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https://www.readbyqxmd.com/read/28422671/structured-learning-of-tree-potentials-in-crf-for-image-segmentation
#1
Fayao Liu, Guosheng Lin, Ruizhi Qiao, Chunhua Shen
We propose a new approach to image segmentation, which exploits the advantages of both conditional random fields (CRFs) and decision trees. In the literature, the potential functions of CRFs are mostly defined as a linear combination of some predefined parametric models, and then, methods, such as structured support vector machines, are applied to learn those linear coefficients. We instead formulate the unary and pairwise potentials as nonparametric forests--ensembles of decision trees, and learn the ensemble parameters and the trees in a unified optimization problem within the large-margin framework...
April 13, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28422233/detection-of-stiff-nanoparticles-within-cellular-structures-by-contact-resonance-atomic-force-microscopy-subsurface-nanomechanical-imaging
#2
Melania Reggente, Daniele Passeri, Livia Angeloni, Francesca Anna Scaramuzzo, Mario Barteri, Francesca De Angelis, Irene Persiconi, Maria Egle De Stefano, Marco Rossi
Detecting stiff nanoparticles buried in soft biological matrices by atomic force microscopy (AFM) based techniques represents a new frontier in the field of scanning probe microscopies, originally developed as surface characterization methods. Here we report the detection of stiff (magnetic) nanoparticles (NPs) internalized in cells by using contact resonance AFM (CR-AFM) employed as a potentially non-destructive subsurface characterization tool. Magnetite (Fe3O4) NPs were internalized in microglial cells from cerebral cortices of mouse embryos of 18 days by phagocytosis...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28407904/characterization-and-functionalities-study-of-hemicellulose-and-cellulose-components-isolated-from-sorghum-bran-bagasse-and-biomass
#3
Shuang Qiu, Madhav P Yadav, Lijun Yin
This study was undertaken to isolate and characterize three carbohydrate-rich fractions: Hemicellulose A (Hemi. A), Hemicellulose B (Hemi. B) and cellulose-rich residue (CRF) from sorghum bran (SBR), sorghum bagasse (SBA) and sorghum biomass (SBI). The monosaccharide composition of the Hemi. A and Hemi. B fractions was determined, indicating that SBR has a highly branched structure. The analysis of insoluble dietary fiber (IDF), soluble dietary fiber (SDF) and total dietary fiber (TDF) showed that TDF and IDF contents in original sorghum materials were in the following order: SBA˃SBI˃SBR...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28398773/genetic-characterization-of-a-unique-recombinant-strain-identified-in-yunnan-with-genome-comprised-of-b-and-c
#4
Xiaolin Wang, Min Zhang, Jianjian Li, Tianyi Li, Changrong Sun, Hanping Li, Yongjian Liu, Siyang Liu, Daomin Zhuang, Zuoyi Bao, Jingwan Han, Jingyun Li, Lin Li
Since the first identification of HIV-1 outbreak in Dehong, Yunnan province has been the epidemic center of HIV in China. Due to the special geographic location and the frequent population mobility, Yunnan province contained complex HIV subtype distribution. Many new CRFs and URFs have been found in recently years. In this study, a unique HIV-1 recombinant strain (URF) genome (YN10134) was characterized from an HIV-positive female in Yunnan, China. This virus genome had a complex intersubtype recombinant structure with 8 breakpoints, composed of subtype B and subtype C...
February 10, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28333019/a-comparison-between-low-dose-rate-brachytherapy-with-or-without-androgen-deprivation-external-beam-radiation-therapy-with-or-without-androgen-deprivation-and-radical-prostatectomy-with-or-without-adjuvant-or-salvage-radiation-therapy-for-high-risk-prostate
#5
Jay P Ciezki, Michael Weller, Chandana A Reddy, Jeffrey Kittel, Harguneet Singh, Rahul Tendulkar, Kevin L Stephans, James Ulchaker, Kenneth Angermeier, Andrew Stephenson, Steven Campbell, Georges-Pascal Haber, Eric A Klein
PURPOSE: We compare the efficacy and toxicity among the 3 major modalities available used to treat high-risk prostate cancer (HRCaP). METHODS AND MATERIALS: From 1996 to 2012, 2557 HRCaP patients were treated: 734 received external beam radiation therapy (EBRT) with or without androgen deprivation therapy (ADT), 515 received low-dose-rate prostate brachytherapy (LDR) with or without ADT, and 1308 received radical prostatectomy (RP) with or without EBRT. Biochemical relapse-free survival (bRFS), clinical relapse-free survival (cRFS), and prostate cancer-specific mortality (PCSM) were assessed...
