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Hannah M Gustafson, Peter A Cripton, Stephen J Ferguson, Benedikt Helgason
The purpose of this study was to load cadaveric vertebral bodies (n=6) in compression and compare the response, measured with digital image correlation (DIC) on the cortex, with the predicted response from specimen-specific vertebral finite element (FE) models. Five modulus-density relationships were evaluated, and for the strongest modulus-density relationship, the correlation between the DIC and FE displacements had R(2) values from 0.75 to 0.93. The stiffnesses derived from the DIC measurements were strongly predicted by the FE stiffnesses (R(2)=0...
October 7, 2016: Journal of the Mechanical Behavior of Biomedical Materials
Jessica A Nash, Albert L Kwansa, James Samuel Peerless, Ho Shin Kim, Yaroslava G Yingling
Nanoparticles (NPs) play increasingly important roles in nanotechnology and nanomedicine where nanoparticle surface chemistry allows for control over interactions with other nanoparticles and biomolecules. In particular, for applications in drug and gene delivery, a fundamental understanding of the NP-nucleic acid interface allows for development of more efficient and effective nanoparticle carriers. Computational modeling can provide insights of processes occurring at the inorganic NP-nucleic interface, in detail which is difficult to access by experimental methods...
October 24, 2016: Bioconjugate Chemistry
Cristian Torres-Díaz, Jorge Gallardo-Cerda, Paris Lavin, Rómulo Oses, Fernando Carrasco-Urra, Cristian Atala, Ian S Acuña-Rodríguez, Peter Convey, Marco A Molina-Montenegro
Most climate and environmental change models predict significant increases in temperature and precipitation by the end of the 21st Century, for which the current functional output of certain symbioses may also be altered. In this context we address the following questions: 1) How the expected changes in abiotic factors (temperature, and water) differentially affect the ecophysiological performance of the plant Colobanthus quitensis? and 2) Will this environmental change indirectly affect C. quitensis photochemical performance and biomass accumulation by modifying its association with fungal endophytes? Plants of C...
2016: PloS One
Mohammad Islamuddin, Garima Chouhan, Muzamil Yaqub Want, Hani A Ozbak, Hassan A Hemeg, Farhat Afrin
BACKGROUND: The therapy of visceral leishmaniasis (VL) is limited by resistance, toxicity and decreased bioavailability of the existing drugs coupled with dramatic increase in HIV-co-infection, non-availability of vaccines and down regulation of cell-mediated immunity (CMI). Thus, we envisaged combating the problem with plant-derived antileishmanial drug that could concomitantly mitigate the immune suppression of the infected hosts. Several plant-derived compounds have been found to exert leishmanicidal activity via immunomodulation...
October 2016: PLoS Neglected Tropical Diseases
Chen Wang, Ying Duan Lei, Frank Wania
Dissolved inorganic salt(s) influence the partitioning of organic compounds into the aqueous phase. This influence is especially significant in atmospheric aerosol, which usually contains large amount of ions, including sodium, ammonium, chloride, sulfate and nitrate. However, empirical data on this salt effect are very sparse. Here, the partitioning of numerous organic compounds into solutions of Na2SO4, NH4Cl and NH4NO3 was measured and compared with existing data for NaCl and (NH4)2SO4. Salt mixtures were also tested in order to establish whether the salt effect is additive...
October 24, 2016: Environmental Science & Technology
Kathryn M Kingsmore, Daniel K Logsdon, Desiree H Floyd, Shayn M Peirce, Benjamin W Purow, Jennifer M Munson
Glioblastoma (GBM) prognosis remains dismal due in part to the invasiveness of GBM cells. Interstitial fluid flow (IFF) has been shown to increase invasion of glioma cells in vitro through the CXCR4 receptor interacting with autologous, pericellular gradients of CXCL12 (autologous chemotaxis) or through the CD44 receptor interactions with the extracellular matrix (hyaluronan-mediated mechanotransduction). These mechanisms have not been examined together and thus we hypothesized that both mechanisms contribute to invasion in populations of cancer cells...
