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https://www.readbyqxmd.com/read/28641399/compannotate-a-comparative-approach-to-annotate-base-pairing-interactions-in-rna-3d-structures
#1
Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641321/identifying-and-acting-on-potentially-inappropriate-care-inadequacy-of-current-hospital-coding-for-this-task
#2
P David Cooper, David R Smart
INTRODUCTION: Recent Australian attempts to facilitate disinvestment in healthcare, by identifying instances of 'inappropriate' care from large Government datasets, are subject to significant methodological flaws. Amongst other criticisms has been the fact that the Government datasets utilized for this purpose correlate poorly with datasets collected by relevant professional bodies. Government data derive from official hospital coding, collected retrospectively by clerical personnel, whilst professional body data derive from unit-specific databases, collected contemporaneously with care by clinical personnel...
June 2017: Diving and Hyperbaric Medicine: the Journal of the South Pacific Underwater Medicine Society
https://www.readbyqxmd.com/read/28641300/prenatal-diagnosis-of-dextrocardia-with-complex-congenital-heart-disease-using-fetal-intelligent-navigation-echocardiography-fine-and-a-literature-review
#3
Lami Yeo, Suchaya Luewan, Dor Markush, Navleen Gill, Roberto Romero
Fetal dextrocardia is a type of cardiac malposition where the major axis from base to apex points to the right side. This condition is usually associated with a wide spectrum of complex cardiac defects. As a result, dextrocardia is conceptually difficult to understand and diagnose on prenatal ultrasound. The advantage of four-dimensional sonography with spatiotemporal image correlation (STIC) is that this modality can facilitate fetal cardiac examination. A novel method known as fetal intelligent navigation echocardiography (FINE) allows automatic generation of nine standard fetal echocardiography views in normal hearts by applying intelligent navigation technology to STIC volume datasets...
June 23, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28641273/learning-and-recognition-of-clothing-genres-from-full-body-images
#4
Shintami C Hidayati, Chuang-Wen You, Wen-Huang Cheng, Kai-Lung Hua
According to the theory of clothing design, the genres of clothes can be recognized based on a set of visually differentiable style elements, which exhibit salient features of visual appearance and reflect high-level fashion styles for better describing clothing genres. Instead of using less-discriminative low-level features or ambiguous keywords to identify clothing genres, we proposed a novel approach for automatically classifying clothing genres based on the visually differentiable style elements. A set of style elements, that are crucial for recognizing specific visual styles of clothing genres, were identified based on the clothing design theory...
June 19, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28641262/scalable-multi-view-semi-supervised-classification-via-adaptive-regression
#5
Hong Tao, Chenping Hou, Feiping Nie, Jubo Zhu, Dongyun Yi
With the advent of multi-view data, multi-view learning has become an important research direction in machine learning and image processing. Considering the difficulty of obtaining labeled data in many machine learning applications, we focus on the multi-view semi-supervised classification problem. In this paper, we propose an algorithm named Multi-View Semi-Supervised Classification via Adaptive Regression (MVAR) to address this problem. Specifically, regression based loss functions with ℓ2,1 matrix norm are adopted for each view and the final objective function is formulated as the linear weighted combination of all the loss functions...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641261/robust-web-image-annotation-via-exploring-multi-facet-and-structural-knowledge
#6
Mengqiu Hu, Yang Yang, Fumin Shen, Luming Zhang, Heng Tao Shen, Xuelong Li
Driven by the rapid development of Internet and digital technologies, we have witnessed the explosive growth of Web images in recent years. Seeing that labels can reflect the semantic contents of the images, automatic image annotation, which can further facilitate the procedure of image semantic indexing, retrieval and other image management tasks, has become one of the most crucial research directions in multimedia. Most of the existing annotation methods heavily rely on well-labeled training data (expensive to collect) and/or single view of visual features (insufficient representative power)...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641251/robust-face-recognition-with-kernelized-locality-sensitive-group-sparsity-representation
#7
Shoubiao Tan, Xi Sun, Wentao Chan, Lei Qu, Ling Shao
In this paper, a novel joint sparse representation method is proposed for robust face recognition. We embed both group sparsity and kernelized locality-sensitive constraints into the framework of sparse representation. The group sparsity constraint is designed to utilize the grouped structure information in the training data. The local similarity between test and training data is measured in the kernel space instead of the Euclidian space. As a result, the embedded nonlinear information can be effectively captured, leading to a more discriminative representation...
June 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641247/modeling-task-fmri-data-via-deep-convolutional-autoencoder
#8
Heng Huang, Xintao Hu, Yu Zhao, Milad Makkie, Qinglin Dong, Shijie Zhao, Lei Guo, Tianming Liu
Task-based fMRI (tfMRI) has been widely used to study functional brain networks under task performance. Modeling tfMRI data is challenging due to at least two problems: the lack of the ground truth of underlying neural activity and the highly complex intrinsic structure of tfMRI data. To better understand brain networks based on fMRI data, data-driven approaches have been proposed, for instance, Independent Component Analysis (ICA) and Sparse Dictionary Learning (SDL). However, both ICA and SDL only build shallow models, and they are under the strong assumption that original fMRI signal could be linearly decomposed into time series components with their corresponding spatial maps...
June 15, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28641246/gracker-a-graph-based-planar-object-tracker
#9
Tao Wang, Haibin Ling
Matching-based algorithms have been commonly used in planar object tracking. They often model a planar object as a set of keypoints, and then find correspondences between keypoint sets via descriptor matching. In previous work, unary constraints on appearances or locations are usually used to guide the matching. However, these approaches rarely utilize structure information of the object, and are thus suffering from various perturbation factors. In this paper, we proposed a graph-based tracker, named Gracker, which is able to fully explore the structure information of the object to enhance tracking performance...
