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https://www.readbyqxmd.com/read/28916782/predicting-clinical-outcomes-from-large-scale-cancer-genomic-profiles-with-deep-survival-models
#1
Safoora Yousefi, Fatemeh Amrollahi, Mohamed Amgad, Chengliang Dong, Joshua E Lewis, Congzheng Song, David A Gutman, Sameer H Halani, Jose Enrique Velazquez Vega, Daniel J Brat, Lee A D Cooper
Translating the vast data generated by genomic platforms into accurate predictions of clinical outcomes is a fundamental challenge in genomic medicine. Many prediction methods face limitations in learning from the high-dimensional profiles generated by these platforms, and rely on experts to hand-select a small number of features for training prediction models. In this paper, we demonstrate how deep learning and Bayesian optimization methods that have been remarkably successful in general high-dimensional prediction tasks can be adapted to the problem of predicting cancer outcomes...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28914779/simultaneous-recognition-and-relative-pose-estimation-of-3d-objects-using-4d-orthonormal-moments
#2
Sergio Dominguez
Both three-dimensional (3D) object recognition and pose estimation are open topics in the research community. These tasks are required for a wide range of applications, sometimes separately, sometimes concurrently. Many different algorithms have been presented in the literature to solve these problems separately, and some to solve them jointly. In this paper, an algorithm to solve them simultaneously is introduced. It is based on the definition of a four-dimensional (4D) tensor that gathers and organizes the projections of a 3D object from different points of view...
September 15, 2017: Sensors
https://www.readbyqxmd.com/read/28914089/art-museum-based-intervention-to-promote-emotional-well-being-and-improve-quality-of-life-in-people-with-dementia-the-artemis-project
#3
Arthur Schall, Valentina A Tesky, Ann-Katrin Adams, Johannes Pantel
ARTEMIS (ART Encounters: Museum Intervention Study) is an art-based intervention designed especially for people with dementia and their care partners that involves a combination of museum visits and artistic activity. This paper reports the results of a randomized wait-list controlled study on the influence of the ARTEMIS intervention on the emotional state, well-being, and quality of life of dementia patients. People with mild-to-moderate dementia (n = 44) and their care partners (n = 44) visited the Frankfurt Städel Museum once a week on six pre-arranged occasions...
January 1, 2017: Dementia
https://www.readbyqxmd.com/read/28912708/remodeling-pearson-s-correlation-for-functional-brain-network-estimation-and-autism-spectrum-disorder-identification
#4
Weikai Li, Zhengxia Wang, Limei Zhang, Lishan Qiao, Dinggang Shen
Functional brain network (FBN) has been becoming an increasingly important way to model the statistical dependence among neural time courses of brain, and provides effective imaging biomarkers for diagnosis of some neurological or psychological disorders. Currently, Pearson's Correlation (PC) is the simplest and most widely-used method in constructing FBNs. Despite its advantages in statistical meaning and calculated performance, the PC tends to result in a FBN with dense connections. Therefore, in practice, the PC-based FBN needs to be sparsified by removing weak (potential noisy) connections...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28912079/solid-anaerobic-digestion-state-of-art-scientific-and-technological-hurdles
#5
REVIEW
Laura André, André Pauss, Thierry Ribeiro
In this paper, a state-of-art about solid anaerobic digestion (AD), focused on recent progress and trends of research is proposed. Solid anaerobic digestion should be the most appropriate process for degradation of by-products with high total solid (TS) content, especially lignocellulosic materials like agricultural waste (straw, manure), household waste and food waste. Solid AD is already widely used in waste water treatment plant for treating plant for sewage sludge but could be more developed for lignocellulosic materials with high TS content...
September 5, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28910776/fastetch-a-fast-sketch-based-assembler-for-genomes
#6
Priyanka Ghosh, Ananth Kalyanaraman
De novo genome assembly describes the process of reconstructing an unknown genome from a large collection of short (or long) reads sequenced from the genome. A single run of a Next-Generation Sequencing (NGS) technology can produce billions of short reads, making genome assembly computationally demanding (both in terms of memory and time). One of the major computational steps in modern day short read assemblers involves the construction and use of a string data structure called the de Bruijn graph. In fact, a majority of short read assemblers build the complete de Bruijn graph for the set of input reads, and subsequently traverse and prune low-quality edges, in order to generate genomic "contigs"-the output of assembly...
September 11, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28910771/a-general-framework-for-linear-distance-preserving-hashing
#7
Min Wang, Wengang Zhou, Qi Tian, Houqiang Li
Binary hashing approaches the approximate nearest neighbor search problem by transferring the data to Hamming space with explicit or implicit distance preserving constraint. With compact data representation, binary hashing identifies the approximate nearest neighbors via very efficient Hamming distance computation. In this paper, we propose a generic hashing framework with a new linear pairwise distance preserving objective and point-wise constraint. In our framework, the direct distance preserving objective aims to keep the linear relationship between the Euclidean distance and the Hamming distance of data points...
