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Sample records for molecular marker-based estimation

  1. Marker-based estimation of genetic parameters in genomics.

    PubMed

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets. PMID:25025305

  2. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  3. The use and abuse of genetic marker-based estimates of relatedness and inbreeding

    PubMed Central

    Taylor, Helen R

    2015-01-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. PMID:26357542

  4. Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses.

    PubMed

    Schrag, Tobias A; Möhring, Jens; Maurer, Hans Peter; Dhillon, Baldev S; Melchinger, Albrecht E; Piepho, Hans-Peter; Sørensen, Anker P; Frisch, Matthias

    2009-02-01

    In hybrid breeding, the prediction of hybrid performance (HP) is extremely important as it is difficult to evaluate inbred lines in numerous cross combinations. Recent developments such as doubled haploid production and molecular marker technologies have enhanced the prospects of marker-based HP prediction to accelerate the breeding process. Our objectives were to (1) predict HP using a combined analysis of hybrids and parental lines from a breeding program, (2) evaluate the use of molecular markers in addition to phenotypic and pedigree data, (3) evaluate the combination of line per se data with marker-based estimates, (4) study the effect of the number of tested parents, and (5) assess the advantage of haplotype blocks. An unbalanced dataset of 400 hybrids from 9 factorial crosses tested in different experiments and data of 79 inbred parents were subjected to combined analyses with a mixed linear model. Marker data of the inbreds were obtained with 20 AFLP primer-enzyme combinations. Cross-validation was used to assess the performance prediction of hybrids of which no or only one parental line was testcross evaluated. For HP prediction, the highest proportion of explained variance (R (2)), 46% for grain yield (GY) and 70% for grain dry matter content (GDMC), was obtained from line per se best linear unbiased prediction (BLUP) estimates plus marker effects associated with mid-parent heterosis (TEAM-LM). Our study demonstrated that HP was efficiently predicted using molecular markers even for GY when testcross data of both parents are not available. This can help in improving greatly the efficiency of commercial hybrid breeding programs. PMID:19048224

  5. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats.

    PubMed

    Konovalov, Fedor A; Goncharov, Nikolay P; Goryunova, Svetlana; Shaturova, Aleksandra; Proshlyakova, Tatyana; Kudryavtsev, Alexander

    2010-06-01

    Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive. PMID:20407790

  6. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    PubMed Central

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  7. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    PubMed

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  8. Development of molecular markers, based on chloroplast and ribosomal DNA regions, to discriminate three popular medicinal plant species, Cynanchum wilfordii, Cynanchum auriculatum, and Polygonum multiflorum.

    PubMed

    Han, Eun-Heui; Cho, KyeMan; Goo, YoungMin; Kim, ManBae; Shin, Young-Wook; Kim, Yun-Hee; Lee, Shin-Woo

    2016-04-01

    Identification of plant species is important for standardizing herbal medicine. Cynanchum wilfordii (Baekshuoh in Korean) and Polygonum multiflorum (Hashuoh in Korean) are important oriental medicinal herbs in Korea, Japan, and China. Cynanchum auriculatum is a faster growing and more productive plant than C. wilfordii; and, it is not recognized as a medicinal plant in the Korean Pharmacopoeia. C. wilfordii, P. multiflorum, and C. auriculatum are often misidentified in the Korean herbal medicine marketplace due to their morphological similarities and similar names. In this study, we investigated molecular authentication of these three medicinal plants using DNA sequences in the TrnL-F chloroplast intergenic region. Specific species identification was achieved by detecting allelic variations of single nucleotide polymorphisms (SNPs) using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and high resolution melting curve analysis. Our results demonstrate that the intraspecific genetic distance between C. wilfordii and C. auriculatum is relatively low. We also developed a quantitative PCR assay using species-specific TrnL-F primers, which allowed us to estimate the ratio of C. wilfordii and C. auriculatum using varying ratios of mixed genomic DNA template from the two species. Additionally, to identify species in hybrid plants produced by cross-fertilization, we analyzed nuclear ribosomal DNA internal transcribed spacer regions in C. wilfordii and C. auriculatum by ARMS-PCR. Our results indicate that SNP-based molecular markers, usable to barcode tools could provide efficient and rapid authentication of these closely related medicinal plant species, and will be useful for preventing the distribution of products contaminated with adulterants. PMID:26902862

  9. Two molecular markers based on mitochondrial genomes for varieties identification of the northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids.

    PubMed

    Xincheng, Zhang; Kunci, Chen; Xinping, Zhu; Jian, Zhao; Qing, Luo; Xiaoyou, Hong; Wei, Li; Fengfang, Xiao

    2015-08-01

    The northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids have played important roles in the Chinese freshwater aquaculture industry, with an annual production in China exceeding 400 thousand tons. While these are popular aquaculture breeds in China, it is not easy to identify northern snakehead, blotched snakehead, and their hybrids. Thus, a method should be developed to identify these varieties. To distinguish between the reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculata ♀ × C. argus ♂), the mitochondrial genome sequences of northern snakehead and blotched snakehead and their reciprocal hybrids were compared. Following the alignment and analysis of mtDNA sequences of northern snakehead, blotched snakehead and their hybrids, two pairs of specific primers were designed based on identified differences ranging from 12S rRNA to 16S rRNA gene. The BY1 primers amplified the same bands in the blotched snakehead and the hybrid (C. maculata ♀ × C. argus ♂), while producing no products in northern snakehead and the hybrid (C. argus ♀ × C. maculata ♂). Amplification with WY1 yielded the opposite results. Then, 30 individuals per fish were randomized to verify the primers, and the results showed that the primers were specific for breeds, as intended. The specific primers can not only simply distinguish between two kinds of hybrids, but also rapidly identify the two parents. This study provides a method of molecular marker identification to identify reciprocal hybrids. PMID:24438305

  10. Citrus (Rutaceae) SNP markers based on Competitive Allele-Specific PCR; transferability across the Aurantioideae subfamily1

    PubMed Central

    Garcia-Lor, Andres; Ancillo, Gema; Navarro, Luis; Ollitrault, Patrick

    2013-01-01

    • Premise of the study: Single nucleotide polymorphism (SNP) markers based on Competitive Allele-Specific PCR (KASPar) were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra- and intergeneric levels and systematic germplasm bank characterization. • Methods and Results: Forty-two SNP markers were developed using KASPar technology. Forty-one were successfully genotyped in all of the Citrus germplasm, where intra- and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. • Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and should be useful for germplasm fingerprinting at a much broader diversity level. PMID:25202535

  11. Expression Marker-Based Strategy to Improve Beef Quality

    PubMed Central

    Cassar-Malek, Isabelle; Picard, Brigitte

    2016-01-01

    For beef cattle research, a main objective is to control concomitantly the development of muscles and the qualities of beef cuts. Beef quality is a complex phenotype that is only detectable after slaughter and is highly variable. The beef industry is in need of tools to estimate beef quality of live cattle or online in abattoirs, with specific attention towards sensory attributes (tenderness, juiciness, flavour, and colour). Identification of relevant genetic and genomic markers is ongoing, especially for tenderness—a top priority quality attribute. In this paper, we describe the steps of an expression marker-based strategy to improve beef sensory quality, from the discovery of biomarkers that identify consistent beef and the biological functions governing beef tenderness to the integration of the knowledge into detection tests for desirable animals. These tools should soon be available for the management of sensory quality in the beef production chain for meeting market's demands and assuring good quality standards. PMID:27066527

  12. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent

    PubMed Central

    Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J.

    2015-01-01

    Background Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Methodology/Principal Findings Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. Conclusions/Significance This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain

  13. Generalized Mixture Models for Molecular Phylogenetic Estimation

    PubMed Central

    Evans, Jason; Sullivan, Jack

    2012-01-01

    The rapidly growing availability of multigene sequence data during the past decade has enabled phylogeny estimation at phylogenomic scales. However, dealing with evolutionary process heterogeneity across the genome becomes increasingly challenging. Here we develop a mixture model approach that uses reversible jump Markov chain Monte Carlo (MCMC) estimation to permit as many distinct models as the data require. Each additional model considered may be a fully parametrized general time-reversible model or any of its special cases. Furthermore, we expand the usual proposal mechanisms for topology changes to permit hard polytomies (i.e., zero-length internal branches). This new approach is implemented in the Crux software toolkit. We demonstrate the feasibility of using reversible jump MCMC on mixture models by reexamining a well-known 44-taxon mammalian data set comprising 22 concatenated genes. We are able to reproduce the results of the original analysis (with respect to bipartition support) when we make identical assumptions, but when we allow for polytomies and/or use data-driven mixture model estimation, we infer much lower bipartition support values for several key bipartitions. PMID:21873377

  14. Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

    PubMed Central

    Ho, Simon Y.W.

    2015-01-01

    Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred. PMID:25780773

  15. Estimating metazoan divergence times with a molecular clock

    PubMed Central

    Peterson, Kevin J.; Lyons, Jessica B.; Nowak, Kristin S.; Takacs, Carter M.; Wargo, Matthew J.; McPeek, Mark A.

    2004-01-01

    Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are ≈555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) ≈900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla. PMID:15084738

  16. Estimating metazoan divergence times with a molecular clock.

    PubMed

    Peterson, Kevin J; Lyons, Jessica B; Nowak, Kristin S; Takacs, Carter M; Wargo, Matthew J; McPeek, Mark A

    2004-04-27

    Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are approximately 555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) approximately 900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla. PMID:15084738

  17. Improved estimates of coordinate error for molecular replacement

    SciTech Connect

    Oeffner, Robert D.; Bunkóczi, Gábor; McCoy, Airlie J.; Read, Randy J.

    2013-11-01

    A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded. The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the r.m.s.d. lead to good estimates of the variance term in the likelihood functions, which increases signal to noise and hence success rates in the MR search. Phaser has hitherto used an estimate of the r.m.s.d. that only depends on the sequence identity between the model and target and which was not optimized for the MR likelihood functions. Variance-refinement functionality was added to Phaser to enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. Variance refinement was subsequently performed on a database of over 21 000 MR problems that sampled a range of sequence identities, protein sizes and protein fold classes. Success was monitored using the translation-function Z-score (TFZ), where a TFZ of 8 or over for the top peak was found to be a reliable indicator that MR had succeeded for these cases with one molecule in the asymmetric unit. Good estimates of the r.m.s.d. are correlated with the sequence identity and the protein size. A new estimate of the r.m.s.d. that uses these two parameters in a function optimized to fit the mean of the refined variance is implemented in Phaser and improves MR outcomes. Perturbing the initial estimate of the r.m.s.d. from the mean of the distribution in steps of standard deviations of the distribution further increases MR success rates.

  18. Comparison of Markerless and Marker-Based Motion Capture Technologies through Simultaneous Data Collection during Gait: Proof of Concept

    PubMed Central

    Cobelli, Claudio

    2014-01-01

    During the last decade markerless motion capture techniques have gained an increasing interest in the biomechanics community. In the clinical field, however, the application of markerless techniques is still debated. This is mainly due to a limited number of papers dedicated to the comparison with the state of the art of marker based motion capture, in term of repeatability of the three dimensional joints' kinematics. In the present work the application of markerless technique to data acquired with a marker-based system was investigated. All videos and external data were recorded with the same motion capture system and included the possibility to use markerless and marker-based methods simultaneously. Three dimensional markerless joint kinematics was estimated and compared with the one determined with traditional marker based systems, through the evaluation of root mean square distance between joint rotations. In order to compare the performance of markerless and marker-based systems in terms of clinically relevant joint angles estimation, the same anatomical frames of reference were defined for both systems. Differences in calibration and synchronization of the cameras were excluded by applying the same wand calibration and lens distortion correction to both techniques. Best results were achieved for knee flexion-extension angle, with an average root mean square distance of 11.75 deg, corresponding to 18.35% of the range of motion. Sagittal plane kinematics was estimated better than on the other planes also for hip and ankle (root mean square distance of 17.62 deg e.g. 44.66%, and 7.17 deg e.g. 33.12%), meanwhile estimates for hip joint were the most incorrect. This technique enables users of markerless technology to compare differences with marker-based in order to define the degree of applicability of markerless technique. PMID:24595273

  19. Utilizing Ion-Mobility Data to Estimate Molecular Masses

    NASA Technical Reports Server (NTRS)

    Duong, Tuan; Kanik, Isik

    2008-01-01

    A method is being developed for utilizing readings of an ion-mobility spectrometer (IMS) to estimate molecular masses of ions that have passed through the spectrometer. The method involves the use of (1) some feature-based descriptors of structures of molecules of interest and (2) reduced ion mobilities calculated from IMS readings as inputs to (3) a neural network. This development is part of a larger effort to enable the use of IMSs as relatively inexpensive, robust, lightweight instruments to identify, via molecular masses, individual compounds or groups of compounds (especially organic compounds) that may be present in specific environments or samples. Potential applications include detection of organic molecules as signs of life on remote planets, modeling and detection of biochemicals of interest in the pharmaceutical and agricultural industries, and detection of chemical and biological hazards in industrial, homeland-security, and industrial settings.

  20. In situ marker-based assessment of leaf trait evolutionary potential in a marginal European beech population.

    PubMed

    Bontemps, A; Lefèvre, F; Davi, H; Oddou-Muratorio, S

    2016-03-01

    Evolutionary processes are expected to be crucial for the adaptation of natural populations to environmental changes. In particular, the capacity of rear edge populations to evolve in response to the species limiting conditions remains a major issue that requires to address their evolutionary potential. In situ quantitative genetic studies based on molecular markers offer the possibility to estimate evolutionary potentials manipulating neither the environment nor the individuals on which phenotypes are measured. The goal of this study was to estimate heritability and genetic correlations of a suite of leaf functional traits involved in climate adaptation for a natural population of the tree Fagus sylvatica, growing at the rear edge of the species range. Using two marker-based quantitative genetics approaches, we obtained consistent and significant estimates of heritability for leaf phenological (phenology of leaf flush), morphological (mass, area, ratio mass/area) and physiological (δ(13)C, nitrogen content) traits. Moreover, we found only one significant positive genetic correlation between leaf area and leaf mass, which likely reflected mechanical constraints. We conclude first that the studied population has considerable genetic diversity for important ecophysiological traits regarding drought adaptation and, second, that genetic correlations are not likely to impose strong genetic constraints to future population evolution. Our results bring important insights into the question of the capacity of rear edge populations to evolve. PMID:26679342

  1. Estimating Arrhenius parameters using temperature programmed molecular dynamics

    NASA Astrophysics Data System (ADS)

    Imandi, Venkataramana; Chatterjee, Abhijit

    2016-07-01

    Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.

  2. Estimating Arrhenius parameters using temperature programmed molecular dynamics.

    PubMed

    Imandi, Venkataramana; Chatterjee, Abhijit

    2016-07-21

    Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times. PMID:27448871

  3. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

    PubMed Central

    Roger, Andrew J; Hug, Laura A

    2006-01-01

    Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods

  4. Intra-population comparison of vegetative and floral trait heritabilities estimated from molecular markers in wild Aquilegia populations.

    PubMed

    Castellanos, Maria Clara; Alcántara, Julio M; Rey, Pedro J; Bastida, Jesus M

    2011-09-01

    Measuring heritable genetic variation is important for understanding patterns of trait evolution in wild populations, and yet studies of quantitative genetic parameters estimated directly in the field are limited by logistic constraints, such as the difficulties of inferring relatedness among individuals in the wild. Marker-based approaches have received attention because they can potentially be applied directly to wild populations. For long-lived, self-compatible plant species where pedigrees are inadequate, the regression-based method proposed by Ritland has the appeal of estimating heritabilities from marker-based estimates of relatedness. The method has been difficult to implement in some plant populations, however, because it requires significant variance in relatedness across the population. Here, we show that the method can be readily applied to compare the ability of different traits to respond to selection, within populations. For several taxa of the perennial herb genus Aquilegia, we estimated heritabilities of floral and vegetative traits and, combined with estimates of natural selection, compared the ability to respond to selection of both types of traits under current conditions. The intra-population comparisons showed that vegetative traits have a higher potential for evolution, because although they are as heritable as floral traits, selection on them is stronger. These patterns of potential evolution are consistent with macroevolutionary trends in the European lineage of the genus. PMID:21504491

  5. Infrared marker-based tracking in an indoor unknown environment for augmented reality applications

    NASA Astrophysics Data System (ADS)

    Huang, Yetao; Weng, Dongdong; Liu, Yue; Wang, Yongtian

    2009-11-01

    Marker based tracking requires complicated preparation work that impedes its use in augmented reality applications. This paper presents a novel tracking scheme to be used in an indoor unknown scene by adapting simultaneous localization and mapping (SLAM) algorithms. An infrared (IR) marker system is specifically designed to simplify the feature recognition and tracking in SLAM process. With one initial IR marker, the other markers can be projected randomly onto a large-area environment. The pose of camera can be estimated with a monocular IR camera in real time. Experimental result demonstrates that the proposed system meets the requirements of accuracy for large-area tracking. A prototype system is built to show its feasibility in unknown environment and potential use in applications.

