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The Phylogeny of Sleep Database: A New Resource for Sleep Scientists
Patrick McNamara, Isabella Capellini, Erica Harris, Charles L. Nunn, Robert A. Barton and Brian Preston
The Open Sleep Journal , 2008, DOI: 10.2174/1874620900801010011]
Abstract: We have constructed a database that describes the sleeping characteristics of 127 different mammalian species representing 46 families across 17 orders. The data were extracted from 178 separate references that were found using standardized search protocols, and for each study includes information on the time spent in REM and NREM sleep, sleep cycle length, the number of animals sampled, their sex and age, and reference citation. Importantly, we also coded nine laboratory condition scores as a way to control for the procedures that were used to collect the data. We created a website that contains the database (http://www.bu.edu/phylogeny/) from which others can both download the data and submit new results. This database is being used to address fundamental questions concerning the evolution of mammalian sleep; similar databases on other groups of organisms will enable sleep biologists to understand patterns of sleep at broader phylogenetic scales.
PubChem3D: conformer ensemble accuracy  [cached]
Kim Sunghwan,Bolton Evan E,Bryant Stephen H
Journal of Cheminformatics , 2013, DOI: 10.1186/1758-2946-5-1
Abstract: Background PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules. Results The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (STST-opt) and combo-Tanimoto (ComboTST-opt), and color-optimized color-Tanimoto (CTCT-opt) and combo-Tanimoto (ComboTCT-opt). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 ), and decreasing the STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively). Conclusion This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D sampling on 3-D similarity measures shows that there is a linear degradation of average accuracy with respect to molecular size and flexibility. Generally speaking, one can likely expect the worst-case minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, and 1.13, in terms of STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt, respectively. This expected accuracy improves linearly as the molecule becomes smaller or less flexible.
CerealsDB 2.0: an integrated resource for plant breeders and scientists  [cached]
Wilkinson Paul A,Winfield Mark O,Barker Gary LA,Allen Alexandra M
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-219
Abstract: Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.
New Classes of Codes for Cryptologists and Computer Scientists  [PDF]
W. B. Vasantha Kandasamy,Florentin Smarandache
Mathematics , 2008,
Abstract: In this book, we have introduced several new classes of codes to aid cryptologists and computer scientists. We have explained these codes very non-technically so that a strong mathematical foundation is not needed to understand them. This book also provides an easy method to detect and correct errors that occur during transmission. Further, some of the codes are constructed so as to mislead an intruder/ hacker. False n-codes, whole n-codes can serve this pupose. These codes can be used to ensure security in networks and safe transmission of identity. We have named a few new classes of codes after Periyar, the south-Indian social leader, to mark his services to humanity. This book is divided into three chapters. Chapter one is introductory in nature. The notion of bicodes and their generalization, and n-codes are introduced in the second chapter. Periyar linear codes are introduced in the third chapter. We have used two methods, viz. pseudo best n-approximations and n-coset leader properties to detect and correct errors.
New geographies of resource extraction  [cached]
Géraud Magrin,Laetitia Perrier-Bruslé
EchoGéo , 2012,
Abstract: Following up on a previous dossier devoted to mining in West Africa, EchoGéo now extends its exploration of the geography of resource extraction today by focusing on some new areas (Burkina Faso, Guyana, Gabon, Gulf of Guinea, South Asia, and East Africa) and a variety of resources (gold, iron, oil, precious stones). The five articles in this dossier explore a range of sites, strategies, relationships between parties involved and between the parties and their environments. In all these proces...
The need for scientists and judges to work together: regarding a new European network  [cached]
Santosuosso Amedeo,Redi Carlo
Health and Quality of Life Outcomes , 2003,
Abstract: Is it always true to say that science is, by definition, universal whilst laws and the courts which apply them are a classic state and national expression? Yes and no. In recent years a new scenario has opened all over the world. Courts intervene more and more in disputes on matters related to scientific procedures in the biological field. In doing so the courts' decisions are affected by scientific issues and ways of reasoning and, on the other hand, affect the scientific field and its way of reasoning. While the old matter of bioethics was still alive and while judges were improving their skill in dealing with hard matters, like refusal of medical treatments, abortion, euthanasia et cetera, a new challenge appeared on the horizon, the challenge of biological sciences, and especially of the most troubled field of human genetics. A completely new awareness is developing among judges that they belong to an international judiciary community, as informal as it is real. Such a community is, even at an embryonic stage, sufficiently universal to be able to come together with the international scientific community. The authors maintain we are in urgent need for new interaction between judges and scientists and of new international means in the light of such cooperation. Judges and jurists need to become better acquainted with scientific questions and learn to exchange ideas with scientists. They also need to set themselves against the latters' conceptual systems and be willing to put their own up for discussion. A European Network for Life Sciences, Health and the Courts is taking its first steps, and judges and scientists are working side by side to tackle the new challenges. The provisional headquarters are located at the University of Pavia (I), Laboratorio di Biologia dello Sviluppo and Collegio Ghislieri (e-mail:. enlsc@unipv.it). ENLSC activity is inspired by the following idea: to be against science is as much antiscientific as to be acritically pro-science.
