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https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#1
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651260/the-cdd-system-in-computed-tomographic-diagnosis-of%C3%A2-diverticular-disease
#2
Daniel Pustelnik, Fabian Henry Jürgen Elsholtz, Christian Bojarski, Bernd Hamm, Stefan Markus Niehues
Purpose This overview sums up the Classification of Diverticular Disease (CDD) with regard to its application in computed tomographic diagnosis and briefly recapitulates its targeted advantages over preliminary systems. Primarily, application of the CDD in computed tomography diagnostics is described. Differences with respect to the categories of the older systems are pointed out on the level of each CDD type using imaging examples. Materials and Methods The presented images are derived from our institute according to the S2k criteria...
June 26, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28651184/computational-study-of-structural-optoelectronic-and-nonlinear-optical-properties-of-dynamic-solid-state-chalcone-derivatives
#3
Aijaz Rasool Chaudhry, Ahmad Irfan, Shabbir Muhammad, Abdullah G Al-Sehemi, R Ahmed, Zhang Jingping
In the present study, we use the state of art density functional theory (DFT) techniques to calculate the structural, optoelectronic and nonlinear optical (NLO) properties for two novel chalcone derivatives. The geometrical structures of chalcone derivatives compound 1 and 2 are optimized using periodic boundary conditions (PBC) in solid-state phase as well as isolated single molecular geometry in the gas phase. The reasonable agreement is found among experimental, solid-state and gas phase single molecular geometries, which provide us, further confidence to explore the potential of above-entitled derivatives as good functional materials for electro-optical applications...
May 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28650863/prediction-models-for-prostate-cancer-outcomes-what-is-the-state-of-the-art-in-2017
#4
James T Kearns, Daniel W Lin
PURPOSE OF REVIEW: Prostate cancer (PCa) remains a significant public health burden, with multiple points for decision-making at all stages of the disease. Given the amount and variety of data that may influence disease management, prediction models have been published to assist clinicians and patients in making decisions about the best next course of action at many disease states. We sought to review the most important studies related to PCa prediction models since 2016 and evaluate their impact upon the evolving field of risk modeling in PCa...
June 24, 2017: Current Opinion in Urology
https://www.readbyqxmd.com/read/28650846/dosimetric-verification-in-water-of-a-monte-carlo-treatment-planning-tool-for-proton-helium-carbon-and-oxygen-ion-beams-at-the-heidelberg-ion-beam-therapy-center
#5
Thomas Tessonnier, Till Tobias Boehlen, Francesco Cerutti, Alfredo Ferrari, Paola Roberta Sala, Stephan Brons, Thomas Haberer, Juergen Debus, Katia Parodi, Andrea Mairani
The introduction of "new" ion species in particle therapy needs to be supported by a thorough assessment of their dosimetric properties and by treatment planning comparisons with clinically used proton and carbon ion beams. In addition to the latter two ions, helium and oxygen ion beams are foreseen at the Heidelberg Ion beam Therapy (HIT) center as potential assets for improving clinical outcomes in the near future. We present in this study a dosimetric validation of a FLUKA-based Monte Carlo Treatment Planning tool (MCTP) for protons, helium, carbon and oxygen ions for spread-out Bragg peaks...
June 26, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28650837/heterogeneous-face-recognition-by-margin-based-cross-modality-metric-learning
#6
Jing Huo, Yang Gao, Yinghuan Shi, Wanqi Yang, Hujun Yin
Heterogeneous face recognition deals with matching face images from different modalities or sources. The main challenge lies in cross-modal differences and variations and the goal is to make cross-modality separation among subjects. A margin-based cross-modality metric learning (MCM²L) method is proposed to address the problem. A cross-modality metric is defined in a common subspace where samples of two different modalities are mapped and measured. The objective is to learn such metrics that satisfy the following two constraints...
June 26, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28650832/committee-based-active-learning-for-surrogate-assisted-particle-swarm-optimization-of-expensive-problems
#7
Handing Wang, Yaochu Jin, John Doherty
Function evaluations (FEs) of many real-world optimization problems are time or resource consuming, posing a serious challenge to the application of evolutionary algorithms (EAs) to solve these problems. To address this challenge, the research on surrogate-assisted EAs has attracted increasing attention from both academia and industry over the past decades. However, most existing surrogate-assisted EAs (SAEAs) either still require thousands of expensive FEs to obtain acceptable solutions, or are only applied to very low-dimensional problems...
