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https://www.readbyqxmd.com/read/28430868/most-visualization-software-for-producing-automated-textbook-style-maps-of-genome-scale-metabolic-networks
#1
James J Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S Lun
Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: 1. automation, since GEMs can be quite large; 2. production of understandable maps that provide ease in identification of pathways, reactions, and metabolites; and 3. visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (1), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (2) and comes close to satisfying (3)...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430744/activation-of-a-c-jun-n-terminal-kinase-mediated-autophagy-pathway-attenuates-the-anticancer-activity-of-gemcitabine-in-human-bladder-cancer-cells
#2
Xiao-Long Huang, Hao Zhang, Xiao-Yu Yang, Xiao-Yong Dong, Xiang-Yu Xie, Hu-Bin Yin, Xin Gou, Yong Lin, Wei-Yang He
The role of autophagy in the anticancer activity of gemcitabine (GEM) in bladder cancer is unclear. The aim of this study is to determine whether GEM activates autophagy, the role of autophagy in the anticancer activity of GEM, and the underlying mechanism by which GEM induces autophagy. Human bladder cancer cell lines T24 and BIU87 were treated with GEM in vitro. Cell viability was measured using the Cell Counting Kit-8 assay. Apoptosis was detected by annexin V assay and western blot. Autophagy was measured by western blot and transmission electron microscopy...
April 20, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28430453/ag-initiated-gem-difluoromethylenation-of-the-nitrogen-center-of-arenediazonium-salts-to-gem-difluoromethylene-azo-compounds
#3
Haizhen Jiang, Yunrong Chen, Bo Chen, Hui Xu, Wen Wan, Hongmei Deng, Kesen Ma, Shaoxiong Wu, Jian Hao
An efficient method for the synthesis of the thermally stable and pharmaceutically important gem-difluoromethylene azo compounds is developed. This protocol achieved gem-difluoromethylenation of the nitrogen center of arenediazonium salts through in situ generated benzo-1,3-diazolic difluoromethylene radical addition to arenediazonium salts under mild Ag-initiated conditions.
April 21, 2017: Organic Letters
https://www.readbyqxmd.com/read/28426279/combination-of-gemcitabine-and-docetaxel-regress-both-gastric-leiomyosarcoma-proliferation-and-invasion-in-an-imageable-patient-derived-orthotopic-xenograft-ipdox-model
#4
Kei Kawaguchi, Kentaro Igarashi, Takashi Murakami, Tasuku Kiyuna, Scott D Nelson, Sarah M Dry, Yunfeng Li, Tara A Russell, Arun S Singh, Bartosz Chmielowski, Michiaki Unno, Fritz C Eilber, Robert M Hoffman
Gastric leiomyosarcoma is a recalcitrant cancer and chemotherapy strategy is controversial. The present study used a patient-derived orthotopic xenograft (PDOX) nude mouse model of gastric leiomyosarcoma to identify an effective therapeutic regimen in order to develop individualized precision medicine for this disease. A gastric leiomyosarcoma obtained from a patient was first grown in transgenic nude mice ubiquitously expressing red fluorescent protein (RFP) in order to stably label the tumor stroma. The RFP-expressing tumor was then passaged orthotopically in the gastric wall of non-transgenic nude mice to establish an imageable PDOX (iPDOX) model...
April 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28426085/n-heterocyclic-carbene-catalyzed-stereoselective-construction-of-olefinic-carbon-sulfur-bonds-via-cross-coupling-reaction-of-gem-difluoroalkenes-and-thiols
#5
Zi-Song Cong, Yang-Guo Li, Lei Chen, Fen Xing, Guang-Fen Du, Cheng-Zhi Gu, Lin He
A novel organocatalytic olefinic carbon-sulfur bond forming reaction was developed. Under the catalysis of 10 mol% stable N-heterocyclic carbene, thiols undergo direct nucleophilic substitution reaction with gem-difluoroalkenes to produce α-fluorovinyl thioethers in high yields with excellent Z-selectivity. In this process, bases are not necessary.
