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Laboratory data prediction models

Catherine C Bell, Anita C A Dankers, Volker M Lauschke, Rowena Sison-Young, Roz Jenkins, Cliff Rowe, Chris Goldring, Kevin Park, Sophie Regan, Tracy Walker, Chris Schofield, Audrey Baze, Alison J Foster, Dominic Williams, Amy W M van de Ven, Frank Jacobs, Jos van Houdt, Tuula Lähteenmäki, Jan Snoeys, Satu Juhila, Lysiane Richert, Magnus Ingelman-Sundberg
Primary human hepatocytes (PHH) are commonly used for in vitro studies of drug-induced liver injury. However, when cultured as 2D monolayers, PHH lose crucial hepatic functions within hours. This dedifferentiation can be ameliorated when PHH are cultured in sandwich configuration (2Dsw), particularly when cultures are regularly re-overlaid with extracellular matrix, or as 3D spheroids. In this study, the six participating laboratories evaluated the robustness of these two model systems made from cryopreserved PHH from the same donors considering both inter-donor and inter-lab variability and compared their suitability for use in repeated-dose toxicity studies using 5 different hepatotoxins with different toxicity mechanisms...
January 10, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
Iván León-Merino, Raúl Rodríguez-Segundo, Daniel J Arismendi-Arrieta, Rita Prosmiti
Recently, empty hydrate structures sI, sII, sH and others have been proposed as low-density ice structures by both experimental observations and computer simulations. Some of them have been synthesized in the laboratory and motivates to reexamine the stability of such guest-free clathrate structures. Using empirical and ab initio-based water models, as well as dispersion-corrected density functional theory approaches, we predict their stability, including cooperative many-body effects, in comparison with reference data from converged wavefunction-based DF-MP2 electronic structure calculations...
January 12, 2018: Journal of Physical Chemistry. A
Carlijn R Hooijmans, Rob B M de Vries, Merel Ritskes-Hoitinga, Maroeska M Rovers, Mariska M Leeflang, Joanna IntHout, Kimberley E Wever, Lotty Hooft, Hans de Beer, Ton Kuijpers, Malcolm R Macleod, Emily S Sena, Gerben Ter Riet, Rebecca L Morgan, Kristina A Thayer, Andrew A Rooney, Gordon H Guyatt, Holger J Schünemann, Miranda W Langendam
Laboratory animal studies are used in a wide range of human health related research areas, such as basic biomedical research, drug research, experimental surgery and environmental health. The results of these studies can be used to inform decisions regarding clinical research in humans, for example the decision to proceed to clinical trials. If the research question relates to potential harms with no expectation of benefit (e.g., toxicology), studies in experimental animals may provide the only relevant or controlled data and directly inform clinical management decisions...
2018: PloS One
Bhargava K Reddy, Dursun Delen, Rupesh K Agrawal
Crohn's disease is among the chronic inflammatory bowel diseases that impact the gastrointestinal tract. Understanding and predicting the severity of inflammation in real-time settings is critical to disease management. Extant literature has primarily focused on studies that are conducted in clinical trial settings to investigate the impact of a drug treatment on the remission status of the disease. This research proposes an analytics methodology where three different types of prediction models are developed to predict and to explain the severity of inflammation in patients diagnosed with Crohn's disease...
January 1, 2018: Health Informatics Journal
Mohamed Gamil, Mohamed Alboraie, Mohammad El-Sayed, Aisha Elsharkawy, Noha Asem, Tamer Elbaz, Mohammad Mohey, Bahaa Abbas, Mai Mehrez, Gamal Esmat
BACKGROUND: Serum levels of alpha-fetoprotein (AFP) were reported to increase in patients with significant or advanced hepatic fibrosis. Combination of non-invasive tests decreases the use of liver biopsy in large proportion of chronic HCV patients. AIM: To compare and combine AFP with commonly used non-invasive fibrosis tests in novel scores for prediction of different stages of hepatic fibrosis. PATIENTS AND METHODS: Six hundred and fifty two treatment naïve chronic hepatitis C patients were enrolled...
January 6, 2018: Journal of Medical Virology
Marietta Landgraf, Jacqui A McGovern, Peter Friedl, Dietmar W Hutmacher
The laboratory mouse is widely considered as a valid and affordable model organism to study human disease. Attempts to improve the relevance of murine models for the investigation of human pathologies led to the development of various genetically engineered, xenograft and humanized mouse models. Nevertheless, most preclinical studies in mice suffer from insufficient predictive value when compared with cancer biology and therapy response of human patients. We propose an innovative strategy to improve the predictive power of preclinical cancer models...
