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https://www.readbyqxmd.com/read/28641315/sequential-vs-concurrent-epirubicin-and-docetaxel-as-adjuvant-chemotherapy-for-high-risk-node-negative-early-breast-cancer-an-interim-analysis-of-a-randomised-phase-iii-study-from-the-hellenic-oncology-research-group
#1
Dimitrios Mavroudis, Emmanouil Saloustros, Ioannis Boukovinas, Pavlos Papakotoulas, Stylianos Kakolyris, Nikolaos Ziras, Charalampos Christophylakis, Nikolaos Kentepozidis, Georgios Fountzilas, Georgios Rigas, Ioannis Varthalitis, Konstantinos Kalbakis, Sofia Agelaki, Dora Hatzidaki, Vasilios Georgoulias
BACKGROUND: Sequential anthracyclines and taxanes are standard adjuvant chemotherapy for patients with high-risk axillary node-positive breast cancer. We compared a sequential to a concurrent regimen in high-risk node-negative early breast cancer. METHODS: Patients were eligible if they had tumours >2 cm or T1c with two of the following characteristics: no oestrogen receptor (ER) and progesterone receptor (PR) expression, histological grade III, Ki67 >40% and vascular, lymphovascular or perineural invasion...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#2
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641267/a-cpu-mic-collaborated-parallel-framework-for-gromacs-on-tianhe-2-supercomputer
#3
Shaoliang Peng, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao
Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer...
June 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28640879/dual-targeting-of-a-virus-movement-protein-to-er-and-plasma-membrane-subdomains-is-essential-for-plasmodesmata-localization
#4
Kazuya Ishikawa, Masayoshi Hashimoto, Akira Yusa, Hiroaki Koinuma, Yugo Kitazawa, Osamu Netsu, Yasuyuki Yamaji, Shigetou Namba
Plant virus movement proteins (MPs) localize to plasmodesmata (PD) to facilitate virus cell-to-cell movement. Numerous studies have suggested that MPs use a pathway either through the ER or through the plasma membrane (PM). Furthermore, recent studies reported that ER-PM contact sites and PM microdomains, which are subdomains found in the ER and PM, are involved in virus cell-to-cell movement. However, functional relationship of these subdomains in MP traffic to PD has not been described previously. We demonstrate here the intracellular trafficking of fig mosaic virus MP (MPFMV) using live cell imaging, focusing on its ER-directing signal peptide (SPFMV)...
June 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28640838/next-generation-sequencing-of-the-clonal-igh-rearrangement-detects-ongoing-mutations-and-interfollicular-trafficking-in-in-situ-follicular-neoplasia
#5
Perikles Kosmidis, Irina Bonzheim, Claudia Dufke, Sema Colak, Thomas Hentrich, Christopher Schroeder, Peter Bauer, Patrick Adam, Falko Fend
Follicular lymphoma (FL) is characterized genetically by a significant intraclonal diversity of rearranged immunoglobulin heavy chain (IGH) genes and a substantial cell migration activity (follicular trafficking). Recently, in situ follicular neoplasia (ISFN), characterized by accumulations of immunohistochemically strongly BCL2-positive, t(14;18)+ clonal B cells confined to germinal centers in reactive lymph nodes, has been identified as a precursor lesion of FL with low risk of progression to manifest FL...
