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https://www.readbyqxmd.com/read/28110480/casubtype-an-r-package-to-identify-gene-sets-predictive-of-cancer-subtypes-and-clinical-outcomes
#1
Hualei Kong, Pan Tong, Xiaodong Zhao, Jielin Sun, Hua Li
In the past decade, molecular classification of cancer has gained high popularity owing to its high predictive power on clinical outcomes as compared with traditional methods commonly used in clinical practice. In particular, using gene expression profiles, recent studies have successfully identified a number of gene sets for the delineation of cancer subtypes that are associated with distinct prognosis. However, identification of such gene sets remains a laborious task due to the lack of tools with flexibility, integration and ease of use...
January 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28110465/spectroscopic-physicochemical-and-photophysical-investigation-of-biologically-active-2-oxo-quinoline-3-carbonitrile-derivative
#2
Mohie E M Zayed, Parveen Kumar
4-(2,3,4-trimethoxyphenyl)-8-methoxy-2-oxo-1,2,5,6 tetrahydrobenzo [h] quinoline-3-carbonitrile (TMTQ) dye was synthesized by one-pot multicomponent reactions (MCRs) of 2,3,4 trimethoxybenzaldehyd, ethyl cyanoacetate, 6-methoxy-1,2,3,4-tetrahydro-naphthalin-1-one and ammonium acetate under microwave irradiation. The structures of the synthesized compound was established by spectroscopic (FT-IR, (1)H-NMR, (13)C-NMR, EI-MS) and elemental analysis. In addition, spectroscopic and physicochemical parameters, including electronic absorption, excitation coefficient, Stokes shift, oscillator strength, transition dipole moment and fluorescence quantum yield have investigated in order to explore the analytical potential of synthesized compounds...
January 21, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28110458/experimental-evaluation-of-new-chitin-chitosan-graft-for-duraplasty
#3
M Pogorielov, A Kravtsova, G C Reilly, V Deineka, G Tetteh, O Kalinkevich, O Pogorielova, R Moskalenko, G Tkach
Natural materials such as collagen and alginate have promising applications as dural graft substitutes. These materials are able to restore the dural defect and create optimal conditions for the development of connective tissue at the site of injury. A promising material for biomedical applications is chitosan-a linear polysaccharide obtained by the deacetylation of chitin. It has been found to be nontoxic, biodegradable, biofunctional and biocompatible in addition to having antimicrobial characteristics. In this study we designed new chitin-chitosan substitutes for dura mater closure and evaluated their effectiveness and safety...
February 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28110425/functional-effector-memory-t-cells-contribute-to-protection-from-superinfection-with-heterologous-simian-immunodeficiency-virus-or-simian-human-immunodeficiency-virus-isolates-in-chinese-rhesus-macaques
#4
Ming Sun, Huiwen Zheng, Yingpeng Xie, Bingxiang Li, Haiting Long, Ge Guo, Lei Guo, Jingjing Wang, Ruotong Ning, Yue Li, Longding Liu
Many studies have revealed a protective effect of infection of an individual with an immunodeficiency virus against subsequent infection with a heterologous strain. However, the extent of protection against superinfection conferred by the first infection and the biological consequences of superinfection are not well understood. Here, we report that a rhesus monkey model of mucosal superinfection was established to investigate the protective immune response. Protection against superinfection was shown to correlate with the extent of the polyfunctionality of CD4(+) effector memory T cells, whereas neutralizing antibody responses did not protect against superinfection in this model...
January 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28110416/lasiokaurin-derivatives-synthesis-antimicrobial-and-antitumor-biological-evaluation-and-apoptosis-inducing-effects
#5
Da-Hong Li, Ping Hu, Sheng-Tao Xu, Chun-Yan Fang, Shuang Tang, Xin-Yu Wang, Xing-Yan Sun, He Li, Ying Xu, Xiao-Ke Gu, Jin-Yi Xu
Herein, a series of lasiokaurin derivatives were designed and synthesized. All the derivatives together with lasiokaurin and oridonin were tested for their antimicrobial and antiproliferative activity. Compound 16 showed the most promising antimicrobial activity with MICs of 2.0 and 1.0 μg/mL against Gram-Positive bacteria S. aureus and B. subtilis, respectively. All the synthetic lasiokaurin derivatives showed better antiproliferative activity than parent compound lasiokaurin 1. Compound 10 exhibited the strongest cytotoxicity with IC50 values of 0...
