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predictive analytics

Hendrik Treutler, Steffen Neumann
Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92 % of the cases...
October 20, 2016: Metabolites
Shuo Kang, Ab F Nieuwenhuis, Klaus Mathwig, Dileep Mampallil, Zinaida A Kostiuchenko, Serge G Lemay
The diffusive mass transport of individual redox molecules was probed experimentally in microfabricated nanogap electrodes. The residence times for molecules inside a well-defined detection volume were extracted and the resulting distribution was compared with quantitative analytical predictions from random-walk theory for the time of first passage. The results suggest that a small number of strongly adsorbing sites strongly influence mass transport at trace analyte levels.
October 24, 2016: Faraday Discussions
Enrico Ubaldi, Nicola Perra, Márton Karsai, Alessandro Vezzani, Raffaella Burioni, Alessandro Vespignani
The dynamic of social networks is driven by the interplay between diverse mechanisms that still challenge our theoretical and modelling efforts. Amongst them, two are known to play a central role in shaping the networks evolution, namely the heterogeneous propensity of individuals to i) be socially active and ii) establish a new social relationships with their alters. Here, we empirically characterise these two mechanisms in seven real networks describing temporal human interactions in three different settings: scientific collaborations, Twitter mentions, and mobile phone calls...
October 24, 2016: Scientific Reports
Xavier LeSaout, Matteo Costioli, Lynn Jordan, Jeremy Lambert, Ross Beighley, Laurel Provencher, Brian Gerwe, Kevin McGuire, Nico Verlinden, Andrew Barry
Small-scale protein purification presents opportunities for accelerated process development of biotherapeutic molecules. Miniaturization of purification conditions reduces time and allows for parallel processing of samples, thus offering increased statistical significance and greater breadth of variables. The ability of the miniaturized platform to be predictive of larger scale purification schemes is of critical importance. The PerkinElmer JANUS BioTx Pro and Pro-Plus workstations were developed as intuitive, flexible, and automated devices capable of performing parallel small-scale analytical protein purification...
March 2016: Engineering in Life Sciences
Ebrahim Alipanahpour Dil, Mehrorang Ghaedi, Arash Asfaram, Shaaker Hajati, Fatemeh Mehrabi, Alireza Goudarzi
Copper oxide nanoparticle-loaded activated carbon (CuO-NP-AC) was synthesized and characterized using different techniques such as FE-SEM, XRD and FT-IR. It was successfully applied for the ultrasound-assisted simultaneous removal of Pb(2+) ions and malachite green (MG) dye in binary system from aqueous solution. The effect of important parameters was modeled and optimized by artificial neural network (ANN) and response surface methodology (RSM). Maximum simultaneous removal percentages (>99.0%) were found at 25mgL(-1), 20mgL(-1), 0...
January 2017: Ultrasonics Sonochemistry
Ebrahim Alipanahpour Dil, Mehrorang Ghaedi, Arash Asfaram
Present study is based on describing an ultrasound-assisted dispersive liquid-liquid microextraction coupled with derivative spectrophotometry (UAS-DLLME-UV-vis) as useful technique for selective determination of crystal violet (CV) and azure b (Az-B). The significant factors like pH, extractor volume, disperser value and extraction time contribution and their numerical coefficient in quadratic model were calculated according to central composite design (CCD). According to desirability function (DF) as good criterion the best experimental conditions was adjusted and selected at pH of 7...
January 2017: Ultrasonics Sonochemistry
N S Al-Maskari, D A McAdams, J N Reddy
Nacre is a tough yet stiff natural composite composed of microscopic mineral polygonal tablets bonded by a tough biopolymer. The high stiffness of nacre is known to be due to its high mineral content. However, the remarkable toughness of nacre is explained by its ability to deform past a yield point and develop large inelastic strain over a large volume around defects and cracks. The high strain is mainly due to sliding and waviness of the tablets. Mimicking nacre's remarkable properties, to date, is still a challenge due in part to fabrication challenges as well as a lack of models that can predict its properties or properties of a bulk material given specific constituent materials and material structure...
