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Search Results: 1 - 10 of 236024 matches for " Thomas Lütteke "
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The use of glycoinformatics in glycochemistry
Thomas Lütteke
Beilstein Journal of Organic Chemistry , 2012, DOI: 10.3762/bjoc.8.104
Abstract: Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein–carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed.
pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files
Thomas Lütteke, Claus-W von der Lieth
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-69
Abstract: The pdb-care program http://www.glycosciences.de/tools/pdb-care/ webcite is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported.Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.Carbohydrates are involved in a variety of fundamental biological processes (cellular differentiation, embryonic development, fertilization) and pathological situations (bacterial and viral infections, inflammatory diseases, cancer) [1-3]. They therefore have a large pharmaceutical and diagnostic potential. Protein-carbohydrate interactions are intensively investigated using a variety of experimental methods. Among these, X-ray and NMR measurements provide a detailed 3D picture of the spatial location of the ligand as well as the protein.About 70% of all proteins deposited in sequence databases show potential N-glycosylation sites, which can be identified by the presence of the Asn-X-Ser/Thr sequon [4,5]. For reasons that are still unclear, not all such sequons are glycosylated. It is estimated that more than half of all the proteins in the human body have carbohydrate molecules attached (see Fig. 1a). Unfortunately, extensive analytical procedures are required to determine which of these potential sites are occupied, even if the protein in question is known to be glycosylated. Due to several reasons, the absence of carbohydrate data in 3D structural data taken from X-ray cryst
In silico Study on Sulfated and Non-Sulfated Carbohydrate Chains from Proteoglycans in Cnidaria and Interaction with Collagen  [PDF]
Thomas Eckert, Sabine St?tzel, Monika Burg-Roderfeld, Judith Sewing, Thomas Lütteke, Nikolay E. Nifantiev, Johannes F. G. Vliegenthart, Hans-Christian Siebert
Open Journal of Physical Chemistry (OJPC) , 2012, DOI: 10.4236/ojpc.2012.22017
Abstract: Proteoglycans and collagen molecules are interacting with each other thereby forming various connective tissues. The sulfation pattern of proteoglycans differs depending on the kind of tissue and/or the degree of maturation. Tissues from Cnidaria are suitable examples for exploration of the effects in relation to the presence and the absence of sulfate groups, when studying characteristic fragments of the long proteoglycan carbohydrate chains in silico. It has been described that a non-sulfated chondroitin appears as a scaffold in early morphogenesis of all nematocyst types in Hydra. On the other hand, sulfated glucosaminoglycans play an important role in various developmental processes of Cnidaria. In order to understand this biological phenomenon on a sub-molecular level we have analysed the structures of sulfated and non-sulfated proteoglycan carbohydrate chains as well as the structure of diverse collagen molecules with computational methods including quantum chemical calculations. The strong interactions between the sulfate groups of the carbohydrates moieties in proteoglycans and positively charged regions of collagen are essential in stabilizing various Cnidaria tissues but could hinder the nematocyst formation and its proper function. The results of our quantum chemical calculations show that the sulfation pattern has a significant effect on the conformation of chondroitin structures under study.
A New Strategy for Solving Two Cosmological Constant Problems in Hadron Physics  [PDF]
Thomas L. Wilson
Journal of Modern Physics (JMP) , 2013, DOI: 10.4236/jmp.2013.45096
Abstract:

A new approach to solving two of the cosmological constant problems (CCPs) is proposed by introducing the Abbott-Deser (AD) method for defining Killing charges in asymptotic de Sitter space as the only consistent means for defining the ground-state vacuum for the CCP. That granted, Einstein gravity will also need to be modified at short-distance nuclear scales, using instead a nonminimally coupled scalar-tensor theory of gravitation that provides for the existence of QCD’s two-phase vacuum having two different zero-point energy states as a function of temperature. Einstein gravity alone cannot accomplish this. The scalar field will be taken from bag theory in hadron physics, and the origin of the bag constant B is accounted for by gravity’s CC as \"\" B—noting that the Higgs mechanism does not account for either the curved-space origin of λ or the mass of composite hadrons. A small Hubble-scale graviton mass mg10-33eV naturally appears external to the hadron bag, induced by λ≠0. This mass is unobservable and gravitationally gauge-dependent. It is shown to be related to the cosmological event horizon in asymptotic de Sitter space.

