping Lin, Mei Han, Qiang Liu, Xiaoxi Zeng, Yuliang Zhao, Yupei Li, Baihai Su, Songmin Huang, Lichuan Yang
The specific timing for discontinuing renal replacement therapy (RRT) in acute kidney injury (AKI) patients is debatable. The predictive abilities of variables at the time of discontinuation of RRT for the long-term prognoses of patients have not been explored. This study aimed to explore the prognostic factors upon discontinuation of RRT for long-term chronic dialysis and death of patients with acute RRT-requiring AKI, thus improving decision making regarding the discontinuation of RRT and the follow-up of patients thereafter...
May 23, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28543353/effect-of-pathologic-revision-and-ki67-and-erg-immunohistochemistry-on-predicting-radical-prostatectomy-outcome-in-men-initially-on-active-surveillance
#5
Leonard P Bokhorst, Monique J Roobol, Chris H Bangma, Geert J van Leenders
OBJECTIVE: To investigate if pathologic biopsy reevaluation and implementation of immunohistochemical biomarkers could improve prediction of radical prostatectomy outcome in men initially on active surveillance. METHODS: Biopsy specimens from diagnosis until switching to radical prostatectomy in men initially on active surveillance in the Dutch part of the Prostate cancer Research International Active Surveillance (PRIAS) study were collected and revised by a single pathologist...
May 24, 2017: Prostate
https://www.readbyqxmd.com/read/28542627/predictive-features-of-chronic-kidney-disease-in-atypical-haemolytic-uremic-syndrome
#6
Matthieu Jamme, Quentin Raimbourg, Dominique Chauveau, Amélie Seguin, Claire Presne, Pierre Perez, Pierre Gobert, Alain Wynckel, François Provôt, Yahsou Delmas, Christiane Mousson, Aude Servais, Laurence Vrigneaud, Agnès Veyradier, Eric Rondeau, Paul Coppo
Chronic kidney disease (CKD) is a frequent and serious complication of atypical haemolytic uremic syndrome (aHUS). We aimed to develop a simple accurate model to predict the risk of renal dysfunction in aHUS based on clinical and biological features available at hospital admission. Renal function at 1-year follow-up, based on an estimated glomerular filtration rate < 60mL/min/1.73m2 as assessed by the Modification of Diet in Renal Disease equation, was used as an indicator of significant CKD. Prospectively collected data from a cohort of 156 aHUS patients who did not receive eculizumab were used to identify predictors of CKD...
2017: PloS One
https://www.readbyqxmd.com/read/28538950/association-of-adjuvant-chemotherapy-with-survival-in-patients-with-stage-ii-or-iii-gastric-cancer
#7
Yuming Jiang, Tuanjie Li, Xiaoling Liang, Yanfeng Hu, Lei Huang, Zhenchen Liao, Liying Zhao, Zhen Han, Shuguang Zhu, Menglan Wang, Yangwei Xu, Xiaolong Qi, Hao Liu, Yang Yang, Jiang Yu, Wei Liu, Shirong Cai, Guoxin Li
Importance: The current staging system of gastric cancer is not adequate for defining a prognosis and predicting the patients most likely to benefit from chemotherapy. Objective: To construct a survival prediction model based on specific tumor and patient characteristics that enables individualized predictions of the net survival benefit of adjuvant chemotherapy for patients with stage II or stage III gastric cancer. Design, Setting, and Participants: In this multicenter retrospective analysis, a survival prediction model was constructed using data from a training cohort of 746 patients with stage II or stage III gastric cancer who satisfied the study's inclusion criteria and underwent surgery between January 1, 2004, and December 31, 2012, at Nanfang Hospital in Guangzhou, China...