April 1, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28325857/treatment-trends-for-retinopathy-of-prematurity-in-the-uk-active-surveillance-study-of-infants-at-risk
#6
Gillian G W Adams, Catey Bunce, Wen Xing, Lucilla Butler, Vernon Long, Aravind Reddy, Annegret H Dahlmann-Noor
OBJECTIVES: To estimate the incidence of severe retinopathy of prematurity (ROP) requiring treatment and describe current treatment patterns in the UK. DESIGN: Nationwide population-based case ascertainment study via the British Ophthalmic Surveillance Unit and a national collaborative ROP special interest group. Practitioners completed a standardised case report form (CRF). SETTING: All paediatric ophthalmologists providing screening and/or treatment for retinopathy in the UK were invited to take part...
March 21, 2017: BMJ Open
https://www.readbyqxmd.com/read/28318764/increasing-hiv-1-subtype-diversity-in-seven-states-united-states-2006-2013
#7
Alexandra M Oster, William M Switzer, Angela L Hernandez, Neeraja Saduvala, Joel O Wertheim, Ndidi Nwangwu-Ike, M Cheryl Ocfemia, Ellsworth Campbell, H Irene Hall
PURPOSE: The aim of the analysis was to explore HIV-1 subtype diversity in the United States and understand differences in prevalence of non-B subtypes and circulating recombinant forms (CRFs) between demographic/risk groups and over time. METHODS: We included HIV-1 polymerase sequences reported to the National HIV Surveillance System for HIV infections diagnosed during 2006-2013 in seven states. We assigned subtype or CRF using the automated subtyping tool COMET, assessed subtype/CRF prevalence by demographic characteristics and country of birth, and determined changes in subtype/CRF by HIV diagnosis year...
February 22, 2017: Annals of Epidemiology
https://www.readbyqxmd.com/read/28303425/common-data-elements-for-clinical-research-in-mitochondrial-disease-a-national-institute-for-neurological-disorders-and-stroke-project
#8
Amel Karaa, Shamima Rahman, Anne Lombès, Patrick Yu-Wai-Man, Muniza K Sheikh, Sherita Alai-Hansen, Bruce H Cohen, David Dimmock, Lisa Emrick, Marni J Falk, Shana McCormack, David Mirsky, Tony Moore, Sumit Parikh, John Shoffner, Tanja Taivassalo, Mark Tarnopolsky, Ingrid Tein, Joanne C Odenkirchen, Amy Goldstein
OBJECTIVES: The common data elements (CDE) project was developed by the National Institute of Neurological Disorders and Stroke (NINDS) to provide clinical researchers with tools to improve data quality and allow for harmonization of data collected in different research studies. CDEs have been created for several neurological diseases; the aim of this project was to develop CDEs specifically curated for mitochondrial disease (Mito) to enhance clinical research. METHODS: Nine working groups (WGs), composed of international mitochondrial disease experts, provided recommendations for Mito clinical research...
March 16, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28278130/cardiometabolic-risk-factors-among-1-3-million-adults-with-overweight-or-obesity-but-not-diabetes-in-10-geographically-diverse-regions-of-the-united-states-2012-2013
#9
Gregory A Nichols, Michael Horberg, Corinna Koebnick, Deborah Rohm Young, Beth Waitzfelder, Nancy E Sherwood, Matthew F Daley, Assiamira Ferrara
INTRODUCTION: Various phenotypes of overweight and obesity pose various health risks. The objective of this study was to determine the prevalence of 4 commonly measured cardiometabolic risk factors (CRFs) among adults with overweight or obesity, but not diabetes, at the time of the study. METHODS: We analyzed data for 1,294,174 adults (aged ≥20 y) who were members of one of 4 integrated health systems. Each cohort member had a body mass index in 2012 or 2013 that indicated overweight or obesity...