  6. ESTIMATION OF MOLECULAR DIFFUSIVITY IN ISOLATED ANIMAL TISSUES

    EPA Science Inventory

    If molecular transport of a lipophilic toxicant in isolated tissues is truly a diffusion process, then it should be possible to describe the process in terms of mathematical equations commonly used to describe the conduction of heat in homogenous and isotropic solids. The present...

  7. Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

    PubMed

    Clarke, Julia A; Boyd, Clint A

    2015-01-01

    Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have also treated molecular divergence estimates younger than previously assessed fossil minimum estimates of clade age as if they were the same as cases in which they were older. However, these cases are not the same. Recovered divergence dates younger than compared oldest known occurrences require prior hypotheses regarding the phylogenetic position of the compared fossil record and standard assumptions about the relative timing of morphological and molecular change to be incorrect. Older molecular dates, by contrast, are consistent with an incomplete fossil record and do not require prior assessments of the fossil record to be unreliable in some way. Here, we compare previous approaches and introduce two new descriptive metrics. Both metrics explicitly incorporate information on uncertainty by utilizing the 95% confidence intervals on estimated divergence dates and data on stratigraphic uncertainty concerning the age of the compared fossils. Metric scores are maximized when these ranges are overlapping. MDI (minimum divergence incongruence) discriminates between situations where molecular estimates are younger or older than known fossils reporting both absolute fit values and a number score for incompatible nodes. DIG range (divergence implied gap range) allows quantification of the minimum increase in implied missing fossil record induced by enforcing a given set of molecular-based estimates. These metrics are used

  8. Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

    PubMed

    Abend, Michael; Port, Matthias

    2016-08-01

    The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers. PMID:27356062

  9. Time-dependent estimates of molecular evolutionary rates: evidence and causes.

    PubMed

    Ho, Simon Y W; Duchêne, Sebastián; Molak, Martyna; Shapiro, Beth

    2015-12-01

    We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates. PMID:26769402

  10. Estimation of biliary excretion of foreign compounds using properties of molecular structure.

    PubMed

    Sharifi, Mohsen; Ghafourian, Taravat

    2014-01-01

    Biliary excretion is one of the main elimination pathways for drugs and/or their metabolites. Therefore, an insight into the structural profile of cholephilic compounds through accurate modelling of the biliary excretion is important for the estimation of clinical pharmacokinetics in early stages of drug discovery. The aim of this study was to develop quantitative structure-activity relationships as computational tools for the estimation of biliary excretion and identification of the molecular properties controlling this process. The study used percentage of dose excreted intact into bile measured in vivo in rat for a diverse dataset of 217 compounds. Statistical techniques were multiple linear regression analysis, regression trees, random forest and boosted trees. A simple regression tree model generated using the CART algorithm was the most accurate in the estimation of the percentage of bile excretion of compounds, and this outperformed the more sophisticated boosted trees and random forest techniques. Analysis of the outliers indicated that the models perform best when lipophilicity is not too extreme (log P < 5.35) and for compounds with molecular weight above 280 Da. Molecular descriptors selected by all these models including the top ten incorporated in boosted trees and random forest indicated a higher biliary excretion for relatively hydrophilic compounds especially if they are anionic or cationic, and have a large molecular size. A statistically validated molecular weight threshold for potentially significant biliary excretion was above 348 Da. PMID:24202722

  11. IMPROVED METHOD FOR ESTIMATING MOLECULAR WEIGHTS OF VOLATILE ORGANIC COMPOUNDS FROM LOW RESOLUTION MASS SPECTRA

    EPA Science Inventory

    An improved method of estimating molecular weights of volatile organic compound from their mass spectra has been developed and implemented with an expert system. he method is based on the strong correlation of MAXMASS, the highest mass with an intensity of 5% of the base peak in ...

  12. LARGE SCALE EVALUATION OF A PATTERN RECOGNITION/EXPERT SYSTEM FOR MASS SPECTRAL MOLECULAR WEIGHT ESTIMATION

    EPA Science Inventory

    A fast, personal-computer based method of estimating molecular weights of organic compounds from low resolution mass I spectra has been thoroughly evaluated. he method is based on a rule-based pattern,recognition/expert system approach which uses empirical linear corrections whic...

  13. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 72 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lesquerella oil. The ratios of ion signal intensities (or relative abundances) of ...

  14. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 74 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using HPLC and the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lequerella oil. The ratios of relative abundances of the fragment ions fr...

  15. A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models

    PubMed Central

    2014-01-01

    Background Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear. Results Complete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400 Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190 Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters. Conclusions Our molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here. PMID:24884411

  16. Comparison of mode estimation methods and application in molecular clock analysis

    NASA Technical Reports Server (NTRS)

    Hedges, S. Blair; Shah, Prachi

    2003-01-01

    BACKGROUND: Distributions of time estimates in molecular clock studies are sometimes skewed or contain outliers. In those cases, the mode is a better estimator of the overall time of divergence than the mean or median. However, different methods are available for estimating the mode. We compared these methods in simulations to determine their strengths and weaknesses and further assessed their performance when applied to real data sets from a molecular clock study. RESULTS: We found that the half-range mode and robust parametric mode methods have a lower bias than other mode methods under a diversity of conditions. However, the half-range mode suffers from a relatively high variance and the robust parametric mode is more susceptible to bias by outliers. We determined that bootstrapping reduces the variance of both mode estimators. Application of the different methods to real data sets yielded results that were concordant with the simulations. CONCLUSION: Because the half-range mode is a simple and fast method, and produced less bias overall in our simulations, we recommend the bootstrapped version of it as a general-purpose mode estimator and suggest a bootstrap method for obtaining the standard error and 95% confidence interval of the mode.

  17. Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock

    PubMed Central

    Piganeau, Gwenaël; Eyre-Walker, Adam

    2003-01-01

    We present a method for estimating the distribution of fitness effects of new amino acid mutations when those mutations can be assumed to be slightly advantageous, slightly deleterious, or strongly deleterious. We apply the method to mitochondrial data from several different species. In the majority of the data sets, the shape of the distribution is approximately exponential. Our results provide an estimate of the distribution of fitness effects of weakly selected mutations and provide a possible explanation for why the molecular clock is fairly constant across taxa and time. PMID:12925735

  18. Molecular marker based characterization and genetic diversity of wheat genotypes in relation to boron efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Boron deficient soils pose a critical problem to wheat production in many areas of the world including Bangladesh and causes significant yield reduction. Therefore, in the present study, 21 diverse wheat (Triticum aestivum L.) genotypes collected from three different countries (Bangladesh, India, a...

  19. Quantification of the effects of molecular marker oxidation on source apportionment estimates for motor vehicles

    NASA Astrophysics Data System (ADS)

    Roy, Anirban A.; Wagstrom, Kristina M.; Adams, Peter J.; Pandis, Spyros N.; Robinson, Allen L.

    2011-06-01

    Molecular markers are individual organic compounds used in receptor models to apportion fine particulate matter to sources. These models currently assume that molecular markers are chemically stable; however, recent laboratory experiments suggest they may be significantly oxidized on atmospherically relevant time scales. To investigate the effects of photo-oxidation, we extended a 3-D chemical transport model (PMCAMx) to simulate norhopane concentrations over the eastern United States during July 2001. Norhopane is an important molecular marker for motor vehicle exhaust. We examined eight different simulation scenarios, using different combinations of reaction rates and source profiles. The simulations including norhopane oxidation better reproduced the observed spatial patterns of norhopane concentrations than the non-reactive cases. Chemical mass balance (CMB) analysis was performed using the PMCAMx-predicted motor vehicle norhopane and elemental carbon (EC) concentrations to quantify the bias caused by oxidation on source apportionment estimates. Norhopane oxidation caused CMB to underestimate total vehicle OC by 10-50%, with larger biases in rural areas. This underestimation was largely due to changes in the amount of OC apportioned to gasoline vehicles which was reduced by as much as 100%. The OC apportioned to diesel vehicle emissions was relatively insensitive to norhopane reaction. Therefore, oxidation can substantially alter CMB estimates regarding the relative importance of gasoline and diesel vehicle emissions.

  20. Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data

    PubMed Central

    Sill, Martin; Saadati, Maral; Benner, Axel

    2015-01-01

    Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso, to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca. Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25861969

  1. Semiempirical molecular orbital estimation of the relative stability of bianthryls produced by anthracene pyrolysis

    SciTech Connect

    Mulholland, J.A.; Mukherjee, J.; Wornat, M.J.; Sarofim, A.F.; Rutledge, G.C. . Dept. of Chemical Engineering)

    1993-08-01

    The pyrolysis of pure anthracene at temperatures between 1,200 and 1,500 K produced all six bianthryl isomers whose relative yields appear to be related to steric factors. To evaluate the hypothesis that thermodynamic factors govern the product distribution of bianthryls in this system, the relative enthalpies and entropies of biaryl isomers were estimated by molecular orbital modeling, using the semiempirical AM1 (Austin Model 1). Computational analysis of several isomer sets demonstrates that the relative stabilities of a large number of biaryl isomers are determined largely by steric interactions caused by structural features defined as bays, coves, and fjords. These steric factors affect both the degree of biaryl twist in the preferred conformation and the freedom of internal rotation. Molecular orbital modeling supports the hypothesis that a thermodynamic distribution of bianthryl isomers is produced by anthracene pyrolysis.

  2. Estimation of Linear Viscoelasticity of Polymer Melts in Molecular Dynamics Simulations Based on Relaxation Mode Analysis

    NASA Astrophysics Data System (ADS)

    Iwaoka, Nobuyuki; Hagita, Katsumi; Takano, Hiroshi

    2014-03-01

    On the basis of relaxation mode analysis (RMA), we present an efficient method to estimate the linear viscoelasticity of polymer melts in a molecular dynamics (MD) simulation. Slow relaxation phenomena appeared in polymer melts cause a problem that a calculation of the stress relaxation function in MD simulations, especially in the terminal time region, requires large computational efforts. Relaxation mode analysis is a method that systematically extracts slow relaxation modes and rates of the polymer chain from the time correlation of its conformations. We show the computational cost may be drastically reduced by combining a direct calculation of the stress relaxation function based on the Green-Kubo formula with the relaxation rates spectra estimated by RMA. N. I. acknowledges the Graduate School Doctoral Student Aid Program from Keio University.

  3. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

    PubMed Central

    Votapka, Lane W.; Amaro, Rommie E.

    2015-01-01

    The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2 −, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor. PMID:26505480

  4. Estimating the timing of early eukaryotic diversification with multigene molecular clocks

    PubMed Central

    Parfrey, Laura Wegener; Lahr, Daniel J. G.; Knoll, Andrew H.; Katz, Laura A.

    2011-01-01

    Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages. PMID:21810989

  5. Estimation of Molecular Acidity via Electrostatic Potential at the Nucleus and Valence Natural Atomic Orbitals

    PubMed Central

    Liu, Shubin; Pedersen, Lee G.

    2009-01-01

    An effective approach of estimating molecular pKa values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pKa values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pKa data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pKa values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules. PMID:19317439

  6. Pedigree-Free Estimates of Heritability in the Wild: Promising Prospects for Selfing Populations

    PubMed Central

    Gay, Laurene; Siol, Mathieu; Ronfort, Joelle

    2013-01-01

    Estimating the genetic variance available for traits informs us about a population’s ability to evolve in response to novel selective challenges. In selfing species, theory predicts a loss of genetic diversity that could lead to an evolutionary dead-end, but empirical support remains scarce. Genetic variability in a trait is estimated by correlating the phenotypic resemblance with the proportion of the genome that two relatives share identical by descent (‘realized relatedness’). The latter is traditionally predicted from pedigrees (ΦA: expected value) but can also be estimated using molecular markers (average number of alleles shared). Nevertheless, evolutionary biologists, unlike animal breeders, remain cautious about using marker-based relatedness coefficients to study complex phenotypic traits in populations. In this paper, we review published results comparing five different pedigree-free methods and use simulations to test individual-based models (hereafter called animal models) using marker-based relatedness coefficients, with a special focus on the influence of mating systems. Our literature review confirms that Ritland’s regression method is unreliable, but suggests that animal models with marker-based estimates of relatedness and genomic selection are promising and that more testing is required. Our simulations show that using molecular markers instead of pedigrees in animal models seriously worsens the estimation of heritability in outcrossing populations, unless a very large number of loci is available. In selfing populations the results are less biased. More generally, populations with high identity disequilibrium (consanguineous or bottlenecked populations) could be propitious for using marker-based animal models, but are also more likely to deviate from the standard assumptions of quantitative genetics models (non-additive variance). PMID:23825602

  7. Marker-Based Hierarchical Segmentation and Classification Approach for Hyperspectral Imagery

    NASA Technical Reports Server (NTRS)

    Tarabalka, Yuliya; Tilton, James C.; Benediktsson, Jon Atli; Chanussot, Jocelyn

    2011-01-01

    The Hierarchical SEGmentation (HSEG) algorithm, which is a combination of hierarchical step-wise optimization and spectral clustering, has given good performances for hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. First, pixelwise classification is performed and the most reliably classified pixels are selected as markers, with the corresponding class labels. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. The experimental results show that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for hyperspectral image analysis.

  8. Ultraspectral sounder data compression using a novel marker-based error-resilient arithmetic coder

    NASA Astrophysics Data System (ADS)

    Huang, Bormin; Sriraja, Y.; Wei, Shih-Chieh

    2006-08-01

    Entropy coding techniques aim to achieve the entropy of the source data by assigning variable-length codewords to symbols with the code lengths linked to the corresponding symbol probabilities. Entropy coders (e.g. Huffman coding, arithmetic coding), in one form or the other, are commonly used as the last stage in various compression schemes. While these variable-length coders provide better compression than fixed-length coders, they are vulnerable to transmission errors. Even a single bit error in the transmission process can cause havoc in the subsequent decoded stream. To cope with it, this research proposes a marker-based sentinel mechanism in entropy coding for error detection and recovery. We use arithmetic coding as an example to demonstrate this error-resilient technique for entropy coding. Experimental results on ultraspectral sounder data indicate that the marker-based error-resilient arithmetic coder provides remarkable robustness to correct transmission errors without significantly compromising the compression gains.

  9. Estimated Soft X-Ray Spectrum and Ionization of Molecular Hydrogen in the Central Molecular Zone of the Galactic Center

    NASA Astrophysics Data System (ADS)

    Notani, Masahiro; Oka, Takeshi

    2014-06-01

    From observed high H_3^+ column densities in the Central Molecular Zone (CMZ), a region with a radius of ˜150 pc at the center of our Milky Way Galaxy, H_2 ionization rates of ζ ˜ 3 × 10-15 s-1 have been reported. This ionization rate which is higher than those in dense clouds and diffuse clouds in the Galactic disk by ˜100 and ˜10, respectively, have been ascribed to high flux of cosmic rays due to the high density of supernova remnants in the region. We are studying the ionization rate due to X-rays intensely observed in the CMZ as a possible competing process. Last year we reported the estimated ionization rate due to observable X-rays with energy 1 - 10 keV as negligible compared to the observed ζ. However, just like cosmic ray ionization is dominated by low energy (E≤ 100 MeV) cosmic rays that are not directly observable because of deflection by solar magnetic field, the X-ray ionization is dominated by soft X-rays (E≤ 1 keV) that are not observable due to optical depth of the foreground gas. Our task therefore resembles those by Hayakawa et al. (1961) and Spitzer and Tomasko (1968) who estimated the cosmic ray ionization rate ζ based on high energy (> 1 GeV) cosmic ray observations. We use theoretical X-ray spectrum and interpolate the observed X-rays at 4 keV, which are observable nearly un-attenuated from the CMZ, to the low energy region. Two theoretical spectra are presented, one due to Bremsstrahlung with variable temperature and proper cut off and the other the advection-dominated accretion flow (ADAF) model. Discussion of the calculations and the results will be presented. Oka, T., Geballe, T. R., Goto, M., Usuda, T., and McCall, B. J. 2005, ApJ, 632 882 Geballe, T. R., and Oka, T. 2010, ApJ, 709 L70. Hayakawa,S.,Nishimura, S., Takayanagi, K. 1961, PASJ, 18 184 Spitzer,L. T., Tomasko, M. G. 1968, ApJ, 152 971 Yuan, F., Quataert, E., Narayan, R. 2003, JPJ, 598 301.