June 16, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28641234/improved-boundary-segmentation-of-skin-lesions-in-high-frequency-3d-ultrasound
#10
B Sciolla, P Delachartre, L Cowell, T Dambry, B Guibert
In this article, we propose a segmentation algorithm for skin lesions in 3D high-frequency ultrasound images. The segmentation is done on melanoma and Basal-cell carcinoma tumors, the most common skin cancer types, and could be used for diagnosis and surgical excision planning in a clinical context. Compared with previously proposed algorithms, which tend to underestimate the size of the lesion, we propose two new boundary terms which provide significant improvements of the accuracy. The first is a probabilistic boundary expansion (PBE) term designed to broaden the segmented area at the boundaries, which uses the feature asymmetry criterion...
June 15, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28640988/does-half-life-matter-after-antipsychotic-discontinuation-a-relapse-comparison-in-schizophrenia-with-3-different-formulations-of-paliperidone
#11
Peter J Weiden, Edward Kim, Jason Bermak, Ibrahim Turkoz, Srihari Gopal, Joris Berwaerts
OBJECTIVE: To evaluate the effect of 1 oral and 2 distinct long-acting injectable (LAI) formulations of the same antipsychotic on times to relapse following medication discontinuation. METHODS: Data were drawn from 3 similarly designed, multicenter, double-blind, placebo-controlled, randomized-withdrawal studies of paliperidone in adults with a schizophrenia diagnosis (according to DSM-IV criteria for ≥ 1 year before screening): once-daily extended-release oral paliperidone (ORAL paliperidone), once-monthly paliperidone palmitate (PP1M), and once-every-3-months paliperidone palmitate (PP3M)...
June 20, 2017: Journal of Clinical Psychiatry
https://www.readbyqxmd.com/read/28640908/evaluating-diagnostic-tests-for-bovine-tuberculosis-in-the-southern-part-of-germany-a-latent-class-analysis
#12
Valerie-Beau Pucken, Gabriela Knubben-Schweizer, Dörte Döpfer, Andreas Groll, Angela Hafner-Marx, Stefan Hörmansdorfer, Carola Sauter-Louis, Reinhard K Straubinger, Pia Zimmermann, Sonja Hartnack
Germany has been officially free of bovine tuberculosis since 1996. However, in the last years there has been an increase of bovine tuberculosis cases, particularly in the southern part of Germany, in the Allgäu region. As a consequence a one-time tuberculosis surveillance program was revisited with different premortal and postmortal tests. The aim of this paper was to estimate diagnostic sensitivities and specificities of the different tests used within this surveillance program. In the absence of a perfect test with 100% sensitivity and 100% specificity, thus in the absence of a gold standard, a Bayesian latent class approach with two different datasets was performed...
2017: PloS One
https://www.readbyqxmd.com/read/28640836/craniofacial-similarity-analysis-through-sparse-principal-component-analysis
#13
Junli Zhao, Fuqing Duan, Zhenkuan Pan, Zhongke Wu, Jinhua Li, Qingqiong Deng, Xiaona Li, Mingquan Zhou
The computer-aided craniofacial reconstruction (CFR) technique has been widely used in the fields of criminal investigation, archaeology, anthropology and cosmetic surgery. The evaluation of craniofacial reconstruction results is important for improving the effect of craniofacial reconstruction. Here, we used the sparse principal component analysis (SPCA) method to evaluate the similarity between two sets of craniofacial data. Compared with principal component analysis (PCA), SPCA can effectively reduce the dimensionality and simultaneously produce sparse principal components with sparse loadings, thus making it easy to explain the results...
2017: PloS One
https://www.readbyqxmd.com/read/28640819/the-importance-of-data-quality-for-generating-reliable-distribution-models-for-rare-elusive-and-cryptic-species
#14
Keith B Aubry, Catherine M Raley, Kevin S McKelvey
The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina)...
2017: PloS One
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#15
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28637310/the-metagenomic-data-life-cycle-standards-and-best-practices
#16
Petra Ten Hoopen, Robert D Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing.Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#17
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637286/structure-seq2-sensitive-and-accurate-genome-wide-profiling-of-rna-structure-in-vivo
#18
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637215/managerial-ownership-in-nursing-homes-staffing-quality-and-financial-performance
#19
Sean Shenghsiu Huang, John R Bowblis
Purpose of the Study: Ownership of nursing homes (NHs) has primarily focused broadly on differences between for-profit (FP), nonprofit (NFP), and government-operated facilities. Yet, among FPs, the understanding of detailed ownership structures at individual NHs is rather limited. Particularly, NH administrators may hold significant equity interests in their facilities, leading to heterogeneous financial incentives and NH outcomes. Through the principal-agent theory, this article studies how managerial ownership of individual facilities affects NH outcomes...
June 20, 2017: Gerontologist
https://www.readbyqxmd.com/read/28636999/impact-of-insurance-status-on-the-survival-of-gallbladder-cancer-patients
#20
Zhiqiang Chen, Wen Gao, Liyong Pu, Long Zhang, Guoyong Han, Qin Zhu, Xiangcheng Li, Jindao Wu, Xuehao Wang
The prognostic significance of insurance status has been investigated in many types of malignancies, however, its impact on gallbladder cancer is yet not known. The purpose of this study was to determine the relationship between insurance status and gallbladder cancer survival. We searched the Surveillance, Epidemiology, and End Results dataset, and identified 1,729 gallbladder cancer cases. Kaplan-Meier methods and multivariable Cox regression models were used to analyze survival outcomes and risk factors...
June 6, 2017: Oncotarget
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