October 24, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
B Caglar, M Olus Ozbek, J W Hans Niemantsverdriet, C J Kees-Jan Weststrate
The adsorption and decomposition of ethanol on Rh(100) was studied as a model reaction to understand the role of C-OH functionalities in the surface chemistry of biomass-derived molecules. A combination of experimental surface science and computational techniques was used: (i) temperature programmed reaction spectroscopy (TPRS), reflection absorption infrared spectroscopy (RAIRS), work function measurements (Kelvin Probe - KP), and density functional theory (DFT). Ethanol produces ethoxy (CH3CH2O) species via O-H bond breaking upon adsorption at 100 K...
October 24, 2016: Physical Chemistry Chemical Physics: PCCP
Kelly D Moynihan, Cary F Opel, Gregory L Szeto, Alice Tzeng, Eric F Zhu, Jesse M Engreitz, Robert T Williams, Kavya Rakhra, Michael H Zhang, Adrienne M Rothschilds, Sudha Kumari, Ryan L Kelly, Byron H Kwan, Wuhbet Abraham, Kevin Hu, Naveen K Mehta, Monique J Kauke, Heikyung Suh, Jennifer R Cochran, Douglas A Lauffenburger, K Dane Wittrup, Darrell J Irvine
Checkpoint blockade with antibodies specific for cytotoxic T lymphocyte-associated protein (CTLA)-4 or programmed cell death 1 (PDCD1; also known as PD-1) elicits durable tumor regression in metastatic cancer, but these dramatic responses are confined to a minority of patients. This suboptimal outcome is probably due in part to the complex network of immunosuppressive pathways present in advanced tumors, which are unlikely to be overcome by intervention at a single signaling checkpoint. Here we describe a combination immunotherapy that recruits a variety of innate and adaptive immune cells to eliminate large tumor burdens in syngeneic tumor models and a genetically engineered mouse model of melanoma; to our knowledge tumors of this size have not previously been curable by treatments relying on endogenous immunity...
October 24, 2016: Nature Medicine
Rui Zhang, Shiping Zhu, Qin Zhou
Infrared image segmentation is a challenging topic because infrared images are characterized by high noise, low contrast, and weak edges. Active contour models, especially gradient vector flow, have several advantages in terms of infrared image segmentation. However, the GVF (Gradient Vector Flow) model also has some drawbacks including a dilemma between noise smoothing and weak edge protection, which decrease the effect of infrared image segmentation significantly. In order to solve this problem, we propose a novel generalized gradient vector flow snakes model combining GGVF (Generic Gradient Vector Flow) and NBGVF (Normally Biased Gradient Vector Flow) models...
October 21, 2016: Sensors
Jaka Kravanja, Mario Žganec, Jerneja Žganec-Gros, Simon Dobrišek, Vitomir Štruc
Depth image acquisition with structured light approaches in outdoor environments is a challenging problem due to external factors, such as ambient sunlight, which commonly affect the acquisition procedure. This paper presents a novel structured light sensor designed specifically for operation in outdoor environments. The sensor exploits a modulated sequence of structured light projected onto the target scene to counteract environmental factors and estimate a spatial distortion map in a robust manner. The correspondence between the projected pattern and the estimated distortion map is then established using a probabilistic framework based on graphical models...
October 19, 2016: Sensors
Ali Fatih Demir, Qammer Abbasi, Zekeriyya Esat Ankarali, Akram Alomainy, Khalid Qaraqe, Erchin Serpedin, Huseyin Arslan
In vivo wireless body area networks (WBANs) and their associated technologies are shaping the future of healthcare by providing continuous health monitoring and noninvasive surgical capabilities, in addition to remote diagnostic and treatment of diseases. To fully exploit the potential of such devices, it is necessary to characterize the communication channel which will help to build reliable and high-performance communication systems. This paper presents an in vivo wireless communication channel characterization for male torso both numerically and experimentally (on a human cadaver) considering various organs at 915 MHz and 2...
October 19, 2016: IEEE Journal of Biomedical and Health Informatics
Jiaxiang Huang, Maoguo Gong, Lijia Ma
Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyse the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations...
October 19, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Jian Zhang, Haiting Chai, Bo Gao, Guifu Yang, Zhiqiang Ma
Heme is an essential biomolecule that widely exists in numerous extant organisms. Accurately identifying heme binding residues (HEMEs) is of great importance in disease progression and drug development. In this study, a novel predictor named HEMEsPred was proposed for predicting HEMEs. First, several sequence- and structure-based features, including amino acid composition, motifs, surface preferences and secondary structure, were collected to construct feature matrices. Second, a novel fast-adaptive ensemble learning scheme was designed to overcome the serious class-imbalance problem as well as to enhance the prediction performance...