  10. Estimation of gas permeability of a zeolite membrane, based on a molecular simulation technique and permeation model

    SciTech Connect

    Suzuki, Shigejirou; Takaba, Hiromitsu; Yamaguchi, Takeo; Nakao, Shinichi

    2000-03-09

    A method for estimating gas permeability through a zeolite membrane, using a molecular simulation technique and a theoretical permeation model, is presented. The estimate of permeability is derived from a combination of an absorption isotherm and self-diffusion coefficient based on the adsorption-diffusion model. The adsorption isotherm and self-diffusion coefficients needed for the estimation were calculated using conventional Monte Carlo and molecular dynamics simulations. The calculated self-diffusion coefficient was converted to the mutual diffusion coefficient and the permeability estimated using the Fickian equation. The method was applied to the prediction of permeabilities of methane and ethylene in silicalite at 301 K. Calculated permeabilities were larger than the experimental values by more than an order of magnitude. However, the anisotropic permeability was consistent with the experimental data and the results obtained using a grand canonical ensemble molecular dynamics technique (Pohl et al., Mol.Phys. 1996, 89(6), 1725--1731).

  11. Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera.

    PubMed

    Li, Qin-Qin; Zhou, Song-Dong; Huang, De-Qing; He, Xing-Jin; Wei, Xian-Qin

    2016-01-01

    A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum, (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian-American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to

  12. Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera

    PubMed Central

    Li, Qin-Qin; Zhou, Song-Dong; Huang, De-Qing; He, Xing-Jin; Wei, Xian-Qin

    2016-01-01

    A primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum, (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK, trnH-psbA, rps16) were used to reconstruct the phylogeny of Allium subgen. Anguinum. RbcL sequences were used to estimate divergences time for Allium, and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian–American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to

  13. Cherenkov radiation fluence estimates in tissue for molecular imaging and therapy applications

    NASA Astrophysics Data System (ADS)

    Glaser, Adam K.; Zhang, Rongxiao; Andreozzi, Jacqueline; Gladstone, David; Pogue, Brian

    2016-03-01

    Cherenkov radiation has emerged as a novel source of light with a number of applications in the biomedical sciences. It's unique properties, including its broadband emission spectrum, spectral weighting in the ultraviolet and blue wavebands, and local generation of light within a given tissue have made it an attractive source of light for techniques ranging from widefield imaging to oximetry and phototherapy. To help guide the future development of this field in the context of molecular imaging, quantitative estimates of the light fluence rates of Cherenkov radiation from a number of radionuclide and external radiotherapy beams in tissue was explored for the first time. Using Monte Carlo simulations, these values were found to be on the order of 0.1 - 1 nW/cm2 per MBq/g for radionuclides and 1 - 10 μW/cm2 per Gy/sec for external radiotherapy beams, dependent on the given waveband and optical properties. For phototherapy applications, the total light fluence was found to be on the order of nJ/cm2 for radionuclides, and mJ/cm2 for radiotherapy beams. To validate these findings, experimental validation was completed with an MV x-ray photon beam incident onto a tissue phantom, confirming the magnitudes of the simulation values. The results indicate that diagnostic potential is reasonable for Cherenkov excitation of molecular probes, but phototherapy may remain elusive at these relatively low fluence values.

  14. High Sensitivity Method to Estimate Distribution of Hyaluronan Molecular Sizes in Small Biological Samples Using Gas-Phase Electrophoretic Mobility Molecular Analysis

    PubMed Central

    Do, Lan; Dahl, Christen P.; Kerje, Susanne; Hansell, Peter; Mörner, Stellan; Lindqvist, Ulla; Engström-Laurent, Anna; Larsson, Göran; Hellman, Urban

    2015-01-01

    Hyaluronan is a negatively charged polydisperse polysaccharide where both its size and tissue concentration play an important role in many physiological and pathological processes. The various functions of hyaluronan depend on its molecular size. Up to now, it has been difficult to study the role of hyaluronan in diseases with pathological changes in the extracellular matrix where availability is low or tissue samples are small. Difficulty to obtain large enough biopsies from human diseased tissue or tissue from animal models has also restricted the study of hyaluronan. In this paper, we demonstrate that gas-phase electrophoretic molecular mobility analyzer (GEMMA) can be used to estimate the distribution of hyaluronan molecular sizes in biological samples with a limited amount of hyaluronan. The low detection level of the GEMMA method allows for estimation of hyaluronan molecular sizes from different parts of small organs. Hence, the GEMMA method opens opportunity to attain a profile over the distribution of hyaluronan molecular sizes and estimate changes caused by disease or experimental conditions that has not been possible to obtain before. PMID:26448761

  15. Divergence date estimation and a comprehensive molecular tree of extant cetaceans.

    PubMed

    McGowen, Michael R; Spaulding, Michelle; Gatesy, John

    2009-12-01

    Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene-Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning approximately 10 million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea. PMID:19699809

  16. Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs.

    PubMed

    Ivy, Jamie A; Putnam, Andrea S; Navarro, Asako Y; Gurr, Jessica; Ryder, Oliver A

    2016-09-01

    Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P < 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs. PMID:27208150

  17. Cherenkov radiation fluence estimates in tissue for molecular imaging and therapy applications.

    PubMed

    Glaser, Adam K; Zhang, Rongxiao; Andreozzi, Jacqueline M; Gladstone, David J; Pogue, Brian W

    2015-09-01

    Cherenkov radiation has recently emerged as an interesting phenomenon for a number of applications in the biomedical sciences. Its unique properties, including broadband emission spectrum, spectral weight in the ultraviolet and blue wavebands, and local generation of light within a given tissue, have made it an attractive new source of light within tissue for molecular imaging and phototherapy applications. While several studies have investigated the total Cherenkov light yield from radionuclides in units of [photons/decay], further consideration of the light propagation in tissue is necessary to fully consider the utility of this signal in vivo. Therefore, to help further guide the development of this novel field, quantitative estimates of the light fluence rate of Cherenkov radiation from both radionuclides and radiotherapy beams in a biological tissue are presented for the first time. Using Monte Carlo simulations, these values were found to be on the order of 0.01-1 nW cm(-2) per MBq g(-1) for radionuclides, and 1-100 μW cm(-2) per Gy s(-1) for external radiotherapy beams, dependent on the given waveband, optical properties, and radiation source. For phototherapy applications, the total light fluence was found to be on the order of nJ cm(-2) for radionuclides, and mJ cm(-2) for radiotherapy beams. The results indicate that diagnostic potential is reasonable for Cherenkov excitation of molecular probes, but phototherapy may remain elusive at such exceedingly low fluence values. The results of this study are publicly available for distribution online at www.dartmouth.edu/optmed/. PMID:26270125

  18. Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data.

    PubMed

    Beimforde, Christina; Feldberg, Kathrin; Nylinder, Stephan; Rikkinen, Jouko; Tuovila, Hanna; Dörfelt, Heinrich; Gube, Matthias; Jackson, Daniel J; Reitner, Joachim; Seyfullah, Leyla J; Schmidt, Alexander R

    2014-09-01

    The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered. PMID:24792086

  19. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    PubMed

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times. PMID:27391254

  20. Contribution of molecular analyses to the estimation of the risk of congenital myotonic dystrophy.

    PubMed Central

    Cobo, A M; Poza, J J; Martorell, L; López de Munain, A; Emparanza, J I; Baiget, M

    1995-01-01

    A molecular analysis of the maternal and child CTG repeat size and intergenerational amplification was performed in order to estimate the risk of having a child with congenital myotonic dystrophy (CMD). In a study of 124 affected mother-child pairs (42 mother-CMD and 82 mother-non-CMD) the mean maternal CTG allele in CMD cases was three times higher (700 repeats) than in non-CMD cases (236 repeats). When the maternal allele was in the 50-300 repeats range, 90% of children were non-CMD. In contrast, when the maternal allele was greater than 300 repeats, 59% inherited the congenital form. Furthermore, the risk of having a CMD child is also related to the intergenerational amplification, which was significantly greater in the mother-CMD pairs than in the mother-non-CMD pairs. Although the risk of giving birth to a CMD child always exists for affected mothers, our data show that such a risk is considerably higher if the maternal allele is greater than 300 repeats. Images PMID:7760317

  1. Organic molecular markers for estimating the biodegradation of petroleum hydrocarbons in soil

    SciTech Connect

    Voos, G.; Mills, G.; O`Neill, J.; Jones, W.A.

    1995-12-01

    The weathering of petroleum hydrocarbons in the soil environment is the sum of biological, physical and chemical processes. It is often difficult to clearly discern microbial from abiotic contributions to the overall process. Our study was initiated to investigate the use of molecular marker compounds (e.g., pristane and phytane) to estimate the biodegradation of petroleum compounds in diesel fuel contaminated soil. This experiment was conducted using mesocosms to simulate the environmental conditions in the SRS soil bioremediation facility. Soil samples were analyzed for hydrocarbon components using high-resolution gas chromatography and gas chromatography-mass spectrometry. The ratios nC17/pristane and nC18/phytane declined during the 64-day experiment. The rate of decline of the marker compounds was significantly less than that of the n-alkanes C17 and C18, but was proportional to the decline in total extractable petroleum hydrocarbons. Analysis for other marker compounds, including diterpenoid hydrocarbons and the ratio of polynuclear aromatic hydrocarbons (PAHs) to methylated PAHs, is continuing.

  2. Estimation of the mutual orientation and intermolecular interaction of C12Ex from molecular dynamics simulations.

    PubMed

    Velinova, Maria; Tsoneva, Yana; Ivanova, Anela; Tadjer, Alia

    2012-04-26

    Nonionic surfactants, such as poly(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent-solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined. PMID:22448734

  3. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

    PubMed

    Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

    2015-12-01

    Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. PMID:26433028

  4. ESTIMATION OF GAS-LIQUID CHROMATOGRAPHIC RETENTION TIMES FROM MOLECULAR STRUCTURE

    EPA Science Inventory

    A new type of computer program called SPARC (SPARC Performs Automated Reasoning in Chemistry) was developed to predict chemical reactivity parameters and physical properties of organic molecules from their molecular structures based on fundamental chemical structure theory. PARC'...

  5. Varations of molecular weight estimation by HP-size exclusion chromatography with UVA versus online DOC detection.

    PubMed

    Her, Namguk; Amy, Gary; Foss, David; Chow, Jaeweon

    2002-08-01

    High performance size exclusion chromatography (HPSEC) with ultraviolet absorbance (UVA) detection has been widely utilized to estimate the molecular weight (MW) and MW distribution of natural organic matter (NOM). However, the estimation of MW with UVA detection is inherently inaccurate because UVA at 254 nm only detects limited components (mostly pi bonded molecules) of NOM, and the molar absorptivity of these different NOM constituents is not equal. In comparison, a SEC chromatogram obtained with a DOC detector showed significant differences compared to a corresponding UVA chromatogram, resulting in different MW values as well as different estimates of polydispersivity. The MWs of Suwannee River humic acid (SRHA), Suwannee River fulvic acid (SRFA), and various mixtures thereof were estimated with HPSEC coupled with UVA and DOC detectors. The results show that UVA is not an adequate detector for quantitative analysis of MW estimation but rather can be used only for limited qualitative analysis. The NOM in several natural waters (Irvine Ranch, California groundwater, and Barr Lake, Colorado surface water) were also characterized to demonstrate the different MWs obtained with the two detectors. The results of the SEC-DOC chromatograms revealed NOM constituent peaks that went undetected by UVA. Utilizing online DOC detection, a better representation of NOM MWs was suggested, with NOM displaying higher weight-averaged MW (Mw) and lower number-averaged MW (Mn) as well as higher polydispersivity. A method for estimation of the MWs of NOM fractional components and polydispersivities is presented. PMID:12188370

  6. a Marker-Based Eulerian-Lagrangian Method for Multiphase Flow with Supersonic Combustion Applications

    NASA Astrophysics Data System (ADS)

    Fan, Xiaofeng; Wang, Jiangfeng

    2016-06-01

    The atomization of liquid fuel is a kind of intricate dynamic process from continuous phase to discrete phase. Procedures of fuel spray in supersonic flow are modeled with an Eulerian-Lagrangian computational fluid dynamics methodology. The method combines two distinct techniques and develops an integrated numerical simulation method to simulate the atomization processes. The traditional finite volume method based on stationary (Eulerian) Cartesian grid is used to resolve the flow field, and multi-component Navier-Stokes equations are adopted in present work, with accounting for the mass exchange and heat transfer occupied by vaporization process. The marker-based moving (Lagrangian) grid is utilized to depict the behavior of atomized liquid sprays injected into a gaseous environment, and discrete droplet model 13 is adopted. To verify the current approach, the proposed method is applied to simulate processes of liquid atomization in supersonic cross flow. Three classic breakup models, TAB model, wave model and K-H/R-T hybrid model, are discussed. The numerical results are compared with multiple perspectives quantitatively, including spray penetration height and droplet size distribution. In addition, the complex flow field structures induced by the presence of liquid spray are illustrated and discussed. It is validated that the maker-based Eulerian-Lagrangian method is effective and reliable.

  7. Marker-based monitoring of seated spinal posture using a calibrated single-variable threshold model.

    PubMed

    Walsh, Pauline; Dunne, Lucy E; Caulfield, Brian; Smyth, Barry

    2006-01-01

    This work, as part of a larger project developing wearable posture monitors for the work environment, seeks to monitor and model seated posture during computer use. A non-wearable marker-based optoelectronic motion capture system was used to monitor seated posture for ten healthy subjects during a calibration exercise and a typing task. Machine learning techniques were used to select overall spinal sagittal flexion as the best indicator of posture from a set of marker and vector variables. Overall flexion data from the calibration exercise were used to define a threshold model designed to classify posture for each subject, which was then applied to the typing task data. Results of the model were analysed visually by qualified physiotherapists with experience in ergonomics and posture analysis to confirm the accuracy of the calibration. The calibration formula was found to be accurate on 100% subjects. This process will be used as a comparative measure in the evaluation of several wearable posture sensors, and to inform the design of the wearable system. PMID:17946301

  8. The lognormal and gamma distribution models for estimating molecular weight distributions of polymers using PGSE NMR.

    PubMed

    Williamson, Nathan H; Nydén, Magnus; Röding, Magnus

    2016-06-01

    We present comprehensive derivations for the statistical models and methods for the use of pulsed gradient spin echo (PGSE) NMR to characterize the molecular weight distribution of polymers via the well-known scaling law relating diffusion coefficients and molecular weights. We cover the lognormal and gamma distribution models and linear combinations of these distributions. Although the focus is on methodology, we illustrate the use experimentally with three polystyrene samples, comparing the NMR results to gel permeation chromatography (GPC) measurements, test the accuracy and noise-sensitivity on simulated data, and provide code for implementation. PMID:27116223

  9. The lognormal and gamma distribution models for estimating molecular weight distributions of polymers using PGSE NMR

    NASA Astrophysics Data System (ADS)

    Williamson, Nathan H.; Nydén, Magnus; Röding, Magnus

    2016-06-01

    We present comprehensive derivations for the statistical models and methods for the use of pulsed gradient spin echo (PGSE) NMR to characterize the molecular weight distribution of polymers via the well-known scaling law relating diffusion coefficients and molecular weights. We cover the lognormal and gamma distribution models and linear combinations of these distributions. Although the focus is on methodology, we illustrate the use experimentally with three polystyrene samples, comparing the NMR results to gel permeation chromatography (GPC) measurements, test the accuracy and noise-sensitivity on simulated data, and provide code for implementation.

  10. Adaptive Green-Kubo estimates of transport coefficients from molecular dynamics based on robust error analysis

    NASA Astrophysics Data System (ADS)

    Jones, Reese E.; Mandadapu, Kranthi K.

    2012-04-01

    We present a rigorous Green-Kubo methodology for calculating transport coefficients based on on-the-fly estimates of: (a) statistical stationarity of the relevant process, and (b) error in the resulting coefficient. The methodology uses time samples efficiently across an ensemble of parallel replicas to yield accurate estimates, which is particularly useful for estimating the thermal conductivity of semi-conductors near their Debye temperatures where the characteristic decay times of the heat flux correlation functions are large. Employing and extending the error analysis of Zwanzig and Ailawadi [Phys. Rev. 182, 280 (1969)], 10.1103/PhysRev.182.280 and Frenkel [in Proceedings of the International School of Physics "Enrico Fermi", Course LXXV (North-Holland Publishing Company, Amsterdam, 1980)] to the integral of correlation, we are able to provide tight theoretical bounds for the error in the estimate of the transport coefficient. To demonstrate the performance of the method, four test cases of increasing computational cost and complexity are presented: the viscosity of Ar and water, and the thermal conductivity of Si and GaN. In addition to producing accurate estimates of the transport coefficients for these materials, this work demonstrates precise agreement of the computed variances in the estimates of the correlation and the transport coefficient with the extended theory based on the assumption that fluctuations follow a Gaussian process. The proposed algorithm in conjunction with the extended theory enables the calculation of transport coefficients with the Green-Kubo method accurately and efficiently.

  11. Estimating Animal Abundance in Ground Beef Batches Assayed with Molecular Markers

    PubMed Central

    Hu, Xin-Sheng; Simila, Janika; Platz, Sindey Schueler; Moore, Stephen S.; Plastow, Graham; Meghen, Ciaran N.

