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https://www.readbyqxmd.com/read/28628667/characterization-of-hiv-1-crf90_bf1-and-putative-novel-crfs_bf1-in-central-west-north-and-northeast-brazilian-regions
#1
Mônica Nogueira da Guarda Reis, Gonzalo Bello, Monick Lindenmeyer Guimarães, Mariane Martins Araújo Stefani
The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates...
2017: PloS One
https://www.readbyqxmd.com/read/28586300/assessment-of-the-clinical-utility-of-adding-common-single-nucleotide-polymorphism-genetic-scores-to-classical-risk-factor-algorithms-in-coronary-heart-disease-risk-prediction-in-uk-men
#2
Katherine E Beaney, Jackie A Cooper, Fotios Drenos, Steve E Humphries
BACKGROUND: Risk prediction algorithms for coronary heart disease (CHD) are recommended for clinical use. However, their predictive ability remains modest and the inclusion of genetic risk may improve their performance. METHODS: QRISK2 was used to assess CHD risk using conventional risk factors (CRFs). The performance of a 19 single nucleotide polymorphism (SNP) gene score (GS) for CHD including variants identified by genome-wide association study and candidate gene studies (weighted using the results from the CARDIoGRAMplusC4D meta-analysis) was assessed using the second Northwick Park Heart Study (NPHSII) of 2775 healthy UK men (284 cases)...
June 6, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28586246/characterization-of-a-new-hiv-1-crf01_ae-crf07_bc-recombinant-virus-in-guangxi-china
#3
Desheng Kong, Yan Wang, Chen Wang, Shujia Liang, Yi Feng, Yuhua Ruan, Yiming Shao, Liying Ma
Currently, more and more kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in China. A novel second-generation CCR5-tropic HIV-1 recombinant virus (GX2016EU09) was identified here, which was isolated from a HIV-1 infected man who had sex with men (MSM) in Guangxi, China. Phylogenetic analysis of near full-length genome (NFLG) showed that the novel HIV-1 recombinant GX2016EU09 clustered with CRF01_AE reference sequences, but set up a distinct branch. Recombinant analysis showed that the NFLG of GX2016EU09 composed of CRF01_AE (as the backbone) and CRF07_BC, with 9 recombination break points observed in the gag, pol, vif, vpr, tat, rev, vpu, env and nef regions...
June 6, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28574343/exploring-context-with-deep-structured-models-for-semantic-segmentation
#4
Guosheng Lin, Chunhua Shen, Anton van den Hengel, Ian Reid
We propose an approach for exploiting contextual information in semantic image segmentation, and particularly investigate the use of patch-patch context and patch-background context in deep CNNs. We formulate deep structured models by combining CNNs and Conditional Random Fields (CRFs) for learning the patch-patch context between image regions. Specifically, we formulate CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied in order to avoid repeated expensive CRF inference during the course of back propagation...
May 26, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28536270/different-signal-enhancement-pathways-of-attention-and-consciousness-underlie-perception-in-humans
#5
Jeroen J A van Boxtel
It is not yet known whether attention and consciousness operate through similar or largely different mechanisms. Visual processing mechanisms are routinely characterized by measuring contrast response functions (CRFs). In this report, behavioral CRFs were obtained in humans (both males and females) by measuring afterimage durations over the entire range of inducer stimulus contrasts to reveal visual mechanisms behind attention and consciousness. Deviations relative to the standard CRF, i.e., gain functions, describe the strength of signal enhancement, which were assessed for both changes due to attentional task and conscious perception...