January 21, 2017: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/28110346/prognostic-value-of-molecular-and-imaging-biomarkers-in-patients-with-supratentorial-glioma
#6
Egesta Lopci, Marco Riva, Laura Olivari, Fabio Raneri, Riccardo Soffietti, Arnoldo Piccardo, Alberto Bizzi, Pierina Navarria, Anna Maria Ascolese, Roberta Rudà, Bethania Fernandes, Federico Pessina, Marco Grimaldi, Matteo Simonelli, Marco Rossi, Tommaso Alfieri, Paolo Andrea Zucali, Marta Scorsetti, Lorenzo Bello, Arturo Chiti
PURPOSE: We evaluated the relationship between (11)C-methionine PET ((11)C-METH PET) findings and molecular biomarkers in patients with supratentorial glioma who underwent surgery. METHODS: A consecutive series of 109 patients with pathologically proven glioma (64 men, 45 women; median age 43 years) referred to our Institution from March 2012 to January 2015 for tumour resection and who underwent preoperative (11)C-METH PET were analysed. Semiquantitative evaluation of the (11)C-METH PET images included SUVmax, region of interest-to-normal brain SUV ratio (SUVratio) and metabolic tumour volume (MTV)...
January 21, 2017: European Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/28110292/biomartr-genomic-data-retrieval-with-r
#7
Hajk-Georg Drost, Jerzy Paszkowski
MOTIVATION: Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, biomartr, which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses...
January 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28110279/walking-the-c4-pathway-past-present-and-future
#8
REVIEW
Robert T Furbank
The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO2 pool was not understood for a number of years, and the nature of C4 as a biochemical CO2 pump then linked the unique Kranz anatomy of C4 plants to their biochemical specialization...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110251/gold-nanomaterials-for-the-selective-capturing-and-sers-diagnosis-of-toxins-in-aqueous-and-biological-fluids
#9
Waleed A Hassanain, Emad L Izake, Michael S Schmidt, Godwin A Ayoko
A highly sensitive nanosensing method for the combined selective capture and SERS detection of Microcystin-LR (MC-LR) in blood plasma has been developed. The new method utilizes gold coated magnetic nanoparticles that are functionalized with anti MC-LR antibody Fab' fragments for the selective capture of MC-LR from aqueous media and blood plasma. Using an oriented immobilization approach, the Fab' fragments are covalently attached to gold surface to form a monolayer with high capture efficiency towards the toxin...
January 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28110241/autopsy-tissues-as-biological-monitors-of-human-exposure-to-environmental-pollutants-a-case-study-concentrations-of-metals-and-pcdd-fs-in-subjects-living-near-a-hazardous-waste-incinerator
#10
José L Domingo, Francisco García, Martí Nadal, Marta Schuhmacher
Human biomonitoring is of tremendous importance to prevent potential adverse effects derived from human exposure to chemicals. Blood and urine are among the biological monitors more frequently used. However, biological matrices such as breast milk, hair, nails, saliva, feces, teeth, and expired air are also often used. In addition, and focused mainly on long-term exposure, adipose tissue and other human tissues like bone, liver, brain or kidney, are also used as biological monitors of certain substances, especially for long-term biomonitoring...
