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MMsPred: a bioactivity and toxicology predictive system Nature Precedings
Joel Masciocchi; Luca Pireddu; Ricardo Medda; Piergiorgio Palla; Matteo Floris; Luca Pani; Patricia Rodriguez-Tome.
In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption, distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could provide solutions to this problem.
The goal of my research is to develop classifiers that accurately discriminate between active and inactive...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Pharmacology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4188/version/1
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Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips Nature Precedings
Donald C. Cooper; Bryan Callahan; Phil Callahan; Lee Burnett.
Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. These data were then used to create standard curves to allow quantification of COC/BE in biological samples. MIR quantification of COC and BE...
Tipo: Manuscript Palavras-chave: Biotechnology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/6827/version/1
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Molecular Bio-imprinting of Biocatalysts Nature Precedings
Israr Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5665/version/1
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Molecular Modeling study of Protein Kinase PKnB from Mycobacterium Tuberculosis with derivatives of 1, 3, 4- Thiadiazoles Nature Precedings
Vivek Gupta; Asif Naqvi; Jayendra Tanwar; Kaushlesh Mishra.
Tuberculosis causes more than two million deaths per year. Faced with this global threat it is crucial to better understand the physiology of the causative organism, Mycobacterium Tuberculosis, in order to develop efficient therapeutic strategies. PKnB from Mycobacterium tuberculosis is a crucial receptor-like protein kinase involved in signal transduction. M. tuberculosis PKnB is a trans-membrane Ser/Thr protein kinase (STPK) highly conserved in Gram-positive bacteria and apparently essential for Mycobacterial viability. We have attempted with the help of virtual screening and docking approaches to expound the extent of specificity of protein kinase B towards different classes of Thiadiazoles (an anti-tubercular agent). The selected Thiadiazoles were...
Tipo: Manuscript Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6136/version/1
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Molecular Static and Dynamic Analyses reveal Flaw in Murine Model used by US FDA to Detect Drug Carcinogenicity Nature Precedings
Trevor Marshall.
The US FDA currently accepts carcinogenicity studies of pharmaceutical drugs based on murine models. In addition to 6 month studies with p53(+/-) and ras.H2 transgenic mice, lifetime studies (typically 2 years) in WT mice or rats are also considered as evidence that a drug lacks carcinogenic activity. This model is not always exhaustive. For example, during the acceptance testing of the ARB Olmesartan[1], possible carcinogenicity observed in hamsters was not able to be duplicated in rats, or in transgenic mice. We have previously used the static molecular modeling of AutoDock to demonstrate that Olmesartan has agonostic activity in the PDB:1DB1 model of the human VDR Nuclear Receptor[2], while it has antagonistic activity in the PDB:1RK3 model of the rat...
Tipo: Poster Palavras-chave: Biotechnology; Cancer; Immunology; Pharmacology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/52/version/1
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Multi-drug resistance (MDR1) gene and P-glycoprotein influence on pharmacokinetic and pharmacodymanic of therapeutic drugs Ciência Rural
Linardi,Renata Lehn; Natalini,Cláudio Corrêa.
(MDR1) gene expressed in tumor cells and also in several normal tissues, such as intestine, liver, kidney, blood-brain barrier, spinal cord, and placenta. P-gp has been identified in mice, rat, bovine, monkey, rodents, and human beings and has been receiving a particular clinical relevance because this protein expression limits brain access and intestinal absorption of many drugs. This protein plays a role as a protective barrier against a wide variety of substrates, avoiding drug entry into the central nervous system. P-glycoprotein also interferes with drug bioavailability and disposition, including absorption, distribution, metabolization, and excretion, influencing pharmacokinetic and pharmacodynamic of drugs. Modulation of P-gp may help the efficacy...
Tipo: Info:eu-repo/semantics/article Palavras-chave: MDR1 gene; P-glycoprotein; Therapeutics; Pharmacology.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782006000100056
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Multidrug resistance of non-adherent cancer cells Nature Precedings
Navneet Singh; Subhas Chakrabarty; Guangming Liu.
Metastases are the cause of 90% of human cancer deaths. Cancer in _situ_ can usually be effectively removed by surgery. Once cancer cells disseminate from the original site and start to circulate in blood, lymph, or other body fluids, the disease becomes almost incurable. Here we show that cancer cells in a non-adherent, 3-dimentional growth pattern are highly drug resistant compared to their adherent counterparts that grow in monolayer, attaching to the wall of tissue culture plates. The non-adherent cancer cells retain the adhering potential and can attach to an appropriate surface to reacquire adherent phenotype. Once the non-adherent cancer cells become attached, they regain drug response, similar to the original adherent cells. A significant increase...
Tipo: Manuscript Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4488/version/1
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Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the 'logic gate' spectrum Nature Precedings
Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological 'logic gates' having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6413/version/1
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Multi-scale network biology model & the model library Nature Precedings
Jianghui Xiong.
Multi-scale network biology model & the model library
Tipo: Presentation Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5778/version/1
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Mummification in a Bitch: A case report Nature Precedings
Perumal P; Venkateswaralu B; D.N. Mohanty; Srinibas Das; Ashok Kumar Barik; P.C. Mishra.
A pug aged 5 years was admitted in the Lyka pet clinic with difficulty in parturition. Breeding history of the dog was collected from the owner. X-ray was conducted which confirmed the presence of foetus. The bitch was manually handled to relieve the Dystocia following intravenous drip of N.S.S. and oxytocin. In the vent of unsuccessful attempt the bitch was surgically operated for C.S. and six fetuses of which four normal and two mummified were relieved. Routine post operative care were undertaken and the bitch recovered normally with out any complication. Photographic recording was also made during the recovery of mummified foetus.