June 22, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28650823/bi-level-and-bi-objective-p-median-type-problems-for-integrative-clustering-application-to-analysis-of-cancer-gene-expression-and-drug-response-data
#8
Anton V Ushakov, Xenia Klimentova, Igor Vasilyev
Recent advances in high-throughput technologies have given rise to collecting large amounts of multidimensional heterogeneous data that provide diverse information on the same biological samples. Integrative analysis of such multisource datasets may reveal new biological insights into complex biological mechanisms and therefore remains an important research field in systems biology. Most of the modern integrative clustering approaches rely on independent analysis of each dataset and consensus clustering, probabilistic or statistical modeling, while flexible distance-based integrative clustering techniques are sparsely covered...
October 27, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28650819/towards-high-quality-visualization-of-superfluid-vortices
#9
Yulong Guo, Xiaopei Liu, Chi Xiong, Xuemiao Xu, Chi-Wing Fu
Superfluidity is a special state of matter exhibiting macroscopic quantum phenomena and acting like a fluid with zero viscosity. In such a state, superfluid vortices exist as phase singularities of the model equation with unique distributions. This paper presents novel techniques to aid the visual understanding of superfluid vortices based on the state-of-the-art non-linear Klein-Gordon equation, which evolves a complex scalar field, giving rise to special vortex lattice/ring structures with dynamic vortex formation, reconnection, and Kelvin waves, etc...
June 26, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28650814/multi-label-classification-by-semi-supervised-singular-value-decomposition
#10
Liping Jing, Chenyang Shen, Liu Yang, Jian Yu, Michael K Ng
Multi-label problems arise in various domains including automatic multimedia data categorization, and have generated significant interest in computer vision and machine learning community. However, existing methods do not adequately address two key challenges: exploiting correlations between labels and making up for the lack of labeled data or even missing labeled data. In this paper, we proposed to use a semi-supervised singular value decomposition to handle these two challenges. The proposed model takes advantage of the nuclear norm regularization on the singular value decomposition to effectively capture the label correlations...
June 26, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28650812/alpha-matting-with-kl-divergence-based-sparse-sampling
#11
Levent Karacan, Aykut Erdem, Erkut Erdem
In this paper, we present a new sampling-based alpha matting approach for the accurate estimation of foreground and background layers of an image. Previous sampling-based methods typically rely on certain heuristics in collecting representative samples from known regions, and thus their performance deteriorates if the underlying assumptions are not satisfied. To alleviate this, we take an entirely new approach and formulate sampling as a sparse subset selection problem where we propose to pick a small set of candidate samples that best explains the unknown pixels...
June 22, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28650806/3d-active-contour-segmentation-based-on-sparse-linear-combination-of-training-shapes-scots
#12
M Mehdi Farhangi, Hichem Frigui, Albert Seow, Amir A Amini
SCoTS captures a sparse representation of shapes in an input image through a linear span of previously delineated shapes in a training repository. The model updates shape prior over level set iterations and captures variabilities in shapes by a sparse combination of the training data. The level set evolution is therefore driven by a data term as well as a term capturing valid prior shapes. During evolution, the shape prior influence is adjusted based on shape reconstruction, with the assigned weight determined from the degree of sparsity of the representation...
June 26, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28650801/300-fps-salient-object-detection-via-minimum-directional-contrast
#13
Xiaoming Huang, Yu-Jin Zhang
Global contrast considers the color difference between a target region or pixel and the rest of the image. It is frequently used to measure the saliency of the region or pixel. In previous global contrast-based methods, saliency is usually measured by the sum of contrast from the entire image. We find that the spatial distribution of contrast is one important cue of saliency that is neglected by previous works. Foreground pixel usually has high contrast from all directions, since it is surrounded by the background...
September 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28650798/coherent-semantic-visual-indexing-for-large-scale-image-retrieval-in-the-cloud
#14
Richang Hong, Lei Li, Junjie Cai, Dapeng Tao, Meng Wang, Qi Tian
The rapidly increasing number of images on the internet has further increased the need for efficient indexing for digital image searching of large databases. The design of a cloud service that provides high efficiency but compact image indexing remains challenging, partly due to the well-known semantic gap between user queries and the rich semantics of large-scale data sets. In this paper, we construct a novel joint semantic-visual space by leveraging visual descriptors and semantic attributes, which narrows the semantic gap by combining both attributes and indexing into a single framework...
