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Signatures of spatial organizations – From the universe of proteins to the universe in general Nature Precedings
Aditya Mittal.
Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that,...
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6038/version/1
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Performance of the ALOGPS 2.1 program for octanol-water partition coefficient prediction with organic chemicals on the Canadian Domestic Substances List Nature Precedings
Sierra Rayne; Kaya Forest.
The KOWWIN and ALOGPS octanol-water partition coefficient (K~ow~) estimation software programs were compared for their capacity to accurately predict log K~ow~ values of 1596 organic compounds on the publicly available Domestic Substances List (DSL) from Environment Canada for which experimental data is available. KOWWIN contained a significantly lower number and magnitude of prediction errors compared to ALOGPS, particularly at experimental log K~ow~ values <2. Substantial predictive differences were observed between the two programs for 9093 compounds not having experimental K~ow~ data on the Canadian DSL. Predictive differences of up to 40 log K~ow~ units were found between KOWWIN and ALOGPS, and in some cases, the discrepancies were...
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3882/version/1
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Hierarchical nanomechanics of collagen microfibrils Nature Precedings
Alfonso Gautieri; Simone Vesentini; Alberto Redaelli; Markus J. Buehler.
Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to organisms and is thus the prime construction materials in biology. Collagen is also the dominating material in the extracellular matrix and its stiffness controls cell differentiation, growth and pathology. However, the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response remains unknown. By using x-ray diffraction data of a collagen fibril (Orgel et al., PNAS, 2006) here we present an experimentally validated model of the nanomechanics of a collagen microfibril that incorporates the full biochemical details of the amino acid sequence of constituting...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4995/version/2
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Characteristics of Uremic Cardiomyopathy with Reversible Systolic Dysfunction Nature Precedings
Srilakshmi Adhyapak; Shamanna Iyengar.
Background: There exists a sub group of patients with uremic cardiomyopathy who experience resolution of heart failure following hemodialysis. It has been hypothesized that these patients are fluid overloaded, and following hemodialysis, show improvements in cardiac geometry and function. We wanted to study their clinical, biochemical and echocardiographic features to define any other additional characteristics.

Aim: To define characteristics of reversible systolic dysfunction.

Methods: We studied 72 patients with chronic kidney disease on hemodialysis of whom 52 presented with congestive heart failure, over a period of 190 days. We studied their echocardiographic profile and blood...
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology.
Ano: 2009 URL: http://precedings.nature.com/documents/3199/version/1
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Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth Nature Precedings
I. C. Baianu.
Experimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7128/version/1
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Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents Nature Precedings
Jean-Claude Bradley; Cameron Neylon; Rajarshi Guha; Antony J. Williams; Bill Hooker; Andrew S. I. D. Lang; Brent Friesen; Tim Bohinski; David Bulger; Matthew Federici; Jenny Hale; Jenna Mancinelli; Khalid B. Mirza; Marshall J. Moritz; Daniel Rein; Cedric Tchakounte; Hai T. Truong.
This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference. The Challenge was sponsored by Submeta, Nature and Sigma-Aldrich.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4243/version/2
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Determinative atom model and the nature of chemical bond Nature Precedings
Wanchung Hu.
Quantum mechanics including Schrodinger and Dirac’s equations are used to describe the atom model. However, the basic assumption assuming electron energy can be described by E=h’w is wrong. If E=h’w, then the total energy of the electron will be E=rmv^2 in contrary to E=rmc^2 from special relativity. Here, I propose a new atom model integrating frame-dragging force, centrifugal force, electrostatic force, and magnetic force. In this new model, the proton group and neutron group in atomic nucleus are rotating in different direction. Thus, they provide equal and opposite frame-dragging force for orbiting electrons. The electrons are orbiting in the equator plane of nucleus. There is no net force or net acceleration for...
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/6719/version/1
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Ten reasons NOT to fix the numerical value of the Avogadro constant Nature Precedings
Nigel Wheatley.
This discussion paper, circulated in advance of the 17th meeting of the Consultative Committee for Amount of Substance, addresses the proposed redefinition of the mole in terms of a fixed numerical value for the Avogadro constant. It gives ten reasons why the Avogadro constant should not be given a fixed numerical value in the International System of Units, noting that there would be no metrological benefit from such a change, and that the proposed redefinition would be more conceptually complex that the current one and divorced from practical measurement and historical background. As the conditions for redefinition of the kilogram have not been met, and no mise en pratique has been produced for the proposed new definition, the paper concludes that the...
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/5828/version/1
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Stir Bar Sorptive Extraction – A method for detection of volatiles from potato plants? Nature Precedings
Katrin Beyer; Angelika Ziegler; Detlef Ulrich; Kirsten Weiß; René Grünwald; Ralf Wilhelm.