Tipo: Presentation Palavras-chave: Microbiology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7063/version/1
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Neem leaf glucosamine stimulates Interleukin-2 (IL-2) in swiss albino mice Nature Precedings
Santhosh Kumar Venugopalan; Navaratnam Viswesharan; Rajasekaran Aiyalu; Nair N K.
Neem leaf glucosamine-mediated immune stimulation was studied in male swiss albino mice. Mice were treated with three doses of Neem leaf glucosamine (266, 400 and 800 µg/30gm mouse, intraperitoneal injection) one dose per week for four weeks. At doses of 266, 400 and 800 µg/30gm mouse a significant increase in Interleukin-2 in mice serum was observed when compared to the control group and also an increase in relative organ weight of the thymus was observed but there was a mild increase in liver and kidney weights. The immune stimulatory response of Neem leaf glucosamine was also observed in T-lymphocyte proliferation. Overall, Neem leaf glucosamine showed a stimulatory effect on immune functions in mice. The immunostimulatory effect of...
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2011 URL: http://precedings.nature.com/documents/5923/version/1
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Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models Nature Precedings
I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6206/version/1
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Neuronal plasticity: cell-based strategy for target identification and validation Nature Precedings
Ana Mingorance-Le Meur; Timothy P. O'Connor.
While growing neurites are relatively plastic during development, their plasticity levels drop rapidly as neurons mature and become integrated into neuronal networks. As a consequence, the central nervous system ability to reorganize itself in response to injury or disease is insufficient. One of the main limitations for the design of therapeutic strategies to enhance neurite sprouting following neurological diseases is our poor understanding of the mechanisms underlying neurite structural plasticity. 

To overcome this limitation, we have implemented a strategy to identify, characterize and validate the most therapeutically relevant drug targets to modulate neuronal plasticity. This strategy is based on the hypothesis...
Tipo: Poster Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2009 URL: http://precedings.nature.com/documents/2780/version/1
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New insight into DNA damage by cisplatin at the atomic scale Nature Precedings
Raji Heyrovska.
Cisplatin is cis-diamminedichloroplatinum (II) of chemical formula, Pt(NH3)Cl2, abbreviated as cis-DDP and known commercially as platinol. It is used widely as an anticancer drug for various types of cancer, ever since its discovery two centuries ago and has become a target of extensive researches. Transplatin, trans-DDP on the other hand, is found to be less or ineffective to treat cancers. Cisplatin is known to interact mainly with the N(7) nitrogen of guanine in nucleic acids, after a water molecule takes away one of the chlorines by hydrolysis. This initiates the damage of nucleic acids and eventually leads to apoptosis. However the way how this happens and why transplatin is less effective is not completely clear. Here the author brings some new...
Tipo: Manuscript Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6891/version/1
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New source for L-iditol and taxanes Nature Precedings
Liu Xi-Kui; Liu Jian-Jun.
We describe the first report of the recovery of L-iditol and Taxane from an angiosperm- Yunnanopilia longistaminata (W.Z.Li) C.Y.Wu et D.Z.Li (Opiliaceae). Two taxane compounds and L-iditol were isolated from the tender burgeon of Yunnanopilia longistaminata, and their structure were identified as Taxayunnansin B, Taxumairol E and L-iditol on the basis of NMR and MS spectrum, respectively. It is a new plant source for L-iditol and taxanes.
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1502/version/1
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Nicotinic α7 acetylcholine receptor-mediated currents are not modulated by the tryptophan metabolite kynurenic acid in adult hippocampal interneurons Nature Precedings
Peter Dobelis; Andrew L. Varnell; Kevin J. Staley; Donald C. Cooper.
The  tryptophan  metabolite,  kynurenic  acid (KYNA),  is  classically  known  to  be  an antagonist  of ionotropic glutamate receptors. Within the last decade several reports have been published suggesting that KYNA also blocks nicotinic acetylcholine receptors (nAChRs) containing the α7 subunit (α7*). Most of these reports involve either indirect measurements of KYNA effects on α7 nAChR function, or are reports of KYNA effects in complicated in vivo systems.  However, a recent report investigating KYNA interactions with α7 nAChRs failed to detect an interaction using direct measurements of...
Tipo: Manuscript Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011 URL: http://precedings.nature.com/documents/6277/version/1
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NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents Nature Precedings
I. C. Baianu; Jun Guo.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer’s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6611/version/1
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NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents [v.2] Nature Precedings
I. C. Baianu; Jun Guo; Randall L. Nelson; Tiefeng You; Doina M. Costescu.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer’s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6611/version/2
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Novel network pharmacology methods for drug mechanism of action identification, pre-clinical drug screening and drug repositioning Nature Precedings
Jianghui Xiong.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Here we present two methodology innovations on network pharmacology modeling. (1) We hypothesize that the gene network associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. We proposed a novel in vivo genetic interaction between genes as ‘synergistic outcome determination’, in a similar way to ‘synthetic lethality’. We scanned above genetic interactions based on microarray profiling for cancer prognosis, and identified a cluster of important yet epigenetically regulated gene modules. By...
Tipo: Presentation Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6455/version/1
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Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos Nature Precedings
I. C. Baianu; Tiefeng You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1μ^2^.
Tipo: Poster Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6591/version/2
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