bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances and some recent applications of the origin-free modulus sum function
Authors: Rius Jordi 
Published: December 2004

Abstract
Since its discovery, the direct methods origin-free modulus sum function [Rius, J., Acta Cryst A49 (1993) 406—409] has been responsible for the solution of a number of difficult crystal structures of minerals and other inorganic compounds from powder diffraction data. This is principally due to the efficiency, robustness and simplicity of implementation of this phase refinement function. The first part of the contribution describes some recent examples on the application of the origin-free modulus sum function to complex structures. In the second part, a powerful variant of this function is introduced which discriminates even better the correct solutions from the wrong ones. This is illustrated with its application to single-crystal data of three selected organic structures. One of these test structures contains 317-atom molecules and is regarded as one of the most difficult structures to be solved with reciprocal space direct methods. This variant could also be useful for those phase refinement strategies based on alternating reciprocal- and real-space procedures, provided that the weak reflections are known.
A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction
Authors: Favre-Nicolin Vincent , Černý Radovan 
Published: December 2004

Abstract

Ab initio structure determination using direct-space methods, although relying on an essentially brute-force approach, can be greatly improved through smarter algorithms. The most basic improvement involves the use of prior information to reduce the number of configurations evaluated to find the structure solution. It is however vitally important that the parametrization used to incorporate this prior information does not reduce the efficiency with which the configuration space is explored. We will show that this can be achieved by defining molecules and polyhedra through a set of restraints associated to dedicated random changes, allowing to solve structures up to three times as fast as with the ‘standard’ approach where atomic positions are parametrized directly from bond lengths, bond angles and dihedral angles.
To further enhance the efficiency of the algorithm, it is also possible to ‘tune’ the convergence criterion used to compare the structural model to the observed diffraction data (usually χ
2 or Rwp
). By using Maximum Likelihood principles, it is shown that incorporating the fact that the model is approximate in the χ
2 evaluation can improve the algorithm convergence towards the structure solution.
Structure solution of zeolites from powder diffraction data
Authors: Burton Allen W. 
Published: December 2004

AbstractThis article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.Ab initiostructure determination of zeolites from powder data has made great progress within the past 10 years. In particular, the developments of the ZEFSAII, FOCUS, and XLENS algorithms have allowed rapid structure solutions of zeolites, in some cases a few days after their initial discoveries.
Structure determination of thermal decomposition products from laboratory X-ray powder diffraction
Authors: Bataille Thierry , Audebrand Nathalie , Boultif Ali , Louër Daniel 
Published: December 2004

Abstract

Ab initio structure determination from powder diffraction data of compounds resulting from solid state transformations is still rather limited. Two major factors influence the stages of the structure elucidation of these solids, i.e. the lower precision in peak position for indexing and the strong line overlap for extracting integrated intensities. The present study deals with the consideration of these two problems for solving the crystal structure of two thermal-decomposition inorganic products, Nd(NO3)3 · 4 H2O and Pb3O2(NO3)2. The new features of DICVOL04, as zero shift refinement, a priori zero search and tolerance of spurious lines have been used for indexing several phases obtained during the thermal treatment of neodymium nitrate hexahydrate. The crystal structures of Nd(NO3)3 · 4 H2O and Pb3O2(NO3)2 have been solved with the direct methods and the structure model of Pb3O2(NO3)2 has been completed using a global optimisation approach. The monoclinic structure of neodymium nitrate tetrahydrate [a = 10.1744(4) Å, b = 8.9716(5) Å, c = 11.7295(5) Å, β = 97.384(4)°, V = 1061.80 Å3, S.G. P21/c] is built from isolated ten-fold coordinated Nd polyhedra. The orthorhombic structure of lead oxide nitrate [a = 7.6034(4) Å, b = 5.7691(4) Å, c = 18.5817(9) Å, V = 815.09 Å3, S.G. Pnma] is built from double chains of edge-sharing OPb4 tetrahedra connected by nitrate groups. In order to estimate the chance of solving crystal structure of nanocrystalline powdered compounds, a comparison of the efficiency of direct methods and direct-space approaches is made from powder diffraction patterns simulated for various crystallite sizes from the crystal structure of the decomposition product γ-Zn2P2O7.
Studying the structure of metal-organic polymers using in-house powder X-ray diffraction data: structural transformations induced by thermal treatment
Authors: Neels Antonia , Wang Yi , Stoeckli-Evans Helen 
Published: December 2004