April 20, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28425853/evaluation-of-the-in-vitro-chemosensitivity-and-correlation-with-clinical-outcomes-in-lung-cancer-using-the-atp-tca
#6
Zhiyao Chen, Shichao Zhang, Sheng Ma, Chang Li, Chun Xu, Yinfang Shen, Jun Zhao, Liyan Miao
BACKGROUND AND OBJECTIVE: Multiple drug resistance (MDR) to chemotherapeutic agents often leads to a failure to respond to chemotherapy. We utilized an in vitro chemosensitivity test to identify sensitive and effective chemotherapeutic drugs and further elucidated the correlation between the in vivo chemosensitivity and clinical outcomes. METHODS: Here, we evaluated the in vitro chemosensitivity and MDR of 120 lung cancer patients to eight single-drug chemotherapies and of 291 lung cancer patients to seven chemotherapy regimens using an ATP-based tumour chemosensitivity assay (ATP-TCA)...
April 19, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28425294/reactivity-of-a-base-stabilized-germanium-i-dimer-toward-group-9-metal-i-chloride-and-dimanganese-decacarbonyl
#7
Muhammad Luthfi Bin Ismail, Fu-Quan Liu, Wai-Leung Yim, Rakesh Ganguly, Yongxin Li, Cheuk-Wai So
The reactivity of the 2-imino-5,6-methylenedioxylphenylgermanium(I) dimer toward group 9 metal(I) chloride and dimanganese decacarbonyl is described. [LGe:]2 (1, L = 2-imino-5,6-methylenedioxylphenyl) underwent a disproportionation reaction with 1.5 equiv of group 9 metal(I) chloride [MCl(cod)]2 (M = Rh, Ir) in toluene to afford a mixture of the group 9 metallogermylene-chlorometal(I) complexes [LGeμ-{M(cod)}2Cl] (M = Rh (2), Ir (4)) and chlorogermylene-chlorometal(I) complexes [L(Cl)GeM(cod)Cl] (M = Rh (3), Ir (5)), respectively...
April 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28422841/evaluation-of-gemcitabine-efficacy-after-the-folfirinox-regimen-in-patients-with-advanced-pancreatic-adenocarcinoma
#8
Marine Gilabert, Brice Chanez, Young Soo Rho, Marc Giovanini, Olivier Turrini, Gerald Batist, Petr Kavan, Jean Luc Raoul
To evaluate gemcitabine efficacy in advanced pancreatic cancer patients after the FOLFIRINOX regimen.Patients with locally-advanced or metastatic pancreatic adenocarcinoma from French and Canadian centers, who were treated with the first-line FOLFIRINOX regimen (FFX L1), followed by gemcitabine monotherapy as a second-line treatment (GEM L2), were retrospectively evaluated. Statistical analyses were performed on the demographic, toxicity, and response rate data. Overall survival (OS) and progression-free survival (PFS) were assessed using the Kaplan-Meier method...
April 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28420130/gaseous-elemental-mercury-and-total-and-leached-mercury-in-building-materials-from-the-former-hg-mining-area-of-abbadia-san-salvatore-central-italy
#9
Orlando Vaselli, Barbara Nisi, Daniele Rappuoli, Jacopo Cabassi, Franco Tassi
Mercury has a strong environmental impact since both its organic and inorganic forms are toxic, and it represents a pollutant of global concern. Liquid Hg is highly volatile and can be released during natural and anthropogenic processes in the hydrosphere, biosphere and atmosphere. In this study, the distribution of Gaseous Elemental Mercury (GEM) and the total and leached mercury concentrations on paint, plaster, roof tiles, concrete, metals, dust and wood structures were determined in the main buildings and structures of the former Hg-mining area of Abbadia San Salvatore (Siena, Central Italy)...
April 15, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28420113/synthesis-and-spectral-properties-of-meso-arylbacteriochlorins-including-insights-into-essential-motifs-of-their-hydrodipyrrin-precursors
#10
Muthyala Nagarjuna Reddy, Shaofei Zhang, Han-Je Kim, Olga Mass, Masahiko Taniguchi, Jonathan S Lindsey
Synthetic bacteriochlorins-analogues of bacteriochlorophylls, Nature's near-infrared absorbers-are attractive for diverse photochemical studies. meso-Arylbacteriochlorins have been prepared by the self-condensation of a dihydrodipyrrin-carbinol or dihydrodipyrrin-acetal following an Eastern-Western (E-W) or Northern-Southern (N-S) joining process. The bacteriochlorins bear a gem-dimethyl group in each pyrroline ring to ensure stability toward oxidation. The two routes differ in the location of the gem-dimethyl group at the respective 3- or 2-position in the dihydrodipyrrin, and the method of synthesis of the dihydrodipyrrin...
