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https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#1
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28722802/pathology-imagebase-a-reference-image-database-for-standardization-of-pathology
#2
Lars Egevad, John Cheville, Andrew J Evans, Jonas Hörnblad, James G Kench, Glen Kristiansen, Katia R M Leite, Cristina Magi-Galluzzi, Chin-Chen Pan, Hemamali Samaratunga, John R Srigley, Lawrence True, Ming Zhou, Mark Clements, Brett Delahunt
AIMS: Despite efforts to standardize histopathology practice through the development of guidelines, the interpretation of morphology is still hampered by subjectivity. We here describe Pathology Imagebase, a novel mechanism for establishing an international standard for the interpretation of pathology specimens. METHODS AND RESULTS: The International Society of Urological Pathology (ISUP) established a reference image database through the input of experts in the field...
July 19, 2017: Histopathology
https://www.readbyqxmd.com/read/28722314/prospective-motion-correction-using-coil-mounted-cameras-cross-calibration-considerations
#3
Julian Maclaren, Murat Aksoy, Melvyn B Ooi, Benjamin Zahneisen, Roland Bammer
PURPOSE: Optical prospective motion correction substantially reduces sensitivity to motion in neuroimaging of human subjects. However, a major barrier to clinical deployment has been the time-consuming cross-calibration between the camera and MRI scanner reference frames. This work addresses this challenge. METHODS: A single camera was mounted onto the head coil for tracking head motion. Two new methods were developed: (1) a rapid calibration method for camera-to-scanner cross-calibration using a custom-made tool incorporating wireless active markers, and (2) a calibration adjustment method to compensate for table motion between scans...
July 19, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28720978/extraction-and-preparation-of-high-aroma-and-low-caffeine-instant-green-teas-by-the-novel-column-chromatographic-extraction-method-with-gradient-elution
#4
Qing-Rong Li, Min Wu, Rui-Jie Huang, Ya-Fei Chen, Chan-Jian Chen, Hui Li, He Ni, Hai-Hang Li
The lack of aroma and natural taste is a critical problem in production and consumption of instant green teas. A method to prepare instant green teas high in-natural-aroma and low-caffeine by the novel column chromatographic extraction with gradient elution is reported. This method simultaneously extracted aroma (or volatile) and non-aroma compounds from green tea. Green tea was loaded into columns with 2.0-fold of petroleum ether (PE): ethanol (8:2). After standing for 3 h until the aroma compounds dissolved, the column was sequentially eluted with 3...
June 2017: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#5
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28719921/-patient-s-autonomy-and-information-in-psycho-oncology-computer-based-distress-screening-for-an-interactive-treatment-planning-epos-react
#6
Norbert Schäffeler, Jana Sedelmaier, Hannah Möhrer, Katrin Ziser, Johanna Ringwald, Martin Wickert, Sara Brucker, Florian Junne, Stephan Zipfel, Martin Teufel
To identify distressed patients in oncology using screening questionnaires is quite challenging in clinical routine. Up to now there is no evidence based recommendation which instrument is most suitable and how to put a screening to practice. Using computer based screening tools offers the possibility to automatically analyse patient's data, inform psycho-oncological and medical staff about the results, and use reactive questionnaires. Studies on how to empower patients in decision making in psycho-oncology are rare...
July 2017: Psychotherapie, Psychosomatik, Medizinische Psychologie
https://www.readbyqxmd.com/read/28719763/two-equals-one-two-human-actions-during-social-interaction-are-grouped-as-one-unit-in-working-memory
#7
Xiaowei Ding, Zaifeng Gao, Mowei Shen
Every day, people perceive other people performing interactive actions. Retaining these actions of human agents in working memory (WM) plays a pivotal role in a normal social life. However, whether the semantic knowledge embedded in the interactive actions has a pervasive impact on the storage of the actions in WM remains unknown. In the current study, we investigated two opposing hypotheses: (a) that WM stores the interactions individually (the individual-storage hypothesis) and (b) that WM stores the interactions as chunks (the chunk-storage hypothesis)...
