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https://www.readbyqxmd.com/read/28732212/ualcan-a-portal-for-facilitating-tumor-subgroup-gene-expression-and-survival-analyses
#1
Darshan S Chandrashekar, Bhuwan Bashel, Sai Akshaya Hodigere Balasubramanya, Chad J Creighton, Israel Ponce-Rodriguez, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally
Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. The large sample numbers in TCGA offer an excellent opportunity to address questions associated with tumo heterogeneity. Exploration of the data by cancer researchers and clinicians is imperative to unearth novel therapeutic/diagnostic biomarkers. Various computational tools have been developed to aid researchers in carrying out specific TCGA data analyses; however there is need for resources to facilitate the study of gene expression variations and survival associations across tumors...
July 18, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28732211/psychological-health-and-pediatric-urology-the-missing-chapter-in%C3%A2-our%C3%A2-surgical-atlas
#2
EDITORIAL
Alexandra Rehfuss, Barry Kogan
No abstract text is available yet for this article.
July 18, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28731045/renal-cell-tumors-with-clear-cell-histology-and-intact-vhl-and-chromosome-3p-a-histological-review-of-tumors-from-the-cancer-genome-atlas-database
#3
Laura Favazza, Dhananjay A Chitale, Ravi Barod, Craig G Rogers, Shanker Kalyana-Sundaram, Nallasivam Palanisamy, Nilesh S Gupta, Sean R Williamson
Clear cell renal cell carcinoma is by far the most common form of kidney cancer; however, a number of histologically similar tumors are now recognized and considered distinct entities. The Cancer Genome Atlas published data set was queried (http://cbioportal.org) for clear cell renal cell carcinoma tumors lacking VHL gene mutation and chromosome 3p loss, for which whole-slide images were reviewed. Of the 418 tumors in the published Cancer Genome Atlas clear cell renal cell carcinoma database, 387 had VHL mutation, copy number loss for chromosome 3p, or both (93%)...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28730682/structure-and-development-of-the-subesophageal-zone-of-the-drosophila-brain-i-segmental-architecture-compartmentalization-and-lineage-anatomy
#4
Volker Hartenstein, Jaison J Omoto, Kathy T Ngo, Darren Wong, Philipp A Kuert, Heinrich Reichert, Jennifer K Lovick, Amelia Younossi-Hartenstein
The subesophageal zone (SEZ) of the Drosophila brain houses the circuitry underlying feeding behavior and is involved in many other aspects of sensory processing and locomotor control. Formed by the merging of four neuromeres, the internal architecture of the SEZ can be best understood by identifying segmentally reiterated landmarks emerging in the embryo and larva, and following the gradual changes by which these landmarks become integrated into the mature SEZ during metamorphosis. In previous works, the system of longitudinal fibers (connectives) and transverse axons (commissures) has been utilized as a scaffold that provides internal landmarks for the neuromeres of the larval ventral nerve cord...
July 21, 2017: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/28729943/relationship-between-cerebellar-structure-and-emotional-memory-in-depression
#5
Li-Yan Xu, Fang-Cheng Xu, Can Liu, Yi-Fu Ji, Jin-Min Wu, Ying Wang, Hai-Bao Wang, Yong-Qiang Yu
BACKGROUND: A few studies have been conducted on the relationship between cerebellar volume and emotional memory or clinical severity in major depressive disorder (MDD). In this study, we aimed to compare the volume and density of the cerebellar gray matter (GM) in patients with MDD and in healthy controls (HCs) and explore the association between these cerebellar parameters and measurements of emotional memory and clinical severity. METHOD: Voxel-based morphometry (VBM) and Individual Brain Atlases using Statistical Parametric Mapping (IBASPM) were used to assess GM density and volume in the cerebellum, respectively, in patients with MDD and the HCs...
July 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28729829/cortex-parcellation-associated-whole-white-matter-parcellation-in-individual-subjects
#6
Patrick Schiffler, Jan-Gerd Tenberge, Heinz Wiendl, Sven G Meuth
The investigation of specific white matter areas is a growing field in neurological research and is typically achieved through the use of atlases. However, the definition of anatomically based regions remains challenging for the white matter and thus hinders region-specific analysis in individual subjects. In this article, we focus on creating a whole white matter parcellation method for individual subjects where these areas can be associated to cortex regions. This is done by combining cortex parcellation and fiber tracking data...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28728854/potential-use-of-american-college-of-radiology-bi-rads-mammography-atlas-for-reporting-and-assessing-lesions-detected-on-dedicated-breast-ct-imaging-preliminary-study
#7
Hae Kyoung Jung, Cherie M Kuzmiak, Keum Won Kim, Na Mi Choi, Hye Jeong Kim, Eun Lee Langman, Sora Yoon, Doreen Steen, Donglin Zeng, Fei Gao
RATIONALE AND OBJECTIVES: Dedicated breast computed tomography (DBCT) is an emerging and promising modality for breast lesions. The objective of this study was to evaluate the potential use of applying the BI-RADS Mammography Atlas 5th Edition for reporting and assessing breast lesions on DBCT. Currently, no atlas exists for DBCT. MATERIALS AND METHODS: Four radiologists trained in breast imaging were recruited in this institutional review board-approved, Health Insurance Portability and Accountability Act-compliant study...