    2012-01-01

    Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources in a single product batch, which produces a high heterogeneity in capture probability. In order to estimate animal abundance through DNA profiling of ground beef constituents, two parameter-based statistical models were developed for incidence data. Simulations were applied to evaluate the maximum likelihood estimate (MLE) of a joint likelihood function from multiple surveys, showing superiority in the presence of high capture heterogeneity with small sample sizes, or comparable estimation in the presence of low capture heterogeneity with a large sample size when compared to other existing models. Our model employs the full information on the pattern of the capture-recapture frequencies from multiple samples. We applied the proposed models to estimate animal abundance in six manufacturing beef batches, genotyped using 30 single nucleotide polymorphism (SNP) markers, from a large scale beef grinding facility. Results show that between 411∼1367 animals were present in six manufacturing beef batches. These estimates are informative as a reference for improving recall processes and tracing finished meat products back to source. PMID:22479559

  12. Friction tensor for a pair of Brownian particles: Spurious finite-size effects and molecular dynamics estimates

    SciTech Connect

    Bocquet, L.; Hansen, J.P.; Piasecki, J.

    1997-10-01

    In this work, we show that in any finite system, the binary friction tenser for two Brownian particles cannot be directly estimated from an evaluation of the microscopic Green Kubo formula, involving the time integral of force-force autocorrelation functions. This pitfall is associated with a subtle inversion of the thermodynamic and long-time limits and leads to spurious results for the estimates of the friction matrix based on molecular dynamics simulations. Starting from a careful analysis of the coupled Langevin equations for two interacting Brownian particles, we derive a method to circumvent these effects and extract the binary friction tenser from the correlation function matrix of the instantaneous forces exerted by the bath particles on the fixed Brownian particles, and from the relaxation of the total momentum of the bath in a finite system. The general methodology is applied to the case of two hard or soft Brownian spheres in a bath of light particles. Numerical estimates of the relevant correlation functions and of the resulting self and mutual components of the matrix of friction tensors are obtained by molecular dynamics simulations for various spacings between the Brownian particles.

  13. Residual Seminal Vesicle Displacement in Marker-Based Image-Guided Radiotherapy for Prostate Cancer and the Impact on Margin Design

    SciTech Connect

    Smitsmans, Monique H.P.; Bois, Josien de; Sonke, Jan-Jakob; Catton, Charles N.; Jaffray, David A.; Lebesque, Joos V.; Herk, Marcel van

    2011-06-01

    Purpose: The objectives of this study were to quantify residual interfraction displacement of seminal vesicles (SV) and investigate the efficacy of rotation correction on SV displacement in marker-based prostate image-guided radiotherapy (IGRT). We also determined the effect of marker registration on the measured SV displacement and its impact on margin design. Methods and Materials: SV displacement was determined relative to marker registration by using 296 cone beam computed tomography scans of 13 prostate cancer patients with implanted markers. SV were individually registered in the transverse plane, based on gray-value information. The target registration error (TRE) for the SV due to marker registration inaccuracies was estimated. Correlations between prostate gland rotations and SV displacement and between individual SV displacements were determined. Results: The SV registration success rate was 99%. Displacement amounts of both SVs were comparable. Systematic and random residual SV displacements were 1.6 mm and 2.0 mm in the left-right direction, respectively, and 2.8 mm and 3.1 mm in the anteroposterior (AP) direction, respectively. Rotation correction did not reduce residual SV displacement. Prostate gland rotation around the left-right axis correlated with SV AP displacement (R{sup 2} = 42%); a correlation existed between both SVs for AP displacement (R{sup 2} = 62%); considerable correlation existed between random errors of SV displacement and TRE (R{sup 2} = 34%). Conclusions: Considerable residual SV displacement exists in marker-based IGRT. Rotation correction barely reduced SV displacement, rather, a larger SV displacement was shown relative to the prostate gland that was not captured by the marker position. Marker registration error partly explains SV displacement when correcting for rotations. Correcting for rotations, therefore, is not advisable when SV are part of the target volume. Margin design for SVs should take these uncertainties into

  14. Estimation of Henry's Law Constant for a Diverse Set of Organic Compounds from Molecular Structure

    EPA Science Inventory

    The SPARC (SPARC Performs Automated Reasoning in Chemistry) vapor pressure and activity coefficient models were coupled to estimate Henry’s Law Constant (HLC) in water and in hexadecane for a wide range of non-polar and polar organic compounds without modification or additional p...

  15. Estimation of Current Breed Differences in Multibreed Genetic Evaluations Using Quantitative and Molecular Approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this presentation were to review methods used in multibreed approaches in national cattle evaluation, suggest guidelines for utilizing information for research estimates of breed differences, describe the design of the multibreed research program (germplasm evaluation; GPE) at the ...

  16. Clinical, cytogenetic, and molecular diagnosis of Angelman syndrome: Estimated prevalence rate in a Danish country

    SciTech Connect

    Petersen, M.B.; Brondum-Nielsen, K.; Hansen, L.K.; Wulff, K.

    1995-06-19

    Angelman syndrome (AS) was initially considered a rather rare abnormality, but in later years, with the possibilities for cytogenetic and molecular diagnosis an increasing number of patients have been reported. The incidence is quoted to be around 1:20,000. The etiology of AS is associated with the lack of maternal allele(s) of one or more loci at 15q11-q13, and is considered an effect of parental imprinting of that region, since a similar deficiency of paternal alleles leads to Prader-Willi syndrome. 9 refs., 1 tab.

  17. Development of marker-based tracking methods for augmented reality applied to NPP maintenance work support and its experimental evaluation

    SciTech Connect

    Ishii, H.; Fujino, H.; Bian, Z.; Sekiyama, T.; Shimoda, H.; Yoshikawa, H.

    2006-07-01

    In this study, two types of marker-based tracking methods for Augmented Reality have been developed. One is a method which employs line-shaped markers and the other is a method which employs circular-shaped markers. These two methods recognize the markers by means of image processing and calculate the relative position and orientation between the markers and the camera in real time. The line-shaped markers are suitable to be pasted in the buildings such as NPPs where many pipes and tanks exist. The circular-shaped markers are suitable for the case that there are many obstacles and it is difficult to use line-shaped markers because the obstacles hide the part of the line-shaped markers. Both methods can extend the maximum distance between the markers and the camera compared to the legacy marker-based tracking methods. (authors)

  18. Estimation of the low-density (beta) lipoproteins of serum in health and disease using large molecular weight dextran sulphate

    PubMed Central

    Walton, K. W.; Scott, P. J.

    1964-01-01

    Studies have been made of the factors affecting the specificity of the interaction between high molecular weight dextran sulphate and low-density lipoproteins, both in pure solution and in serum. The results have been used in the development of a simple assay method for the serum concentration of low-density lipoproteins in small volumes of serum. The results obtained by this assay procedure have been found to correlate acceptably with parallel estimations of low-density lipoproteins by an ultracentrifugal technique and by paper electrophoresis. The technique has been applied to a survey of serum levels of these proteins in a normal population. The results have been compared with data in the literature. Satisfactory agreement was found between mean levels, matched for age and sex, between the dextran sulphate method and those methods based ultimately on chemical estimation of one or more components of the isolated lipoproteins. A systematic difference was observed when the dextran sulphate method was compared with estimates based on analytical ultracentrifugation or turbidimetry using amylopectin sulphate. Some indication of the range of application of the dextran sulphate method in clinical chemistry is provided. Images PMID:14227432

  19. Molecular Phylogenetic Analysis of Infidum similis, Including Morphological Data and Estimation of its Genome Size.

    PubMed

    Martínez-Salazar, Elizabeth A; Rosas-Valdez, Rogelio; Gregory, T Ryan; Violante-González, Juan

    2016-08-01

    :   Infidum similis Travassos, 1916 (Dicrocoeliidae: Leipertrematinae) was found in the gall bladder of Leptophis diplotropis Günther, 1872 from El Podrido, Acapulco, Guerrero, Mexico. A phylogenetic analysis based on partial sequences of the 28S ribosomal RNA using maximum likelihood (ML) and Bayesian inference (BI) analyses was carried out to assess its phylogenetic position within suborder Xiphidiata, alongside members of the superfamilies Gorgoderoidea and Plagiorchoidea. The phylogenetic trees showed that the genus is most-closely related to the Plagiorchoidea rather than to the Gorgoderoidea, in keeping with previous taxonomic designations. Phylogenies obtained from ML and BI analysis of the 28S rDNA gene revealed a well supported clade in which Choledocystus hepaticus (Lutz, 1928) Sullivan, 1977 is sister to I. similis. On the other hand, a tree obtained using a partial sequence of the cytochrome c oxidase subunit 1 (cox1) mtDNA gene (ML and BI analysis), with species supposed to be closely related to I. similis according to 28S, does not support this relatedness. Based on the independence of Infidum from the subfamily Leipertrematinae Yamaguti, 1958 , our results clearly demonstrated that the genus corresponds to a different family and with species closely related to C. hepaticus within Plagiorchoidea. New data are presented about the tegumental surface of I. similis by scanning electron microscopy as well as the estimation of its haploid genome size using Feulgen Image Analysis Densitometry of sperm nuclei as part of the characterization of this species. This is the first genome size estimated for a member of Plagiorchiida, and these data will provide a new source of knowledge on helminth diversity and evolutionary studies. This constitutes the first host record, and new geographical distribution, for this species in Mexico. PMID:26998629

  20. Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields.

    PubMed

    Šebesta, Filip; Sláma, Vladislav; Melcr, Josef; Futera, Zdeněk; Burda, Jaroslav V

    2016-08-01

    Force-field parameters of the first row transition metals together with a few additional common elements such as those from the second (Rh, Ru) and third (Hg, Pt) rows of elements in ligated forms were determined based on the density functional theory calculations. Bonding characteristics were determined by averaging metal-ligand force constants in optimal geometries from several chosen complexes of each metal in the most common oxidation numbers and structural arrangements. Parameters of Lennard-Jones potential were determined based on a supermolecular model. Our determined molecular mechanical parameters are compared with presently available parameters published by other groups. We performed two different kinds of testing in order to demonstrate the reliability of these parameters in the case of ligated metallo complexes. First, the nonbonding potential was constructed for an additional set of 19 larger systems containing common complexes with organic molecules. The second test compares the Pt-O and Pt-H radial distribution functions for cisplatin in a box of TIP3P water with lately published studies. PMID:27337427

  1. Mass estimates for very cold (<8 K) gas in molecular cloud cores

    NASA Astrophysics Data System (ADS)

    Steinacker, J.; Linz, H.; Beuther, H.; Henning, Th.; Bacmann, A.

    2016-09-01

    Context. The mass of prestellar cores is an essential ingredient to understand the onset of star formation in the core. The low level of emission from cold dust may keep parts of this dust hidden from observation. Aims: We aim to determine the fraction of core mass in the temperature range <8 K that can be expected for typical low- and high-mass star formation regions. Methods: We calculated the dust temperature within standard spherically symmetric prestellar cores for a grid of density power laws in the outer core regions, core masses, and variations in the external multicomponent radiation field. We assume the dust is composed of amorphous silicate and carbon and we discuss variations of its optical properties. As a measure for the distribution of cores and clumps, we used core mass functions derived for various environments. In view of the high densities in very cold central regions, dust and gas temperatures are assumed to be equal. Results: We find that the fraction of mass with temperatures <8 K in typical low- and high-mass cores is <20%. It is possible to obtain higher fractions of very cold gas by placing intermediate- or high-mass cores in a typical low-mass star formation environment. We show that the mass uncertainty arising from far-infrared to mm modeling of very cold dust emission is smaller than the mass uncertainty owing to the unknown dust opacities. Conclusions: Under typical star formation conditions, dust with temperatures <8 K covers a small mass fraction in molecular cloud cores, but may play a more important role for special cases. The major unknown in determining the total core mass from thermal dust emission is the uncertainty in the dust opacity, not in the underestimated very cold dust mass.

  2. Optical coherence tomography in estimating molecular diffusion of drugs and analytes in ocular tissues

    NASA Astrophysics Data System (ADS)

    Ghosn, Mohamad G.; Tuchin, Valery V.; Larin, Kirill V.

    2009-02-01

    Aside from other ocular drug delivery methods, topical application and follow up drug diffusion through the cornea and sclera of the eye remain the favored method, as they impose the least pain and discomfort to the patient. However, this delivery route suffers from the low permeability of epithelial tissues and drug washout, thus reducing the effectiveness of the drug and ability to reach its target in effective concentrations. In order to better understand the behavioral characteristics of diffusion in ocular tissue, a method for noninvasive imaging of drug diffusion is needed. Due to its high resolution and depth-resolved imaging capabilities, optical coherence tomography (OCT) has been utilized in quantifying the molecular transport of different drugs and analytes in vitro in the sclera and the cornea. Diffusion of Metronidazole (0.5%), Dexamethasone (0.2%), Ciprofloxacin (0.3%), Mannitol (20%), and glucose solution (20%) in rabbit sclera and cornea were examined. Their permeability coefficients were calculated by using OCT signal slope and depth-resolved amplitude methods as function of time and tissue depth. For instance, mannitol was found to have a permeability coefficient of (8.99 +/- 1.43) × 10-6 cm/s in cornea (n=4) and (6.18 +/- 1.08) × 10-6 cm/s in sclera (n=5). We also demonstrate the capability of OCT technique for depth-resolved monitoring and quantifying of glucose diffusion in different layers of the sclera. We found that the glucose diffusion rate is not uniform throughout the tissue and is increased from approximately (2.39 +/- 0.73) × 10-6 cm/s at the epithelial side to (8.63 +/- 0.27) × 10-6 cm/s close to the endothelial side of the sclera. In addition, discrepancy in the permeability rates of glucose solutions with different concentrations was observed. Such diffusion studies could enhance our knowledge and potentially pave the way for advancements of therapeutic and diagnostic techniques in the treatment of ocular diseases.

  3. Marker based standardization of polyherbal formulation (SJT-DI-02) by high performance thin layer chromatography method

    PubMed Central

    Ladva, Bhakti J.; Mahida, Vijay M.; Kantaria, Urmi D.; Gokani, Rina H.

    2014-01-01

    Background: Preparation of highly standardized herbal products with respect to chemical composition and biological activity is considered to be a valuable approach in this field. SJT-DI-02 polyherbal formulation was successfully developed at our institute and filed for patent at Mumbai patent office. Objective: The present work was marker based standardization of patented, novel and efficacious polyherbal formulation namely SJT-DI-02 for the treatment of diabetes. The SJT-DI-02 was comprised of dried extracts of rhizomes of Acorus calamus, leaves of Aegle marmelose, fruits of Benincasa hispida, roots of Chlorophytum arendinaceum, seeds of Eugenia jambolana, leaves of Ocimum sanctum, pericarp of Punica granatum, seeds of Tamarindus indica. Selected plants were collected, dried and extracted with suitable solvents. The formulation was prepared by mixing different fractions of extracts. Materials and Methods: For successful and best standardization, first of all selection and procurement was carried out. Selection is done on the basis of therapeutic efficacy and amount of the marker present in the particular plant part. At the time of procurement side by side phytochemical screening and estimation of phytoconstituents was carried out. After completion of preliminary screening using characterized markers, we tried to develop best TLC systems using selected solvent composition. Finally well-developed TLC systems were applied in HPTLC. In the present study polyherbal formulation was standardized by using different four markers. TLC Densitometric methods were developed using HPTLC for the quantification of these marker compounds. Solvent systems were optimized to achieve best resolution of the marker compounds from other components of the sample extract. The identity of the bands in the sample extracts were confirmed by comparing the Rf and the absorption spectra by overlaying their UV absorption spectra with those of their respective standards. The purity of the bands

  4. Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations.

    PubMed

    Kittel, Rebecca N; Austin, Andrew D; Klopfstein, Seraina

    2016-08-01

    Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov

  5. SSR and SRAP marker-based linkage map of Vitis vinifera L.

    PubMed Central

    Guo, Yinshan; Lin, Hong; Liu, Zhendong; Zhao, Yuhui; Guo, Xiuwu; Li, Kun

    2014-01-01

    An F1 population was created by the cross ‘87-1’ × ‘9-22’. The female parent ‘87-1’ was an extremely early maturing cultivar with strong flavour. The male parent was an excellent breeding line producing large berries maturing late. The mapping population included 149 randomly chosen individuals. Molecular genetic map for each parent and the consensus map were constructed using simple sequence repeat and sequence-related amplified polymorphism markers by software JoinMap 3.0. The ‘87-1’ map covers a total length of 1272.9 cM distributed in 21 linkage groups and consists of 163 molecular markers with an average distance between adjacent markers of 8.9 cM. The ‘9-22’ map covers a total length of 1267.4 cM distributed in 20 linkage groups and consists of 158 molecular markers with an average distance between adjacent markers of 9.1 cM. The consensus map covers a total length of 1537.1 cM distributed in 21 linkage groups and one doublet and consists of 217 molecular markers with an average distance of 7.8 cM between adjacent markers. The length of the linkage groups is 69.8 cM on average. The map covers the 19 chromosomes of the Vitis genome and can lay a solid foundation for further studies such as quantative trait loci (QTL) mapping of correlated traits and marker-assisted selection. PMID:26019507

  6. Variability of Marker-Based Rectal Dose Evaluation in HDR Cervical Brachytherapy

    SciTech Connect

    Wang Zhou; Jaggernauth, Wainwright; Malhotra, Harish K.; Podgorsak, Matthew B.