Abstract
The use of X-ray powder diffraction for the structure determination of inorganic, organic and metal-organic compounds has grown impressively over the last ten years. In supramolecular chemistry, the knowledge of the three-dimensional structure of a material is essential for the discussion of its macroscopic behaviour, and as a result the design of new functionalized materials.
The ab initio crystal structure determination of previously unknown metal-organic compounds is still rare but is a field of high interest and activity. Here we describe the formation of 1D coordination polymers and the phase transformation processes that lead to the formation of 3D polymers on heating, accompanied by colour changes.
The reaction of pyrazine-2,5-dimethyl-3,6-dicarboxylic acid with first row transition metal salts lead to the formation of coordination polymers always in the form of microcrystalline powders. With manganese and nickel salts isostructural 1D coordination polymers were obtained. With zinc chloride and copper chloride isomorphous 1D coordination polymers were obtained. The thermal decomposition of the nickel and copper polymers were studied and it was shown that on the loss of the coordinated water molecules new 3D coordination polymers could be obtained. In both the 1D and 3D coordination polymers the metal atoms have octahedral geometry in N2O4 environments. The crystal structures of all six complexes have been determined from powder X-ray diffraction data. Crystal data: (1) crystal symmetry monoclinic [space group P21/c, a = 7.4645(1), b = 8.9472(2), c = 7.6166(1) Å, β = 92.198(2)°]; (2) crystal symmetry orthorhombic [space group Pmna, a = 7.4060(2), b = 7.1857(2), c = 9.0661(2) Å]; (3) crystal symmetry monoclinic [space group P21/c, a = 6.9376(9), b = 7.1306(12), c = 8.5852(20) Å, β = 113.299(18)°]; (4) crystal symmetry orthorhombic [space group Pbcn, a = 9.0593(2), b = 7.4410(1), c = 14.6697(2) Å]; (5) crystal symmetry orthorhombic [space group Pbcn, a = 8.9727(1), b = 7.2354(1), c = 15.0444(2) Å]; (6) crystal symmetry monoclinic [space group P21/c, a = 6.9133(4), b = 7.9927(6), c = 8.2084(6) Å, β = 110.066(6)°].
A Separation-of-Timescales Approach to the Coalescent in a Continuous Population
Authors: Wilkins Jon F 
Published: December 2004

AbstractThis article presents an analysis of a model of isolation by distance in a continuous, two-dimensional habitat. An approximate expression is derived for the distribution of coalescence times for a pair of sequences sampled from specific locations in a rectangular habitat. Results are qualitatively similar to previous analyses of isolation by distance, but account explicitly for the location of samples relative to the habitat boundaries. A separation-of-timescales approach takes advantage of the fact that the sampling locations affect only the recent coalescent behavior. When the population size is larger than the number of generations required for a lineage to cross the habitat range, the long-term genealogical process is reasonably well described by Kingman's coalescent with time rescaled by the effective population size. This long-term effective population size is affected by the local dispersal behavior as well as the geometry of the habitat. When the population size is smaller than the time required to cross the habitat, deep branches in the genealogy are longer than would be expected under the standard neutral coalescent, similar to the pattern expected for a panmictic population whose population size was larger in the past.
Robust Transmission/Disequilibrium Test for Incomplete Family Genotypes
Authors: Sebastiani Paola , Abad Maria M , Alpargu Gülhan , Ramoni Marco F 
Published: December 2004

Abstract
Several solutions have been proposed to extend the transmission disequilibrium test (TDT) to include cases with missing parental genotype. However, completion of the missing parental genotype may bias the test if the underlying missing data mechanism is informative. Furthermore, all these solutions resolve the problem of missing parental genotype, while offspring with missing genotypes are typically ignored. We propose here an extension to the TDT, called robust TDT (rTDT), able to handle incomplete genotypes on both parents and children and that does not rest on any assumption about the missing data mechanism. rTDT returns minimum and maximum values of TDT that are consistent with all the possible completions of the missing data. We also show that, in some situations, rTDT can achieve both greater power and greater significance than the popular TDT analysis of incomplete data. rTDT is applied to a database of markers of susceptibility to Crohn's disease and it shows that only 2 of the 11 markers originally associated with the phenotype do not depend on assumptions about the missing data mechanism.
Selective Phenotyping for Increased Efficiency in Genetic Mapping Studies
Authors: Jin Chunfang , Lan Hong , Attie Alan D , Churchill Gary A , Bulutuglo Dursun , Yandell Brian S 
Published: December 2004