September 11, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28910756/coresets-for-triangulation
#8
Qianggong Zhang, Tat-Jun Chin
Multiple-view triangulation by l∞ minimisation has become established in computer vision. State-of-the-art l∞ triangulation algorithms exploit the quasiconvexity of the cost function to derive iterative update rules that deliver the global minimum. Such algorithms, however, can be computationally costly for large problem instances that contain many image measurements, e.g., from web-based photo sharing sites or long-term video recordings. In this paper, we prove that l∞ triangulation admits a coreset approximation scheme, which seeks small representative subsets of the input data called coresets...
September 11, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28910755/siminet-a-novel-method-for-quantifying-brain-network-similarity
#9
Ahmad Mheich, Mahmoud Hassan, Mohamad Khalil, Vincent Gripon, Olivier Dufor, Fabrice Wendling
Quantifying the similarity between two networks is critical in many applications. A number of algorithms have been proposed to compute graph similarity, mainly based on the properties of nodes and edges. Interestingly, most of these algorithms ignore the physical location of the nodes, which is a key factor in the context of brain networks involving spatially defined functional areas. In this paper, we present a novel algorithm called "SimiNet" for measuring similarity between two graphs whose nodes are defined a priori within a 3D coordinate system...
September 8, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28905236/diagnosis-of-coronary-artery-disease-using-an-efficient-hash-table-based-closed-frequent-itemsets-mining
#10
Ramesh Dhanaseelan, M Jeya Sutha
This paper proposes an efficient hash table based closed frequent itemsets (HCFI) mining algorithm to envisage coronary artery disease early. HCFI algorithm generates closed frequent itemsets efficiently by performing intersection operation on transaction id's of itemset without considering the name of item/itemset. The employed hash table reduces search efficiency to O(1) or constant time. HCFI algorithm is applied on the UCI (University of California, Irvine) Cleveland dataset, a biological database of cardiovascular disease to generate closed frequent itemsets on the dataset...
September 14, 2017: Medical & Biological Engineering & Computing
https://www.readbyqxmd.com/read/28901609/adaptive-non-local-means-on-local-principle-neighborhood-for-noise-artifacts-reduction-in-low-dose-ct-images
#11
Yuanke Zhang, Hongbing Lu, Junyan Rong, Jing Meng, Junliang Shang, Pinghong Ren, Junying Zhang
PURPOSE: Low-dose CT (LDCT) technique can reduce the x-ray radiation exposure to patients at the cost of degraded images with severe noise and artifacts. Non-local means (NLM) filtering has shown its potential in improving LDCT image quality. However, currently most NLM-based approaches employ a weighted average operation directly on all neighbor pixels with a fixed filtering parameter throughout the NLM filtering process, ignoring the non-stationary noise nature of LDCT images. In this paper, an adaptive NLM filtering scheme on local principle neighborhoods (PC-NLM) is proposed for structure-preserving noise/artifacts reduction in LDCT images...
September 2017: Medical Physics
https://www.readbyqxmd.com/read/28900898/methods-for-practising-ethics-in-research-and-innovation-a-literature-review-critical-analysis-and-recommendations
#12
Wessel Reijers, David Wright, Philip Brey, Karsten Weber, Rowena Rodrigues, Declan O'Sullivan, Bert Gordijn
This paper provides a systematic literature review, analysis and discussion of methods that are proposed to practise ethics in research and innovation (R&I). Ethical considerations concerning the impacts of R&I are increasingly important, due to the quickening pace of technological innovation and the ubiquitous use of the outcomes of R&I processes in society. For this reason, several methods for practising ethics have been developed in different fields of R&I. The paper first of all presents a systematic search of academic sources that present and discuss such methods...
September 12, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28895906/silicon-nitride-photonic-integration-platforms-for-visible-near-infrared-and-mid-infrared-applications
#13
Pascual Muñoz, Gloria Micó, Luis A Bru, Daniel Pastor, Daniel Pérez, José David Doménech, Juan Fernández, Rocío Baños, Bernardo Gargallo, Rubén Alemany, Ana M Sánchez, Josep M Cirera, Roser Mas, Carlos Domínguez
Silicon nitride photonics is on the rise owing to the broadband nature of the material, allowing applications of biophotonics, tele/datacom, optical signal processing and sensing, from visible, through near to mid-infrared wavelengths. In this paper, a review of the state of the art of silicon nitride strip waveguide platforms is provided, alongside the experimental results on the development of a versatile 300 nm guiding film height silicon nitride platform.
September 12, 2017: Sensors
https://www.readbyqxmd.com/read/28894460/an-automatic-gastrointestinal-polyp-detection-system-in-video-endoscopy-using-fusion-of-color-wavelet-and-convolutional-neural-network-features
#14
Mustain Billah, Sajjad Waheed, Mohammad Motiur Rahman
Gastrointestinal polyps are considered to be the precursors of cancer development in most of the cases. Therefore, early detection and removal of polyps can reduce the possibility of cancer. Video endoscopy is the most used diagnostic modality for gastrointestinal polyps. But, because it is an operator dependent procedure, several human factors can lead to misdetection of polyps. Computer aided polyp detection can reduce polyp miss detection rate and assists doctors in finding the most important regions to pay attention to...