June 14, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28482717/radiation-therapy-improves-survival-in-patients-with-testicular-diffuse-large-b-cell-lymphoma
#6
Jennifer C Ho, Bouthaina S Dabaja, Sarah A Milgrom, Grace L Smith, Jay P Reddy, Ali Mazloom, Ken H Young, Lijuan Deng, L Jeffrey Medeiros, Wenli Dong, Pamela K Allen, Therese Y Andraos, Nathan H Fowler, Loretta J Nastoupil, Yasuhiro Oki, Luis E Fayad, Francesco Turturro, Sattva S Neelapu, Jason Westin, Fredrick B Hagemeister, Maria Alma Rodriguez, Chelsea C Pinnix
In 120 Stage I-IV testicular diffuse large B-cell lymphoma (DLBCL) patients treated from 1964 to 2015, we assessed the benefits of prophylactic contralateral testicular radiation (RT) and prophylactic central nervous system (CNS) therapy on overall, progression free, testicular relapse free, and CNS relapse free survival (OS, PFS, TRFS, and CRFS, respectively). Seventy percent of patients received RT, 53% received anthracyclines and rituximab (modern therapy), and 61% received CNS prophylaxis. On univariate analysis RT was associated with improved TRFS, PFS, and trended toward improved OS...
May 9, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28468996/temporally-evolving-gain-mechanisms-of-attention-in-macaque-area-v4
#7
Ilaria Sani, Elisa Santandrea, Maria Concetta Morrone, Leonardo Chelazzi
Cognitive attention and perceptual saliency jointly govern our interaction with the environment. Yet, we still lack a universally accepted account of the interplay between attention and luminance contrast - a fundamental dimension of saliency. We measured the attentional modulation of V4 neurons' Contrast Response Functions (CRFs) in awake, behaving macaque monkeys and applied a new approach which emphasizes the temporal dynamics of cell responses. We found that attention modulates CRFs via different gain mechanisms during subsequent epochs of visually driven activity: an early contrast-gain - strongly dependent on pre-stimulus activity changes (baseline shift), a time-limited stimulus-dependent multiplicative modulation, reaching its maximal expression around 150 ms after stimulus onset, and a late resurgence of contrast-gain modulation...
May 3, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28468684/a-chronology-of-ratios-between-black-smoke-and-pm10-and-pm2-5-in-the-context-of-comparison-of-air-pollution-epidemiology-concentration-response-functions
#8
Mathew R Heal, Iain J Beverland
BACKGROUND: For many air pollution epidemiological studies in Europe, 'black smoke' (BS) was the only measurement available to quantify ambient particulate matter (PM), particularly for exposures prior to the mid-1990s when quantification via the PM10 and/or PM2.5 metrics was introduced. The aim of this work was to review historic BS and PM measurements to allow comparison of health concentration-response functions (CRF) derived using BS as the measure of exposure with CRFs derived using PM10 or PM2...
May 3, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28463186/deeplab-semantic-image-segmentation-with-deep-convolutional-nets-atrous-convolution-and-fully-connected-crfs
#9
Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, Alan L Yuille
In this work we address the task of semantic image segmentation with Deep Learning and make three main contributions that are experimentally shown to have substantial practical merit. First, we highlight convolution with upsampled filters, or 'atrous convolution', as a powerful tool in dense prediction tasks. Atrous convolution allows us to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks. It also allows us to effectively enlarge the field of view of filters to incorporate larger context without increasing the number of parameters or the amount of computation...
April 27, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28422671/structured-learning-of-tree-potentials-in-crf-for-image-segmentation
#10
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
#11
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...
May 4, 2017: Nanoscale
https://www.readbyqxmd.com/read/28407904/characterization-and-functionalities-study-of-hemicellulose-and-cellulose-components-isolated-from-sorghum-bran-bagasse-and-biomass
#12
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-comprising-b-and-c
#13
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. Owing to the special geographic location and the frequent population mobility, Yunnan province contained complex HIV subtype distribution. Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been found in recent years. In this study, a unique HIV-1 recombinant strain genome (YN10134) was characterized from an HIV-positive female in Yunnan, China. This virus genome had a complex intersubtype recombinant structure with eight breakpoints, composed of subtypes B and C...
June 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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