    2010-01-01

    In film-based intracavitary brachytherapy for cervical cancer, position of the rectal markers may not accurately represent the anterior rectal wall. This study was aimed at analyzing the variability of rectal dose estimation as a result of interfractional variation of marker placement. A cohort of five patients treated with multiple-fraction tandem and ovoid high-dose-rate (HDR) brachytherapy was studied. The cervical os point and the orientation of the applicators were matched among all fractional plans for each patient. Rectal points obtained from all fractions were then input into each clinical treated plan. New fractional rectal doses were obtained and a new cumulative rectal dose for each patient was calculated. The maximum interfractional variation of distances between rectal dose points and the closest source positions was 1.1 cm. The corresponding maximum variability of fractional rectal dose was 65.5%. The percentage difference in cumulative rectal dose estimation for each patient was 5.4%, 19.6%, 34.6%, 23.4%, and 13.9%, respectively. In conclusion, care should be taken when using rectal markers as reference points for estimating rectal dose in HDR cervical brachytherapy. The best estimate of true rectal dose for each fraction should be determined by the most anterior point among all fractions.

  7. Assessing performance of single-sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed.

    PubMed

    Menéndez, Juan; Álvarez, Isabel; Fernandez, Iván; Menéndez-Arias, Nuria A; Goyache, Félix

    2016-07-01

    Estimating effective population size (N e ) using linkage disequilibrium (LD) information (N e( LD ) ) has the operational advantage of using a single sample. However, N e( LD ) estimates assume discrete generations and its performance are constrained by demographic issues. However, such concerns have received little empirical attention so far. The pedigree of the endangered Gochu Asturcelta pig breed includes individuals classified into discrete filial generations and individuals with generations overlap. Up to 780 individuals were typed with a set of 17 microsatellites. Performance of N e( LD ) was compared with N e estimates obtained using genealogical information, molecular coancestry (N e(M) ) and a temporal (two-sample) method (N e( JR ) ). Molecular-based estimates of N e exceeded those obtained using pedigree data. Estimates of N e( LD ) for filial generations F3 and F4 (17.0 and 17.3, respectively) were lower and steadier than those obtained using yearly or biannual samplings. N e( LD ) estimated for samples including generations overlap could only be compared with those obtained for the discrete filial generations when sampling span approached a generation interval and demographic correction for bias was applied. Single-sample N e(M) estimates were lower than their N e( LD ) counterparts. N e(M) estimates are likely to partially reflect the number of founders rather than population size. In any case, estimates of LD and molecular coancestry tend to covary and, therefore, N e(M) and N e( LD ) can hardly be considered independent. Demographically adjusted estimates of N e( JR ) and N e( LD ) took comparable values when: (1) the two samples used for the former were separated by one equivalent to discrete generations in the pedigree and (2) sampling span used for the latter approached a generation interval. Overall, the empirical evidence given in this study suggested that the advantage of using single-sample methods to obtain molecular-based estimates of N e

  8. A Marker-Based Approach for the Automated Selection of a Single Segmentation from a Hierarchical Set of Image Segmentations

    NASA Technical Reports Server (NTRS)

    Tarabalka, Y.; Tilton, J. C.; Benediktsson, J. A.; Chanussot, J.

    2012-01-01

    The Hierarchical SEGmentation (HSEG) algorithm, which combines region object finding with region object clustering, has given good performances for multi- and hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. Two classification-based approaches for automatic marker selection are adapted and compared for this purpose. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. Three different implementations of the M-HSEG method are proposed and their performances in terms of classification accuracies are compared. The experimental results, presented for three hyperspectral airborne images, demonstrate that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for remote sensing image analysis.

  9. Molecular techniques in ecohealth research toolkit: facilitating estimation of aggregate gastroenteritis burden in an irrigated periurban landscape.

    PubMed

    Tserendorj, Ariuntuya; Anceno, Alfredo J; Houpt, Eric R; Icenhour, Crystal R; Sethabutr, Orntipa; Mason, Carl S; Shipin, Oleg V

    2011-09-01

    Assessment of microbial hazards associated with certain environmental matrices, livelihood strategies, and food handling practices are constrained by time-consuming conventional microbiological techniques that lead to health risk assessments of narrow geographic or time scope, often targeting very few pathogens. Health risk assessment based on one or few indicator organisms underestimates true disease burden due a number of coexisting causative pathogens. Here, we employed molecular techniques in a survey of Cryptosporidium parvum, Giardia lamblia, Campylobacter jejuni, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio cholera, and Rotavirus A densities in canal water with respect to seasonality and spatial distribution of point-nonpoint pollution sources. Three irrigational canals stretching across nearly a 150-km(2) periurban landscape, traditionally used for agricultural irrigation but function as vital part of municipal wastewater stabilization in recent years, were investigated. Compiled stochastic data (pathogen concentration, susceptible populations) and literature-obtained deterministic data (pathogen dose-response model parameter values) were used in estimating waterborne gastroenteritis burden. Exposure scenarios include swimming or fishing, consuming canal water-irrigated vegetables, and ingesting or inhaling water aerosols while working in canal water-irrigated fields. Estimated annual gastroenteritis burden due individual pathogens among the sampling points was -10.6log(10) to -2.2log(10) DALYs. Aggregated annual gastroenteritis burden due all the target pathogens per sampling point was -3.1log(10) to -1.9log(10) DALYs, far exceeding WHO acceptable limit of -6.0log(10) DALYs. The present approach will facilitate the comprehensive collection of surface water microbiological baseline data and setting of benchmarks for interventions aimed at reducing microbial hazards in similar landscapes worldwide. PMID:22146856

  10. Cellular and molecular research to reduce uncertainties in estimates of health effects from low-level radiation

    SciTech Connect

    Elkind, M.M.; Bedford, J.; Benjamin, S.A.; Waldren, C.A. ); Gotchy, R.L. )

    1990-10-01

    A study was undertaken by five radiation scientists to examine the feasibility of reducing the uncertainties in the estimation of risk due to protracted low doses of ionizing radiation. In addressing the question of feasibility, a review was made by the study group: of the cellular, molecular, and mammalian radiation data that are available; of the way in which altered oncogene properties could be involved in the loss of growth control that culminates in tumorigenesis; and of the progress that had been made in the genetic characterizations of several human and animal neoplasms. On the basis of this analysis, the study group concluded that, at the present time, it is feasible to mount a program of radiation research directed at the mechanism(s) of radiation-induced cancer with special reference to risk of neoplasia due to protracted, low doses of sparsely ionizing radiation. To implement a program of research, a review was made of the methods, techniques, and instruments that would be needed. This review was followed by a survey of the laboratories and institutions where scientific personnel and facilities are known to be available. A research agenda of the principal and broad objectives of the program is also discussed. 489 refs., 21 figs., 14 tabs.

  11. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

    PubMed Central

    2015-01-01

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

  12. Effect of thermal processing on estimated metabolizable protein supply to dairy cattle from camelina seeds: relationship with protein molecular structural changes.

    PubMed

    Peng, Quanhui; Khan, Nazir A; Wang, Zhisheng; Zhang, Xuewei; Yu, Peiqiang

    2014-08-20

    This study evaluated the effect of thermal processing on the estimated metabolizable protein (MP) supply to dairy cattle from camelina seeds (Camelina sativa L. Crantz) and determined the relationship between heat-induced changes in protein molecular structural characteristics and the MP supply. Seeds from two camelina varieties were sampled in two consecutive years and were either kept raw or were heated in an autoclave (moist heating) or in an air-draft oven (dry heating) at 120 °C for 1 h. The MP supply to dairy cattle was modeled by three commonly used protein evaluation systems. The protein molecular structures were analyzed by Fourier transform/infrared-attenuated total reflectance molecular spectroscopy. The results showed that both the dry and moist heating increased the contents of truly absorbable rumen-undegraded protein (ARUP) and total MP and decreased the degraded protein balance (DPB). However, the moist-heated camelina seeds had a significantly higher (P < 0.05) content of ARUP and total MP and a significantly lower (P < 0.05) content of DPB than did the dry-heated camelina seeds. The regression equations showed that intensities of the protein molecular structural bands can be used to estimate the contents of ARUP, MP, and DPB with high accuracy (R(2) > 0.70). These results show that protein molecular structural characteristics can be used to rapidly assess the MP supply to dairy cattle from raw and heat-treated camelina seeds. PMID:25046194

  13. A comparison of morphological and molecular-based surveys to estimate the species richness of Chaetoceros and Thalassiosira (bacillariophyta), in the Bay of Fundy.

    PubMed

    Hamsher, Sarah E; LeGresley, Murielle M; Martin, Jennifer L; Saunders, Gary W

    2013-01-01

    The goal of this study was to compare the ability of morphology and molecular-based surveys to estimate species richness for two species-rich diatom genera, Chaetoceros Ehrenb. and Thalassiosira Cleve, in the Bay of Fundy. Phytoplankton tows were collected from two sites at intervals over two years and subsampled for morphology-based surveys (2010, 2011), a culture-based DNA reference library (DRL; 2010), and a molecular-based survey (2011). The DRL and molecular-based survey utilized the 3' end of the RUBISCO large subunit (rbcL-3P) to identify genetic species groups (based on 0.1% divergence in rbcL-3P), which were subsequently identified morphologically to allow comparisons to the morphology-based survey. Comparisons were compiled for the year (2011) by site (n = 2) and by season (n = 3). Of the 34 taxa included in the comparisons, 50% of taxa were common to both methods, 35% were unique to the molecular-based survey, and 12% were unique to the morphology-based survey, while the remaining 3% of taxa were unidentified genetic species groups. The morphology-based survey excelled at identifying rare taxa in individual tow subsamples, which were occasionally missed with the molecular approach used here, while the molecular methods (the DRL and molecular-based survey), uncovered nine cryptic species pairs and four previously overlooked species. The last mentioned were typically difficult to identify and were generically assigned to Thalassiosira spp. during the morphology-based survey. Therefore, for now we suggest a combined approach encompassing routine morphology-based surveys accompanied by periodic molecular-based surveys to monitor for cryptic and difficult to identify taxa. As sequencing technologies improve, molecular-based surveys should become routine, leading to a more accurate representation of species composition and richness in monitoring programs. PMID:24130665

  14. Methods for Locating the Tibio-Femoral Contact Pathway in Total Knee Replacements Using Marker-Based Gait Analysis and Standard Radiography

    PubMed Central

    Lundberg, Hannah J; Swanson, Andrea; Knowlton, Christopher; Inoue, Nozomu; Wimmer, Markus A

    2014-01-01

    Introduction The purpose of this study was to develop and test techniques for tracking the path of contact between the tibial and femoral total knee replacement components during level over-ground walking. The tibio-femoral path of contact could be an indicator of the in vivo performance of a total knee replacement as an estimator of areas of contact between the implant components. A longer contact path, indicative of more sliding between the implant components during walking, could indicate an implant at risk for increased wear. In addition, the tibio-femoral contact path determines the position and length of the muscle and ligament lever arms about the knee, and can subsequently influence knee contact force calculations. Methods Two methods were developed to predict the tibio-femoral contact pathways for total knee replacement devices. Both methods used patient-specific knee kinematics obtained during gait analysis, standard radiographs obtained during clinical follow-ups, and point-clouds of the tibial and femoral bearing surfaces. The validity of the techniques was evaluated with knee wear simulator tests and comparisons to wear scars on postmortem retrieved tibial components. Results The average total anterior-posterior distance covered by the contact path for ten patients implanted with a total knee replacement was 29.01 mm on the lateral side, and 21.80 mm on the medial side. Both methods for predicting the tibiofemoral contact pathways yielded similar results, and fell within the wear scars of simulator-tested and postmortem retrieved implants. Conclusions The methods for predicting the tibio-femoral contact pathway using marker-based gait analysis and standard clinical radiographs are computationally simple, and reliably predict contact path characteristics as evaluated against wear scars from knee wear simulator tests and postmortem retrieved implants. PMID:25328466

  15. Effective one step-iterative fiducial marker-based compensation for involuntary motion in weight-bearing C-arm cone-beam CT scanning of knees

    NASA Astrophysics Data System (ADS)

    Choi, Jang-Hwan; Maier, Andreas; Berger, Martin; Fahrig, Rebecca

    2014-03-01

    We previously introduced three different fiducial marker-based correction methods (2D projection shifting, 2D projection warping, and 3D image warping) for patients' involuntary motion in the lower body during weight-bearing Carm CT scanning. The 3D warping method performed better than 2D methods since it could more accurately take into account the lower body motion in 3D. However, as the 3D warping method applies different rotational and translational movement to the reconstructed image for each projection frame, distance-related weightings were slightly twisted and thus result in overlaying background noise over the entire image. In order to suppress background noise and artifacts (e.g. metallic marker-caused streaks), the 3D warping method has been improved by incorporating bilateral filtering and a Landwebertype iteration in one step. A series of projection images of five healthy volunteers standing at various flexion angles were acquired using a C-arm cone-beam CT system with a flat panel. A horizontal scanning trajectory of the C-arm was calibrated to generate projection matrices. Using the projection matrices, the static reference marker coordinates in 3D were estimated and used for the improved 3D warping method. The improved 3D warping method effectively reduced background noise down below the noise level of 2D methods and also eliminated metal-generated streaks. Thus, improved visibility of soft tissue structures (e.g. fat and muscle) was achieved while maintaining sharp edges at bone-tissue interfaces. Any high resolution weight-bearing cone-beam CT system can apply this method for motion compensation.

  16. Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau

    NASA Astrophysics Data System (ADS)

    McFadden, C. S.; Brown, A. S.; Brayton, C.; Hunt, C. B.; van Ofwegen, L. P.

    2014-06-01

    The application of DNA barcoding to anthozoan cnidarians has been hindered by their slow rates of mitochondrial gene evolution and the failure to identify alternative molecular markers that distinguish species reliably. Among octocorals, however, multilocus barcodes can distinguish up to 70 % of morphospecies, thereby facilitating the identification of species that are ecologically important but still very poorly known taxonomically. We tested the ability of these imperfect DNA barcodes to estimate species richness in a biodiversity survey of the shallow-water octocoral fauna of Palau using multilocus ( COI, mtMutS, 28S rDNA) sequences obtained from 305 specimens representing 38 genera of octocorals. Numbers and identities of species were estimated independently (1) by a taxonomic expert using morphological criteria and (2) by assigning sequences to molecular operational taxonomic units (MOTUs) using predefined genetic distance thresholds. Estimated numbers of MOTUs ranged from 73 to 128 depending on the barcode and distance threshold applied, bracketing the estimated number of 118 morphospecies. Concordance between morphospecies identifications and MOTUs ranged from 71 to 75 % and differed little among barcodes. For the speciose and ecologically dominant genus Sinularia, however, we were able to identify 95 % of specimens correctly simply by comparing mtMutS sequences and in situ photographs of colonies to an existing vouchered database. Because we lack a clear understanding of species boundaries in most of these taxa, numbers of morphospecies and MOTUs are both estimates of the true species diversity, and we cannot currently determine which is more accurate. Our results suggest, however, that the two methods provide comparable estimates of species richness for shallow-water Indo-Pacific octocorals. Use of molecular barcodes in biodiversity surveys will facilitate comparisons of species richness and composition among localities and over time, data that do not

  17. Pleistocene Speciation in North American Lichenized Fungi and the Impact of Alternative Species Circumscriptions and Rates of Molecular Evolution on Divergence Estimates

    PubMed Central

    Leavitt, Steven D.; Lumbsch, H. Thorsten; Stenroos, Soili; Clair, Larry L. St.

