Additional Examples (additional + example)

Distribution by Scientific Domains


Selected Abstracts


rSNP_Guide: An integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites,

HUMAN MUTATION, Issue 4 2002
Julia V. Ponomarenko
Abstract Since the human genome was sequenced in draft, single nucleotide polymorphism (SNP) analysis has become one of the keynote fields of bioinformatics. We have developed an integrated database-tools system, rSNP_Guide (http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/), devoted to prediction of transcription factor (TF) binding sites, alterations of which could be associated with disease phenotype. By inputting data on alterations in DNA sequence and in DNA binding pattern of an unknown TF, rSNP_Guide searches for a known TF with alterations in the recognition score calculated on the basis of TF site's sequence and consistent with the input alterations in DNA binding to the unknown TF. Our system has been tested on many relationships between known TF sites and diseases, as well as on site-directed mutagenesis data. Experimental verification of rSNP_Guide system was made on functionally important SNPs in human TDO2and mouse K-ras genes. Additional examples of analysis are reported involving variants in the human ,A-globin (HBG1), hsp70(HSPA1A), and Factor IX (F9) gene promoters. Hum Mutat 20:239,248, 2002. © 2002 Wiley-Liss, Inc. [source]


Simultaneous untangling and smoothing of moving grids

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 7 2008
Ezequiel J. López
Abstract In this work, a technique for simultaneous untangling and smoothing of meshes is presented. It is based on an extension of an earlier mesh smoothing strategy developed to solve the computational mesh dynamics stage in fluid,structure interaction problems. In moving grid problems, mesh untangling is necessary when element inversion happens as a result of a moving domain boundary. The smoothing strategy, formerly published by the authors, is defined in terms of the minimization of a functional associated with the mesh distortion by using a geometric indicator of the element quality. This functional becomes discontinuous when an element has null volume, making it impossible to obtain a valid mesh from an invalid one. To circumvent this drawback, the functional proposed is transformed in order to guarantee its continuity for the whole space of nodal coordinates, thus achieving the untangling technique. This regularization depends on one parameter, making the recovery of the original functional possible as this parameter tends to 0. This feature is very important: consequently, it is necessary to regularize the functional in order to make the mesh valid; then, it is advisable to use the original functional to make the smoothing optimal. Finally, the simultaneous untangling and smoothing technique is applied to several test cases, including 2D and 3D meshes with simplicial elements. As an additional example, the application of this technique to a mesh generation case is presented. Copyright © 2008 John Wiley & Sons, Ltd. [source]


Influence of the mother's reproductive state on the hormonal status of daughters in marmosets (Callithrix kuhlii)

AMERICAN JOURNAL OF PRIMATOLOGY, Issue 1 2004
Alyssa M. Puffer
Abstract Behavioral and endocrine suppression of reproduction in subordinate females produces the high reproductive skew that characterizes callitrichid primate mating systems. Snowdon et al. [American Journal of Primatology 31:11,21, 1993] reported that the eldest daughters in tamarin families exhibit further endocrinological suppression immediately following the birth of siblings, and suggested that dominant females exert greater control over subordinate endocrinology during this energetically challenging phase of reproduction. We monitored the endocrine status of five Wied's black tufted-ear marmoset daughters before and after their mother delivered infants by measuring concentrations of urinary estradiol (E2), pregnanediol glucuronide (PdG), testosterone (T), and cortisol (CORT). Samples were collected from marmoset daughters 4 weeks prior to and 9 weeks following three consecutive sibling-litter births when the daughters were prepubertal (M=6.1 months of age), peripubertal (M=11.9 months), and postpubertal (M=17.6 months). The birth of infants was associated with reduced ovarian steroid excretion only in the prepubertal daughters. In contrast, ovarian steroid levels tended to increase in the postpubertal daughters. Urinary E2 and T levels in the postpubertal daughters were 73.8% and 37.6% higher, respectively, in the 3 weeks following the birth of infants, relative to prepartum levels. In addition, peak urinary PdG concentrations in peri- and postpubertal daughters were equivalent to luteal phase concentrations in nonpregnant, breeding adult females, and all of the peri- and postpubertal daughters showed clear ovulatory cycles. Cortisol excretion did not change in response to the reproductive status of the mother, nor did the concentrations change across age. Our data suggest that marmoset daughters of potential breeding age are not hormonally suppressed during the mother's peripartum period or her return to fertility. These findings provide an additional example of species diversity in the social regulation of reproduction in callitrichid primates. Am. J. Primatol. 64:29,37, 2004. © 2004 Wiley-Liss, Inc. [source]


The wealth of species: ecological communities, complex systems and the legacy of Frank Preston