March 9, 2017: Preventing Chronic Disease
https://www.readbyqxmd.com/read/28275889/automatic-anatomical-labeling-of-arteries-and-veins-using-conditional-random-fields
#10
Takayuki Kitasaka, Mitsuru Kagajo, Yukitaka Nimura, Yuichiro Hayashi, Masahiro Oda, Kazunari Misawa, Kensaku Mori
PURPOSE: For safe and reliable laparoscopic surgery, it is important to determine individual differences of blood vessels such as the position, shape, and branching structures. Consequently, a computer-assisted laparoscopy that displays blood vessel structures with anatomical labels would be extremely beneficial. This paper details an automated anatomical labeling method for abdominal arteries and veins extracted from 3D CT volumes. METHODS: The proposed method represents a blood vessel tree as a probabilistic graphical model by conditional random fields (CRFs)...
March 8, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28252395/discriminative-training-of-deep-fully-connected-continuous-crfs-with-task-specific-loss
#11
Fayao Liu, Guosheng Lin, Chunhua Shen
Recent works on deep conditional random fields (CRFs) have set new records on many vision tasks involving structured predictions. Here, we propose a fully connected deep continuous CRF model with task-specific losses for both discrete and continuous labeling problems. We exemplify the usefulness of the proposed model on multi-class semantic labeling (discrete) and the robust depth estimation (continuous) problems. In our framework, we model both the unary and the pairwise potential functions as deep convolutional neural networks (CNNs), which are jointly learned in an end-to-end fashion...
May 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28239528/prevalence-of-cardiovascular-risk-factors-in-people-with-epilepsy
#12
Rosa Maria Vivanco-Hidalgo, Alejandra Gomez, Antia Moreira, Laura Díez, Roberto Elosua, Jaume Roquer
OBJECTIVES: Epilepsy has been associated with cardiovascular comorbidity. This study aimed to assess the potential association between cardiovascular risk factors (CRFs), antiepileptic drugs (AEDs), and etiology. MATERIAL AND METHODS: A single-center retrospective epilepsy cohort from the decade of 2004-2013 was assessed. Poisson regression models with robust variance were estimated to obtain CRF prevalence ratios (PR) according to AED prescription and etiology...
February 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28198547/phylogenetic-characteristics-of-hiv-1-among-travelers-entering-china-from-myanmar-a-retrospective-study
#13
Li Zhang, Binhui Wang, Yaobo Liang, Yue Feng, Shuwei Dong, Yajuan Wang, Yaping Li, A-Mei Zhang, Li Liu, Weihong Qin, Xueshan Xia
Due to the open policy of the Chinese government, a large number of Burmese individuals enter China at land ports in Yunnan province for travel or business. However, the situation of HIV-1 infection and its phylogenetic characteristics among these travelers remains unclear, which is a potential threat to public health. From January 2003 to December 2012, a total of 1,961 travelers were detected to be positive for HIV-1 infection at land ports between Myanmar and Yunnan province, China. From 1153 (58.8%) Burmese of them, we randomly collected 489 serum samples for HIV-1 subtype/recombinant analysis...
February 15, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28193549/identification-of-rare-hiv-1-group-n-hbv-ae-and-htlv-3-strains-in-rural-south-cameroon
#14
M A Rodgers, A S Vallari, B Harris, J Yamaguchi, V Holzmayer, K Forberg, M G Berg, J Kenmenge, C Ngansop, B Awazi, D Mbanya, L Kaptue, C Brennan, G Cloherty, N Ndembi
Surveillance of emerging viral variants is critical to ensuring that blood screening and diagnostic tests detect all infections regardless of strain or geographic location. In this study, we conducted serological and molecular surveillance to monitor the prevalence and diversity of HIV, HBV, and HTLV in South Cameroon. The prevalence of HIV was 8.53%, HBV was 10.45%, and HTLV was 1.04% amongst study participants. Molecular characterization of 555 HIV-1 specimens identified incredible diversity, including 7 subtypes, 12 CRFs, 6 unclassified, 24 Group O and 2 Group N infections...