2017: International Journal of Biomedical Imaging
https://www.readbyqxmd.com/read/28892843/emd-regression-for-modelling-multi-scale-relationships-and-application-to-weather-related-cardiovascular-mortality
#15
Pierre Masselot, Fateh Chebana, Diane Bélanger, André St-Hilaire, Belkacem Abdous, Pierre Gosselin, Taha B M J Ouarda
In a number of environmental studies, relationships between nat4ural processes are often assessed through regression analyses, using time series data. Such data are often multi-scale and non-stationary, leading to a poor accuracy of the resulting regression models and therefore to results with moderate reliability. To deal with this issue, the present paper introduces the EMD-regression methodology consisting in applying the empirical mode decomposition (EMD) algorithm on data series and then using the resulting components in regression models...
September 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28891436/radio-localization-of-non-palpable-breast-lesions-under-ultrasonographic-guidance-current-status-and-future-perspectives
#16
Giulia Anna Follacchio, Francesco Monteleone, Maria Letizia Meggiorini, Maria Paola Nusiner, Carlo De Felice, Giuseppe De Vincentis, Mauro Liberatore
BACKGROUND: Due to the spread of mammographic screening programs, a constant increase of clinically-occult breast cancer diagnosis has been registered. A correct approach to non-palpable breast lesions requires an accurate intra-operative localization in order to achieve a complete surgical resection. Aim of this paper is to describe the state of the art of the US-guided procedures such as Radio-guided Occult Lesion Localization (ROLL) and Radio-guided Seed Localization (RSL) in comparison to the most widely adopted Wire-Guided Localization (WGL)...
September 8, 2017: Current Radiopharmaceuticals
https://www.readbyqxmd.com/read/28891044/considerations-for-evaluating-treatment-effects-from-randomized-clinical-trials
#17
Stephen J Ruberg, Mouna Akacha
This paper focuses on the choice of treatment effect measures in randomized clinical trials (RCT). Traditionally, an intention-to-treat (ITT) analysis is conducted with an implicit understanding that a treatment-policy effect is of greatest interest. In this paper we contend that this approach may not always provide accurate information about clinically meaningful treatment effects, and we present an argument that for any RCT it is desirable to require an explicit definition of what treatment effect is of primary interest, known as the 'estimand'...
September 10, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28890755/architectural-patterns-for-differential-diagnosis-of-proliferative-breast-lesions-from-histopathological-images
#18
L Nguyen, A B Tosun, J L Fine, D L Taylor, S C Chennubhotla
The differential diagnosis of proliferative breast lesions, benign usual ductal hyperplasia (UDH) versus malignant ductal carcinoma in situ (DCIS) is challenging. This involves a pathologist examining histopathologic sections of a biopsy using a light microscope, evaluating tissue structures for their architecture or size, and assessing individual cell nuclei for their morphology. Imposing diagnostic boundaries on features that otherwise exist on a continuum going from benign to atypia to malignant is a challenge...
April 2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
https://www.readbyqxmd.com/read/28890341/cueing-for-people-with-parkinson-s-disease-with-freezing-of-gait-a-narrative-review-of-the-state-of-the-art-and-novel-perspectives
#19
REVIEW
Ginis Pieter, Nackaerts Evelien, Nieuwboer Alice, Heremans Elke
Freezing, which manifests during gait and other movements, is an incapacitating motor symptom experienced by many patients with Parkinson's disease (PD). In rehabilitation, auditory and visual cueing methods are commonly applied to evoke a more goal-directed type of motor control and, as such, reduce freezing severity in patients with PD. In this narrative review, we summarize the current evidence regarding the effects of external cueing in patients with PD with freezing of gait (FOG) and provide suggestions on how to further improve cueing effectiveness with emerging technological developments...
September 7, 2017: Annals of Physical and Rehabilitation Medicine
https://www.readbyqxmd.com/read/28888170/cortexpert-a-model-based-method-for-automatic-renal-cortex-segmentation
#20
Dehui Xiang, Ulas Bagci, Chao Jin, Fei Shi, Weifang Zhu, Jianhua Yao, Milan Sonka, Xinjian Chen
This paper introduces a model-based approach for a fully automatic delineation of kidney and cortex tissue from contrast-enhanced abdominal CT scans. The proposed framework, named CorteXpert, consists of two new strategies for kidney tissue delineation: cortex model adaptation and non-uniform graph search. CorteXpert was validated on a clinical data set of 58 CT scans using the cross-validation evaluation strategy. The experimental results indicated the state-of-the-art segmentation accuracies (as dice coefficient): 97...
August 23, 2017: Medical Image Analysis
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