January 5, 2018: Trends in Biotechnology
Pao-Jen Kuo, Shao-Chun Wu, Peng-Chen Chien, Cheng-Shyuan Rau, Yi-Chun Chen, Hsiao-Yun Hsieh, Ching-Hua Hsieh
OBJECTIVES: This study aimed to build and test the models of machine learning (ML) to predict the mortality of hospitalised motorcycle riders. SETTING: The study was conducted in a level-1 trauma centre in southern Taiwan. PARTICIPANTS: Motorcycle riders who were hospitalised between January 2009 and December 2015 were classified into a training set (n=6306) and test set (n=946). Using the demographic information, injury characteristics and laboratory data of patients, logistic regression (LR), support vector machine (SVM) and decision tree (DT) analyses were performed to determine the mortality of individual motorcycle riders, under different conditions, using all samples or reduced samples, as well as all variables or selected features in the algorithm...
January 5, 2018: BMJ Open
Xing Chen, Li Huang, Di Xie, Qi Zhao
Associations between microRNAs (miRNAs) and human diseases have been identified by increasing studies and discovering new ones is an ongoing process in medical laboratories. To improve experiment productivity, researchers computationally infer potential associations from biological data, selecting the most promising candidates for experimental verification. Predicting potential miRNA-disease association has become a research area of growing importance. This paper presents a model of Extreme Gradient Boosting Machine for MiRNA-Disease Association (EGBMMDA) prediction by integrating the miRNA functional similarity, the disease semantic similarity, and known miRNA-disease associations...
January 5, 2018: Cell Death & Disease
Satbir Singh Thakur, Haocheng Li, Angela M Y Chan, Roxana Tudor, Gilbert Bigras, Don Morris, Emeka K Enwere, Hua Yang
Ki67 is a commonly used marker of cancer cell proliferation, and has significant prognostic value in breast cancer. In spite of its clinical importance, assessment of Ki67 remains a challenge, as current manual scoring methods have high inter- and intra-user variability. A major reason for this variability is selection bias, in that different observers will score different regions of the same tumor. Here, we developed an automated Ki67 scoring method that eliminates selection bias, by using whole-slide analysis to identify and score the tumor regions with the highest proliferative rates...
2018: PloS One
Nabihah Tayob, Peter Richardson, Donna L White, Xiaoying Yu, Jessica A Davila, Fasiha Kanwal, Ziding Feng, Hashem B El-Serag
BACKGROUND: Hepatocellular carcinoma (HCC) has limited treatment options in patients with advanced stage disease and early detection of HCC through surveillance programs is a key component towards reducing mortality. The current practice guidelines recommend that high-risk cirrhosis patients are screened every six months with ultrasonography but these are done in local hospitals with variable quality leading to disagreement about the benefit of HCC surveillance. The well-established diagnostic biomarker α-Fetoprotein (AFP) is used widely in screening but the reported performance varies widely across studies...
January 4, 2018: BMC Medical Research Methodology
Naama Schwartz, Ali Sakhnini, Naiel Bisharat
Despite overwhelming data on predictors of inpatient mortality, it is unclear which variables are the most instructive in predicting mortality of patients in departments of internal medicine. This study aims to identify the most informative predictors of inpatient mortality, and builds a prediction model on an individual level, given a constellation of patient characteristics. We use a penalized method for developing the prediction model by applying the least-absolute-shrinkage and selection-operator regression...
December 30, 2017: Internal and Emergency Medicine
Zhao Li, Liwen Jing, Ross Murch
Acoustic wave propagation (up to 50 kHz) within a water-filled high-density polyethylene (HDPE) pipeline is studied using laboratory experiments and theoretical analysis. Experiments were carried out in a 15 m length of cylindrical HDPE pipeline using acoustic transducers to acquire signals uniformly spaced along the axis of the pipe. By proposing the use of the iterative quadratic maximum likelihood algorithm to this experimental configuration, wavenumbers, attenuations, and mode amplitudes could be accurately extracted from the measurement data...
December 2017: Journal of the Acoustical Society of America
Tatiana G Akhmetshina, Vladislav A Blatov, Davide M Proserpio, Alexander P Shevchenko
More than 38 000 substances made only of metal atoms are collected in modern structural databases; we may call them intermetallic compounds. They have important industrial applications, and yet they are terra incognita for most of our undergraduate students. Their structural complexity and synthesis are not easily adaptable to first years laboratories, keeping them away from the standard curricula. They have been described over the years following alternative and complementary views such as coordination polyhedra, atomic layers, and polyatomic clusters...
December 29, 2017: Accounts of Chemical Research
Giuseppe De Nisco, Peng Zhang, Karol Calò, Xiao Liu, Raffaele Ponzini, Cristina Bignardi, Giovanna Rizzo, Xiaoyan Deng, Diego Gallo, Umberto Morbiducci
Personalized computational hemodynamics (CH) is a promising tool to clarify/predict the link between low density lipoproteins (LDL) transport in aorta, disturbed shear and atherogenesis. However, CH uses simplifying assumptions that represent sources of uncertainty. In particular, modelling blood-side to wall LDL transfer is challenged by the cumbersomeness of protocols needed to obtain reliable LDL concentration profile estimations. This paucity of data is limiting the establishment of rigorous CH protocols able to balance the trade-offs among the variety of in vivo data to be acquired, and the accuracy required by biological/clinical applications...