The application of Stir Bar Sorptive Extraction (SBSE) as a method for extraction of emitted volatile compounds of potato leaves using GC/MS will be studied. A suitable efficient method shall be developed to describe differences in the spectrum of volatile compounds of potato varieties. It was shown that SBSE yields results similar to other established methods but with less effort. The method will be optimized further. The use of the spectrum of volatile compounds as a parameter for variety assessment (e.g.: plant health, plant protection, biosafety) is planned.
Tipo: Presentation Palavras-chave: Chemistry; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5736/version/1
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Nuclear Medicine and Early Discovery of Disease Nature Precedings
I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer’s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major consequences for the society.
Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) CAT/CT and Nuclear Magnetic Resonance Imaging (NMRI/MRI). These nuclear medicine techniques are discussed together with their clinical and research applications to early diagnosis of Alzheimer's Disease (AD) and cancers. Novel approaches to early detection and modeling of AD and cancers are then...
Tipo: Presentation Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6196/version/1
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Chemical Topology of Crystalline Matter and the Transcendental Numbers ϕ , e and π Nature Precedings
Michael J. Bucknum; Eduardo A. Castro.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F. Wells in the 20th century.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2008 URL: http://precedings.nature.com/documents/1587/version/2
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Use of Semantic Technologies - Semantic Chemistry Nature Precedings
Alexandru Todor; Adrian Paschke; Stephan Heineke.
Our Chemical e-Science Information Cloud (ChemCloud) – a Semantic Web based eScience infrastructure – integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and...
Tipo: Presentation Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/5649/version/1
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Induced fit, conformational selection and independent dynamic segments: an extended view of binding events Nature Precedings
Peter Csermely; Robin Palotai; Ruth Nussinov.
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (‘discrete breathers’) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4422/version/1
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Early Diagnosis of Alzheimer's disease by NIRF Spectroscopy and Nuclear Medicine-v.4.0 Nature Precedings
I Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer’s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics & Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6273/version/1
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Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades Nature Precedings
Henry L. Niman; Magdi D. Saad; Mona M. Aly; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/459/version/3
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Suppression of 12-O-tetradecanoylphorbol-13-acetate-induced ornithine decarboxylase activity by resveratrol derivatives Nature Precedings
Suaib Luqman; Tamara P. Kondratyuk; Juma Hosino; Mark Cushman; John M. Pezzuto.
As demonstrated previously, resveratrol (3,4',5-trihydroxy-trans-stilbene) inhibits 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced ornithine decarboxylase (ODC), the key rate limiting enzyme in mammalian polyamine synthesis. Using human bladder epithelial carcinoma HTB-24 cells in culture where resveratrol inhibits induction with an IC50 of 8.8 µM, we now report potential metabolites demonstrate greater activity [tetrabutylammonium (E)-4-(3,5-dihydroxystyryl)phenyl sulfate (IC50 1.2 µM), resveratrol tripotassium 3,5,4'-trisulfate (IC50 1.8 µM), resveratrol tripotassium 3,4'-disulfate (IC50 1.8 µM), and resveratrol tripotassium 3,5-disulfate (IC50 2.3 µM)]. Based on RT-PCR...
Tipo: Poster Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6908/version/1
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Isoglitter Nature Precedings
Michael J. Bucknum; Eduardo A. Castro; Bin Wen.
Described herein is a novel crystalline pattern in space group Ammm, that is a model of a C allotrope. This so-called isoglitter structure-type is a model of a graphite-diamond hybrid. A DFT geometry optimization and band structure calculation indicates that the lattice is metallic in a C realization.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/6483/version/2
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Chemical Physics of Phonons & Superconductivity: A Heuristic Approach Nature Precedings
Michael J. Bucknum.
Several lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity. The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that Badger's rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the mechanism of superconductivity.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2008 URL: http://precedings.nature.com/documents/1586/version/1
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Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and Cosmology: Graphene, Boron Nitride and Coronene Nature Precedings
Raji Heyrovska; Lakshmi Atchison; Sara Narayan.
Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and thereby their precise atomic structures, for the first time. Considered here are three nanomaterials with hexagonal structures, but of quite different properties, namely, graphene (an electrical conductor), boron nitride (an insulator) and coronene (indicators of life...
Tipo: Poster Palavras-chave: Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4357/version/1
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Open Chemistry Nature Precedings
Peter Murray-Rust.
An invited article on Open Chemistry discussing the importance of Open Access and Open Data and stressing the emerging role of the blogosphere
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2007 URL: http://precedings.nature.com/documents/1200/version/1
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