January 19, 2017: Environmental Research
https://www.readbyqxmd.com/read/28110218/hydrogen-peroxide-as-a-central-redox-signaling-molecule-in-physiological-oxidative-stress-oxidative-eustress
#11
REVIEW
Helmut Sies
Hydrogen peroxide emerged as major redox metabolite operative in redox sensing, signaling and redox regulation. Generation, transport and capture of H2O2 in biological settings as well as their biological consequences can now be addressed. The present overview focuses on recent progress on metabolic sources and sinks of H2O2 and on the role of H2O2 in redox signaling under physiological conditions (1-10nM), denoted as oxidative eustress. Higher concentrations lead to adaptive stress responses via master switches such as Nrf2/Keap1 or NF-κB...
January 5, 2017: Redox Biology
https://www.readbyqxmd.com/read/28110195/geometric-protein-localization-cues-in-bacterial-cells
#12
REVIEW
Taylor B Updegrove, Kumaran S Ramamurthi
Bacterial cells are highly organized at a molecular level. Understanding how specific proteins localize to their proper subcellular address has been a major challenge in bacterial cell biology. One mechanism, which appears to be increasingly more common, is the use of 'geometric cues' for protein localization. In this model, certain shape-sensing proteins recognize, and preferentially embed into, either negatively or positively curved (concave or convex, respectively) membranes. Here, we review examples of bacterial proteins that reportedly localize by sensing geometric cues and highlight emerging mechanistic understandings of how proteins may recognize subtle differences in membrane curvature...
January 19, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28110192/effects-of-osteogenic-protein-1-on-intervertebral-disc-regeneration-a-systematic-review-of-animal-studies
#13
REVIEW
Pei Li, Ruijie Zhang, Yibo Gan, Liyuan Wang, Chen Zhao, Lei Luo, Chengmin Zhang, Qiang Zhou
Osteogenic protein (OP)-1 delivery into discs has achieved some success in disc regeneration in animals, though conflicting outcomes exist. This study aimed to systematically review the animal studies that assessed the effect of OP-1 on disc regeneration. Relevant literature was searched in the following databases: PubMed, MEDLINE, EMBASE, the Cochrane Library, China National Knowledge Internet (CNKI) and Chinese BioMedical Literature Database (CBM). Animal species, disc degeneration model, OP-1 delivery method, and follow-up methodology including disc histology, disc matrix alteration, disc height, MRI T2 signal intensity and OP-1 treatment complications were extracted and reviewed...
January 19, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28110189/anticancer-activity-of-baicalein-and-luteolin-studied-in-colorectal-adenocarcinoma-lovo-cells-and-in-drug-resistant-lovo-dx-cells
#14
Anna Palko-Labuz, Kamila Sroda-Pomianek, Anna Uryga, Edyta Kostrzewa-Suslow, Krystyna Michalak
Due to the type-specific diversity of cancer cells, an analysis and elucidation of molecular mechanisms responsible for anticancer properties of biologically active compounds are essential. Plant-derived polyphenolic compounds such as flavonoids may be useful in cancer chemoprevention or treatment because they influence diverse molecular pathways in cancer cells. In these studies anticancer activity of natural occurring flavones, baicalein and luteolin was investigated in colon cancer cells LoVo and in their drug resistant subline LoVo/Dx...
January 19, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28110183/noncovalent-interaction-assisted-fullerene-for-the-transportation-of-some-brain-anticancer-drugs-a-theoretical-study
#15
Pabitra Narayan Samanta, Kalyan Kumar Das
The treatment of brain cancer like glioblastoma multiforme often uses chemotherapeutic drugs like temozolomide, procarbazine, carmustine, and lomustine. Fullerene loaded with these drugs help to cross the blood brain barriers. The adsorptions of the four drug molecules on the surface of the fullerene are studied mostly by using density functional theory (DFT) based method at the M06-2X/6-31G(d) level of calculations. In all four cases, the estimated interactions are noncovalent type and the average adsorption energy lies in between -5 and -11kcal/mol in the gas phase...
