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https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#1
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29325889/early-cell-response-of-osteogenic-cells-on-differently-modified-implant-surfaces-sequences-of-cell-proliferation-adherence-and-differentiation
#2
Sebastian Blatt, Andreas Max Pabst, Eik Schiegnitz, Marco Hosang, Thomas Ziebart, Christian Walter, Bilal Al-Nawas, Marcus Oliver Klein
OBJECTIVES: Osseointegration of dental implants is a crucial prerequisite for long-term survival. Therefore, surface modifications are needed to interact with the extracellular environment and to trigger osteogenic cell responses such as cell proliferation, adherence, and differentiation. The purpose of this study was to investigate different surface modifications in vitro over 2 weeks. MATERIALS AND METHODS: Commercially available cells from a human osteogenic cell line (HHOB-c) were cultivated on the following surfaces: titanium with smooth surfaces (polished titanium (P), machined titanium (M), polyetheretherketone (Peek)), titanium with rough and hydrophilised surfaces (acid etched titanium (A), sandblasted acid etched titanium (SA and SA2), sandblasted acid etched hydrophilised (SAH), titanium plasma painted titanium (TPS)), titanium with calcium phosphate-containing surfaces (titanium plasma painted calcium phosphate modified titanium (TPS-CaP), sandblasted calcium phosphate modified titanium (S-CaP), sandblasted acid etched calcium phosphate modified titanium (SA-CaP)), and zirconium-oxide (yttrium amplified zirconium (Z), yttrium amplified Ca2+ delivering zirconium (Z-Ca))...
December 26, 2017: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/29298691/volition-adaptive-control-for-gait-training-using-wearable-exoskeleton-preliminary-tests-with-incomplete-spinal-cord-injury-individuals
#3
Vijaykumar Rajasekaran, Eduardo López-Larraz, Fernando Trincado-Alonso, Joan Aranda, Luis Montesano, Antonio J Del-Ama, Jose L Pons
BACKGROUND: Gait training for individuals with neurological disorders is challenging in providing the suitable assistance and more adaptive behaviour towards user needs. The user specific adaptation can be defined based on the user interaction with the orthosis and by monitoring the user intentions. In this paper, an adaptive control model, commanded by the user intention, is evaluated using a lower limb exoskeleton with incomplete spinal cord injury individuals (SCI). METHODS: A user intention based adaptive control model has been developed and evaluated with 4 incomplete SCI individuals across 3 sessions of training per individual...
January 3, 2018: Journal of Neuroengineering and Rehabilitation
https://www.readbyqxmd.com/read/29298056/full-enyzme-complex-simulation-interactions-in-human-pyruvate-dehydrogenase-complex
#4
Samira Hezaveh, An-Ping Zeng, Uwe Jandt
The pyruvate dehydrogenase complex (PDC) is a large macromolecular machine consisting of dozens of interacting enzymes that are connected and regulated by highly flexible domains, also called swinging arms. The overall structure and function of these domains and how they organize the complex function is rarely elucidated yet. This lack of structural and dynamic understanding is frequently observed in multi domain enzymatic complexes. Here we present the first full and dynamic structural model of full human PDC (hPDC), including the linking arms binding to the surrounding E1 and E3 enzymes via their binding domains with variable stoichiometries...
January 3, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29297285/effective-computational-detection-of-pirnas-using-n-gram-models-and-support-vector-machine
#5
Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Piwi-interacting RNAs (piRNAs) are a new class of small non-coding RNAs that are known to be associated with RNA silencing. The piRNAs play an important role in protecting the genome from invasive transposons in the germline. Recent studies have shown that piRNAs are linked to the genome stability and a variety of human cancers. Due to their clinical importance, there is a pressing need for effective computational methods that can be used for computational identification of piRNAs...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29291527/improve-ground-level-pm2-5-concentration-mapping-using-a-random-forests-based-geostatistical-approach
#6
Ying Liu, Guofeng Cao, Naizhuo Zhao, Kevin Mulligan, Xinyue Ye
Accurate measurements of ground-level PM2.5 (particulate matter with aerodynamic diameters equal to or less than 2.5 μm) concentrations are critically important to human and environmental health studies. In this regard, satellite-derived gridded PM2.5 datasets, particularly those datasets derived from chemical transport models (CTM), have demonstrated unique attractiveness in terms of their geographic and temporal coverage. The CTM-based approaches, however, often yield results with a coarse spatial resolution (typically at 0...
December 29, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29261283/transparent-and-self-powered-multi-stage-sensation-matrix-for-mechanosensation-application
#7
Qian Zhang, Tao Jiang, Dong Hae Ho, Shanshan Qin, Xixi Yang, Jeong Ho Cho, Qijun Sun, Zhong Lin Wang
Electronic skin based on multimodal sensing array is ready to detect various stimuli in different categories by utilizing highly sensitive materials, sophisticated geometry designs, and integration of multifunctional sensors. However, it is still difficult to distinguish multiple and complex mechanical stimuli in a local position by conventional multimodal E-skin, which is significantly important in the signals feedback of robotic fine motions and human-machine interactions. Here, we present a transparent, flexible and self-powered multi-stage sensation matrix based on piezoelectric nanogenerators (NGs) constructed in a crossbar design...