May 24, 2017: JAMA Surgery
https://www.readbyqxmd.com/read/28538622/towards-precision-medicine-accurate-predictive-modeling-of-infectious-complications-in-combat-casualties
#8
Christopher J Dente, Matthew Bradley, Seth Schobel, Beverly Gaucher, Timothy Buchman, Allan D Kirk, Eric Elster
BACKGROUND: The biomarker profile of trauma patients may allow for the creation of models to assist bedside decision making & prediction of complications. We sought to determine the utility of modeling in the prediction of bacteremia & pneumonia in combat casualties. METHODS: This is a prospective, observational trial of patients with complex wounds treated at Walter Reed National Military Medical Center (2007-2012). Tissue, serum and wound effluent samples were collected during operative interventions until wound closure...
May 22, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28536207/impaired-cerebral-autoregulation-measurement-and-application-to-stroke
#9
REVIEW
Li Xiong, Xiuyun Liu, Ty Shang, Peter Smielewski, Joseph Donnelly, Zhen-Ni Guo, Yi Yang, Thomas Leung, Marek Czosnyka, Rong Zhang, Jia Liu, Ka Sing Wong
Cerebral autoregulation (CA) is a protective mechanism that maintains cerebral blood flow at a relatively constant level despite fluctuations of cerebral perfusion pressure or arterial blood pressure. It is a universal physiological mechanism that may involve myogenic, neural control as well as metabolic regulations of cerebral vasculature in response to changes in pressure or cerebral blood flow. Traditionally, CA has been represented by a sigmoid curve with a wide plateau between about 50 mm Hg and 170 mm Hg of steady-state changes in mean arterial pressure, defined as static CA...
June 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/28534462/associations-between-alcohol-dehydrogenase-genes-and-alcohol-use-across-early-and-middle-adolescence-moderation-%C3%A3-preventive-intervention
#10
H Harrington Cleveland, Gabriel L Schlomer, David J Vandenbergh, Pedro S A Wolf, Mark E Feinberg, Mark T Greenberg, Richard L Spoth, Cleve Redmond
Data from the in-school sample of the PROSPER preventive intervention dissemination trial were used to investigate associations between alcohol dehydrogenase genes and alcohol use across adolescence, and whether substance misuse interventions in the 6th and 7th grades (targeting parenting, family functioning, social norms, youth decision making, and peer group affiliations) modified associations between these genes and adolescent use. Primary analyses were run on a sample of 1,885 individuals and included three steps...
May 23, 2017: Development and Psychopathology
https://www.readbyqxmd.com/read/28533984/predictive-ability-of-the-mini-nutritional-assessment-short-form-mna-sf-in-a-free-living-elderly-population-a-cross-sectional-study
#11
Raimunda Montejano Lozoya, Nieves Martínez-Alzamora, Gonzalo Clemente Marín, Silamani J A Guirao-Goris, Rosa María Ferrer-Diego
BACKGROUND: Various scales have been used to perform a quick and first level nutritional assessment, and the MNA is one of the most used and recommended by experts in the elderly in all areas. This scale has a short form, the MNA-SF, revised and validated in 2009, which has two versions: the BMI-MNA-SF contains the first six items of the full scale including Body Mass Index while the CC-MNA-SF includes Calf Circumference instead of BMI. OBJECTIVE: To evaluate the predictive ability for nutritional status of the two versions of the MNA-SF against the MNA in free-living elderly in the province of Valencia...
2017: PeerJ
https://www.readbyqxmd.com/read/28533475/first-line-palliative-her2-targeted-therapy-in-her2-positive-metastatic-breast-cancer-is-less-effective-after-previous-adjuvant-trastuzumab-based-therapy
#12
Hánah N Rier, Mark-David Levin, Joost van Rosmalen, Monique M E M Bos, Jan C Drooger, Paul de Jong, Johanneke E A Portielje, Elisabeth M P Elsten, Albert-Jan Ten Tije, Stefan Sleijfer, Agnes Jager
BACKGROUND: Survival of patients with human epidermal growth receptor 2 (HER2)-positive metastatic breast cancer (MBC) has improved dramatically since trastuzumab has become available, although the disease eventually progresses in most patients. This study investigates the outcome (overall survival [OS] and time to next treatment [TNT]) in MBC patients pretreated with trastuzumab in the adjuvant setting (TP-group) compared with trastuzumab-naïve patients (TN-group) in order to investigate the possibility of trastuzumab resistance...