July 1, 2017: Psychological Science
https://www.readbyqxmd.com/read/28719614/beat-id-towards-a-computationally-low-cost-single-heartbeat-biometric-identity-check-system-based-on-electrocardiogram-wave-morphology
#8
Joana S Paiva, Duarte Dias, João P S Cunha
In recent years, safer and more reliable biometric methods have been developed. Apart from the need for enhanced security, the media and entertainment sectors have also been applying biometrics in the emerging market of user-adaptable objects/systems to make these systems more user-friendly. However, the complexity of some state-of-the-art biometric systems (e.g., iris recognition) or their high false rejection rate (e.g., fingerprint recognition) is neither compatible with the simple hardware architecture required by reduced-size devices nor the new trend of implementing smart objects within the dynamic market of the Internet of Things (IoT)...
2017: PloS One
https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#9
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28719009/diagnosis-of-chronic-heart-failure-by-the-soluble-suppression-of-tumorigenicity-2-and-n-terminal-pro-brain-natriuretic-peptide
#10
Xiao-Ling Jin, Ning Huang, Hui Shang, Ming-Cheng Zhou, Yi Hong, Wen-Zheng Cai, Jie Huang
OBJECTIVE: Our study was to explore the roles between serum soluble suppression of tumorigenicity 2 (sST2) and N-terminal pro-brain natriuretic peptide (NT-proBNP) while evaluating ventricular function to properly diagnose chronic heart failure (CHF). METHODS: In total, 197 CHF patients were recruited and classified into ventricular function's II, III, and IV groups, and 106 healthy people into normal control group. To detect concentrations of Sst2 and NT-proBNP, ELISA and electro-chemiluminescence immuno assay were implemented...
July 18, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28718781/latent-variable-method-for-automatic-adaptation-to-background-states-in-motor-imagery-bci
#11
Nikolay Dagaev, Ksenia Volkova, Alexei Ossadtchi
<i>Objective</i>. Brain-computer interface (BCI) systems are known to be vulnerable to variabilities in background states of a user. Usually, no detailed information on these states is available even during the training stage. Thus there is a need in a method which is capable of taking background states into account in an unsupervised way. <i>Approach</i>. We propose a latent variable method that is based on a probabilistic model with a discrete latent variable. In order to estimate the model's parameters, we suggest to use the expectation maximization (EM) algorithm...
July 18, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28718773/mouse-epileptic-seizure-detection-with-multiple-eeg-features-and-simple-thresholding-technique
#12
Quang M Tieng, Ashwin Anbazhagan, Min Chen, David Charles Reutens
Epilepsy is a common neurological disorder characterized by recurrent, unprovoked seizures. The search for new treatments for seizures and epilepsy relies upon studies in animal models of epilepsy. To capture data on seizures, many applications require prolonged electroencephalography (EEG) with recordings that generate voluminous data. The desire for efficient evaluation of these recordings motivates the development of automated seizure detection algorithms. Approach: A new seizure detection method is proposed, based on multiple features and a simple thresholding technique...
July 18, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28718523/error-rate-of-automated-calculation-for-wound-surface-area-using-a-digital-photography
#13
S Yang, J Park, H Lee, J B Lee, B U Lee, B H Oh
BACKGROUND: Although measuring would size using digital photography is a quick and simple method to evaluate the skin wound, the possible compatibility of it has not been fully validated. PURPOSE: To investigate the error rate of our newly developed wound surface area calculation using digital photography. METHODS: Using a smartphone and a digital single lens reflex (DSLR) camera, four photographs of various sized wounds (diameter: 0.5-3.5 cm) were taken from the facial skin model in company with color patches...
July 17, 2017: Skin Research and Technology
https://www.readbyqxmd.com/read/28718516/control-of-the-fluid-viscosity-in-a-mock-circulation
#14
Stefan Boës, Gregor Ochsner, Raffael Amacher, Anastasios Petrou, Mirko Meboldt, Marianne Schmid Daners
A mock circulation allows the in vitro investigation, development, and testing of ventricular assist devices. An aqueous-glycerol solution is commonly used to mimic the viscosity of blood. Due to evaporation and temperature changes, the viscosity of the solution drifts from its initial value and therefore, deviates substantially from the targeted viscosity of blood. Additionally, the solution needs to be exchanged to account for changing viscosities when mimicking different hematocrits. This article presents a method to control the viscosity in a mock circulation...