January 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
Yong-Jun Ye, Xin-Tao Dai, De-Xin Ding, Ya-Li Zhao
In this study, a one-dimensional steady-state mathematical model of radon transport in fragmented uranium ore was established according to Fick's law and radon transfer theory in an air-water interface. The model was utilized to obtain an analytical solution for radon concentration in the air-water, two-phase system under steady state conditions, as well as a corresponding radon exhalation rate calculation formula. We also designed a one-dimensional experimental apparatus for simulating radon diffusion migration in the uranium ore with various water levels to verify the mathematical model...
October 19, 2016: Journal of Environmental Radioactivity
Somayeh Beirami, Hadi Rahimzadeh Barzoki, Nader Bahramifar
Preconcentration of trace amounts of diazinon by carbon mesoporous CMK-3 in water and biological samples and measurement by high-performance liquid chromatography were investigated. CMK-3, was prepared using hexagonal SBA-15 as the template. The synthesized materials were characterized by XRD, FT-IR, BET, TEM and Boehm titration method. The preconcentration procedure was optimized using a multivariate optimization approach following a two-stage process. Effect of analytical parameters including the amount of the CMK-3 as an adsorbent, pH, type and volume of eluent, flow rate of eluent and sample were studied by screening project, then the effective parameters were optimized by response surface methodology based on central composite design...
October 21, 2016: Biomedical Chromatography: BMC
Guillaume Martin, Lionel Roques
Various models describe asexual evolution by mutation, selection and drift. Some focus directly on fitness, typically modelling drift but ignoring or simplifying both epistasis and the distribution of mutation effects (travelling wave models). Others follow the dynamics of quantitative traits determining fitness (Fisher's geometrical model), imposing a complex but fixed form of mutation effects and epistasis, and often ignoring drift. In all cases, predictions are typically obtained in high or low mutation rate limits and for long-term stationary regimes, thus loosing information on transient behaviors and the effect of initial conditions...
October 21, 2016: Genetics
Tomasz Czaja, Sylwester Mazurek, Roman Szostak
Diffuse reflectance Fourier transform infrared spectroscopy (DRIFTS) is a fast, reliable and cost effective analytical method, requiring minimal or no sample preparation. It is commonly used in the course of qualitative and quantitative analysis of pharmaceutical ingredients and food. We demonstrate that simpler and cheaper specular reflectance (SR) accessory working in a DRIFTS like mode (SR-DL) can be an alternative for DIRFTS attachment. An application of a modified SR accessory for quantitative analysis of solids samples is presented...
December 1, 2016: Talanta
L M M Lê, A Tfayli, J Zhou, P Prognon, A Baillet-Guffroy, E Caudron
Raman spectroscopy is a rapid, non-destructive and non-invasive method that is a promising tool for real-time analytical control of drug concentrations. This study evaluated a handheld Raman device to discriminate and quantify two isomeric drugs used to treat cancer. Doxorubicin (DOXO) and epirubicin (EPIR) samples were analyzed at therapeutic concentrations from 0.1 to 2mg/mL (n=90) and 0.08-2mg/mL (n=90) by non-invasive measurements using a portable Raman spectrometer. The discrimination of these two molecules was demonstrated for all concentrations (n=180) by qualitative analysis using partial least square discriminant analysis (PLS-DA) with 100% classification accuracy, sensitivity and specificity and 0% error rate...
December 1, 2016: Talanta
Lukasz P Kozlowski
BACKGROUND: Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. RESULTS: Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets...
October 21, 2016: Biology Direct
Richard C Harrington, Brant C Faircloth, Ron I Eytan, W Leo Smith, Thomas J Near, Michael E Alfaro, Matt Friedman
BACKGROUND: Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS)...
October 21, 2016: BMC Evolutionary Biology
Zhiwei Zhou, Xiaotao Shen, Jia Tu, Zheng-Jiang Zhu
The rapid development of metabolomics has significantly advanced health and disease related research. However, metabolite identification remains a major analytical challenge for untargeted metabolomics. While the use of collision cross-section (CCS) values obtained in ion mobility - mass spectrometry (IM-MS) effectively increases identification confidence of metabolites, it is restricted by the limited number of available CCS values for metabolites. Here, we demonstrated the use of a machine-learning algorithm called support vector regression (SVR) to develop a prediction method that utilized 14 common molecular descriptors to predict CCS values for metabolites...