Inconsistencies in Theoretical Physics, with Focus on the Higgs Mechanism  [PDF]
Thomas L. Wilson
Journal of Modern Physics (JMP) , 2015, DOI: 10.4236/jmp.2015.63027
Abstract: In spite of tremendous progress in experimental high-energy physics such as the apparent discovery of the Higgs boson at CERN, there exist a number of inconsistencies in theoretical physics which continue to go either unnoticed or unstated. These include the Higgs mechanism itself as well as recent discussions of problems with inflationary cosmology. The subject will be addressed in the context of this author’s recent paper [1] on the requirement for compatible asymptotic states in the study of the cosmological constant problem (CCP). Inconsistency in the Higgs mechanism is eliminated by using scalar-tensor gravity where the scalar field is a gravitational field with zero spin that represents the spontaneous symmetry breaking potential.
After-School Physical Activity Interventions on Child and Adolescent Physical Activity and Health: A Review of Reviews  [PDF]
Yolanda Demetriou, Fiona Gillison, Thomas L. McKenzie
Advances in Physical Education (APE) , 2017, DOI: 10.4236/ape.2017.72017
Abstract: Schools are a critical setting for children to accrue recommended levels of physical activity, and after-school programmes are suggested to supplement existing programmes such as physical education. This review of reviews provides a comprehensive picture of the effects of after-school physical activity programmes on student physical activity and health. We completed a literature search of electronic databases and identified six existing systematic reviews and meta-analyses of the effects of after-school programmes on child and adolescent physical activity and health. We compared these reviews on numerous factors, including the databases searched, aims, outcome variables, physical activity measures, inclusion criteria, and quality of original studies. Our review of reviews identified considerable differences among the published reviews in the number and type of studies included, and in the conclusions drawn. In general, the reviews identified better outcomes when conducting the programmes in school rather than community settings, providing sessions on two or more days a week, and ensuring high programme attendance rates. Subgroup analyses indicated that girls were more receptive than boys to intervention programmes that promoted weight control. Additionally, there were some benefits for increasing physical activity levels among over-weight youth and boys. This review of reviews suggests there is currently only modest support of the benefits of after-school programmes on child and adolescent physical activity levels and body composition. Many questions remain unanswered, and there is further need to design, implement, and assess quality after-school interventions that target physical activity in diverse settings.
Anatase Titanium Dioxide Coated Single Wall Carbon Nanotubes Manufactured by Sonochemical-Hydrothermal Technique  [PDF]
Paul Clemens, Xin Wei, Bobby L. Wilson, Renard L. Thomas
Open Journal of Composite Materials (OJCM) , 2013, DOI: 10.4236/ojcm.2013.32A004
Abstract:

A novel, cost effective, sonochemical-hydrothermal technique was used for the deposition of nanosized anatase titanium dioxide (TiO2) onto single wall carbon nanotubes (SWCNTs). This technique is described and the characterization of the synthesized TiO2-SWCNTs is reported. The characterization techniques employed include scanning electron microscopy (SEM), Raman spectroscopy, and X-ray diffraction (XRD). From the characterization the size and morphology of the synthesized TiO2 nanoparticles (deposited on the SWCNTs) are reported. Furthermore, it is demonstrated that the created TiO2 nanoparticles are chemically attached to the SWCNTs. Also, an important correlation between calculated TiO2 crystal size and the red shifts in the lowest Raman TiO2 (E.g.) predominate peak is reported. The synthesized TiO2-SWCNTs have potential for large scale production and application in a variety of new technologies such as clean energy power generation devices, electrical storage devices, photocatalysts, and sensors.

A reproductive history of mothers with spina bifida offspring-a new look at old issues
Thomas L Farley
Fluids and Barriers of the CNS , 2006, DOI: 10.1186/1743-8454-3-10
Abstract: Data from 271 mothers was collected by interview 18.3 mean years after the affected child's birth. Data analysis was by χ-square, Fisher exact test and t test with a p value less than 0.05 considered significant.Females made up 56.5% of affected offspring (probands) and 53.1% of unaffected offspring. The spina bifida and anencephaly recurrence rate was 4.0%. The twinning rate was 8.6/1000 live births. 24.4% of mothers had a history of spontaneous abortion and the rate varied by pregnancy order from 87 to 185/1000 live births. Duration of pregnancies subsequent to probands was shorter for female than male probands. Mean birth weight of probands with high lesions exceeded those with low lesions. A spontaneous abortion preceded female probands more often than males as compared to live births. Affected males with high lesions conceived by white mothers were at greater risk to be spontaneously aborted. Previous inter-gestational interval for mothers with no history of spontaneous abortion was longer for probands than unaffected offspring but not for mothers with a history of spontaneous abortion.Overall, and for every major subgroup of these mothers, more affected and unaffected female than male offspring were born. Differences by gender and lesion level among probands and between probands and unaffected offspring were consistent with an etiology of unknown genetic factors, hormonal and/or immune system factors.Spina bifida is a disorder of the cerebrospinal fluid system resulting from a failure of neural tube closure in the fetus and associated with accompanying deformities leading to hydrocephalus. Over the past twenty-five years, a number of studies [1] have demonstrated that environmental and genetic factors play an important part in neural tube defect (NTD) etiology. Dietary folic acid fortification [2] and supplementation [3], in particular, have shown success as preventative measures. However, despite such progress, much is still unknown about the complex, multi-f
Reproductive physiology of mango
Davenport, Thomas L.;
Brazilian Journal of Plant Physiology , 2007, DOI: 10.1590/S1677-04202007000400007
Abstract: mango flowering involves hormonal regulation of shoot initiation and induction events resulting in reproductive shoot formation. a balance or ratio of endogenously regulated phytohormones, thought to be auxin from leaves and cytokinins from roots, appears to govern the initiation cycle independently from inductive influences. induction of reproductive or vegetative shoots is thought to be governed by the ratio of a temperature-regulated florigenic promoter and an age regulated vegetative promoter at the time of shoot initiation. management of off-season flowering in mango trees is being accomplished in the tropics by successfully synchronizing shoot initiation through tip pruning and use of nitrate sprays coupled with management of the stem age to induce flowering such that it can be accomplished during any desired week of the year.
Open Access Publishing Practices in a Complex Environment: Conditions, Barriers, and Bases of Power
Thomas L. Reinsfelder
Journal of Librarianship and Scholarly Communication , 2012,
Abstract: The system of scholarly communication is a complex environment made up of various stakeholders including not only researchers, librarians, and publishers, but also academic administrators. This paper examines conditions each group faces while also noting barriers preventing movement toward open access. To further analyze interrelationships and interdependencies among groups, a discussion is presented using French & Raven’s bases of power to describe how members of each stakeholder group exert some degree of power upon all other groups while at the same time being influenced, either directly or indirectly, by external forces. A better understanding of the many existing interactions and dependencies can help those who work within this system navigate ongoing changes while more successfully positioning their organizations for the future.
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