December 15, 2017: Journal of Biomechanics
Lanfang Peng, Zhenqing Shi, Pei Wang, Wei Li, Zhang Lin, Zhi Dang, Donald L Sparks
The kinetics of Zn release from soil is a key process affecting the fate and bioavailability of Zn in soil, which may be complicated by multiple soil binding sites and reactions during the Zn release process. In this study, we developed a novel quantitative model for the dynamic Zn speciation in soil during the Zn release process, by integrating the mechanistic equilibrium model WHAM 7 and molecular level investigation of Zn speciation with X-ray absorption spectroscopy (XAS). The kinetics model specifically considered Zn reactions with soil organic matter (SOM), iron (hydr)oxides, and clay minerals, and dissolution of Zn precipitates...
December 5, 2017: Journal of Colloid and Interface Science
Ouahid Ben Ghanem, Syed Nasir Shah, Jean-Marc Lévêque, M I Abdul Mutalib, Mohanad El-Harbawi, Amir Sada Khan, Mohamad Sahban Alnarabiji, Hamada R H Al-Absi, Zahoor Ullah
Over the past decades, Ionic liquids (ILs) have gained considerable attention from the scientific community in reason of their versatility and performance in many fields. However, they nowadays remain mainly for laboratory scale use. The main barrier hampering their use in a larger scale is their questionable ecological toxicity. This study investigated the effect of hydrophobic and hydrophilic cyclic cation-based ILs against four pathogenic bacteria that infect humans. For that, cations, either of aromatic character (imidazolium or pyridinium) or of non-aromatic nature, (pyrrolidinium or piperidinium), were selected with different alkyl chain lengths and combined with both hydrophilic and hydrophobic anionic moieties...
December 7, 2017: Chemosphere
Tobias Herold, Vindi Jurinovic, Aarif M N Batcha, Stefanos A Bamopoulos, Maja Rothenberg-Thurley, Bianka Ksienzyk, Luise Hartmann, Philipp A Greif, Julia Phillippou-Massier, Stefan Krebs, Helmut Blum, Susanne Amler, Stephanie Schneider, Nikola Konstandin, Maria Cristina Sauerland, Dennis Görlich, Wolfgang E Berdel, Bernhard J Wörmann, Johanna Tischer, Marion Subklewe, Stefan K Bohlander, Jan Braess, Wolfgang Hiddemann, Klaus H Metzeler, Ulrich Mansmann, Karsten Spiekermann
Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model...
December 14, 2017: Haematologica
Chiu-Shia Fen, Yong-Tai Sun, Yuen Cheng, Yuanchin Chen, Whaiwan Yang, Changtai Pan
Variations of gas phase density are responsible for advective and diffusive transports of organic vapors in unsaturated soils. Laboratory experiments were conducted to explore dense gas transport (sulfur hexafluoride, SF6) from different source densities through a nitrogen gas-dry soil column. Gas pressures and SF6 densities at transient state were measured along the soil column for three transport configurations (horizontal, vertically upward and vertically downward transport). These measurements and others reported in the literature were compared with simulation results obtained from two models based on different diffusion approaches: the dusty gas model (DGM) equations and a Fickian-type molar fraction-based diffusion expression...
December 6, 2017: Journal of Contaminant Hydrology
Paola Stefanelli, Maria Fenicia Vescio, Maria Paola Landini, Ivano Dal Conte, Alberto Matteelli, Antonio Cristaudo, Marina Gaino, Marco Cusini, Anna Maria Barbui, Antonella Mencacci, Rosella De Nittis, Valeria Ghisetti, Elena Stroppiana, Anna Carannante
INTRODUCTION: Neisseria gonorrhoeae (NG) antimicrobial susceptibility trends to azithromycin, cefixime and ceftriaxone were analyzed, from 2009 to 2016, to monitor changing antimicrobial susceptibility concomitant with the change in prescribing practice in 2012 from cefixime, or ceftriaxone, to ceftriaxone plus azithromycin. Patient characteristics predictive to be infected by antibiotic resistant N. gonorrhoeae were estimated. Finally, the protocol for the treatment of gonorrhoea, in comparison with the international guidelines, was also evaluated...
2017: PloS One
Itza Mendoza-Sanchez, Robin L Autenrieth, Thomas J McDonald, Jeffrey A Cunningham
We applied a mathematical model to data from experimental column studies to understand the dynamics of successful and unsuccessful reductive dechlorination of chlorinated ethenes in groundwater under different flow conditions. In laboratory column experiments (reported previously), it was observed that complete dechlorination of cis-dichloroethene to ethene was sustained at high flow velocity (0.51 m/d), but that dechlorination failed at medium or low flow velocity (0.080 or 0.036 m/d). The mathematical model applied here accounts for transport of chlorinated ethenes in flowing groundwater, mass transfer of chlorinated ethenes between mobile groundwater and stationary biofilms, and diffusion and biodegradation within the biofilms...
December 13, 2017: Environmental Science & Technology
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