ECOLOGY LETTERS, Issue 3 2007
Jeffrey C. Nekola
Abstract General statistical patterns in community ecology have attracted considerable recent debate. Difficulties in discriminating among mathematical models and the ecological mechanisms underlying them are likely related to a phenomenon first described by Frank Preston. He noted that the frequency distribution of abundances among species was uncannily similar to the Boltzmann distribution of kinetic energies among gas molecules and the Pareto distribution of incomes among wage earners. We provide additional examples to show that four different ,distributions of wealth' (species abundance distributions, species,area and species,time relations, and distance decay of compositional similarity) are not unique to ecology, but have analogues in other physical, geological, economic and cultural systems. Because these appear to be general statistical patterns characteristic of many complex dynamical systems they are likely not generated by uniquely ecological mechanistic processes. [source]


Nucleophilic Carbenes and Pseudo-Cross-Conjugated Mesomeric Betaines of Indazole Starting from Analogues of the Alkaloid-Betaine Nigellicine

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2005
Andreas Schmidt
Abstract The alkaloid Nigellicine possesses the indazolium-3-carboxylate ring system as electronically relevant partial structure which represents a member of the class of pseudo-cross-conjugated mesomeric betaines. Indazolium-3-carboxylate, prepared starting from indazole-3-carboxylic acid by an esterification,methylation,saponification sequence, can be converted into the isoconjugated phenyl- and 4-(nitrophenyl)amidates and the thiocarboxylate as additional examples of pseudo-cross-conjugated systems. In accordance with results of ab initio calculations decarboxylation of indazolium-3-carboxylate with formation of the nucleophilic carbene indazol-3-ylidene begins at approximately 40 °C as evidenced by temperature-dependent NMR spectroscopy. The carbene can be trapped with protons as indazolium salts, and carbon dioxide which reconstitutes the pseudo-cross-conjugated mesomeric betaine. According to the calculations, the carbene adopts a singlet ground state. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]


The Zintl,Klemm concept applied to cations in oxides.

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003

The structures of 94 ternary aluminates are reinterpreted on the basis of the Zintl,Klemm concept and Pearson's generalized octet rule. In aluminates of highly electropositive metals such as alkali, alkaline-earth and rare-earth metals, the Al atoms form three-dimensional skeleta which can be interpreted as if the Al atoms were behaving as Zintl polyanions, adopting the structure of either main-group elements or Zintl polyanions showing the same connectivity. The O atoms are then located close to both the hypothetical two-electron bonds and the lone pairs, giving rise to a tetrahedral coordination. When more electronegative elements, such as W or Si, are present in the compound, the electron transfer towards the Al atoms does not take place. In this case, aluminium behaves as a base, transferring its electrons to the more electronegative atoms and the coordination sphere of aluminium becomes octahedral. In some compounds the Al atoms clearly show amphoteric character so that some Al atoms act as donors (bases) and hence are octahedrally coordinated, whereas others behave as acceptors (acids), adopting a tetrahedral coordination. From this it is concluded that the coordination sphere of aluminium is not a function of the ionic radius of the Al3+ cations, but it depends on the nature of the other cations accompanying them in the structure. The networks formed by these aluminates are, in many instances, similar to those of the binary oxides of the main-group elements. For this reason, a systematic survey of these oxides is also reported. Compounds such as stuffed cristobalites and trydimites and also perov­skites are examples of this new interpretation. Perovskites are then reinterpreted as a stuffed pseudo-TeO3 structure. Other families of compounds such as silicates and phosphates are susceptible to a similar interpretation. This study provides additional examples of how cations recognize themselves in spite of being embedded in an oxygen matrix. [source]


Improved 2,4-Diarylthiazole-Based Antiprion Agents: Switching the Sense of the Amide Group at C5 Leads to an Increase in Potency

CHEMMEDCHEM, Issue 9 2010

Abstract Amide derivatives of 2,4-diarylthiazole-5-carboxylic acids were synthesised and tested for efficacy in a cell line model of prion disease. A number of compounds demonstrating antiprion activity were thereby identified from the screening libraries, showing improved potency and reproducibility of results relative to amide derivatives of the related 2,4-diphenyl-5-aminothiazole, which have been documented previously. Thus, 'switching' the sense of the amide bond at thiazole C5 revealed a more promising lead series of potential prion disease therapeutics. Furthermore, 3,5-diaryl-1,2,4-thiadiazoles isolated as by-products during library synthesis provided a handful of additional examples possessing an antiprion effect, thereby augmenting the set of newly identified active compounds. Evaluation of binding to cellular prion protein (PrPC) showed only weak affinities at best, suggesting that the newly identified antiprion agents do not mediate their biological effect through direct interaction with PrPC. [source]