July 17, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28718208/quantification-of-nasal-airflow-resistance-in-english-bulldogs-using-computed-tomography-and-computational-fluid-dynamics
#15
Eric T Hostnik, Brian A Scansen, Rachel Zielinski, Samir N Ghadiali
Stenotic nares, edematous intranasal turbinates, mucosal swelling, and an elongated, thickened soft palate are common sources of airflow resistance for dogs with brachycephalic airway syndrome. Surgery has focused on enlarging the nasal apertures and reducing tissue of the soft palate. However, objective measures of surgical efficacy are lacking. Twenty-one English bulldogs without previous surgery were recruited for this prospective, pilot study. Computed tomography was performed using conscious sedation and without endotracheal intubation using a 128 multidetector computed tomography scanner...
July 17, 2017: Veterinary Radiology & Ultrasound
https://www.readbyqxmd.com/read/28717902/fusion-of-heart-rate-variability-and-pulse-rate-variability-for-emotion-recognition-using-lagged-poincare-plots
#16
Atefeh Goshvarpour, Ataollah Abbasi, Ateke Goshvarpour
Designing an efficient automatic emotion recognition system based on physiological signals has attracted great interests within the research of human-machine interactions. This study was aimed to classify emotional responses by means of a simple dynamic signal processing technique and fusion frameworks. The electrocardiogram and finger pulse activity of 35 participants were recorded during rest condition and when subjects were listening to music intended to stimulate certain emotions. Four emotion categories, including happiness, sadness, peacefulness, and fear were chosen...
July 17, 2017: Australasian Physical & Engineering Sciences in Medicine
https://www.readbyqxmd.com/read/28717812/a-new-adaptive-home-based-exercise-technology-among-older-adults-living-in-nursing-home-a-pilot-study-on-feasibility-acceptability-and-physical-performance
#17
V Valiani, M Lauzé, D Martel, M Pahor, T M Manini, S Anton, M Aubertin-Leheudre
OBJECTIVES: To explore the feasibility and acceptability of a new home-based exercise technology among older adults and to evaluate its efficacy on physical performance measures. DESIGN: Longitudinal clinical trial. SETTING: Oak Hammock at the University of Florida, a nursing home located in Gainesville, Florida. PARTICIPANTS: Twelve pre-disabled older adults (≥75 years) living in a nursing home with a Short Physical Performance Battery (SPPB) score between 6 and 9 and no diagnosis of dementia...
2017: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/28717569/histogram-analysis-for-smartphone-based-rapid-hematocrit-determination
#18
Uddin M Jalal, Sang C Kim, Joon S Shim
A novel and rapid analysis technique using histogram has been proposed for the colorimetric quantification of blood hematocrits. A smartphone-based "Histogram" app for the detection of hematocrits has been developed integrating the smartphone embedded camera with a microfluidic chip via a custom-made optical platform. The developed histogram analysis shows its effectiveness in the automatic detection of sample channel including auto-calibration and can analyze the single-channel as well as multi-channel images...
July 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28717141/children-s-first-handwriting-productions-show-a-rhythmic-structure
#19
Elena Pagliarini, Lisa Scocchia, Mirta Vernice, Marina Zoppello, Umberto Balottin, Sana Bouamama, Maria Teresa Guasti, Natale Stucchi
Although much research has been concerned with the development of kinematic aspects of handwriting, little is known about the development along with age of two principles that govern its rhythmic organization: Homothety and Isochrony. Homothety states that the ratio between the durations of the single motor events composing a motor act remains invariant and independent from the total duration of the movement. Isochrony refers to the proportional relationship between the speed of movement execution and the length of its trajectory...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716553/regional-analysis-of-age-related-local-bone-loss-in-the-spine-of-a-healthy-population-using-3d-voxel-based-modeling
#20
Alexander Valentinitsch, Stefano Trebeschi, Eva Alarcón, Thomas Baum, Johannes Kaesmacher, Claus Zimmer, Cristian Lorenz, Jan S Kirschke
Local variations in bone loss may be of great importance to individually predict osteoporotic fractures but are neglected by current densitometry techniques. The purpose of this study was to evaluate regional variations of normal bone loss at the spine among different age groups using voxel-based morphometry. Non-contrast MDCT scans of 16 patients under the age of 40 (mean age 26years) without spinal pathology were identified as a reference cohort, where each thoracolumbar vertebra was assessed individually...
July 14, 2017: Bone
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