July 17, 2017: Academic Radiology
https://www.readbyqxmd.com/read/28728584/professionals-perception-of-intimate-partner-violence-in-young-people-a-qualitative-study-in-northern-spain
#8
Amaia Maquibar, Carmen Vives-Cases, Anna-Karin Hurtig, Isabel Goicolea
BACKGROUND: Intimate partner violence (IPV) is a public health problem with devastating effects on young women's health. These negative effects increase when the exposure to IPV lasts for a long time and exposure at an early age increases the risk of adult IPV. Despite efforts made in the last few decades, data show little progress has been made towards its reduction. Thus, the aim of the study reported here is to explore professionals' perceptions regarding intimate partner violence (IPV) among young people, focusing on the characteristics of the phenomenon and their perceptions about existing programmes and campaigns aimed at addressing it...
July 20, 2017: Reproductive Health
https://www.readbyqxmd.com/read/28726143/endoscopic-management-of-post-laparoscopic-sleeve-gastrectomy-stenosis
#9
Valérie Deslauriers, Amélie Beauchamp, Fabio Garofalo, Henri Atlas, Ronald Denis, Pierre Garneau, Radu Pescarus
BACKGROUND: Laparoscopic sleeve gastrectomy (LSG) is the most popular bariatric surgery worldwide. Gastric sleeve stenosis is the most common postoperative complication, occurring in up to 3.9% of the cases. Current treatment options include endoscopic treatments, such as dilatations and stent placement as well as surgical revisions such as laparoscopic Roux-en-Y gastric bypass (LRYGB), wedge gastrectomy or seromyotomy. METHODS: A retrospective analysis of our prospectively collected therapeutical endoscopy database was performed between January 2014 and February 2017...
July 19, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28725522/pathogenetic-analysis-of-sinonasal-teratocarcinosarcomas-reveal-actionable-%C3%AE-catenin-overexpression-and-a-%C3%AE-catenin-mutation
#10
Andrew C Birkeland, Sarah J Burgin, Megan Yanik, Megan V Scott, Carol R Bradford, Jonathan B McHugh, Scott A McLean, Stephen E Sullivan, Jacques E Nor, Erin L McKean, J Chad Brenner
Objective  Sinonasal teratocarcinosarcomas are rare, aggressive tumors of the skull base. Treatment options are limited and outcomes are poor. Little is known in regard to the genetic factors regulating these tumors. Characterization of actionable molecular alterations in these tumors could provide potentially successful therapeutic options. Methods  We performed targeted exome sequencing on an index sinonasal teratocarcinosarcoma specimen to identify potential driver mutations. We performed immunohistochemical stains for β-catenin on paraffin-embedded tissue on the index tumor and a subsequent teratocarcinosarcoma...
August 2017: Journal of Neurological Surgery. Part B, Skull Base
https://www.readbyqxmd.com/read/28723760/bioinformatics-analysis-to-identify-the-critical-genes-micrornas-and-long-noncoding-rnas-in-melanoma
#11
Qian Zhang, Yang Wang, Jiulong Liang, Yaguang Tian, Yu Zhang, Kai Tao
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28723667/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#12
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
June 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28723576/an-atlas-of-human-regulatory-t-helper-like-cells-reveals-features-of-th2-like-tregs-that-support-a-tumorigenic-environment
#13
Leena Halim, Marco Romano, Reuben McGregor, Isabel Correa, Polychronis Pavlidis, Nathali Grageda, Sec-Julie Hoong, Muhammed Yuksel, Wayel Jassem, Rosalind F Hannen, Mark Ong, Olivia Mckinney, Bu'Hussain Hayee, Sophia N Karagiannis, Nicholas Powell, Robert I Lechler, Estefania Nova-Lamperti, Giovanna Lombardi
Regulatory T cells (Tregs) play a pivotal role in maintaining immunological tolerance, but they can also play a detrimental role by preventing antitumor responses. Here, we characterized T helper (Th)-like Treg subsets to further delineate their biological function and tissue distribution, focusing on their possible contribution to disease states. RNA sequencing and functional assays revealed that Th2-like Tregs displayed higher viability and autocrine interleukin-2 (IL-2)-mediated activation than other subsets...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28721443/a-diffusion-spectrum-imaging-based-tractographic-study-into-the-anatomical-subdivision-and-cortical-connectivity-of-the-ventral-external-capsule-uncinate-and-inferior-fronto-occipital-fascicles
#14
Sandip S Panesar, Fang-Cheng Yeh, Christopher P Deibert, David Fernandes-Cabral, Vijayakrishna Rowthu, Pinar Celtikci, Emrah Celtikci, William D Hula, Sudhir Pathak, Juan C Fernández-Miranda
PURPOSE: The inferior fronto-occipital fasciculus (IFOF) and uncinate fasciculus (UF) are major fronto-capsular white matter pathways. IFOF connects frontal areas of the brain to parieto-occipital areas. UF connects ventral frontal areas to anterior temporal areas. Both fascicles are thought to subserve higher language and emotion roles. Controversy pertaining to their connectivity and subdivision persists in the literature, however. METHODS: High-definition fiber tractography (HDFT) is a non-tensor tractographic method using diffusion spectrum imaging data...
