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https://www.readbyqxmd.com/read/27913395/metabolomic-characterization-of-hepatocellular-carcinoma-in-patients-with-liver-cirrhosis-for-biomarker-discovery
#1
Cristina Di Poto, Alessia Ferrarini, Yi Zhao, Rency S Varghese, Chao Tu, Yiming Zuo, Minkun Wang, Mohammad R Nezami Ranjbar, Yue Luo, Chi Zhang, Chirag S Desai, Kirti Shetty, Mahlet G Tadesse, Habtom W Ressom
BACKGROUND: Metabolomics plays an important role in providing insight into the etiology and mechanisms of hepatocellular carcinoma (HCC). This is accomplished by a comprehensive analysis of patterns involved in metabolic alterations in human specimens. This study compares the levels of plasma metabolites in HCC cases versus cirrhotic patients and evaluates the ability of candidate metabolites in distinguishing the two groups. Also, it investigates the combined use of metabolites and clinical covariates for detection of HCC in patients with liver cirrhosis...
December 2, 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/27913367/a-new-method-for-self-estimation-of-the-severity-of-obstructive-sleep-apnea-using-easily-available-measurements-and-neural-fuzzy-evaluation-system
#2
Ming-Feng Wu, Wei-Chang Huang, Chia-Feng Juang, Kai-Ming Chang, Chih-Yu Wen, Yu-Hsuan Chen, Ching-Yi Lin, Yi-Chan Chen, Ching-Cheng Lin
This paper proposes a neural fuzzy evaluation system (NFES) with significant variables selected from stepwise regression to predict apnea-hypopnea index (AHI) for evaluating obstructive sleep apnea (OSA). The variables considered are the change statuses of blood pressure (BP) before going to sleep and early in the morning as well as other five easily available measurements (age, body mass index (BMI) etc.) so that users can use the system for self-evaluation of OSA. A total of 150 subjects are reviewed retrospectively and categorized as training (120 subjects) and validation (30 subjects) sets by a five-fold cross validation scheme with stratified sampling based on the OSA severity...
December 1, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27913357/introducing-a-stable-bootstrap-validation-framework-for-reliable-genomic-signature-extraction
#3
Nikolaos-Kosmas Chlis, Ekaterini S Bei, Michael Zervakis
The application of machine learning methods for the identification of candidate genes responsible for phenotypes of interest, such as cancer, is a major challenge in the field of bioinformatics. These lists of genes are often called genomic signatures and their linkage to phenotype associations may form a significant step in discovering the causation between genotypes and phenotypes. Traditional methods that produce genomic signatures from DNA Microarray data tend to extract significantly different lists under relatively small variations of the training data...
November 29, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27913322/automatic-detection-and-classification-of-high-frequency-oscillations-in-depth-eeg-signals
#4
Nisrine Jrad, Amar Kachenoura, Isabelle Merlet, Fabrice Bartolomei, Anca Nica, Arnaud Biraben, Fabrice Wendling
GOAL: Interictal High Frequency Oscillations (HFOs [30-600 Hz]) have proven to be relevant biomarkers in epilepsy. In this paper, four categories of HFOs are considered: Gamma ([30- 80 Hz]), High-Gamma ([80-120 Hz]), Ripples ([120-250 Hz]) and Fast-Ripples ([250-600 Hz]). A universal detector of the four types of HFOs is proposed. It has the advantages of i) classifying HFOs, and thus being robust to inter- and intra-subject variability; ii) rejecting artefacts, thus being specific. METHODS: Gabor atoms are tuned to cover the physiological bands...
November 29, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27913177/effect-of-trunnion-roughness-and-length-on-the-modular-taper-junction-strength-under-typical-intraoperative-assembly-forces
#5
S Y Jauch-Matt, A W Miles, H S Gill
Modular hip implants are at risk of fretting-induced postoperative complications most likely initiated by micromotion between adjacent implant components. A stable fixation between ball head and stem-neck taper is critical to avoid excessive interface motions. Therefore, the aim of this study was to identify the effect of trunnion roughness and length on the modular taper strength under typical intraoperative assembly forces. Custom-made Titanium trunnions (standard/mini taper, smooth/grooved surface finish) were assembled with modular Cobalt-chromium heads by impaction with peak forces ranging from 2kN to 6kN...
November 29, 2016: Medical Engineering & Physics
https://www.readbyqxmd.com/read/27913119/mechanical-forces-during-muscle-development
#6
REVIEW
Sandra B Lemke, Frank Schnorrer
Muscles are the major force producing tissue in the human body. While certain muscle types specialise in producing maximum forces, others are very enduring. An extreme example is the heart, which continuously beats for the entire life. Despite being specialised, all body muscles share similar contractile mini-machines called sarcomeres that are organised into regular higher order structures called myofibrils. The major sarcomeric components and their organisational principles are conserved throughout most of the animal kingdom...