December 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/29258445/a-biological-network-based-regularized-artificial-neural-network-model-for-robust-phenotype-prediction-from-gene-expression-data
#8
Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek, Kourosh Zarringhalam
BACKGROUND: Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers...
December 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29232832/hybrid-orientation-based-human-limbs-motion-tracking-method
#9
Grzegorz Glonek, Adam Wojciechowski
One of the key technologies that lays behind the human-machine interaction and human motion diagnosis is the limbs motion tracking. To make the limbs tracking efficient, it must be able to estimate a precise and unambiguous position of each tracked human joint and resulting body part pose. In recent years, body pose estimation became very popular and broadly available for home users because of easy access to cheap tracking devices. Their robustness can be improved by different tracking modes data fusion. The paper defines the novel approach-orientation based data fusion-instead of dominating in literature position based approach, for two classes of tracking devices: depth sensors (i...
December 9, 2017: Sensors
https://www.readbyqxmd.com/read/29218909/reading-between-the-genes-computational-models-to-discover-function-from-noncoding-dna
#10
Yves A Lussier, Joanne Berghout, Francesca Vitali, Kenneth S Ramos, Maricel Kann, Jason H Moore
Noncoding DNA - once called "junk" has revealed itself to be full of function. Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements. Variation in these regions has been tied to variation in biological function and human disease. This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218324/intellicount-high-throughput-quantification-of-fluorescent-synaptic-protein-puncta-by-machine-learning
#11
J A Fantuzzo, V R Mirabella, A H Hamod, R P Hart, J D Zahn, Z P Pang
Synapse formation analyses can be performed by imaging and quantifying fluorescent signals of synaptic markers. Traditionally, these analyses are done using simple or multiple thresholding and segmentation approaches or by labor-intensive manual analysis by a human observer. Here, we describe Intellicount, a high-throughput, fully-automated synapse quantification program which applies a novel machine learning (ML)-based image processing algorithm to systematically improve region of interest (ROI) identification over simple thresholding techniques...
November 2017: ENeuro
https://www.readbyqxmd.com/read/29201283/a-comparison-of-network-definitions-for-detecting-sex-differences-in-brain-connectivity-using-support-vector-machines
#12
George W Hafzalla, Anjanibhargavi Ragothaman, Joshua Faskowitz, Neda Jahanshad, Katie L McMahon, Greig I de Zubicaray, Margaret J Wright, Meredith N Braskie, Gautam Prasad, Paul M Thompson
Human brain connectomics is a rapidly evolving area of research, using various methods to define connections or interactions between pairs of regions. Here we evaluate how the choice of (1) regions of interest, (2) definitions of a connection, and (3) normalization of connection weights to total brain connectivity and region size, affect our calculation of the structural connectome. Sex differences in the structural connectome have been established previously. We study how choices in reconstruction of the connectome affect our ability to classify subjects by sex using a support vector machine (SVM) classifier...
2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
https://www.readbyqxmd.com/read/29196723/bayesian-analysis-of-microscale-thermophoresis-data-to-quantify-affinity-of-protein-protein-interactions-with-human-survivin
#13
Maria-Jose Garcia-Bonete, Maja Jensen, Christian V Recktenwald, Sandra Rocha, Volker Stadler, Maria Bokarewa, Gergely Katona
A biomolecular ensemble exhibits different responses to a temperature gradient depending on its diffusion properties. MicroScale Thermophoresis technique exploits this effect and is becoming a popular technique for analyzing interactions of biomolecules in solution. When comparing affinities of related compounds, the reliability of the determined thermodynamic parameters often comes into question. The thermophoresis binding curves can be assessed by Bayesian inference, which provides a probability distribution for the dissociation constant of the interacting partners...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29190724/socioeconomic-characterization-of-regions-through-the-lens-of-individual-financial-transactions
#14
Behrooz Hashemian, Emanuele Massaro, Iva Bojic, Juan Murillo Arias, Stanislav Sobolevsky, Carlo Ratti
People are increasingly leaving digital traces of their daily activities through interacting with their digital environment. Among these traces, financial transactions are of paramount interest since they provide a panoramic view of human life through the lens of purchases, from food and clothes to sport and travel. Although many analyses have been done to study the individual preferences based on credit card transaction, characterizing human behavior at larger scales remains largely unexplored. This is mainly due to the lack of models that can relate individual transactions to macro-socioeconomic indicators...