July 18, 2017: Neuroradiology
https://www.readbyqxmd.com/read/28721358/utah-optrode-array-customization-using-stereotactic-brain-atlases-and-3-d-cad-modeling-for-optogenetic-neocortical-interrogation-in-small-rodents-and-nonhuman-primates
#15
Ronald W Boutte, Sam Merlin, Guy Yona, Brandon Griffiths, Alessandra Angelucci, Itamar Kahn, Shy Shoham, Steve Blair
As the optogenetic field expands, the need for precise targeting of neocortical circuits only grows more crucial. This work demonstrates a technique for using Solidworks(®) computer-aided design (CAD) and readily available stereotactic brain atlases to create a three-dimensional (3-D) model of the dorsal region of area visual cortex 4 (V4D) of the macaque monkey (Macaca fascicularis) visual cortex. The 3-D CAD model of the brain was used to customize an [Formula: see text] Utah optrode array (UOA) after it was determined that a high-density ([Formula: see text]) UOA caused extensive damage to marmoset (Callithrix jacchus) primary visual cortex as assessed by electrophysiological recording of spiking activity through a 1...
October 2017: Neurophotonics
https://www.readbyqxmd.com/read/28720872/associating-transcription-factors-and-conserved-rna-structures-with-gene-regulation-in-the-human-brain
#16
Nikolai Hecker, Stefan E Seemann, Asli Silahtaroglu, Walter L Ruzzo, Jan Gorodkin
Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expression in the human brain. First, we modeled the expression of a gene as a linear combination of the expression of TFs. We devised an approach to select robust TF-gene interactions and to determine localized contributions to gene expression of TFs...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720453/parental-acceptance-of-human-papillomavirus-vaccinations-and-community-pharmacies-as-vaccination-settings-a-qualitative-study-in-alabama
#17
Salisa C Westrick, Lindsey A Hohmann, Stuart J McFarland, Benjamin S Teeter, Kara K White, Tessa J Hastings
PURPOSE: To determine parents' knowledge and attitudes regarding human papillomavirus (HPV) vaccinations in their adolescent children and to describe parents' perceptions of adolescent vaccinations in community pharmacies. METHODS: In-depth interviews were completed with parents or guardians of children ages 11-17 years from Alabama's Lee and Macon counties. One-hour long, open-ended telephonic or in-person interviews were conducted until the saturation point was reached...
June 2017: Papillomavirus Research
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#18
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28718916/the-genetic-landscape-of-endometrial-clear-cell-carcinomas
#19
Deborah F DeLair, Kathleen A Burke, Pier Selenica, Raymond S Lim, Sasinya N Scott, Sumit Middha, Abhinita S Mohanty, Donavan T Cheng, Michael F Berger, Robert A Soslow, Britta Weigelt
Clear cell carcinoma of the endometrium is a rare type of endometrial cancer generally associated with an aggressive clinical behavior. Here we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs) and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs...
July 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28718375/emp3-is-induced-by-twist1-2-and-regulates-epithelial-to-mesenchymal-transition-of-gastric-cancer-cells
#20
Ming Han, Wanpeng Xu
In this study, we aimed to explore new downstream effectors of TWIST1/2 in inducing epithelial-to-mesenchymal transition in gastric cancer. Bioinformatic data mining was performed using data in The Cancer Genome Atlas Stomach Adenocarcinoma. Survival curves were generated using Kaplan-Meier plotter. Gastric cancer cell lines (AGS and SGC-7901) were used as in vitro cell model to investigate the regulative effect of TWIST1/2 on epithelial membrane protein 3 expression and the progression of epithelial-to-mesenchymal transition...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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