Abstract
The power of a genetic mapping study depends on the heritability of the trait, the number of individuals included in the analysis, and the genetic dissimilarity among them. In experiments that involve microarrays or other complex physiological assays, phenotyping can be expensive and time-consuming and may impose limits on the sample size. A random selection of individuals may not provide sufficient power to detect linkage until a large sample size is reached. We present an algorithm for selecting a subset of individuals solely on the basis of genotype data that can achieve substantial improvements in sensitivity compared to a random sample of the same size. The selective phenotyping method involves preferentially selecting individuals to maximize their genotypic dissimilarity. Selective phenotyping is most effective when prior knowledge of genetic architecture allows us to focus on specific genetic regions. However, it can also provide modest improvements in efficiency when applied on a whole-genome basis. Importantly, selective phenotyping does not reduce the efficiency of mapping as compared to a random sample in regions that are not considered in the selection process. In contrast to selective genotyping, inferences based solely on a selectively phenotyped population of individuals are representative of the whole population. The substantial improvement introduced by selective phenotyping is particularly useful when phenotyping is difficult or costly and thus limits the sample size in a genetic mapping study.
The cryptochrome (cry) Gene and a Mating Isolation Mechanism in Tephritid Fruit Flies
Authors: An Xin , Tebo Molly , Song Sunmi , Frommer Marianne , Raphael Kathryn A 
Published: December 2004

Abstract
Two sibling species of tephritid fruit fly, Bactrocera tryoni and Bactrocera neohumeralis, are differentiated by their time of mating, which is genetically determined and requires interactions between the endogenous circadian clock and light intensity. The cryptochrome (cry) gene, a light-sensitive component of the circadian clock, was isolated in the two Bactrocera species. The putative amino acid sequence is identical in the two species. In the brain, in situ hybridization showed that cry is expressed in the lateral and dorsal regions of the central brain where PER immunostaining was also observed and in a peripheral cell cluster of the antennal lobes. Levels of cry mRNA were analyzed in whole head, brain, and antennae. In whole head, cry is abundantly and constantly expressed. However, in brain and antennae the transcript cycles in abundance, with higher levels during the day than at night, and cry transcripts are more abundant in the brain and antennae of B. neohumeralis than in that of B. tryoni. Strikingly, these results are duplicated in hybrid lines, generated by rare mating between B. tryoni and B. neohumeralis and then selected on the basis of mating time, suggesting a role for the cry gene in the mating isolation mechanism that differentiates the species.
The L-Type Cyclin CYL-1 and the Heat-Shock-Factor HSF-1 Are Required for Heat-Shock-Induced Protein Expression in Caenorhabditis elegans
Authors: Hajdu-Cronin Yvonne M , Chen Wen J , Sternberg Paul W 
Published: December 2004

Abstract
In a screen for suppressors of activated GOA-1 (Gαo) under the control of the hsp-16.2 heat-shock promoter, we identified three genetic loci that affected heat-shock-induced GOA-1 expression. The cyl-1 mutants are essentially wild type in appearance, while hsf-1 and sup-45 mutants have egg-laying defects. The hsf-1 mutation also causes a temperature-sensitive developmental arrest, and hsf-1 mutants have decreased life span. Western analysis indicated that mutations in all three loci suppressed the activated GOA-1 transgene by decreasing its expression. Heat-shock-induced expression of hsp-16.2 mRNA was reduced in cyl-1 mutants and virtually eliminated in hsf-1 and sup-45 mutants, as compared to wild-type expression. The mutations could also suppress other transgenes under heat-shock control. cyl-1 and sup-45, but not hsf-1, mutations suppressed a defect caused by a transgene not under heat-shock control, suggesting a role in general transcription or a post-transcriptional aspect of gene expression. hsf-1 encodes the C. elegans homolog of the human heat-shock factor HSF1, and cyl-1 encodes a cyclin most similar to cyclin L. We believe HSF-1 acts in heat-shock-inducible transcription and CYL-1 acts more generally in gene expression.
Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate
Authors: Nikoh Naruo , Duty April , Gibson Greg 
Published: December 2004