April 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28415884/alcohol-quantification-recent-insights-into-amperometric-enzyme-biosensors
#11
Vinita Hooda, Vikas Kumar, Anjum Gahlaut, Vikas Hooda
Biosensors are the switching channels that make sense. The biosensors have found an empirical role in health applications (e.g. clinical diagnostics) as they represent the technological counterpart of living senses. On a global scale, alcohol analysis is indispensable for criminal justice systems, monitoring medical conditions of HIV patients & pregnant women as well as public safety issues regarding pilots, metro drivers, doctors etc. For addressing the clinical and toxicological problems, much advancement in the improvement of biosensors have been witnessed in recent decades...
April 17, 2017: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/28406461/n-2-2-dimethyl-1-quinolin-2-yl-propylidene-arylaminonickel-complexes-and-their-ethylene-oligomerization
#12
Hongyi Suo, Tong Zhao, Yiqing Wang, Qing Ban, Wen-Hua Sun
A series of N-(2,2-dimethyl-1-(quinolin-2-yl)propylidene) arylamines was sophisticatedly synthesized and reacted with nickel(II) bromine for the formation of the corresponding nickel complexes. All the organic compounds were characterized by IR, NMR spectra and elemental analysis, while all the nickel complexes were characterized by IR spectra and elemental analysis. On activation with ethylaluminium sesquichloride (EASC) and modified methylaluminoxane (MMAO), all nickel precatalysts exhibited good activities toward ethylene oligomerization, indicating the positive efficiency of gem-dimethyl substitutents; in which major hexenes were obtained with MMAO...
April 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28394191/the-parp-inhibitor-olaparib-enhances-the-cytotoxicity-of-combined-gemcitabine-busulfan-and-melphalan-in-lymphoma-cells
#13
Benigno C Valdez, Yang Li, David Murray, Yan Liu, Yago Nieto, Richard E Champlin, Borje S Andersson
The combination of gemcitabine (Gem), busulfan (Bu), and melphalan (Mel) is a promising regimen for autologous stem-cell transplantation (SCT) for lymphomas. To further improve the efficacy of [Gem + Bu + Mel], we added poly(ADP-ribose) polymerase (PARP) inhibitor olaparib (Ola). We hypothesized that Ola would inhibit the repair of damaged DNA caused by [Gem + Bu + Mel]. Exposure of J45.01 and Toledo cell lines to IC10-20 of individual drug inhibited proliferation by 6-16%; [Gem + Bu + Mel] by 20-27%; and [Gem + Bu + Mel + Ola] by 61-67%...
April 10, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28380597/optimizing-test-procedures-for-estimating-daily-methane-and-carbon-dioxide-emissions-in-cattle-using-short-term-breath-measures
#14
P F Arthur, I M Barchia, C Weber, T Bird-Gardiner, K A Donoghue, R M Herd, R S Hegarty
Respiration chambers are considered the reference method for quantifying the daily CH production rate (MPR) and CO production rate (CPR) of cattle; however, they are expensive, labor intensive, cannot be used in the production environment, and can be used to assess only a limited number of animals. Alternative methods are now available, including those that provide multiple short-term measures of CH and CO, such as the GreenFeed Emission Monitoring (GEM) system. This study was conducted to provide information for optimizing test procedures for estimating MPR and CPR of cattle from multiple short-term CH and CO records...
February 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28379254/difluorocarbene-transfer-from-a-cobalt-complex-to-an-electron-deficient-alkene
#15
Monalisa Goswami, Bas de Bruin, Wojciech I Dzik
We report the synthesis of the trifluoromethyl cobalt(iii)tetraphenylporphyrinato complex [Co(TPP)CF3], which loses fluoride upon one-electron reduction and transfers a difluorocarbene moiety to n-butyl acrylate to produce the corresponding gem-difluorocyclopropane. Catalytic CF2 transfer from Me3SiCF3 to n-butyl acrylate becomes possible when directly using the divalent cobalt(ii) porphyrin catalysts in the presence of NaI.
