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Daniel Reker, J B Brown
High-throughput and high-content screening campaigns have resulted in the creation of large chemogenomic matrices. These matrices form the training data which is used to build ligand-target interaction models for pharmacological and chemical biology research. While academic, government, and industrial efforts continuously add to the ligand-target data pairs available for modeling, major research efforts are devoted to improving machine learning techniques to cope with the sparseness, heterogeneity, and size of available datasets as well as inherent noise and bias...
2018: Methods in Molecular Biology
Paresh Shrimali, Mathew Peter, Archana Singh, Neha Dalal, Suresh Dakave, Shubhada V Chiplunkar, Prakriti Tayalia
For diseases related to genetic disorders or cancer, many cellular therapies rely on the ex vivo modification of cells for attaining a desired therapeutic effect. The efficacy of such therapies involving the genetic modification of cells relies on the extent of gene expression and subsequent persistence of modified cells when infused into the patient's body. In situ gene delivery implies the manipulation of cells in their in vivo niche such that the effectiveness can be improved by minimizing post manipulation effects like cell death, lack of persistence, etc...
October 18, 2018: Biomaterials Science
Tássia Carla Confortin, Izelmar Todero, Luciana Luft, Juliana Ferreira Soares, Marcio Antonio Mazutti, Giovani Leone Zabot, Marcus Vinícius Tres
The purpose of this review is to assist readers in understanding the importance of Lupinus albescens to nature, farmers, and scientists. L. albescens is mostly found in Argentina, Uruguay, Paraguay, and in "Campanha, Litoral and Missões" regions of State of Rio Grande do Sul (Brazil). Therefore, this review presents information and discussion on this plant that can encourage novel studies in a near future for exploring evermore the biological and physicochemical properties of L. albescens . The plant presents adaptive characteristics of soils with low content of nutrients, being an important plant for the recovering of degraded areas...
October 2018: 3 Biotech
Fengqin Wang, Hengjin Ke
A longstanding challenge in epilepsy research and practice is the need to classify synchronization patterns hidden in multivariate electroencephalography (EEG) data that is routinely superimposed with intensive noise. It is essential to select a suitable feature extraction method to achieve high recognition performance. A typical approach is to extract the mutual information (MI) between pairs of channels. This calculation, which considers the differences between the sequence pairs to build a reasonable partition, can improve the classification performance...
2018: Frontiers in Human Neuroscience
P Tsilifis, R G Ghanem
A novel approach is presented for constructing polynomial chaos representations of scalar quantities of interest (QoI) that extends previously developed methods for adaptation in Homogeneous Chaos spaces. In this work, we develop a Bayesian formulation of the problem that characterizes the posterior distributions of the series coefficients and the adaptation rotation matrix acting on the Gaussian input variables. The adaptation matrix is thus construed as a new parameter of the map from input to QoI, estimated through Bayesian inference...
September 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Alexis Nez, Laetitia Fradet, Frédéric Marin, Tony Monnet, Patrick Lacouture
Magneto-inertial measurement units (MIMUs) are a promising way to perform human motion analysis outside the laboratory. To do so, in the literature, orientation provided by an MIMU is used to deduce body segment orientation. This is generally achieved by means of a Kalman filter that fuses acceleration, angular velocity, and magnetic field measures. A critical point when implementing a Kalman filter is the initialization of the covariance matrices that characterize mismodelling and input error from noisy sensors...
October 16, 2018: Sensors
Habib Hasan Farooqui, Sakthivel Selvaraj, Aashna Mehta, David L Heymann
India was the largest consumer of antibiotics in 2010 in the world. Evidence suggests that countries with high per-capita antibiotic consumption have higher rates of antibiotic resistance. To control antibiotic resistance, not only reduction in antibiotic consumption is required, socio-economic factors like access to clean water and sanitation, regulation of private healthcare sector and better governance are equally important. The key objective of this research was to investigate the five year trends in consumption of major antibiotic classes in India and compare them with European Surveillance of Antimicrobial Consumption Network (ESAC-Net) countries...
2018: PloS One
Samuel R Polio, Aritra Nath Kundu, Carey E Dougan, Nathan P Birch, D Ezra Aurian-Blajeni, Jessica D Schiffman, Alfred J Crosby, Shelly R Peyton
Published data on the mechanical strength and elasticity of lung tissue is widely variable, primarily due to differences in how testing was conducted across individual studies. This makes it extremely difficult to find a benchmark modulus of lung tissue when designing synthetic extracellular matrices (ECMs). To address this issue, we tested tissues from various areas of the lung using multiple characterization techniques, including micro-indentation, small amplitude oscillatory shear (SAOS), uniaxial tension, and cavitation rheology...