October 21, 2016: Analytical Chemistry
Sasha C Voss, Paola Magni, Ian Dadour, Christian Nansen
Forensic entomology is primarily concerned with the estimation of time since death and involves determination of the age of immature insects colonising decomposing remains. Accurate age determination of puparia is usually accomplished by dissection, which means destructive sampling of evidence. As part of improving abilities to correctly identify species and developmental age, it is highly desirable to have available non-destructive methods. In this study, we acquired external hyperspectral imaging (HSI) data (77 spectral bands, 389-892 nm) from the dorsal and ventral sides of individual puparia of two species of blowfly (Diptera: Calliphoridae), Calliphora dubia Macquart 1855 and Chrysomya rufifacies Macquart 1842...
October 21, 2016: International Journal of Legal Medicine
Orsolya Benedek, Andreas Podbielski, Philipp Warnke
BACKGROUND: Chemiluminescent or enzyme-linked fluorescent immunoassays are commonly used to diagnose Clostridium difficile-associated diarrhea. METHODS: The LIAISON analyzer (DiaSorin, Italy) was compared to miniVIDAS (bioMérieux, France) and, furthermore, to culture of toxigenic strains. In total, 249 native stool samples were analyzed. Sensitivities, specificities, and positive and negative predictive values were investigated. Furthermore, performance under routine conditions was assessed...
September 29, 2016: European Journal of Microbiology & Immunology
Alistair E W Johnson, Mohammad M Ghassemi, Shamim Nemati, Katherine E Niehaus, David A Clifton, Gari D Clifford
Clinical data management systems typically provide caregiver teams with useful information, derived from large, sometimes highly heterogeneous, data sources that are often changing dynamically. Over the last decade there has been a significant surge in interest in using these data sources, from simply re-using the standard clinical databases for event prediction or decision support, to including dynamic and patient-specific information into clinical monitoring and prediction problems. However, in most cases, commercial clinical databases have been designed to document clinical activity for reporting, liability and billing reasons, rather than for developing new algorithms...
February 2016: Proceedings of the IEEE
Alex R Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito, Donal Fellows, Antonio Fernandez Guerra, Nuno Ferreira, Yuliya Fetyukova, Bruno Fosso, Jonathan Giddy, Carole Goble, Anton Güntsch, Robert Haines, Vera Hernández Ernst, Hannes Hettling, Dóra Hidy, Ferenc Horváth, Dóra Ittzés, Péter Ittzés, Andrew Jones, Renzo Kottmann, Robert Kulawik, Sonja Leidenberger, Päivi Lyytikäinen-Saarenmaa, Cherian Mathew, Norman Morrison, Aleksandra Nenadic, Abraham Nieva de la Hidalga, Matthias Obst, Gerard Oostermeijer, Elisabeth Paymal, Graziano Pesole, Salvatore Pinto, Axel Poigné, Francisco Quevedo Fernandez, Monica Santamaria, Hannu Saarenmaa, Gergely Sipos, Karl-Heinz Sylla, Marko Tähtinen, Saverio Vicario, Rutger Aldo Vos, Alan R Williams, Pelin Yilmaz
BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science...
October 20, 2016: BMC Ecology
Ryo Suzuki, Kohta Ito, Taeyong Lee, Naomichi Ogihara
Accurate identification of the material properties of the plantar soft tissue is important for computer-aided analysis of foot pathologies and design of therapeutic footwear interventions based on subject-specific models of the foot. However, parameter identification of the hyperelastic material properties of plantar soft tissues usually requires an inverse finite element analysis due to the lack of a practical contact model of the indentation test. In the present study, we derive an analytical contact model of a spherical indentation test in order to directly estimate the material properties of the plantar soft tissue...
September 22, 2016: Journal of the Mechanical Behavior of Biomedical Materials
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