April 5, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28376080/long-term-results-and-recurrence-patterns-from-scalop-a-phase-ii-randomised-trial-of-gemcitabine-or-capecitabine-based-chemoradiation-for-locally-advanced-pancreatic-cancer
#16
C N Hurt, S Falk, T Crosby, A McDonald, R Ray, G Joseph, J Staffurth, R A Abrams, G Griffiths, T Maughan, S Mukherjee
BACKGROUND: SCALOP, a randomised, phase II trial, tested the activity and safety of gemcitabine (GEM)-based and capecitabine (CAP)-based chemoradiation (CRT) for locally advanced pancreatic cancer (LAPC). Here we present the long-term outcomes. METHODS: Eligibility: histologically proven LAPC ⩽7 cm. Following 12 weeks of induction GEMCAP chemotherapy (three cycles: GEM 1000 mg m(-2) days 1, 8, 15; CAP 830 mg m(-2) days 1-21 q28 days) patients with stable/responding disease, tumour ⩽6 cm, and WHO Performance Status 0-1 were randomised to receive one cycle GEMCAP followed by CAP (830 mg m(-2) b...
April 4, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28373469/nab-paclitaxel-and-gemcitabine-in-advanced-pancreatic-cancer-the-one-year-experience-of-the-national-cancer-institute-of-naples
#17
Alessandro Ottaiano, Monica Capozzi, Chiara DE Divitiis, Claudia VON Arx, Elena DI Girolamo, Guglielmo Nasti, Ernesta Cavalcanti, Fabiana Tatangelo, Giovanni Romano, Antonio Avallone, Salvatore Tafuto
BACKGROUND: Pancreas adenocarcinoma is the sixth cause of cancer-related death worldwide with an increasing mortality in the Western countries. Recently, the association between nab-paclitaxel (nab-P) and gemcitabine (GEM) has significantly improved progression-free and overall survival. PATIENTS AND METHODS: Patients affected by metastatic pancreas adenocarcinoma were treated at the Department of Abdominal Oncology of the National Cancer Institute of Naples from July 2015 to July 2016 with nab-P at 125 mg per square meter of body-surface area followed by GEM at 1,000 mg per square meter on days 1, 8 and 15 every 4 weeks...
April 2017: Anticancer Research
https://www.readbyqxmd.com/read/28367990/systems-approach-to-characterize-the-metabolism-of-liver-cancer-stem-cells-expressing-cd133
#18
Wonhee Hur, Jae Yong Ryu, Hyun Uk Kim, Sung Woo Hong, Eun Byul Lee, Sang Yup Lee, Seung Kew Yoon
Liver cancer stem cells (LCSCs) have attracted attention because they cause therapeutic resistance in hepatocellular carcinoma (HCC). Understanding the metabolism of LCSCs can be a key to developing therapeutic strategy, but metabolic characteristics have not yet been studied. Here, we systematically analyzed and compared the global metabolic phenotype between LCSCs and non-LCSCs using transcriptome and metabolome data. We also reconstructed genome-scale metabolic models (GEMs) for LCSC and non-LCSC to comparatively examine differences in their metabolism at genome-scale...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28356963/human-antigen-r-as-a-predictive-marker-for-response-to-gemcitabine-based-chemotherapy-in-advanced-cisplatin-resistant-urothelial-cancer
#19
Yasuyoshi Miyata, Kensuke Mitsunari, Asai Akihiro, Shin-Ichi Watanabe, Tomohiro Matsuo, Kojiro Ohba, Hideki Sakai
In patients with advanced urothelial cancer (UC), a combination of cisplatin (CDDP) and gemcitabine (GEM) is the most commonly used first-line systematic chemotherapy regimen. Although no standard regime for the treatment of CDDP-resistant UC has been established, GEM-based regimens are frequently used in these patients. In other types of cancer, human antigen R (HuR) status in cancer cells is closely associated with patient response to GEM. The aim of the present study was to establish the predictive potential of HuR expression for disease progression and survival in patients with UC who were treated with GEM-based regimens as a first or second-line chemotherapy...
February 2017: Oncology Letters
https://www.readbyqxmd.com/read/28356771/nab-paclitaxel-for-the-treatment-of-pancreatic-cancer
#20
REVIEW
George Kim
BACKGROUND: Nanoparticle albumin-bound paclitaxel (nab-P) plus gemcitabine (Gem) became a standard treatment option for metastatic pancreatic cancer (MPC) following positive results from a global phase III trial (MPACT). A large number of studies have now published results on the use of nab-P/Gem to treat advanced and early-stage disease, warranting a comprehensive review. The main goal of this systematic review is to summarize the efficacy and safety data of nab-P/Gem for the treatment of pancreatic cancer (PC)...
2017: Cancer Management and Research
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