    2013-01-01

    Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree framework. PMID:24386465

  18. Quality Assurance and Commissioning of an Infrared Marker-Based Patient Positioning System for Frameless Extracranial Stereotactic Radiotherapy

    PubMed Central

    Gupta, Tejpal; Phurailatpam, Reena; Ajay, Mishra; Rajeshri, Pai; Pranshu, Mohindra; Supriya, Chopra

    2007-01-01

    Rapid advancements in imaging technology have led to remarkable improvements in identification and localization of tumors, ushering the era of high-precision techniques in contemporary radiotherapy practice. However, uncertainties in patient set-up and organ motion during a course of fractionated radiotherapy can compromise precision of radiation therapy. Excellent accuracy has been achieved with invasive and non-invasive fixation systems for stereotactic radiotherapy. This report describes the commissioning procedure and Quality Assurance studies done to evaluate the accuracy of isocenter localization by an infrared marker-based positioning system (ExacTrac). The ExacTrac has two infrared cameras that emit and detect infrared rays from reflective markers and construct three-dimensional coordinates of each marker. It detects the difference of the actual isocenter position from the planned isocenter coordinates in three translational (lateral, longitudinal, vertical, or x,y,z axes) and three rotational axes (six degree of freedom). This study performed on a flat and static phantom shows excellent accuracy achieved by the ExacTrac system. The positioning accuracy of ExacTrac (± 1 mm translational displacement and ± 1° rotational errors) can be a valuable tool in implementing frameless extracranial stereotactic radiotherapy. Nevertheless, it needs to be further evaluated on patients with inherent motion and greater positional uncertainty before being adopted in clinical practice. PMID:23675057

  19. Model-based approach for human kinematics reconstruction from markerless and marker-based motion analysis systems.

    PubMed

    Sholukha, V; Bonnechere, B; Salvia, P; Moiseev, F; Rooze, M; Van Sint Jan, S

    2013-09-27

    Modeling tools related to the musculoskeletal system have been previously developed. However, the integration of the real underlying functional joint behavior is lacking and therefore available kinematic models do not reasonably replicate individual human motion. In order to improve our understanding of the relationships between muscle behavior, i.e. excursion and motion data, modeling tools must guarantee that the model of joint kinematics is correctly validated to ensure meaningful muscle behavior interpretation. This paper presents a model-based method that allows fusing accurate joint kinematic information with motion analysis data collected using either marker-based stereophotogrammetry (MBS) (i.e. bone displacement collected from reflective markers fixed on the subject's skin) or markerless single-camera (MLS) hardware. This paper describes a model-based approach (MBA) for human motion data reconstruction by a scalable registration method for combining joint physiological kinematics with limb segment poses. The presented results and kinematics analysis show that model-based MBS and MLS methods lead to physiologically-acceptable human kinematics. The proposed method is therefore available for further exploitation of the underlying model that can then be used for further modeling, the quality of which will depend on the underlying kinematic model. PMID:23972432

  20. Estimate of Top-of-Atmosphere Albedo for a Molecular Atmosphere over Ocean using Clouds and the Earth's Radiant Energy System (CERES) Measurements

    NASA Technical Reports Server (NTRS)

    Kato, S.; Loeb, N. G.; Rutledge, C. K.

    2002-01-01

    The shortwave broadband albedo at the top of a molecular atmosphere over ocean between 40deg N and 40deg S is estimated using radiance measurements from the Clouds and the Earth's Radiant Energy System (CERES) instrument and the Visible Infrared Scanner (VIRS) aboard the Tropical Rainfall Measuring Mission (TRMM) satellite. The albedo monotonically increases from 0.059 at a solar zenith angle of 10deg to 0.107 at a solar zenith angle of 60deg. The estimated uncertainty in the albedo is 3.5 x 10(exp -3) caused by the uncertainty in CERES-derived irradiances, uncertainty in VIRS-derived aerosol optical thicknesses, variations in ozone and water vapor, and variations in surface wind speed. The estimated uncertainty is similar in magnitude to the standard deviation of 0.003 that is derived from 72 areas divided by 20deg latitude by 20deg longitude grid boxes. The empirically estimated albedo is compared with the modeled albedo using a radiative transfer model combined with an ocean surface bidirectional reflectivity model. The modeled albedo with standard tropical atmosphere is 0.061 and 0.111 at the solar zenith angles of 10deg and 60deg, respectively. This empirically estimated albedo can be used to estimate the direct radiative effect of aerosols at the top of the atmosphere over oceans.

  1. Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

    NASA Astrophysics Data System (ADS)

    Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R.

    2016-03-01

    A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H2O)n (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculation MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%-65% saving of computational time. The methodology has a potential for application to molecular clusters containing ˜100 atoms.

  2. Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

    PubMed Central

    Fukunishi, Yoshifumi; Nakamura, Haruki

    2012-01-01

    We have developed a method for estimating protein-ligand binding free energy (ΔG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the ΔG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the ΔG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated ΔG values was 0.81, and the average error of ΔG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation. PMID:24281257

  3. Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)-Tuned Range-Separated Density Functional Approach.

    PubMed

    Sun, Haitao; Ryno, Sean; Zhong, Cheng; Ravva, Mahesh Kumar; Sun, Zhenrong; Körzdörfer, Thomas; Brédas, Jean-Luc

    2016-06-14

    We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a nonempirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values, as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials. PMID:27183355

  4. Estimating the Gibbs energy of hydration from molecular dynamics trajectories obtained by integral equations of the theory of liquids in the RISM approximation

    NASA Astrophysics Data System (ADS)

    Tikhonov, D. A.; Sobolev, E. V.

    2011-04-01

    A method of integral equations of the theory of liquids in the reference interaction site model (RISM) approximation is used to estimate the Gibbs energy averaged over equilibrium trajectories computed by molecular mechanics. Peptide oxytocin is selected as the object of interest. The Gibbs energy is calculated using all chemical potential formulas introduced in the RISM approach for the excess chemical potential of solvation and is compared with estimates by the generalized Born model. Some formulas are shown to give the wrong sign of Gibbs energy changes when peptide passes from the gas phase into water environment; the other formulas give overestimated Gibbs energy changes with the right sign. Note that allowance for the repulsive correction in the approximate analytical expressions for the Gibbs energy derived by thermodynamic perturbation theory is not a remedy.

  5. Estimation of octanol/water partition coefficient and aqueous solubility of environmental chemicals using molecular fingerprints and machine learning methods

    EPA Science Inventory

    Octanol/water partition coefficient (logP) and aqueous solubility (logS) are two important parameters in pharmacology and toxicology studies, and experimental measurements are usually time-consuming and expensive. In the present research, novel methods are presented for the estim...

  6. Molecular statics calculations of proton binding to goethite surfaces: A new approach to estimation of stability constants for multisite surface complexation models

    NASA Astrophysics Data System (ADS)

    Rustad, James R.; Felmy, Andrew R.; Hay, Benjamin P.

    1996-05-01

    A new approach to estimating stability constants for proton binding in multisite surface complexation models is presented. The method is based on molecular statics computation of energies for the formation of proton vacancies and interstitials in ideal periodic slabs representing the (100), (110), (010), (001), and (021) surfaces of goethite. Gas-phase energies of clusters representing the hydrolysis products of ferric iron are calculated using the same potential energy functions used for the surface. These energies are linearly related to the hydrolysis constants for ferric iron in aqueous solution. Stability constants for proton binding at goethite surfaces are estimated by assuming the same log K- Δ E relationship for goethite surface protonation reactions. These stability constants predict a pH of zero charge of 8.9, in adequate agreement with measurements on CO 2-free goethite. The estimated stability constants differ significantly from previous estimations based on Pauling bond strength. We find that nearly all the surface oxide ions are reactive; nineteen of the twenty-six surface sites investigated have log Kint between 7.7 and 9.4. This implies a site density between fifteen and sixteen reactive sites/nm for crystals dominated by (110) and (021) crystal faces.

  7. Molecular statics calculations of proton binding to goethite surfaces: A new approach to estimation of stability constants for multisite surface complexation models

    SciTech Connect

    Rustad, J.R.; Felmy, A.R.; Hay, B.P.

    1996-05-01

    A new approach to estimating stability constants for proton binding in multisite surface complexation models is presented. The method is based on molecular statics computation of energies for the formation of proton vacancies and interstitials in ideal periodic slabs representing the (100), (110), (010), (001), and (021) surfaces of goethite. Gas-phase energies of clusters representing the hydrolysis products of ferric iron are calculated using the same potential energy functions used for the surface. These energies are linearly related to the hydrolysis constants for ferric iron in aqueous solution. Stability constants for proton binding at goethite surfaces are estimated by assuming the same log K-{Delta}E relationship for goethite surface protonation reactions. These stability constants predict a pH of zero charge of 8.9, in adequate agreement with measurements on CO{sub 2}-free goethite. The estimated stability constants differ significantly from previous estimations based on Pauling bond strength. We find that nearly all the surface oxide ions are reactive; nineteen of the twenty-six surface sites investigated have log K{sup int} between 7.7 and 9.4. This implies a site density between fifteen and sixteen reactive sites/nm for crystals dominated by (110) and (021) crystal faces. 39 refs., 8 figs., 4 tabs.

  8. Ambient gas/particle partitioning. 3. Estimating partition coefficients of apolar, polar, and ionizable organic compounds by their molecular structure.

    PubMed

    Arp, Hans Peter H; Gosses, Kai-Uwe

    2009-03-15

    Equilibrium gas/particle partitioning coefficients of terrestrial aerosols, Kip, are dependent on various intermolecular interactions that can be quantified by experimentally determined compound-specific descriptors. For many compounds of environmental interest, such as emerging contaminants and atmospheric phototransformation products, these compound-specific descriptors are unknown or immeasurable. Often, only the molecular structure is known. Here we present the ability of two computer programs to predict equilibrium partitioning to terrestrial aerosols solely on the basis of molecular structure: COSMOtherm and SPARC. The greatest hurdle with designing such an approach is to identify suitable molecular surrogates to represent the dominating sorbing phases, which for ambient terrestrial aerosols are the water insoluble organic matter (WIOM) phase and the mixed-aqueous phase. For the WI0M phase, hypothetical urban secondary organic aerosol structural units from Kalberer et al. Science 2004, 303, 1659-1662 were investigated as input surrogates, and for the mixed-aqueous phase mildly acidic water was used as a surrogate. Using a validation data set of more than 1400 experimentally determined Kip values for polar, apolar, and ionic compounds ranging over 9 orders of magnitude (including semivolatile compounds such as PCDD/Fs, pesticides, and PBDEs), SPARC and COSMOtherm were generally able to predict Kip values well within an order of magnitude over an ambient range of temperature and relative humidity. This is remarkable as these two models were not fitted or calibrated to any experimental data. As these models can be used for potentially any organic molecule, they are particularly recommended for environmental screening purposes and for use when experimental compound descriptor data are not available. PMID:19368193

  9. Baseline correction of a correlation model for improving the prediction accuracy of infrared marker-based dynamic tumor tracking.

    PubMed

    Akimoto, Mami; Nakamura, Mitsuhiro; Mukumoto, Nobutaka; Yamada, Masahiro; Tanabe, Hiroaki; Ueki, Nami; Kaneko, Shuji; Matsuo, Yukinori; Mizowaki, Takashi; Kokubo, Masaki; Hiraoka, Masahiro

    2015-01-01

    We previously found that the baseline drift of external and internal respiratory motion reduced the prediction accuracy of infrared (IR) marker-based dynamic tumor tracking irradiation (IR Tracking) using the Vero4DRT system. Here, we proposed a baseline correction method, applied immediately before beam delivery, to improve the prediction accuracy of IR Tracking. To perform IR Tracking, a four-dimensional (4D) model was constructed at the beginning of treatment to correlate the internal and external respiratory signals, and the model was expressed using a quadratic function involving the IR marker position (x) and its velocity (v), namely function F(x,v). First, the first 4D model, F1st(x,v), was adjusted by the baseline drift of IR markers (BDIR) along the x-axis, as function F'(x,v). Next, BDdetect, that defined as the difference between the target positions indicated by the implanted fiducial markers (Pdetect) and the predicted target positions with F'(x,v) (Ppredict) was determined using orthogonal kV X-ray images at the peaks of the Pdetect of the end-inhale and end-exhale phases for 10 s just before irradiation. F'(x,v) was corrected with BDdetect to compensate for the residual error. The final corrected 4D model was expressed as Fcor(x,v) = F1st{(x-BDIR),v}-BDdetect. We retrospectively applied this function to 53 paired log files of the 4D model for 12 lung cancer patients who underwent IR Tracking. The 95th percentile of the absolute differences between Pdetect and Ppredict (|Ep|) was compared between F1st(x,v) and Fcor(x,v). The median 95th percentile of |Ep| (units: mm) was 1.0, 1.7, and 3.5 for F1st(x,v), and 0.6, 1.1, and 2.1 for Fcor(x,v) in the left-right, anterior-posterior, and superior-inferior directions, respectively. Over all treatment sessions, the 95th percentile of |Ep| peaked at 3.2 mm using Fcor(x,v) compared with 8.4 mm using F1st(x,v). Our proposed method improved the prediction accuracy of IR Tracking by correcting the baseline drift

  10. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families

    PubMed Central

    van Tuinen, Marcel; Torres, Christopher R.

    2015-01-01

    Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer

  11. Cytogenetic and molecular characterization of eight new reciprocal translocations in the pig species. Estimation of their incidence in French populations

    PubMed Central

    Ducos, Alain; Pinton, Alain; Yerle, Martine; Séguéla, Anne; Berland, Hélène-Marie; Brun-Baronnat, Corinne; Bonnet, Nathalie; Darré, Roland

    2002-01-01

    Eight new cases of reciprocal translocation in the domestic pig are described. All the rearrangements were highlighted using GTG banding techniques. Chromosome painting experiments were also carried out to confirm the proposed hypotheses and to accurately locate the breakpoints. Three translocations, rcp(4;6)(q21;p14), rcp(2;6)(p17;q27) and rcp(5;17)(p12;q13) were found in boars siring small litters (8.3 and 7.4 piglets born alive per litter, on average, for translocations 2/6 and 5/17, respectively). The remaining five, rcp(5;8)(p12;q21), rcp(15;17)(q24;q21), rcp(7;8)(q24;p21), rcp(5;8)(p11;p23) and rcp(3;15)(q27;q13) were identified in young boars controlled before entering reproduction. A decrease in prolificacy of 22% was estimated for the 3/15 translocation after reproduction of the boar carrier. A parental origin by inheritance of the translocation was established for the (5;8)(p11;p23) translocation. The overall incidence of reciprocal translocations in the French pig populations over the 2000/2001 period was estimated (0.34%). PMID:12081804

  12. Estimating contemporary early life-history dispersal in an estuarine fish: integrating molecular and otolith elemental approaches.

    PubMed

    Bradbury, I R; Campana, S E; Bentzen, P

    2008-03-01

    Dispersal during the early life history of the anadromous rainbow smelt, Osmerus mordax, was examined using assignment testing and mixture analysis of multilocus genotypes and otolith elemental composition. Six spawning areas and associated estuarine nurseries were sampled throughout southeastern Newfoundland. Samples of adults and juveniles isolated by > 25 km displayed moderate genetic differentiation (F(ST) ~ 0.05), whereas nearby (< 25 km) spawning and nursery samples displayed low differentiation (F(ST) < 0.01). Self-assignment and mixture analysis of adult spawning samples supported the hypothesis of independence of isolated spawning locations (> 80% self-assignment) with nearby runs self-assigning at rates between 50 % and 70%. Assignment and mixture analysis of juveniles using adult baselines indicated high local recruitment at several locations (70-90%). Nearby (< 25 km) estuaries at the head of St Mary's Bay showed mixtures of individuals (i.e. 20-40% assignment to adjacent spawning location). Laser ablation inductively coupled mass spectrometry transects across otoliths of spawning adults of unknown dispersal history were used to estimate dispersal among estuaries across the first year of life. Single-element trends and multivariate discriminant function analysis (Sr:Ca and Ba:Ca) classified the majority of samples as estuarine suggesting limited movement between estuaries (< 0.5%). The mixtures of juveniles evident in the genetic data at nearby sites and a lack of evidence of straying in the otolith data support a hypothesis of selective mortality of immigrants. If indeed selective mortality of immigrants reduces the survivorship of dispersers, estimates of dispersal in marine environments that neglect survival may significantly overestimate gene flow. PMID:18321254

  13. An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide.

    PubMed

    Guan, Yihong; Zhu, Qinfang; Huang, Delai; Zhao, Shuyi; Jan Lo, Li; Peng, Jinrong

    2015-01-01

    The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed MW approximately 13 kDa larger than its predicted MW. The first 188 AA in Def is defined by a glutamate-rich region containing ~35.6% of acidic AA. In this report, we analyzed the relationship between the SDS PAGE-displayed MW of thirteen peptides derived from Def and the AA composition in each peptide. We found that the difference between the predicted and SDS PAGE-displayed MW showed a linear correlation with the percentage of acidic AA that fits the equation y = 276.5x - 31.33 (x represents the percentage of acidic AA, 11.4% ≤ x ≤ 51.1%; y represents the average ΔMW per AA). We demonstrated that this equation could be applied to predict the SDS PAGE-displayed MW for thirteen different natural acidic proteins. PMID:26311515

  14. Estimation of interaction between oriented immobilized green fluorescent protein and its antibody by high performance affinity chromatography and molecular docking.