April 2017: Virology
https://www.readbyqxmd.com/read/28178737/hiv-1-molecular-epidemiology-among-newly-diagnosed-hiv-1-individuals-in-hebei-a-low-hiv-prevalence-province-in-china
#15
Xinli Lu, Xianjiang Kang, Yongjian Liu, Ze Cui, Wei Guo, Cuiying Zhao, Yan Li, Suliang Chen, Jingyun Li, Yuqi Zhang, Hongru Zhao
New human immunodeficiency virus type 1 (HIV-1) diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28124495/very-high-risk-prostate-cancer-stratification-by-outcomes-of-radiotherapy-and-long-term-androgen-deprivation-therapy
#16
Natsuo Tomita, Norihito Soga, Yuji Ogura, Takumi Kageyama, Takeshi Kodaira
AIM: The definition of very high-risk (VHR) prostate cancer is currently based on the study of radical prostatectomy. We aimed to identify a suitable definition for VHR group following external beam radiation therapy (EBRT) and long-term androgen-deprivation therapy (ADT). METHODS: This retrospective study included 356 high-risk patients treated with EBRT and long-term ADT. A median follow-up time was 68 months. At first, associations of previously described prognostic factors with biochemical disease-free survival (bDFS), clinical relapse-free survival (cRFS) and prostate cancer-specific survival (CSS) were examined...
January 25, 2017: Asia-Pacific Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28113438/improving-biochemical-named-entity-recognition-performance-using-pso-classifier-selection-and-bayesian-combination-method
#17
Abbas Akkasi, Ekrem Varoglu
Named Entity Recognition (NER) is a basic step for large number of consequent text mining tasks in the biochemical domain. Increasing the performance of such recognition systems is of high importance and always poses a challenge. In this study, a new community based decision making system is proposed which aims at increasing the efficiency of NER systems in the chemical/drug name context. Particle Swarm Optimization (PSO) algorithm is chosen as the expert selection strategy along with the Bayesian combination method to merge the outputs of the selected classifiers as well as evaluate the fitness of the selected candidates...
May 18, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28077647/sensitive-next-generation-sequencing-method-reveals-deep-genetic-diversity-of-hiv-1-in-the-democratic-republic-of-the-congo
#18
Mary A Rodgers, Eduan Wilkinson, Ana Vallari, Carole McArthur, Larry Sthreshley, Catherine A Brennan, Gavin Cloherty, Tulio de Oliveira
As the epidemiological epicenter of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43.02%), but 7 other subtypes (33...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28064308/-structural-studies-of-chromatin-remodeling-factors
#19
REVIEW
O I Volokh, N I Derkacheva, V M Studitsky, O S Sokolova
Changes of chromatin structure require participation of chromatin remodeling factors (CRFs), which are ATP-dependent multisubunit complexes that change the structure of the nucleosome without covalently modifying its components. CRFs act together with other protein factors to regulate the extent of chromatin condensation. Four CRF families are currently distinguished based on their structural and biochemical characteristics: SWI/SNF, ISWI, Mi-2/CHD, and SWR/INO80. X-ray diffraction analysis and electron microscopy are the main methods to obtain structural information about macromolecules...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28062403/mutated-chromatin-regulatory-factors-as-tumor-drivers-in-cancer
#20
REVIEW
Carl Koschmann, Felipe J Nunez, Flor Mendez, Jacqueline A Brosnan-Cashman, Alan K Meeker, Pedro R Lowenstein, Maria G Castro
Genes encoding proteins that regulate chromatin structure and DNA modifications [i.e., chromatin regulatory factors (CRF)] and genes encoding histone proteins harbor recurrent mutations in most human cancers. These mutations lead to modifications in tumor chromatin and DNA structure and an altered epigenetic state that contribute to tumorigenesis. Mutated CRFs have now been identified in most types of cancer and are increasingly regarded as novel therapeutic targets. In this review, we discuss DNA alterations in CRFs and how these influence tumor chromatin structure and function, which in turn leads to tumorigenesis...
January 15, 2017: Cancer Research
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