May 22, 2017: Oncologist
https://www.readbyqxmd.com/read/28530216/-chilaiditi-syndrome-a-case-report
#13
Sławomir Krzemiński
The abnormality being the result of a certain transposition of the large intestine winding in between diaphragm and the liver, owes it's name to a so called Chilaiditi symptom. This symptom is rarely recognized for at most 0,025-0,28% of the whole population statistics - wise. The Chilaiditi symptom can be examined without any serious (abdominal) pain indication, when conducting the gastrointestinal examination with the implication of the different disorders. When carrying out the diagnostic examination, it is strongly recommended to take notice of patients suffering from the pain in abdominal area, especially in case of the patients with the developed air - structure under the right side copula of the diaphragm...
April 21, 2017: Polski Merkuriusz Lekarski: Organ Polskiego Towarzystwa Lekarskiego
https://www.readbyqxmd.com/read/28529606/comparison-of-prognostic-nomograms-based-on-different-nodal-staging-systems-in-patients-with-resected-gastric-cancer
#14
Zi-Xian Wang, Miao-Zhen Qiu, Yu-Ming Jiang, Zhi-Wei Zhou, Guo-Xin Li, Rui-Hua Xu
Purpose: Previous studies addressing the optimal nodal staging system in patients with resected gastric cancer have shown inconsistent results, and the optimal system for development of prognostic nomograms remains unclear. In this study, we compared prognostic nomograms based on the metastatic lymph node (MLN) count, lymph node ratio (LNR), and log odds of metastatic lymph nodes (LODDS) to predict the 5-year overall survival in patients with resected gastric cancer. Methods: We analysed 15,320 patients with resected gastric cancer in the Surveillance, Epidemiology, and End Results (SEER) database between 1988 and 2010...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28526449/predictors-of-vaginal-delivery-in-medically-indicated-early-preterm-induction-of-labor
#15
Rachel A Sievert, Spencer G Kuper, Victoria C Jauk, Melissa Parrish, Joseph R Biggio, Lorie M Harper
BACKGROUND: When delivery is indicated prior to 34 weeks, many providers perform a cesarean delivery (CD) rather than induce labor based on perceptions of a high failure rate. Given the morbidity of CD, an accurate estimate of the success rate and factors associated with success in preterm induction of labor (IOL) is important in management decisions. OBJECTIVE: We sought to develop a prediction model for successful induction of labor in preterm patients using factors known at the time the decision is made to deliver...
May 16, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28523350/comparison-of-a-radiomic-biomarker-with-volumetric-analysis-for-decoding-tumour-phenotypes-of-lung-adenocarcinoma-with-different-disease-specific-survival
#16
Mei Yuan, Yu-Dong Zhang, Xue-Hui Pu, Yan Zhong, Hai Li, Jiang-Fen Wu, Tong-Fu Yu
OBJECTIVES: To compare a multi-feature-based radiomic biomarker with volumetric analysis in discriminating lung adenocarcinomas with different disease-specific survival on computed tomography (CT) scans. METHODS: This retrospective study obtained institutional review board approval and was Health Insurance Portability and Accountability Act (HIPAA) compliant. Pathologically confirmed lung adenocarcinoma (n = 431) manifested as subsolid nodules on CT were identified...