November 29, 2016: Mechanisms of Development
https://www.readbyqxmd.com/read/27912731/predicting-the-recurrence-of-noncoding-regulatory-mutations-in-cancer
#7
Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi
BACKGROUND: One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncoding mutations owing to a limited amount of whole-genome sequenced samples. Hence, it is required to develop a method to predict potentially recurrent mutations. RESULTS: In this work, we developed a random forest classifier that predicts regulatory mutations that may recur based on the features of the mutations repeatedly appearing in a given cohort...
December 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27912165/biomarker-analysis-of-american-toad-anaxyrus-americanus-and-grey-tree-frog-hyla-versicolor-tadpoles-following-exposure-to-atrazine
#8
Marcía N Snyder, W Matthew Henderson, Donna A Glinski, S Thomas Purucker
The objective of the current study was to use a biomarker-based approach to investigate the influence of atrazine exposure on American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles. Atrazine is one of the most frequently detected herbicides in environmental matrices throughout the United States. In surface waters, it has been found at concentrations from 0.04-2859μg/L and thus presents a likely exposure scenario for non-target species such as amphibians. Studies have examined the effect of atrazine on the metamorphic parameters of amphibians, however, the data are often contradictory...
November 21, 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/27912064/modular-assembly-of-the-bacterial-large-ribosomal-subunit
#9
Joseph H Davis, Yong Zi Tan, Bridget Carragher, Clinton S Potter, Dmitry Lyumkis, James R Williamson
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911828/evaluating-the-evaluation-of-cancer-driver-genes
#10
Collin J Tokheim, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Rachel Karchin
Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard, that is, bona fide driver gene mutations. Here, we establish an evaluation framework that can be applied to driver gene prediction methods. We used this framework to compare the performance of eight such methods. One of these methods, described here, incorporated a machine-learning-based ratiometric approach...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911413/fabricating-a-uv-vis-and-raman-spectroscopy-immunoassay-platform
#11
Cynthia Hanson, Nathan D Israelsen, Michael Sieverts, Elizabeth Vargis
Immunoassays are used to detect proteins based on the presence of associated antibodies. Because of their extensive use in research and clinical settings, a large infrastructure of immunoassay instruments and materials can be found. For example, 96- and 384-well polystyrene plates are available commercially and have a standard design to accommodate ultraviolet-visible (UV-Vis) spectroscopy machines from various manufacturers. In addition, a wide variety of immunoglobulins, detection tags, and blocking agents for customized immunoassay designs such as enzyme-linked immunosorbent assays (ELISA) are available...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911353/computer-aided-classification-of-mammographic-masses-using-visually-sensitive-image-features
#12
Yunzhi Wang, Faranak Aghaei, Ali Zarafshani, Yuchen Qiu, Wei Qian, Bin Zheng
PURPOSE: To develop a new computer-aided diagnosis (CAD) scheme that computes visually sensitive image features routinely used by radiologists to develop a machine learning classifier and distinguish between the malignant and benign breast masses detected from digital mammograms. METHODS: An image dataset including 301 breast masses was retrospectively selected. From each segmented mass region, we computed image features that mimic five categories of visually sensitive features routinely used by radiologists in reading mammograms...
November 30, 2016: Journal of X-ray Science and Technology
https://www.readbyqxmd.com/read/27911325/autonomic-nervous-system-dysfunctions-as-a-basis-for-a-predictive-model-of-risk-of%C3%A2-neurological-disorders-in-subjects-with%C3%A2-prior-history-of-traumatic-brain-injury-implications-in-alzheimer-s-disease
#13
Lap Ho, Marc Legere, Tongbin Li, Samara Levine, Ke Hao, Breanna Valcarcel, Giulio M Pasinetti
Autonomic dysfunction is very common in patients with dementia, and its presence might also help in differential diagnosis among dementia subtypes. Various central nervous system structures affected in Alzheimer's disease (AD) are also implicated in the central autonomic nervous system (ANS) regulation. For example, deficits in central cholinergic function in AD could likely lead to autonomic dysfunction. We recently developed a simple, readily applicable evaluation for monitoring ANS disturbances in response to traumatic brain injury (TBI)...