    PubMed

    Li, Qian; Wang, Jing; Yang, Lingjian; Gao, Xiaokang; Chen, Hongwei; Zhao, Xinfeng; Bian, Liujiao; Zheng, Xiaohui

    2015-07-01

    Although green fluorescence protein (GFP) and its antibody are widely used to track a protein or a cell in life sciences, the binding behavior between them remains unclear. In this work, diazo coupling method that synthesized a new stationary GFP was oriented immobilized on the surface of macro-porous silica gel by a phase. The stationary phase was utilized to confirm the validation of injection amount-dependent analysis in exploring protein-protein interaction that use GFP antibody as a probe. GFP antibody was proved to have one type of binding site on immobilized GFP. The number of binding site and association constant were calculated to be (6.41 ± 0.76) × 10(-10) M and (1.39 ± 0.12) × 10(9) M(-1). Further analysis by molecular docking showed that the binding of GFP to its antibody is mainly driven by hydrogen bonds and salt bridges. These results indicated that injection amount-dependent analysis is capable of exploring the protein-protein interactions with the advantages of ligand and time saving. It is a valuable methodology for the ligands, which are expensive or difficult to obtain. PMID:25727342

  15. The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations.

    PubMed

    Vogt, Natalja; Demaison, Jean; Cocinero, Emilio J; Écija, Patricia; Lesarri, Alberto; Rudolph, Heinz Dieter; Vogt, Jürgen

    2016-06-21

    Fructose and deoxyribose (24 and 19 atoms, respectively) are too large for determining accurate equilibrium structures, either by high-level ab initio methods or by experiments alone. We show in this work that the semiexperimental (SE) mixed estimation (ME) method offers a valuable alternative for equilibrium structure determinations in moderate-sized molecules such as these monosaccharides or other biochemical building blocks. The SE/ME method proceeds by fitting experimental rotational data for a number of isotopologues, which have been corrected with theoretical vibration-rotation interaction parameters (αi), and predicate observations for the structure. The derived SE constants are later supplemented by carefully chosen structural parameters from medium level ab initio calculations, including those for hydrogen atoms. The combined data are then used in a weighted least-squares fit to determine an equilibrium structure (r). We applied the ME method here to fructose and 2-deoxyribose and checked the accuracy of the calculations for 2-deoxyribose against the high level ab initio r structure fully optimized at the CCSD(T) level. We show that the ME method allows determining a complete and reliable equilibrium structure for relatively large molecules, even when experimental rotational information includes a limited number of isotopologues. With a moderate computational cost the ME method could be applied to larger molecules, thereby improving the structural evidence for subtle orbital interactions such as the anomeric effect. PMID:27212641

  16. The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils.

    PubMed

    Lenart-Boroń, Anna M; Wolny-Koładka, Katarzyna A; Boroń, Piotr M; Mitka, Józef R

    2014-01-01

    The occurrence of Azotobacter spp., which has beneficial effects on plant development, is related to various soil properties, such as pH and fertility. This study evaluated the prevalence of Azotobacter spp. in industrial (H) and agricultural soils (P) in Nowa Huta, Cracow and determined the phenotypic and genetic diversity of these bacteria. The examined bacteria were present in 40% of H and in 50% of P soils. Taxonomic identification of the bacterial isolates indicated the presence of three species--A. salinestris, A. chroococcum and A. vinelandii. The genetic diversity, determined using two fingerprinting methods--Random Analysis of Polymorphic DNA (RAPD) and Rep-PCR (BOX) revealed high level of population diversity. In AMOVA analysis most of diversity was attributed to within-population variation (76-85%), and only 3.78-6.18% was associated with among-group H and P variation. Global test of differences revealed distinct population structure within bacterial strains isolated from H and P areas only for BOX markers (Fst = 0.05732, P = 0.00275). Phenetic analyses: UPGMA and DCA better discriminated H and P groups based on RAPD data. Both BOX and RAPD methods provided an insight into the genetic complexity of Azotobacter spp. variation in soils of different land-use types. PMID:24798904

  17. A fast tree-based method for estimating column densities in adaptive mesh refinement codes. Influence of UV radiation field on the structure of molecular clouds

    NASA Astrophysics Data System (ADS)

    Valdivia, Valeska; Hennebelle, Patrick

    2014-11-01

    Context. Ultraviolet radiation plays a crucial role in molecular clouds. Radiation and matter are tightly coupled and their interplay influences the physical and chemical properties of gas. In particular, modeling the radiation propagation requires calculating column densities, which can be numerically expensive in high-resolution multidimensional simulations. Aims: Developing fast methods for estimating column densities is mandatory if we are interested in the dynamical influence of the radiative transfer. In particular, we focus on the effect of the UV screening on the dynamics and on the statistical properties of molecular clouds. Methods: We have developed a tree-based method for a fast estimate of column densities, implemented in the adaptive mesh refinement code RAMSES. We performed numerical simulations using this method in order to analyze the influence of the screening on the clump formation. Results: We find that the accuracy for the extinction of the tree-based method is better than 10%, while the relative error for the column density can be much more. We describe the implementation of a method based on precalculating the geometrical terms that noticeably reduces the calculation time. To study the influence of the screening on the statistical properties of molecular clouds we present the probability distribution function of gas and the associated temperature per density bin and the mass spectra for different density thresholds. Conclusions: The tree-based method is fast and accurate enough to be used during numerical simulations since no communication is needed between CPUs when using a fully threaded tree. It is then suitable to parallel computing. We show that the screening for far UV radiation mainly affects the dense gas, thereby favoring low temperatures and affecting the fragmentation. We show that when we include the screening, more structures are formed with higher densities in comparison to the case that does not include this effect. We

  18. Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates.

    PubMed

    Fleischer, R C; McIntosh, C E; Tarr, C L

    1998-04-01

    The Hawaiian Islands form as the Pacific Plate moves over a 'hot spot' in the earth's mantle where magma extrudes through the crust to build huge shield volcanos. The islands subside and erode as the plate carries them to the north-west, eventually to become coral atolls and seamounts. Thus islands are ordered linearly by age, with the oldest islands in the north-west (e.g. Kauai at 5.1 Ma) and the youngest in the south-east (e.g. Hawaii at 0.43 Ma). K-Ar estimates of the date of an island's formation provide a maximum age for the taxa inhabiting the island. These ages can be used to calibrate rates of molecular change under the following assumptions: (i) K-Ar dates are accurate; (ii) tree topologies show that derivation of taxa parallels the timing of island formation; (iii) populations do not colonize long after island emergence; (iv) the coalescent point for sister taxa does not greatly predate the formation of the colonized younger island; (v) saturation effects and (vi) among-lineage rate variation are minimal or correctable; and (vii) unbiased standard errors of distances and regressions can be estimated from multiple pairwise comparisons. We use the approach to obtain overall corrected rate calibrations for: (i) part of the mitochondrial cytochrome b gene in Hawaiian drepanidines (0.016 sequence divergence/Myr); (ii) the Yp1 gene in Hawaiian Drosophila (0.019/Myr Kambysellis et al. 1995); and (iii) parts of the mitochondrial 12S and 16S rRNA and tRNAval in Laupala crickets (0.024-0.102/Myr, Shaw 1996). We discuss the reliability of the estimates given the assumptions (i-vii) above and contrast the results with previous calibrations of Adh in Hawaiian Drosophila and chloroplast DNA in lobeliods. PMID:9628004

  19. Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The widespread use of the set of MTDFREML computer programs for genetic evaluation and estimation of genetic parameters has led to significant improvement in traits of economic importance. The initial version of this software package, however, was generally limited to use of pedigree-based relations...

  20. SU-E-J-24: Can Fiducial Marker-Based Setup Using ExacTrac Be An Alternative to Soft Tissue-Based Setup Using Cone-Beam CT for Prostate IMRT?

    SciTech Connect

    Tanabe, S; Utsunomiya, S; Abe, E; Aoyama, H; Satou, H; Sakai, H; Yamada, T

    2015-06-15

    Purpose: To assess an accuracy of fiducial maker-based setup using ExacTrac (ExT-based setup) as compared with soft tissue-based setup using Cone-beam CT (CBCT-based setup) for patients with prostate cancer receiving intensity-modulated radiation therapy (IMRT) for the purpose of investigating whether ExT-based setup can be an alternative to CBCT-based setup. Methods: The setup accuracy was analyzed prospectively for 7 prostate cancer patients with implanted three fiducial markers received IMRT. All patients were treated after CBCT-based setup was performed and corresponding shifts were recorded. ExacTrac images were obtained before and after CBCT-based setup. The fiducial marker-based shifts were calculated based on those two images and recorded on the assumption that the setup correction was carried out by fiducial marker-based auto correction. Mean and standard deviation of absolute differences and the correlation between CBCT and ExT shifts were estimated. Results: A total of 178 image dataset were analyzed. On the differences between CBCT and ExT shifts, 133 (75%) of 178 image dataset resulted in smaller differences than 3 mm in all dimensions. Mean differences in the anterior-posterior (AP), superior-inferior (SI), and left-right (LR) dimensions were 1.8 ± 1.9 mm, 0.7 ± 1.9 mm, and 0.6 ± 0.8 mm, respectively. The percentages of shift agreements within ±3 mm were 76% for AP, 90% for SI, and 100% for LR. The Pearson coefficient of correlation for CBCT and ExT shifts were 0.80 for AP, 0.80 for SI, and 0.65 for LR. Conclusion: This work showed that the accuracy of ExT-based setup was correlated with that of CBCT-based setup, implying that ExT-based setup has a potential ability to be an alternative to CBCT-based setup. The further work is to specify the conditions that ExT-based setup can provide the accuracy comparable to CBCT-based setup.

  1. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

    PubMed Central

    2014-01-01

    Background Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The

  2. Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds.

    PubMed

    Schrag, Tobias A; Möhring, Jens; Melchinger, Albrecht E; Kusterer, Barbara; Dhillon, Baldev S; Piepho, Hans-Peter; Frisch, Matthias

    2010-01-01

    The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective was to assess the usefulness of pedigree information in combination with the covariance between general combining ability (GCA) and per se performance of parental lines for HP prediction. In addition, we compared the prediction efficiency of AFLP and SSR marker data, estimated marker effects separately for reciprocal allelic configurations (among heterotic groups) of heterozygous marker loci in hybrids, and imputed missing AFLP marker data for marker-based HP prediction. Unbalanced field data of 400 maize dent x flint hybrids from 9 factorials and of 79 inbred parents were subjected to joint analyses with mixed linear models. The inbreds were genotyped with 910 AFLP and 256 SSR markers. Efficiency of prediction (R (2)) was estimated by cross-validation for hybrids having no or one parent evaluated in testcrosses. Best linear unbiased prediction of GCA and specific combining ability resulted in the highest efficiencies for HP prediction for both traits (R (2) = 0.6-0.9), if pedigree and line per se data were used. However, without such data, HP for grain yield was more efficiently predicted using molecular markers. The additional modifications of the marker-based approaches had no clear effect. Our study showed the high potential of joint analyses of hybrids and parental inbred lines for the prediction of performance of untested hybrids. PMID:19916002

  3. Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations.

    PubMed

    Majhi, Amit Kumar; Kanchi, Subbarao; Venkataraman, V; Ayappa, K G; Maiti, Prabal K

    2015-11-28

    Molecular dynamics simulations of electroporation in POPC and DPPC lipid bilayers have been carried out at different temperatures ranging from 230 K to 350 K for varying electric fields. The dynamics of pore formation, including threshold field, pore initiation time, pore growth rate, and pore closure rate after the field is switched off, was studied in both the gel and liquid crystalline (Lα) phases of the bilayers. Using an Arrhenius model of pore initiation kinetics, the activation energy for pore opening was estimated to be 25.6 kJ mol(-1) and 32.6 kJ mol(-1) in the Lα phase of POPC and DPPC lipids respectively at a field strength of 0.32 V nm(-1). The activation energy decreases to 24.2 kJ mol(-1) and 23.7 kJ mol(-1) respectively at a higher field strength of 1.1 V nm(-1). At temperatures below the melting point, the activation energy in the gel phase of POPC and DPPC increases to 28.8 kJ mol(-1) and 34.4 kJ mol(-1) respectively at the same field of 1.1 V nm(-1). The pore closing time was found to be higher in the gel than in the Lα phase. The pore growth rate increases linearly with temperature and quadratically with field, consistent with viscosity limited growth models. PMID:26372335

  4. Photoacoustic imaging of a near-infrared fluorescent marker based on dual wavelength pump-probe excitation

    NASA Astrophysics Data System (ADS)

    Märk, Julia; Theiss, Christoph; Schmitt, Franz-Josef; Laufer, Jan

    2014-03-01

    Photoacoustic imaging has been used to determine the spatial distribution of fluorophores, such as exogenous dyes and genetically expressed proteins, from images acquired in phantoms and in vivo. Most methods involve the acquisition of multiwavelength images and rely on differences in the absorption spectra of the tissue chromophores to estimate the spatial distribution and abundance of the latter using spectral decomposition techniques, such as model based inversion schemes. However, the inversion of 3-D images can be computationally expensive. Experimental approaches to localising contrast agents may therefore be useful, especially if quantification is not essential. This work aims to develop a method for determining the spatial distribution of a near-infrared fluorescent cell marker from images acquired using dual wavelength excitation. The excitation wavelengths coincided with the absorption and emission spectrum of the fluorophore. The contrast mechanism relies on reducing the excited state lifetime of the fluorophore by inducing stimulated emission. This changes the amount of energy thermalized by the fluorophore, and hence the photoacoustic signal amplitude. Since this is not observed in endogenous chromophores, the background may be removed by subtracting two images acquired with and without pulse delay between the pump and probe pulses. To characterise the fluorophore, the signal amplitude is measured in a cuvette as a function of pulse delay, concentration, and fluence. The spatial distribution of the fluorophore is determined from images acquired in realistic tissue phantoms. This method may be suitable for in vivo applications, such as imaging of exogenous or genetically expressed fluorescent cell markers.

  5. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)

    PubMed Central

    Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  6. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

    PubMed

    Han, Bin; Wang, Changbiao; Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  7. SU-E-J-39: Dosimetric Benefit of Implanted Marker-Based CBCT Setup for Definitive Prostatic Radiotherapy

    SciTech Connect

    Zhen, H; Wu, Z; Bluemenfeld, P; Chu, J; Wang, D

    2015-06-15

    Purpose Daily setup for definitive prostatic radiotherapy is challenged by suboptimal visibility of the prostate boundary and daily variation of rectum shape and position. For patients with improved bowel preparation, we conducted a dosimetric comparison between prostate implanted marker (IM)-based daily setup and anterior rectal wall (ARW)-based setup, with the hypothesis that the former leads to adequate target coverage with better rectal sparing. Methods Five IMRT/VMAT prostate cases with implanted markers were selected for analysis. Daily CBCT showed improvement of the rectal volume compared to planning CT. For each patient, the prostate and rectum were contoured on three CBCT images (fraction 5/15/25) with subsequent physician review. The CBCTs were then registered to a planning CT using IM-based registration. The deviation of ARW positions from planning CT to CBCT were analyzed at various sup-inf levels (−1.8 cm to 1.8 cm from level of prostate center). To estimate the potential dosimetric impact from ARW-based setup, the treatment plans were recalculated using A-P shifts ranging from −1mm to +6mm. Clinically important rectum DVH values including Dmax, D3cc and Dmean were computed. Results For the studied patients, we observed on average 32% rectum volume reduction from planning CT to CBCT. As a Results, the ARW on average shifts posteriorly by −1mm to +5mm, depending on the sup-inf level of observation, with larger shifts observed at more superior levels. Recalculation shows that when ARW shifts 1mm posteriorly, ARW-based CBCT setup leads to a 1.0%, 4.2%, and 3.2% increase in rectum Dmax, D3cc, and Dmean, respectively, compared to IM-based setup. The dosimetric deviations increase to 4.7%, 25.8% and 24.7% when ARW shifts 6mm posteriorly. No significant prostate-only dose difference was observed. Conclusion For patients with improved bowel preparation, IM-based CBCT setup leads to accurate prostate coverage along with significantly lower rectal dose

  8. A Preliminary Study of Genetic Variation in Populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, Estimated with AFLP Molecular Markers

    PubMed Central

    Andrade, I. M.; Mayo, S. J.; van den Berg, C.; Fay, M. F.; Chester, M.; Lexer, C.; Kirkup, D.

    2007-01-01

    Background and Aims This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. Methods Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. Key Results The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (FST = 0·1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0·6903, P = 0·002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise ΦPT = 0·137, P = 0·003) and as diverse (Nei's gene diversity, average He = 0·1832, 0·1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average He = 0·127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11·95 %, P = 0·037). Conclusions The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests. PMID:17823112

  9. Molecular sizes of amino acid transporters in the luminal membrane from the kidney cortex, estimated by the radiation-inactivation method.