2017: PloS One
https://www.readbyqxmd.com/read/29186295/systematic-analysis-and-prediction-of-type-iv-secreted-effector-proteins-by-machine-learning-approaches
#15
Jiawei Wang, Bingjiao Yang, Yi An, Tatiana Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I Webb, Richard A Strugnell, Jiangning Song, Trevor Lithgow
In the course of infecting their hosts, pathogenic bacteria secrete numerous effectors, namely, bacterial proteins that pervert host cell biology. Many Gram-negative bacteria, including context-dependent human pathogens, use a type IV secretion system (T4SS) to translocate effectors directly into the cytosol of host cells. Various type IV secreted effectors (T4SEs) have been experimentally validated to play crucial roles in virulence by manipulating host cell gene expression and other processes. Consequently, the identification of novel effector proteins is an important step in increasing our understanding of host-pathogen interactions and bacterial pathogenesis...
November 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29182092/preliminary-assessment-of-a-compliant-gait-exoskeleton
#16
Manuel Cestari, Daniel Sanz-Merodio, Elena Garcia
Current commercial wearable gait exoskeletons contain joints with stiff actuators that cannot adapt to unpredictable environments. These actuators consume a significant amount of energy, and their stiffness may not be appropriate for safe human-machine interactions. Adjustable compliant actuators are being designed and implemented because of their ability to minimize large forces due to shocks, to safely interact with the user, and to store and release energy in passive elastic elements. Introduction of such compliant actuation in gait exoskeletons, however, has been limited by the larger power-to-weight and volume ratio requirement...
June 2017: Soft Robotics
https://www.readbyqxmd.com/read/29172925/parents-experiences-and-responses-to-an-intervention-for-psychological-preparation-of-children-and-families-during-the-child-s-radiotherapy
#17
Charlotte Ångström-Brännström, Viveca Lindh, Tara Mullaney, Kristina Nilsson, Gun Wickart-Johansson, Anna-Maja Svärd, Tufve Nyholm, Jack Lindh, Gunn Engvall
The aim of this study was to evaluate parents' experiences and responses to a systematic intervention for psychological preparation of children and families during the child's radiotherapy (RT) treatment. In this case-control study at 3 pediatric RT centers, an intervention with a preparatory kit, including age-adjusted information on tablets, gift of a stuffed toy or a pair of headphones, a parent booklet, and toy models of the computed tomography and RT machines was implemented. For evaluation, a mixed methods data collection was conducted...
November 1, 2017: Journal of Pediatric Oncology Nursing: Official Journal of the Association of Pediatric Oncology Nurses
https://www.readbyqxmd.com/read/29170578/investigating-changes-in-resting-state-connectivity-from-functional-mri-data-in-patients-with-hiv-associated-neurocognitive-disorder-using-mca-and-machine-learning
#18
Adora M DSouza, Anas Z Abidin, Axel Wismüller
Infection of the brain by the Human Immunodeficiency Virus (HIV) causes irreversible damage to the synaptic connections resulting in cognitive impairment. Patients with HIV infection, showing signs of impairment in multiple cognitive domains, as assessed by neuropsychological testing, are said to exhibit symptoms of HIV Associated Neurocognitive Disorder (HAND). In this study, we use resting-state functional MRI (fMRI) data to distinguish between healthy subjects and subjects with symptoms of HAND. To this end, we first establish a measure of interaction between pairs of regional time-series by quantifying their non-linear functional connectivity using Mutual Connectivity Analysis (MCA)...
March 13, 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/29167655/an-individual-finger-gesture-recognition-system-based-on-motion-intent-analysis-using-mechanomyogram-signal
#19
Huijun Ding, Qing He, Yongjin Zhou, Guo Dan, Song Cui
Motion-intent-based finger gesture recognition systems are crucial for many applications such as prosthesis control, sign language recognition, wearable rehabilitation system, and human-computer interaction. In this article, a motion-intent-based finger gesture recognition system is designed to correctly identify the tapping of every finger for the first time. Two auto-event annotation algorithms are firstly applied and evaluated for detecting the finger tapping frame. Based on the truncated signals, the Wavelet packet transform (WPT) coefficients are calculated and compressed as the features, followed by a feature selection method that is able to improve the performance by optimizing the feature set...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29158606/detecting-macroecological-patterns-in-bacterial-communities-across-independent-studies-of-global-soils
#20
Kelly S Ramirez, Christopher G Knight, Mattias de Hollander, Francis Q Brearley, Bede Constantinides, Anne Cotton, Si Creer, Thomas W Crowther, John Davison, Manuel Delgado-Baquerizo, Ellen Dorrepaal, David R Elliott, Graeme Fox, Robert I Griffiths, Chris Hale, Kyle Hartman, Ashley Houlden, David L Jones, Eveline J Krab, Fernando T Maestre, Krista L McGuire, Sylvain Monteux, Caroline H Orr, Wim H van der Putten, Ian S Roberts, David A Robinson, Jennifer D Rocca, Jennifer Rowntree, Klaus Schlaeppi, Matthew Shepherd, Brajesh K Singh, Angela L Straathof, Jennifer M Bhatnagar, Cécile Thion, Marcel G A van der Heijden, Franciska T de Vries
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries...
November 20, 2017: Nature Microbiology
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