December 1, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910886/sequential-information-in-a-great-ape-utterance
#14
Pawel Fedurek, Klaus Zuberbühler, Christoph D Dahl
Birdsong is a prime example of acoustically sophisticated vocal behaviour, but its complexity has evolved mainly through sexual selection to attract mates and repel sexual rivals. In contrast, non-human primate calls often mediate complex social interactions, but are generally regarded as acoustically simple. Here, we examine arguably the most complex call in great ape vocal communication, the chimpanzee (Pan troglodytes schweinfurthii) 'pant hoot'. This signal consists of four acoustically distinct phases: introduction, build-up, climax and let-down...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910869/multiparameter-mechanical-and-morphometric-screening-of-cells
#15
Mahdokht Masaeli, Dewal Gupta, Sean O'Byrne, Henry T K Tse, Daniel R Gossett, Peter Tseng, Andrew S Utada, Hea-Jin Jung, Stephen Young, Amander T Clark, Dino Di Carlo
We introduce a label-free method to rapidly phenotype and classify cells purely based on physical properties. We extract 15 biophysical parameters from cells as they deform in a microfluidic stretching flow field via high-speed microscopy and apply machine-learning approaches to discriminate different cell types and states. When employing the full 15 dimensional dataset, the technique robustly classifies individual cells based on their pluripotency, with accuracy above 95%. Rheological and morphological properties of cells while deforming were critical for this classification...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910685/measuring-20-100-t-b-fields-using-zeeman-splitting-of-sodium-emission-lines-on-a-500-ka-pulsed-power-machine
#16
J T Banasek, J T Engelbrecht, S A Pikuz, T A Shelkovenko, D A Hammer
We have shown that Zeeman splitting of the sodium (Na) D-lines at 5890 and 5896 Å can be used to measure the magnetic field (B-field) produced in high current pulsed power experiments. We have measured the B-field next to a return current conductor in a hybrid X-pinch experiment near a peak current of about 500 kA. Na is deposited on the conductor and then is desorbed and excited by radiation from the hybrid X-pinch. The D-line emission spectrum implies B-fields of about 20 T with a return current post of 4 mm diameter or up to 120 T with a return current wire of 0...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910670/alignment-and-absolute-wavelength-calibration-of-imaging-bragg-spectrometers
#17
G Bertschinger, O Marchuk, R Barnsley
In the present and the next generation of fusion devices, imaging Bragg spectrometers are key diagnostics to measure plasma parameters in the hot core, especially ion temperature and plasma rotation. The latter quantities are routinely obtained using the Doppler-width and -shift of the emitted spectral lines, respectively. Line shift measurements require absolute accuracies Δλ/λ of about 10 ppm, where λ-is the observed wavelength. For ITER and the present fusion devices, spectral lines of He-and H-like argon, iron, and krypton as well as Ne-like tungsten are foreseen for the measurements...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910583/robust-analysis-of-trends-in-noisy-tokamak-confinement-data-using-geodesic-least-squares-regression
#18
G Verdoolaege, A Shabbir, G Hornung
Regression analysis is a very common activity in fusion science for unveiling trends and parametric dependencies, but it can be a difficult matter. We have recently developed the method of geodesic least squares (GLS) regression that is able to handle errors in all variables, is robust against data outliers and uncertainty in the regression model, and can be used with arbitrary distribution models and regression functions. We here report on first results of application of GLS to estimation of the multi-machine scaling law for the energy confinement time in tokamaks, demonstrating improved consistency of the GLS results compared to standard least squares...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910573/polycapillary-lenses-for-soft-x-ray-transmission-in-iter-model-comparison-with-experiments-and-potential-application
#19
D Mazon, C Liegeard, A Jardin, R Barnsley, M Walsh, M O'Mullane, A Sirinelli, F Dorchies
Measuring Soft X-Ray (SXR) radiation [0.1 keV; 15 keV] in tokamaks is a standard way of extracting valuable information on the particle transport and magnetohydrodynamic activity. Generally, the analysis is performed with detectors positioned close to the plasma for a direct line of sight. A burning plasma, like the ITER deuterium-tritium phase, is too harsh an environment to permit the use of such detectors in close vicinity of the machine. We have thus investigated in this article the possibility of using polycapillary lenses in ITER to transport the SXR information several meters away from the plasma in the complex port-plug geometry...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910541/research-on-the-best-measurement-situation-between-optical-probe-and-tissue-surfaces-in-non-invasive-detection
#20
Xuyao Yu, Rong Liu, Hui Yu, Jiao Wang, Jun Wang, Kexin Xu
Near-infrared spectroscopy is often used for the non-invasive detection of composition in the human body, such as that of blood glucose and haemoglobin, due to its high penetration depth into tissues. Although it is feasible to position the optical probe precisely, contact situation between probe and human tissues is a difficult problem to determine because of physiological tremor and mechanical performance of bio-soft tissue. Here, we proposed a novel estimation method for the situation between the optical probe and tissue surfaces based on the dynamic auto-correlation matrix of two-dimensional correlation spectroscopy (2DCOS) and radar chart...
November 2016: Review of Scientific Instruments
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