September 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28650137/how-to-manage-the-biological-risk-in-a-dental-clinic-state-of-the-art-and-future-perspectives
#15
Matteo Saccucci, Gaetano Ierardo, Carmela Protano, Matteo Vitali, Antonella Polimeni
Dental Personnel (DP) may be exposed to pathogens during dental treatment, either through contact contaminated equipment, or with blood and respiratory secretion. On the other hand, health care professionals are constantly exposed to pathogens and opportunists in their work environment. Consequently, the dental healthcare environment is connected with the risk of exposure to biological agents both for patients and dental workers, and involves a wide number of microorganisms that can be present in biological matrices (gingival fluids, saliva, blood), contaminated and/or non-sanitized surfaces, water used in the dental unit, or emitted by patients suffering or carrier of a transmissible disease...
June 23, 2017: Minerva Stomatologica
https://www.readbyqxmd.com/read/28649961/optoelectronic-device-physics-and-technology-of-nitride-semiconductors-from-the-uv-to-the-terahertz-a-review
#16
Theodore D Moustakas, Roberto Paiella
This paper reviews the device physics and technology of optoelectronic devices based on semiconductors of the GaN family, operating in the spectral regions from deep UV to Terahertz. Such devices include LEDs, lasers, detectors, electroabsorption modulators and devices based on intersubband transitions in AlGaN quantum wells (QWs). After a brief history of the development of the field, we describe how the unique crystal structure, chemical bonding, and resulting spontaneous and piezoelectric polarizations in heterostructures affect the design, fabrication and performance of devices based on these materials...
June 26, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28649883/middle-down-proteomics-a-still-unexploited-resource-for-chromatin-biology
#17
Simone Sidoli, Benjamin A Garcia
Introduction Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac...
June 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28649871/the-potential-role-of-nintedanib-in-treating-colorectal-cancer
#18
Antonio Rossi, Tiziana Pia Latiano, Paola Parente, Cinzia Chiarazzo, Filomena Limosani, Gabriele Di Maggio, Evaristo Maiello
Angiogenesis leads to the growth, progression, and metastases of a variety of solid tumors, including metastatic colorectal cancer (mCRC), involving particularly the family of vascular endothelial growth factors (VEGF) and their receptors (VEGFR). Several anti-angiogenic inhibitors are already registered for mCRC therapy: bevacizumab, aflibercept, ramucirumab, regorafenib. Nintedanib is a new triple angiokinase oral inhibitor that potently blocks the proangiogenic pathways mediated by VEGFR, platelet-derived growth factor receptor (PDGFR), and fibroblast growth factor receptor (FGFR)...
June 26, 2017: Expert Opinion on Pharmacotherapy
https://www.readbyqxmd.com/read/28649599/semi-automated-annotation-of-signal-events-in-clinical-eeg-data
#19
S Yang, S López, M Golmohammadi, I Obeid, J Picone
To be effective, state of the art machine learning technology needs large amounts of annotated data. There are numerous compelling applications in healthcare that can benefit from high performance automated decision support systems provided by deep learning technology, but they lack the comprehensive data resources required to apply sophisticated machine learning models. Further, for economic reasons, it is very difficult to justify the creation of large annotated corpora for these applications. Hence, automated annotation techniques become increasingly important...
December 2016: ... IEEE Signal Processing in Medicine and Biology Symposium. IEEE Signal Processing in Medicine and Biology Symposium
https://www.readbyqxmd.com/read/28649481/cardio-oncology-cancer-therapy-related-cardiovascular-complications-in-a-molecular-targeted-era-new-concepts-and-perspectives
#20
REVIEW
David Hurtado-de-Mendoza, Arturo Loaiza-Bonilla, Paula A Bonilla-Reyes, Gabriel Tinoco, Rodrigo Alcorta
Cardio-oncology is a medical discipline that identifies, prevents, and treats the cardiovascular complications related to cancer therapy. Due to the remarkable proliferation of new cancer therapies causing cardiovascular complications, such as hypertension, heart failure, vascular complications, and cardiac arrhythmia, we provide an extensive, comprehensive revision of the most up-to-date scientific information available on the cardiovascular complications associated with the use of newer, novel chemotherapeutic agents, including their reported incidence, suggested pathophysiology, clinical manifestations, potential treatment, and prevention...
May 18, 2017: Curēus
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