The need for scientists and judges to work together: regarding a new European network
Amedeo Santosuosso, Carlo Redi
Health and Quality of Life Outcomes , 2003, DOI: 10.1186/1477-7525-1-22
Abstract: Is it always true to say that science is, by definition, universal whilst laws and the courts which apply them are a classic state and national expression? Yes and no.In this commentary we point out the new scenario that in recent years has opened all over the world. Courts intervene more and more in disputes on matters related to scientific procedures in the biological field. In doing so the courts' decisions are affected by scientific issues and ways of reasoning and, on the other hand, affect the scientific field and its way of reasoning. Nowadays science affects law more and more and vice versa.We maintain we are in urgent need for new interaction between judges and scientists and of new international means in the light of such cooperation. A European Network for Life Sciences, Health and the Courts is taking its first steps, and judges and scientists are working side by side to tackle the new challenges.Although the intervention of the law in the field of medicine and life sciences is not a novelty, in recent years legal intervention in old bioethical and new science related matters has increased dramatically. Court decisions have become widespread in most countries. Parliamentary acts have regulated many aspects of women's and men's choices regarding their own bodies. Codes of conduct have been enacted in many fields: we may remember, in the field of experimentation on human beings, the Good Clinical Practice or the new issues of the Declaration of Helsinki or the documents by the World Health Organisation. They all lay down greatly important regulations, although not in a strictly legal sense. Finally, a new wave of solemn declarations has sprung up from international institutions. The European Convention on Human Rights and Biomedicine (Oviedo, 1997) is one of these, but not the only one. Let's remember the UNESCO Genome Declaration (1997) and the Charter of Fundamental Rights of the European Union passed by the European Council of Nice, 7th–10th December 20
VAMDC as a Resource for Atomic and Molecular Data and the New Release of VALD  [PDF]
F. Kupka,the VAMDC Collaboration
Physics , 2011,
Abstract: The Virtual Atomic and Molecular Data Centre (VAMDC) (M.L. Dubernet et al. 2010, JQSRT 111, 2151) is an EU-FP7 e-infrastructure project devoted to building a common electronic infrastructure for the exchange and distribution of atomic and molecular data. It involves two dozen teams from six EU member states (Austria, France, Germany, Italy, Sweden, United Kingdom) as well as Russia, Serbia, and Venezuela. Within VAMDC scientists from many different disciplines in atomic and molecular physics collaborate with users of their data and also with scientists and engineers from the information and communication technology community. In this presentation an overview of the current status of VAMDC and its capabilities will be provided. In the second part of the presentation I will focus on one of the databases which have become part of the VAMDC platform, the Vienna Atomic Line Data Base (VALD). VALD has developed into a well-known resource of atomic data for spectroscopy particularly in astrophysics. A new release, VALD-3, will provide numerous improvements over its predecessor. This particularly relates to the data contents where new sets of atomic data for both precision spectroscopy (i.e., with data for observed energy levels) as well as opacity calculations (i.e., with data involving predicted energy levels) have been included. Data for selected diatomic molecules have been added and a new system for data distribution and data referencing provides for more convenience in using the upcoming third release of VALD.
PubChem3D: Conformer generation
Evan E Bolton, Sunghwan Kim, Stephen H Bryant
Journal of Cheminformatics , 2011, DOI: 10.1186/1758-2946-3-4
Abstract: Using the software package OMEGA from OpenEye Scientific Software, Inc., theoretical 3-D conformer models were generated for 25,972 small-molecule ligands, whose 3-D structures were experimentally determined. Different values for primary conformer generation parameters were systematically tested to find optimal settings. Employing a greater fragment sampling rate than the default did not improve the accuracy of the theoretical conformer model ensembles. An ever increasing energy window did increase the overall average accuracy, with rapid convergence observed at 10 kcal/mol and 15 kcal/mol for model building and torsion search, respectively; however, subsequent study showed that an energy threshold of 25 kcal/mol for torsion search resulted in slightly improved results for larger and more flexible structures. Exclusion of coulomb terms from the 94s variant of the Merck molecular force field (MMFF94s) in the torsion search stage gave more accurate conformer models at lower energy windows. Overall average accuracy of reproduction of bioactive conformations was remarkably linear with respect to both non-hydrogen atom count ("size") and effective rotor count ("flexibility"). Using these as independent variables, a regression equation was developed to predict the RMSD accuracy of a theoretical ensemble to reproduce bioactive conformations. The equation was modified to give a minimum RMSD conformer sampling value to help ensure that 90% of the sampled theoretical models should contain at least one conformer within the RMSD sampling value to a "bioactive" conformation.Optimal parameters for conformer generation using OMEGA were explored and determined. An equation was developed that provides an RMSD sampling value to use that is based on the relative accuracy to reproduce bioactive conformations. The optimal conformer generation parameters and RMSD sampling values determined are used by the PubChem3D project to generate theoretical conformer models.PubChem [1-4] is an open
Review: CHIRAL INTERACTIONS AND CHIRAL INVERSIONS – NEW CHALLENGES TO CHIRAL SCIENTISTS  [PDF]
Somagoni Jagan Mohan,Eaga Chandra Mohan,Sunil Reddy,Sarangapani Manda
Pharmacie Globale : International Journal of Comprehensive Pharmacy , 2011,
Abstract: The interest in chirality and its consequences is not a new phenomenon. However, during the last decade it has raised increasing expectations due to scientific and economic reasons, the pharmaceutical industry being the main contributor and driving force. Advances in chemical technologies connected with the synthesis, separation, and analysis of pure enantiomers from racemates, together with administrative regulatory measures, have resulted in an increase in the number of newly registered chiral drugs containing only one of the enantiomers. Though the advantages of using single enantiomer like least possible side effects, reduced metabolic/renal/hepatic drug load and reduced drug interactions with an improved efficacy are so attractive the problems associated with the development of single enantiomer drugs are so challenging and many of them are left unsolved even today. In this article we mainly stressed upon chiral interactions, chiral inversions and impact of in vivo chiral interactions in every stage of the kinetics leading to stereoselective absorption, distribution, metabolism and excretion. Discussion about the rational use of chiral excipients which can enhance the eutomer/distomer ratio of enantiomer release versus time of a racemic drug was made. Finally we also mentioned the list questions which are gradually turning into unsolved challenges and threatening the future research in the chiral area.
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