2017: PloS One
https://www.readbyqxmd.com/read/28640835/bilateral-blockade-of-mek-and-pi3k-mediated-pathways-downstream-of-mutant-kras-as-a-treatment-approach-for-peritoneal-mucinous-malignancies
#6
Murali R Kuracha, Peter Thomas, Brian W Loggie, Venkatesh Govindarajan
Mucinous colorectal adenocarcinomas (MCAs) are clinically and morphologically distinct from nonmucinous colorectal cancers (CRCs), show a distinct spectrum of genetic alterations (higher KRAS mutations, lower p53, high MUC2), exhibit more aggressive behavior (more prone to peritoneal dissemination and lymph node involvement) and are associated with poorer response to chemotherapy with limited treatment options. Here, we report the effectiveness of combinatorial targeting of two KRAS-mediated parallel pathways in reducing MUC2 production and mucinous tumor growth in vitro and in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28640767/surgical-and-pathological-outcomes-of-laparoscopic-versus-abdominal-radical-hysterectomy-with-pelvic-lymphadenectomy-and-or-para-aortic-lymph-node-sampling-for-bulky-early-stage-cervical-cancer
#7
Tao Zhu, Xi Chen, Jianqing Zhu, Yaqing Chen, Aijun Yu, Lu Chen, Huafeng Shou, Meijuan Wu, Ping Zhang
BACKGROUND AND OBJECTIVES: The aim of this study was to compare the feasibility, morbidity, and recurrence rate of total laparoscopic radical hysterectomy (LRH) with those of abdominal radical hysterectomy (ARH) for bulky early-stage cervical cancer. METHODS: We performed a retrospective cohort study of 112 patients with stage IB1 or IIA2 cervical cancer in which the tumor diameter was 3 cm or greater. All patients underwent LRH (n = 30) or ARH (n = 82) with pelvic lymphadenectomy and/or para-aortic lymph node sampling between May 2011 and November 2014...
July 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28640608/numerical-diculties-computing-electrostatic-potentials-near-interfaces-with-the-poisson-boltzmann-equation
#8
Marcia Oliveira Fenley, Alexander H Boschitsch, Robert C Harris
Many researchers compute surface maps of the electrostatic potential with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of electrostatic potential, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of the electrostatic potential) at the surface...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640587/silica-nanoparticle-as-a-lymph-node-targeting-platform-for-vaccine-delivery
#9
Myunggi An, Meng Li, Jingchao Xi, Haipeng Liu
Nanoparticles have emerged as the platform of choice to improve the efficacy and safety of subunit vaccines. A major challenge underlying the use of nanomaterials in vaccines lies in the particle designs that can efficiently target and activate the antigen-presenting cells, especially dendritic cells. Here we show a toll-like receptor 9 (TLR-9) agonist and antigen co-loaded, silica nanoparticles (SiNPs) are able to accumulate in antigen presenting cells in the draining lymph nodes after injection. Vaccine loaded SiNPs led to dramatically enhanced induction of antigen-specific B and T cell responses as compared to soluble vaccines, which in turn drove a protective antitumoral immunity in a murine tumor model...
June 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28637293/conserved-non-exonic-elements-a-novel-class-of-marker-for-phylogenomics
#10
Scott V Edwards, Alison Cloutier, Allan J Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species...
June 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28636989/satb1-overexpression-correlates-with-gastrointestinal-neoplasms-invasion-and-metastasis-a-meta-analysis-for-chinese-population
#11
Tao Xiao, Lei Fu, Zhigang Jie
BACKGROUND: Gastrointestinal neoplasm (GIN) is the most common neoplasm in China. The global chromatin organizer SATB1 (special AT-rich sequence binding protein 1) is aberrantly expressed in multiple human neoplasms. We conducted this meta-analysis to investigate whether the invasion and metastasis of GIN correlates with SATB1 levels in tumor tissues in Chinese patients. MATERIALS AND METHODS: Eligible studies were identified through multiple search strategies in the databases PubMed, Embase, Medline, CNKI, and WANFANG, and the relevant clinicopathological data were extracted...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636956/elicitation-of-robust-tier-2-neutralizing-antibody-responses-in-nonhuman-primates-by-hiv-envelope-trimer-immunization-using-optimized-approaches