2018: PloS One
Fernando Magro, Cláudia Camila Dias, Francisco Portela, Mário Miranda, Samuel Fernandes, Sonia Bernardo, Paula Ministro, Paula Lago, Isadora Rosa, Inês Pita, Luis Correia, Pedro Pereira Rodrigues
Introduction: Ulcerative colitis (UC) is a chronic inflammatory disease often accompanied by severe and distressing symptoms that, in some patients, might require a surgical intervention (colectomy). This study aimed at determining the risk of experiencing progressive disease or requiring colectomy. Material and Methods: This was a multicenter study: patients' data (n=1481) was retrieved from the Portuguese database of inflammatory bowel disease patients. Bayesian networks and logistic regression were used to build risk matrices concerning the outcomes of interest...
October 17, 2018: Journal of Crohn's & Colitis
Caroline Magnain, Jean C Augustinack, Lee Tirrell, Morgan Fogarty, Matthew P Frosch, David Boas, Bruce Fischl, Kathleen S Rockland
Optical coherence tomography is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles. Optical coherence microscopy (OCM) is higher resolution (i.e., 1.25 µm) and is capable of detecting neurons. In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II. In the current method-oriented study, we aimed to determine the colocalization success rate between OCM and Nissl in other brain cortical areas with different laminar arrangements and cell packing density...
October 17, 2018: Brain Structure & Function
Sang Hoon Sung, Sunhyung Kim, Jan Hendricks, Christian Clasen, Kyung Hyun Ahn
We explore the relaxation behavior of model colloidal gels under steady shear flow by means of orthogonal superposition rheometry. Fumed silica and carbon black dispersions in Newtonian matrices are used as a model system. As shear rate increases, the frequency dependent orthogonal moduli of the gels shift along the frequency axis without changing their shape, which finally can be superimposed to yield a single master curve. This indicates that the shear rate tunes a master clock for overall relaxation modes in the sheared colloidal gels to produce a "time-shear rate superposition (TSS)", as temperature does in polymeric liquids to produce a time-temperature superposition (TTS)...
October 17, 2018: Soft Matter
Athanasia A Septevani, David A C Evans, Alireza Hosseinmardi, Darren J Martin, John Simonsen, John F Conley, Pratheep K Annamalai
Analysis of cellulose nanocrystals (CNCs) at low volume fractions in polymer nanocomposites through conventional electron microscopy still remains a challenge due to insufficient contrast between CNCs and organic polymer matrices. Herein, a methodology for enhancing the contrast of CNC, through atomic layer deposition (ALD) of alumina (Al2 O3 ) on CNCs is demonstrated. The metal oxide coated CNC allows clear visualization by transmission electron microscopy, when they are dispersed in water and polyol. A coating of about 6 ± 1 nm thick alumina layer on the CNC is achieved after 50 ALD cycles...
October 16, 2018: Small
Serkan Tuylu, Atac Bascetin, Deniz Adiguzel
Environmental impacts resulting from conventional tailings disposal such as tailings dam accidents are a common problem for base metal mines around the world. In this context, laboratory-scale studies have been carried out on the Surface Paste Disposal (SPD) method, which is one of the alternative surface storage methods. In this study, three different SPD designs were tested; and volumetric water content, oxygen consumption, and matric suction sensors in first, fifth and 10th paste layers plus pH- electric conductivity (EC) values were all measured...
October 13, 2018: Journal of Environmental Management
Silas Bossert, Elizabeth A Murray, Eduardo A B Almeida, Seán G Brady, Bonnie B Blaimer, Bryan N Danforth
Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineages is now a standard method, it is still not clear if UCE data can be readily combined with published transcriptomes. In this study, we evaluate the combination of UCEs and transcriptomes in a single analysis using genome-, transcriptome-, and UCE data for 79 bees in the largest and most biologically diverse bee family, Apidae...