May 18, 2017: European Radiology
https://www.readbyqxmd.com/read/28516344/defining-optimal-cutoff-value-of-mgmt-promoter-methylation-by-roc-analysis-for-clinical-setting-in-glioblastoma-patients
#17
Guoqiang Yuan, Liang Niu, Yinian Zhang, Xiaoqing Wang, Kejun Ma, Hang Yin, Junqiang Dai, Wangning Zhou, Yawen Pan
Resistance to temozolomide (TMZ) chemotherapy poses a significant challenge in the treatment of glioblastoma (GBM). Hypermethylation in O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is thought to play a critical role in this resistance. Pyrosequencing (PSQ) has been shown to be accurate and robust for MGMT promoter methylation testing. The unresolved issue is the determination of a cut-off value for dichotomization of quantitative MGMT PSQ results into "MGMT methylated" and "MGMT unmethylated" patient subgroups as a basis for further treatment decisions...
May 17, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28515807/external-validation-of-the-procars-nomograms-and-comparison-of-existing-risk-stratification-tools-for-localized-prostate-cancer
#18
David Tiberi, George Rodrigues, Tom Pickles, Jim Morris, Juanita Crook, Andre-Guy Martin, Fabio Cury, Charles Catton, Himu Lukka, Andrew Warner, Daniel Taussky
INTRODUCTION: The purpose of this study was to perform a direct comparison of several existing risk-stratification tools for localized prostate cancer in terms of their ability to predict for biochemical failure-free survival (BFFS). Two large databases were used and an external validation of two recently developed nomograms on an independent cohort was also performed in this analysis. METHODS: Patients who were treated with external beam radiotherapy (EBRT) and/or brachytherapy for localized prostate cancer were selected from the multi-institutional Genitourinary Radiation Oncologists of Canada (GUROC) Prostate Cancer Risk Stratification (ProCaRS) database (n=7974) and the Centre Hospitalier de l'Université de Montréal (CHUM) validation database (n=2266)...
March 2017: Canadian Urological Association Journal, Journal de L'Association des Urologues du Canada
https://www.readbyqxmd.com/read/28512173/clinical-utility-of-risk-models-to-refer-patients-with-adnexal-masses-to-specialized-oncology-care-multicenter-external-validation-using-decision-curve-analysis
#19
Laure Wynants, Dirk Timmerman, Jan Verbakel, Antonia Testa, Luca Savelli, Daniela Fischerová, Dorella Franchi, Caroline D Van Holsbeke, Elisabeth Epstein, Wouter Froyman, Stefano Guerriero, Alberto Rossi, Robert Fruscio, Francesco Leone, Tom Bourne, Lil Valentin, Ben Van Calster
To evaluate the utility of pre-operative diagnostic models for ovarian cancer based on ultrasound and/or biomarkers for referring patients to specialized oncology care. The investigated models were RMI, ROMA, and three models from the International Ovarian Tumor Analysis (IOTA) group (LR2, ADNEX, and the Simple Rules risk score, SRRisks). <p>DESIGN: A secondary analysis of prospectively collected data from two cross-sectional cohort studies performed to externally validate diagnostic models.</p> <p>PARTICIPANTS: A total of 2763 patients (2403 in dataset 1 and 360 in dataset 2) from 18 centers (11 oncology centers and 7 non-oncology hospitals) in 6 countries...
May 16, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28505493/development-of-an-analysis-method-for-determination-of-sulfonamides-and-their-five-acetylated-metabolites-in-baby-foods-by-ultra-high-performance-liquid-chromatography-coupled-to-high-resolution-mass-spectrometry-orbitrap-ms
#20
Ülgen I Konak, Muharrem Certel, Bülent Şık, Timur Tongur
A high sensitive and reliable multiresidue method was developed and validated for determination of twelve sulfonamides and five acetylated metabolites in baby foods by using UHPLC-Orbitrap-MS. The sample preparation included two extraction methods as QuEChERS and ASE. The original QuEChERS method was performed, whereas ASE method was optimized to achieve the best recovery for all analytes. UHPLC-Orbitrap-MS parameters were optimized to obtain good retention and separation in LC and high sensitivity and selectivity in MS...
July 1, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
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