#12
Matthias Pauthner, Colin Havenar-Daughton, Devin Sok, Joseph P Nkolola, Raiza Bastidas, Archana V Boopathy, Diane G Carnathan, Abishek Chandrashekar, Kimberly M Cirelli, Christopher A Cottrell, Alexey M Eroshkin, Javier Guenaga, Kirti Kaushik, Daniel W Kulp, Jinyan Liu, Laura E McCoy, Aaron L Oom, Gabriel Ozorowski, Kai W Post, Shailendra K Sharma, Jon M Steichen, Steven W de Taeye, Talar Tokatlian, Alba Torrents de la Peña, Salvatore T Butera, Celia C LaBranche, David C Montefiori, Guido Silvestri, Ian A Wilson, Darrell J Irvine, Rogier W Sanders, William R Schief, Andrew B Ward, Richard T Wyatt, Dan H Barouch, Shane Crotty, Dennis R Burton
The development of stabilized recombinant HIV envelope trimers that mimic the virion surface molecule has increased enthusiasm for a neutralizing antibody (nAb)-based HIV vaccine. However, there is limited experience with recombinant trimers as immunogens in nonhuman primates, which are typically used as a model for humans. Here, we tested multiple immunogens and immunization strategies head-to-head to determine their impact on the quantity, quality, and kinetics of autologous tier 2 nAb development. A bilateral, adjuvanted, subcutaneous immunization protocol induced reproducible tier 2 nAb responses after only two immunizations 8 weeks apart, and these were further enhanced by a third immunization with BG505 SOSIP trimer...
June 20, 2017: Immunity
https://www.readbyqxmd.com/read/28636829/analysis-of-minimally-invasive-esophagectomy-at-a-single-veterans-affairs-medical-center
#13
Matthew D Skancke, Robert A Grossman, Gustavo Marino, Fredrick J Brody, Gregory D Trachiotis
BACKGROUND: To date, there are no published studies focusing on the benefits of minimally invasive esophagectomy (MIE) versus open esophagectomy at a Veterans Affairs Medical Center (VAMC). Our primary outcome was the incidence of esophageal malignancy in the veteran population and the postoperative morbidity following traditional and MIE for malignancy. DESIGN: Retrospective analysis of the incidence of esophageal malignancy at a Veteran Integrated Service Network (VISN) 5 VAMC reported to the VAMC Esophageal Tumor Registry between 2003 and 2016 and outcomes of the veterans who received esophagectomy for malignancy...
June 21, 2017: Journal of Laparoendoscopic & Advanced Surgical Techniques. Part A
https://www.readbyqxmd.com/read/28636558/prognostic-significance-of-clinicopathological-factors-in-early-breast-cancer-20-years-of-follow-up-in-a-single-center-analysis
#14
Valentina Cocciolone, Katia Cannita, Maria Letizia Calandrella, Enrico Ricevuto, Paola Lanfiuti Baldi, Tina Sidoni, Azzurra Irelli, Stefania Paradisi, Laura Pizzorno, Valter Resta, Alberto Bafile, Edoardo Alesse, Alessandra Tessitore, Corrado Ficorella
BACKGROUND: To quantify the effect of traditional prognostic factors [nodal status, estrogen-receptor (ER), progesterone-receptor (PR), human epidermal growth factor receptor 2 (HER2)] on long-term outcome of patients with early breast cancer (EBC), treated in clinical practice over a period of about twenty years. RESULTS: 1198 consecutive patients were identified. Median DFS (disease-free survival): ER+/PR±/HER2-, 165 months (mo) if node-negative (N0) and 114mo if node-positive (N+) (p < 0...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636557/surgical-management-for-follicular-variant-of-papillary-thyroid-carcinoma
#15
Jianing Tang, Deguang Kong, Lupin Bu, Gaosong Wu
BACKGROUND AND AIMS: For most patients with follicular variant of papillary thyroid carcinoma (FVPTC), surgery is required, while the surgical management remains controversial. We aim to further understanding of treatment of FVPTC and to determine whether specific features could be identified for the decision of surgical strategy. MATERIALS AND METHODS: Data were obtained from the Surveillance, Epidemiology, and End Results (SEER) Program database during 2003 and 2013...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636553/the-prognostic-and-diagnostic-value-of-circulating-tumor-cells-in-bladder-cancer-and-upper-tract-urothelial-carcinoma-a-meta-analysis-of-30-published-studies