October 13, 2018: Molecular Phylogenetics and Evolution
Jacob P Walsh, Justin B Renaud, Shawn Hoogstra, David R McMullin, Ashraf Ibrahim, Cobus Visagie, Joey B Tanney, Ken K-C Yeung, Mark W Sumarah
RATIONALE: Microbial natural products are often biosynthesized as classes of structurally related compounds that have similar MS/MS fragmentation patterns. Mining MS/MS datasets for precursor ions that share diagnostic or common features enables entire chemical classes to be identified, including novel derivatives that have previously been unreported. Analytical data analysis tools that can facilitate a class-targeted approach to rapidly dereplicate known compounds and identify structural variants within complex matrices would be useful for the discovery of new natural products...
October 16, 2018: Rapid Communications in Mass Spectrometry: RCM
Yuanyuan Wu, Shuai Li, Jingxin Song, Bingxue Jiang, ShanShan Chen, Huimin Sun, Xinxin Li
Nano-titanium dioxide (TiO2 ) was modified with the surfactant sodium laurate (SL) via ultrasonic microwave-assisted technology to improve the dispersion of TiO2 in polymer matrices. As revealed by Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscopy analyses, SL was well adsorbed onto the TiO2 surface through chemical bonding, resulting in SL-modified TiO2 (TiO2 -SLx). The hydrophobicity and dispersibility of TiO2 -SLx increased significantly compared to unmodified nano-TiO2 ...
October 16, 2018: Journal of Food Science
Zongliang Hu, Tiejun Tong, Marc G Genton
We propose a likelihood ratio test framework for testing normal mean vectors in high-dimensional data under two common scenarios: the one-sample test and the two-sample test with equal covariance matrices. We derive the test statistics under the assumption that the covariance matrices follow a diagonal matrix structure. In comparison with the diagonal Hotelling's tests, our proposed test statistics display some interesting characteristics. In particular, they are a summation of the log-transformed squared t-statistics rather than a direct summation of those components...
October 16, 2018: Biometrics
Huifeng Pi, Min Li, Lingyun Zou, Min Yang, Ping Deng, Tengfei Fan, Menyu Liu, Li Tian, Manyu Tu, Jia Xie, Mengyan Chen, Huijuan Li, Yu Xi, Lei Zhang, Mindi He, Yonghui Lu, Chunhai Chen, Tao Zhang, Zheng Wang, Zhengping Yu, Feng Gao, Zhou Zhou
Cadmium (Cd) is a toxic metal that is widely found in numerous environmental matrices and induces serious adverse effects in various organs and tissues. Bone tissue seems to be a crucial target of Cd contamination. Macroautophagy/autophagy has been proposed to play a pivotal role in Cd-mediated bone toxicity. However, the mechanisms that underlie Cd-induced autophagy are not yet completely understood. We demonstrated that Cd treatment increased autophagic flux and inhibition of the autophagic process using Atg7 gene silencing blocked the Cd-induced mesenchymal stem cell death...
October 16, 2018: Autophagy
Piret Raudsepp, Julia Koskar, Dea Anton, Kadrin Meremäe, Karmen Kapp, Peeter Laurson, Uko Bleive, Hedi Kaldmäe, Mati Roasto, Tõnu Püssa
BACKGROUND: It is important to find plant materials that can inhibit the growth of Listeria monocytogenes and other food spoiling bacteria both in vitro and in situ. The aim of the study was to compare antibacterial and antioxidative activity of selected plant-ethanol infusions: leaves and berries of black currant (Ribes nigrum L.), berries of chokeberry (Aronia melanocarpa (Michx.) Elliott) and blue honeysuckle (Lonicera caerulea L. var. edulis); petioles and dark and light roots of garden rhubarb (Rheum rhaponticum L...
October 16, 2018: Journal of the Science of Food and Agriculture
Kelly M Hainline, Fangqi Gu, Jacqueline F Handley, Ye F Tian, Yaoying Wu, Larischa de Wet, Donald J Vander Griend, Joel H Collier
Progress in prostate cancer research is presently limited by a shortage of reliable in vitro model systems. The authors describe a novel self-assembling peptide, bQ13, which forms nanofibers and gels useful for the 3D culture of prostate cancer spheroids, with improved cytocompatibility compared to related fibrillizing peptides. The mechanical properties of bQ13 gels can be controlled by adjusting peptide concentration, with storage moduli ranging between 1 and 10 kPa. bQ13's ability to remain soluble at mildly basic pH considerably improved the viability of encapsulated cells compared to other self-assembling nanofiber-forming peptides...
October 15, 2018: Macromolecular Bioscience
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