Abstract
As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal range for Drosophila genes and proteins, and linkage disequilibrium decays rapidly such that haplotype blocks are typically only a few SNPs long. However, intron 1 of 5-HT1A consists of two haplotypes that are at significantly different frequencies in the two populations. Neither this region of the gene nor any of the common amino acid polymorphisms in the three loci associate with either heart rate or heart rate variability. A cluster of SNPs in intron 2 of 5-HT1A, including a triallelic site, do show a highly significant interaction between genotype, sex, and population. While it is likely that a combination of weak, complex selection pressures and population structure has helped shape variation in the serotonin receptors of Drosophila, much larger sampling strategies than are currently adopted in evolutionary genetics will be required to disentangle these effects.
The Population Genetic Theory of Hidden Variation and Genetic Robustness
Authors: Hermisson Joachim , Wagner Günter P 
Published: December 2004

Abstract
One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype.
Direct Estimation of Genetic Principal Components
Authors: Kirkpatrick Mark , Meyer Karin 
Published: December 2004

AbstractEstimating the genetic and environmental variances for multivariate and function-valued phenotypes poses problems for estimation and interpretation. Even when the phenotype of interest has a large number of dimensions, most variation is typically associated with a small number of principal components (eigen-vectors or eigenfunctions). We propose an approach that directly estimates these leading principal components; these then give estimates for the covariance matrices (or functions). Direct estimation of the principal components reduces the number of parameters to be estimated, uses the data efficiently, and provides the basis for new estimation algorithms. We develop these concepts for both multivariate and function-valued phenotypes and illustrate their application in the restricted maximum-likelihood framework.
Expression Level of sarah, a Homolog of DSCR1, Is Critical for Ovulation and Female Courtship Behavior in Drosophila melanogaster
Authors: Ejima Aki , Tsuda Manabu , Takeo Satomi , Ishii Kunimasa , Matsuo Takashi , Aigaki Toshiro 
Published: December 2004

Abstract
To better understand the genetic bases of postmating responses in Drosophila melanogaster females, we screened a collection of P{GS} insertion lines and identified two insertions in sarah (sra), whose misexpression in the nervous system induced high levels of ovulation in virgins. The gene sra encodes a protein similar to human Down syndrome critical region 1 (DSCR1). The ovulation phenotype was reproduced in transgenic virgins expressing UAS-sra in the nervous system. The flies also extruded the ovipositor toward courting males as seen in wild-type mated females, supporting the notion that ovulation and behavioral patterns are physiologically coupled. The sra insertions were found to be hypomorphic alleles with reduced expression levels. Females homozygous for these alleles show: (1) spontaneous ovulation in virgins, (2) sterility with impaired meiotic progression, and (3) compromised postmating responses with lower ovulation level, higher remating rate, and shorter period for restoration of receptivity. No obvious defects were observed in the homozygous males. The gene sra is predominantly expressed in oocytes, nurse cells, and the nervous system. Taken together, these results indicate that the expression level of sra is critical for ovulation and female courtship behavior, including their postmating changes.
Polyandry, Life-History Trade-Offs and the Evolution of Imprinting at Mendelian Loci
Authors: Mills Walter , Moore Tom 
Published: December 2004

AbstractGenomic imprinting causes parental origin-dependent differential expression of a small number of genes in mammalian and angiosperm plant embryos, resulting in non-Mendelian inheritance of phenotypic traits. The “conflict” theory of the evolution of imprinting proposes that reduced genetic relatedness of paternally, relative to maternally, derived alleles in offspring of polygamous females supports parental sex-specific selection at gene loci that influence maternal investment. While the theory's physiological predictions are well supported by observation, the requirement of polyandry in the evolution of imprinting from an ancestral Mendelian state has not been comprehensively analyzed. Here, we use diallelic models to examine the influence of various degrees of polyandry on the evolution of both Mendelian and imprinted autosomal gene loci that influence trade-offs between maternal fecundity and offspring viability. We show that, given a plausible assumption on the physiological relationship between maternal fecundity and offspring viability, low levels of polyandry are sufficient to reinforce exclusively the fixation of “greedy” paternally imprinted alleles that increase offspring viability at the expense of maternal fecundity and “thrifty” maternally imprinted alleles of opposite effect. We also show that, for all levels of polyandry, Mendelian alleles at genetic loci that influence the trade-off between maternal fecundity and offspring viability reach an evolutionary stable state, whereas pairs of reciprocally imprinted alleles do not.
Using Temporally Spaced Sequences to Simultaneously Estimate Migration Rates, Mutation Rate and Population Sizes in Measurably Evolving Populations
Authors: Ewing Greg , Nicholls Geoff , Rodrigo Allen 
Published: December 2004

Abstract
We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.