January 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110179/analysis-the-effect-of-different-geometries-of-afm-s-cantilever-on-the-dynamic-behavior-and-the-critical-forces-of-three-dimensional-manipulation
#16
Moharam Habibnejad Korayem, Maniya B Saraie, Mahdieh B Saraee
An important challenge when using an atomic force microscope (AFM) is to be able to control the force exerted by the AFM for performing various tasks. Nevertheless, the exerted force is proportional to the deflection of the AFM cantilever, which itself is affected by a cantilever's stiffness coefficient. Many papers have been published so far on the methods of obtaining the stiffness coefficients of AFM cantilevers in 2D; however, a comprehensive model is yet to be presented on 3D cantilever motion. The discrepancies between the equations of the 2D and 3D analysis are due to the number and direction of forces and moments that are applied to a cantilever...
January 13, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28110168/ultra-high-performance-liquid-chromatography-tandem-mass-spectrometry-uhplc-ms-ms-for-determination-of-ghb-precursors-and-metabolites-in-different-specimens-application-to-clinical-and-forensic-cases
#17
Francesco Paolo Busardò, Chrystalla Kyriakou, Emilia Marchei, Roberta Pacifici, Daniel Sejer Pedersen, Simona Pichini
Gamma-hydroxybutyric acid (GHB) acts as a precursor and metabolite of the inhibitory central nervous system (CNS) neurotransmitter gamma-aminobutyric acid (GABA). Sodium salt of GHB has been used as a medication for narcolepsy and alcohol withdrawal. Moreover, GHB and its precursor gamma-butyrolactone (GBL), are illegal recreational drugs of abuse. A procedure based on ultra-high-performance liquid chromatography tandem mass spectrometry has been developed and validated in plasma, urine, cerebrospinal fluid and hair for acute and chronic exposure to GHB and in seized preparations coming from black market...
January 9, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28110151/selection-of-an-optimal-set-of-biomarkers-and-comparative-analyses-of-biological-age-estimation-models-in-korean-females
#18
Haemi Jee, Jaehyun Park
To date, an optimal working model which predicts biological age (BA) with a set of working biomarkers has not been devised to represent the Korean female population. Accuracy of prediction and applicability are required of an optimal set of commonly assessed biomarkers to provide information on the health status. The goal of this study was to identify a set of biomarkers that represent the aging process and to develop and compare different BA prediction models to elucidate the most fitting and applicable model for providing information on health status in the Korean female population...
January 12, 2017: Archives of Gerontology and Geriatrics
https://www.readbyqxmd.com/read/28110143/non-denitrifying-polyphosphate-accumulating-organisms-obviate-requirement-for-anaerobic-condition
#19
A Anisa Cokro, Yingyu Law, Rohan B H Williams, Yeshi Cao, Per H Nielsen, Stefan Wuertz
Enhanced biological phosphorus removal (EBPR) is a widely used process in wastewater treatment that requires anaerobic/aerobic or anaerobic/anoxic cycling. Surprisingly, phosphorus (P) release was observed in the presence of nitrate in the anoxic compartment of the activated sludge tank in a full-scale treatment plant with the Modified Ludzack Ettinger configuration. We therefore studied the potential of this full-scale activated sludge community to perform EBPR under anoxic/aerobic cycling. The polyphosphate accumulating organism (PAO) Candidatus Accumulibacter represented 3...
January 3, 2017: Water Research
https://www.readbyqxmd.com/read/28110115/application-of-an-ecosystem-model-to-evaluate-the-importance-of-different-processes-and-food-web-structure-for-transfer-of-13-elements-in-a-shallow-lake
#20
L Konovalenko, C Bradshaw, E Andersson, U Kautsky
In environmental risk assessments of nuclear waste, there is need to estimate the potential risks of a large number of radionuclides over a long time period during which the environment is likely to change. Usually concentration ratios (CRs) are used to calculate the activity concentrations in organisms. However, CRs are not available for all radionuclides and they are not easily scalable to the varying environment. Here, an ecosystem transport model of elements, which estimates concentrations in organisms using carbon flows and food transfer instead of CR is presented...
January 18, 2017: Journal of Environmental Radioactivity
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