October 4, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Dong Qian, Bei Wang, Yun Qing, Tao Zhang, Yu Zhang, Xing Wang, Masatoshi Nakamura
Daytime short nap involves physiological processes, such as alertness, drowsiness and sleep. The study of the relationship between drowsiness and nap based on physiological signals is a great way to have a better understanding of the periodical rhymes of physiological states. A model of Bayesian nonnegative CP decomposition (BNCPD) was proposed to extract common multiway features from the group-level electroencephalogram (EEG) signals. As an extension of the nonnegative CP decomposition, the BNCPD model involves prior distributions of factor matrices, while the underlying CP rank could be determined automatically based on a Bayesian nonparametric approach...
October 19, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Chong Sun, Dong Wang, Huchuan Lu
In this paper, we propose an effective person reidentification method with latent variables, which represents a pedestrian as the mixture of a holistic model and a number of flexible models. Three types of latent variables are introduced to model uncertain factors in the re-identification problem, including vertical misalignments, horizontal misalignments and leg posture variations. The distance between two pedestrians can be determined by minimizing a given distance function with respect to latent variables, and then be used to conduct the re-identification task...
October 19, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Noam Segev, Maayan Harel, Shie Mannor, Koby Crammer, Ran El-Yaniv
We propose novel model transfer-learning methods that refine a decision forest model M learned within a "source" domain using a training set sampled from a "target" domain, assumed to be a variation of the source. We present two random forest transfer algorithms. The first algorithm searches greedily for locally optimal modifications of each tree structure by trying to locally expand or reduce the tree around individual nodes. The second algorithm does not modify structure, but only the parameter (thresholds) associated with decision nodes...
October 18, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
Antonis Sakellarios, Lorenz Raeber, Christos Bourantas, Themis Exarchos, Lambros Athanasiou, Gualtiero Pelosi, Oberdan Parodi, Konstantinos Koskinas, Katerina Naka, Lampros Michalis, Patrick Wjc Serruys, Hector Garcia-Garcia, Stephan Windecker, Dimitrios Fotiadis
OBJECTIVE: The aim of this study is to explore major mechanisms of atherosclerotic plaque growth, presenting a proof-of-concept numerical model. METHODS: To this aim, a human reconstructed left circumflex coronary artery is utilized for a multi-level modeling approach. More specifically, the first level consists of the modeling of blood flow and endothelial shear stress (ESS) computation. The second level includes the modeling of low and high density lipoprotein (LDL, HDL) and monocytes transport through the endothelial membrane to vessel wall...
October 19, 2016: IEEE Transactions on Bio-medical Engineering
A Sangion, P Gramatica
Pharmaceutical and Personal Care Products (PPCPs) became a class of contaminants of emerging concern because are ubiquitously detected in surface water and soil, where they can affect wildlife. Ecotoxicological data are only available for a few PPCPs, thus modelling approaches are essential tools to maximize the information contained in the existing data. In silico methods may be helpful in filling data gaps for the toxicity of PPCPs towards various ecological indicator organisms. The good correlation between toxicity toward Daphnia magna and those on two fish species (Pimephales promelas and Oncorhynchus mykiss), improved by the addition of one theoretical molecular descriptor, allowed us to develop predictive models to investigate the relationship between toxicities in different species...
October 2016: SAR and QSAR in Environmental Research
Cameron Browne
This paper concerns modeling the coupled within-host population dynamics of virus and CTL (Cytotoxic T Lymphocyte) immune response. There is substantial evidence that the CTL immune response plays a crucial role in controlling HIV in infected patients. Recent experimental studies have demonstrated that certain CTL variants can recognize HIV infected cells early in the infected cell lifecycle before viral production, while other CTLs only detect viral proteins (epitopes) presented on the surface of infected cells after viral production...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
H T Banks, John E Banks, R A Everett, John D Stark
We develop statistical and mathematical based methodologies for determining (as the experiment progresses) the amount of information required to complete the estimation of stable population parameters with pre-specified levels of confidence. We do this in the context of life table models and data for growth/death for three species of Daphniids as investigated by J. Stark and J. Banks [17]. The ideas developed here also have wide application in the health and social sciences where experimental data are often expensive as well as difficult to obtain...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
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