#16
Zheng Zhang, Wei Fan, Qiaoling Deng, Shihui Tang, Ping Wang, Peipei Xu, June Wang, Mingxia Yu
There are inconsistent conclusions in the association between circulating tumor cells (CTCs) and urothelial cancer (UC). We performed a meta-analysis to assess the prognostic and diagnostic value of CTCs in UC. We search Medline, Embase and Web of science for relevant studies. The study was set up according to the inclusion/exclusion criteria. 30 published studies with a total of 2161 urothelial cancer patients were included. Meta-analysis showed that CTC-positive was significantly associated with tumor stage (≤ II vs III, IV) (OR = 4...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28635997/a-spin-column-free-approach-to-sodium-hydroxide-based-glycan-permethylation
#17
Yueming Hu, Chad R Borges
Glycan permethylation was introduced as a tool to facilitate the study of glycans in 1903. Since that time, permethylation procedures have been continually modified to improve permethylation efficiency and qualitative applicability. Typically, however, either laborious preparation steps or cumbersome and uneconomical spin columns have been needed to obtain decent permethylation yields on small glycan samples. Here we describe a spin column-free (SCF) glycan permethylation procedure that is applicable to both O- and N-linked glycans and can be employed upstream to intact glycan analysis by MALDI-MS, ESI-MS, or glycan linkage analysis by GC-MS...
June 21, 2017: Analyst
https://www.readbyqxmd.com/read/28635683/blastic-plasmacytoid-dendritic-cell-neoplasm-with-pulmonary-involvement-and-atypical-skin-lesion
#18
Cyndi Myrelle da Silva Barros Romão, Cláudio José Dos Santos Júnior, Luiz Arthur Calheiros Leite, Maria Jordana Rocha Gomes Alves, Nathalia Silva Araújo, Anderson F L Castro, Muriel Silva Moura, Vitória Mikaelly da Silva Gomes, Arthur Moacir Costa Sampaio Batinga, João Antonio S Queiroz, Natanael Barbosa Dos Santos
BACKGROUND Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematodermic malignancy neoplasm with highly aggressive course and poor prognosis. This disease typically presents with cutaneous involvement as the first manifestation, with subsequent or simultaneous spread to bone marrow and peripheral blood.  CASE REPORT Here, we report the case of a 51-year-old woman who presented a violaceus skin lesion on the lateral region of the right thigh, weight loss, fever, and lymphadenopathies. Computed tomography (CT) displayed thoracic and abdominal lymph node and alveolar bleeding...
June 21, 2017: American Journal of Case Reports
https://www.readbyqxmd.com/read/28635678/evaluation-of-classifier-performance-for-multiclass-phenotype-discrimination-in-untargeted-metabolomics
#19
Patrick J Trainor, Andrew P DeFilippis, Shesh N Rai
Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes. Despite this, a comprehensive and rigorous evaluation of the accuracy of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics datasets, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines (SVM), Artificial Neural Network, k-Nearest Neighbors (k-NN), and Naïve Bayes classification techniques for discrimination...
June 21, 2017: Metabolites
https://www.readbyqxmd.com/read/28635623/compressed-sensing-reconstruction-based-on-block-sparse-bayesian-learning-in-bearing-condition-monitoring
#20
Jiedi Sun, Yang Yu, Jiangtao Wen
Remote monitoring of bearing conditions, using wireless sensor network (WSN), is a developing trend in the industrial field. In complicated industrial environments, WSN face three main constraints: low energy, less memory, and low operational capability. Conventional data-compression methods, which concentrate on data compression only, cannot overcome these limitations. Aiming at these problems, this paper proposed a compressed data acquisition and reconstruction scheme based on Compressed Sensing (CS) which is a novel signal-processing technique and applied it for bearing conditions monitoring via WSN...
June 21, 2017: Sensors
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