    PubMed Central

    Béliveau, R; Demeule, M; Jetté, M; Potier, M

    1990-01-01

    Renal brush-border membrane vesicles from rat kidney cortex were irradiated in frozen state with a gamma-radiation source. Initial rates of influx into these vesicles were estimated for substrates such as L-glutamic acid, L-alanine, L-proline and L-leucine to establish the molecular sizes of their carriers. Transport was measured in initial-rate conditions to avoid artifacts arising from a decrease in the driving force caused by a modification of membrane permeability. Initial rates of Na(+)-independent uptakes for those four substrates appeared unaffected in the dose range used (0-6 Mrad), indicating that the passive permeability of the membrane towards these substrates was unaffected. However, at higher doses of irradiation the Na+ influx and the intravesicular volume evaluated by the uptake of glucose at equilibrium were altered by radiation. Thus Na(+)-dependent influx values were corrected for volume changes, and the corrected values were used to compute radiation-inactivation sizes of the transport systems. Their respective values for L-glutamic acid, L-proline, L-leucine and L-alanine carriers were 250, 224, 293 and 274 kDa. The presence of the free-radicals scavenger benzoic acid in the frozen samples during irradiation did not affect the uptake of glucose, phosphate and alkaline phosphatase activity. These results indicate that freezing samples in a cryoprotective medium was enough to prevent secondary inactivation of transporters by free radicals. Uptakes of beta-alanine and L-lysine were much less affected by radiation. The radiation-inactivation size of the Na(+)-dependent beta-alanine carrier was 127 kDa and that of the L-lysine carrier was 90 kDa. PMID:1971509

  10. Development of new candidate gene and EST-based molecular markers for Gossypium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New source of molecular markers accelerates the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum expressed sequence tag (EST) sequences, and validated them through amplification, ge...

  11. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect

    Reid, David M.; Collins, Michael A.

    2013-11-14

    A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

  12. Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

    SciTech Connect

    Yan, Guanghua Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray

    2014-10-15

    Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

  13. Molecular dynamics estimates for the thermodynamic properties of the Fe-S liquid cores of the Moon, Io, Europa, and Ganymede

    NASA Astrophysics Data System (ADS)

    Kuskov, O. L.; Belashchenko, D. K.

    2016-05-01

    A molecular dynamics (MD) simulation is performed for the physical and chemical properties of solid and liquid Fe-S solutions using the embedded atom model (EAM) potential as applied to the internal structure of the Moon, Io, Europa, and Ganymede under the assumption that the satellites' cores can be described by a two-component iron-sulfur system. Calculated results are presented for the thermodynamic parameters including the caloric, thermal, and elastic properties (specific heat, thermal expansion, Grüneisen parameter, density, compression module, velocity of sound, and adiabatic gradient) of the Fe-S solutions at sulfur concentrations of 0-18 at %, temperatures of up to 2500 K, and pressures of up to 14 GPa. The velocity of sound, which increases as pressure rises, is weakly dependent on sulfur concentration and temperature. For the Moon's outer Fe-S core (~5 GPa/2000 K), which contains 6-16 at % (3.5-10 wt %) sulfur, the density and the velocity of sound are estimated at 6.3-7.0 g/cm3 and 4000 ± 50 m/s, respectively. The MD calculations are compared with the interpretation of the Apollo observations (Weber et al., 2011) to show a good consistency of the velocity of P-waves in the Moon's liquid core whereas the thermodynamic density of the Fe-S core is not consistent with the seismic models with ρ = 5.1-5.2 g/cm3 (Garcia et al., 2011; Weber et al., 2011). The revision the density values for the core leads to the revision of its size and mass. At sulfur concentrations of 3.5-10 wt %, the density of the Fe-S melt is 20-30% higher that the seismic density of the core. Therefore, the most likely radius of the Moon's outer core must be less than 330 km (Weber et al., 2011) because, provided that the constraint on the Moon's mass and moment of inertia is satisfied, an increase in the density of the core must lead to a reduction of its radius. For Jupiter's Galilean moons Io, Europa, and Ganymede, constraints are obtained on the size, density, and sound velocity of

  14. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

    PubMed

    Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

    2014-05-21

    In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother

  15. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: Analysis of the accuracy and application to liquid systems

    SciTech Connect

    Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

    2014-05-21

    In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother

  16. ESTIMATION OF HYDROLYSIS RATE CONSTANTS OF CARBOXYLIC ACID ESTER AND PHOSPHATE ESTER COMPOUNDS IN AQUEOUS SYSTEMS FROM MOLECULAR STRUCTURE BY SPARC

    EPA Science Inventory

    SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid ester and phosphate ester compounds in aqueous non- aqueous and systems strictly from molecular structure. The energy diffe...

  17. Accuracy of an infrared marker-based patient positioning system (ExacTrac®) for stereotactic body radiotherapy in localizing the planned isocenter using fiducial markers

    NASA Astrophysics Data System (ADS)

    Montes-Rodríguez, María de los Ángeles; Hernández-Bojórquez, Mariana; Martínez-Gómez, Alma Angélica; Contreras-Pérez, Agustín; Negrete-Hernández, Ingrid Mireya; Hernández-Oviedo, Jorge Omar; Mitsoura, Eleni; Santiago-Concha, Bernardino Gabriel

    2014-11-01

    Stereotactic Body Radiation Therapy (SBRT) requires a controlled immobilization and position monitoring of patient and target. The purpose of this work is to analyze the performance of the imaging system ExacTrac® (ETX) using infrared and fiducial markers. Materials and methods: In order to assure the accuracy of isocenter localization, a Quality Assurance procedure was applied using an infrared marker-based positioning system. Scans were acquired of an inhouse-agar gel and solid water phantom with infrared spheres. In the inner part of the phantom, three reference markers were delineated as reference and one pellet was place internally; which was assigned as the isocenter. The iPlan® RT Dose treatment planning system. Images were exported to the ETX console. Images were acquired with the ETX to check the correctness of the isocenter placement. Adjustments were made in 6D the reference markers were used to fuse the images. Couch shifts were registered. The procedure was repeated for verification purposes. Results: The data recorded of the verifications in translational and rotational movements showed averaged 3D spatial uncertainties of 0.31 ± 0.42 mm respectively 0.82° ± 0.46° in the phantom and the first correction of these uncertainties were of 1.51 ± 1.14 mm respectively and 1.37° ± 0.61°. Conclusions: This study shows a high accuracy and repeatability in positioning the selected isocenter. The ETX-system for verifying the treatment isocenter position has the ability to monitor the tracing position of interest, making it possible to be used for SBRT positioning within uncertainty ≤1mm.

  18. Accuracy of an infrared marker-based patient positioning system (ExacTrac®) for stereotactic body radiotherapy in localizing the planned isocenter using fiducial markers

    SciTech Connect

    Montes-Rodríguez, María de los Ángeles Mitsoura, Eleni; Hernández-Bojórquez, Mariana; Martínez-Gómez, Alma Angélica; Contreras-Pérez, Agustín; Negrete-Hernández, Ingrid Mireya; Hernández-Oviedo, Jorge Omar; Santiago-Concha, Bernardino Gabriel

    2014-11-07

    Stereotactic Body Radiation Therapy (SBRT) requires a controlled immobilization and position monitoring of patient and target. The purpose of this work is to analyze the performance of the imaging system ExacTrac® (ETX) using infrared and fiducial markers. Materials and methods: In order to assure the accuracy of isocenter localization, a Quality Assurance procedure was applied using an infrared marker-based positioning system. Scans were acquired of an inhouse-agar gel and solid water phantom with infrared spheres. In the inner part of the phantom, three reference markers were delineated as reference and one pellet was place internally; which was assigned as the isocenter. The iPlan® RT Dose treatment planning system. Images were exported to the ETX console. Images were acquired with the ETX to check the correctness of the isocenter placement. Adjustments were made in 6D the reference markers were used to fuse the images. Couch shifts were registered. The procedure was repeated for verification purposes. Results: The data recorded of the verifications in translational and rotational movements showed averaged 3D spatial uncertainties of 0.31 ± 0.42 mm respectively 0.82° ± 0.46° in the phantom and the first correction of these uncertainties were of 1.51 ± 1.14 mm respectively and 1.37° ± 0.61°. Conclusions: This study shows a high accuracy and repeatability in positioning the selected isocenter. The ETX-system for verifying the treatment isocenter position has the ability to monitor the tracing position of interest, making it possible to be used for SBRT positioning within uncertainty ≤1mm.

  19. USING CARBOHYDRATES AS MOLECULAR MARKERS TO DETERMINE THE CONTRIBUTION OF AGRICULTURAL SOIL TO AMBIENT FINE AND COURSE PM

    EPA Science Inventory

    Project research optimized the quantification technique for carbohydrates that also allows quantification of other non-polar molecular markers based on using an isotopically labeled internal standard (D-glucose-1,2,3,4,5,6,6-d7) to monitor extraction efficiency, extraction usi...

  20. Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny.

    PubMed

    Bokma, Folmer

    2008-11-01

    Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis-Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny. PMID:18752617

  1. Estimation of molecular upper remission limit for monitoring minimal residual disease in peripheral blood of acute myeloid leukemia patients by WT1 expression

    PubMed Central

    POLÁK, JAROSLAV; HÁJKOVÁ, HANA; MAALAUFOVÁ-SOUKUPOVÁ, JACQUELINE; MARKOVÁ, JANA; ŠÁLEK, CYRIL; SCHWARZ, JIŘÍ; HAŠKOVEC, CEDRIK

    2012-01-01

    To date, approximately one half of acute myeloid leukaemia (AML) patients do not have a suitable specific molecular marker for monitoring minimal residual disease (MRD). The Wilm’s tumour gene (WT1) has been suggested as a possible molecular marker of MRD in AML. The expression of WT1 in peripheral blood (PB) was measured using quantitative real-time reverse transcription-polymerase chain reaction in peripheral leukocytes from 151 patients with AML at diagnosis. WT1 expression was significantly elevated, i.e. up to 3 orders of magnitude in the majority (80%) of AML patients at diagnosis compared to the PB of healthy donors. Sequence samples of the long-term followed-up AML patients treated with chemotherapy and/or allogeneic bone marrow transplantation were analysed for WT1 expression. The results revealed that the hematological relapses were preceded (median, 1.8 months) by an increase in WT1 gene expression. For the practical utility of this gene as a molecular marker of relapse, it was necessary to determine an upper remission limit, crossing which would signal hematological relapse. The upper remission limit was determined in our set of patients to be 0.02 WT1/ABL. The AML patients who consequently relapsed crossed this upper remission limit; however, those in permanent remission did not. Therefore, this upper remission limit could be taken as the border of molecular relapse of AML patients. Moreover, insufficient decline of WT1 expression under the upper remission limit following induction and/or consolidation therapy was associated with markedly high risk of relapse. The results show that our upper remission limit can be taken as the border of molecular relapse of AML patients and WT1 levels following initial therapy as a beneficial prognostic marker. PMID:22969857

  2. Accurate pose estimation using single marker single camera calibration system

    NASA Astrophysics Data System (ADS)

    Pati, Sarthak; Erat, Okan; Wang, Lejing; Weidert, Simon; Euler, Ekkehard; Navab, Nassir; Fallavollita, Pascal

    2013-03-01

    Visual marker based tracking is one of the most widely used tracking techniques in Augmented Reality (AR) applications. Generally, multiple square markers are needed to perform robust and accurate tracking. Various marker based methods for calibrating relative marker poses have already been proposed. However, the calibration accuracy of these methods relies on the order of the image sequence and pre-evaluation of pose-estimation errors, making the method offline. Several studies have shown that the accuracy of pose estimation for an individual square marker depends on camera distance and viewing angle. We propose a method to accurately model the error in the estimated pose and translation of a camera using a single marker via an online method based on the Scaled Unscented Transform (SUT). Thus, the pose estimation for each marker can be estimated with highly accurate calibration results independent of the order of image sequences compared to cases when this knowledge is not used. This removes the need for having multiple markers and an offline estimation system to calculate camera pose in an AR application.

  3. Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. Part I. Numerical model-based optimization

    PubMed Central

    Choi, Jang-Hwan; Fahrig, Rebecca; Keil, Andreas; Besier, Thor F.; Pal, Saikat; McWalter, Emily J.; Beaupré, Gary S.; Maier, Andreas

    2013-01-01

    Purpose: Human subjects in standing positions are apt to show much more involuntary motion than in supine positions. The authors aimed to simulate a complicated realistic lower body movement using the four-dimensional (4D) digital extended cardiac-torso (XCAT) phantom. The authors also investigated fiducial marker-based motion compensation methods in two-dimensional (2D) and three-dimensional (3D) space. The level of involuntary movement-induced artifacts and image quality improvement were investigated after applying each method. Methods: An optical tracking system with eight cameras and seven retroreflective markers enabled us to track involuntary motion of the lower body of nine healthy subjects holding a squat position at 60° of flexion. The XCAT-based knee model was developed using the 4D XCAT phantom and the optical tracking data acquired at 120 Hz. The authors divided the lower body in the XCAT into six parts and applied unique affine transforms to each so that the motion (6 degrees of freedom) could be synchronized with the optical markers’ location at each time frame. The control points of the XCAT were tessellated into triangles and 248 projection images were created based on intersections of each ray and monochromatic absorption. The tracking data sets with the largest motion (Subject 2) and the smallest motion (Subject 5) among the nine data sets were used to animate the XCAT knee model. The authors defined eight skin control points well distributed around the knees as pseudo-fiducial markers which functioned as a reference in motion correction. Motion compensation was done in the following ways: (1) simple projection shifting in 2D, (2) deformable projection warping in 2D, and (3) rigid body warping in 3D. Graphics hardware accelerated filtered backprojection was implemented and combined with the three correction methods in order to speed up the simulation process. Correction fidelity was evaluated as a function of number of markers used (4–12) and

  4. Molecular clocks.

    PubMed

    Lee, Michael S Y; Ho, Simon Y W

    2016-05-23

    In the 1960s, several groups of scientists, including Emile Zuckerkandl and Linus Pauling, had noted that proteins experience amino acid replacements at a surprisingly consistent rate across very different species. This presumed single, uniform rate of genetic evolution was subsequently described using the term 'molecular clock'. Biologists quickly realised that such a universal pacemaker could be used as a yardstick for measuring the timescale of evolutionary divergences: estimating the rate of amino acid exchanges per unit of time and applying it to protein differences across a range of organisms would allow deduction of the divergence times of their respective lineages (Figure 1). PMID:27218841

  5. SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Capillary electrophoresis-based molecular genotyping was conducted on 35 sugarcane cultivars (Saccharum spp. hybrids) and five clones of related wild species with 20 polymorphic SSR DNA markers. A total of 251 alleles were identified with 248 alleles displaying varying degrees of polymorphism and t...

  6. Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera).

    PubMed

    Hu, Jihong; Gui, Songtao; Zhu, Zhixuan; Wang, Xiaolei; Ke, Weidong; Ding, Yi

    2015-01-01

    Genomic resources such as single nucleotide polymorphism (SNPs), insertions and deletions (InDels) and SSRs (simple sequence repeats) are essential for crop improvement and better utilization in genetic breeding. However, the resources for the sacred lotus (Nelumbo nucifera Gaertn.) are still limited. In the present study, to dissect large-scale genomic molecular marker resources for sacred lotus, we re-sequenced a Thailand sacred lotus cultivar 'Chiang Mai wild lotus' and compared with the reported lotus genome 'Middle lake wild lotus'. A total of 3,180,059 SNPs, 328, 251 InDels and 14,191 SVs were found between the two genomes. The functional impact analyses of these SNPs indicated that they may be involved in metabolic processes, binding, catalytic activity, etc. Mining the genome sequences for SSRs showed that 191,657 SSRs were identified with a frequency of one SSR per 4.23 kb and 103,656 SSR primer pairs were designed. Furthermore, 14, 502 EST-SSRs were also indentified using the available RNA-seq data in the NCBI. A subset of 150 SSRs (genomic and EST-SSRs) was randomly selected for validation and genetic diversity analysis. The genotypes could be easily distinguished using these SSR markers and the 'Chiang Mai wild lotus' was obviously differentiated from the other Chinese accessions. This study provides considerable amounts of genomic resources and markers for the quantitative trait locus (QTL) identification and molecular selection of the species, which could have a potential role in various applications in sacred lotus breeding. PMID:26606530

  7. Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera)

    PubMed Central

    Zhu, Zhixuan; Wang, Xiaolei; Ke, Weidong; Ding, Yi

    2015-01-01

    Genomic resources such as single nucleotide polymorphism (SNPs), insertions and deletions (InDels) and SSRs (simple sequence repeats) are essential for crop improvement and better utilization in genetic breeding. However, the resources for the sacred lotus (Nelumbo nucifera Gaertn.) are still limited. In the present study, to dissect large-scale genomic molecular marker resources for sacred lotus, we re-sequenced a Thailand sacred lotus cultivar ‘Chiang Mai wild lotus’ and compared with the reported lotus genome ‘Middle lake wild lotus’. A total of 3,180,059 SNPs, 328, 251 InDels and 14,191 SVs were found between the two genomes. The functional impact analyses of these SNPs indicated that they may be involved in metabolic processes, binding, catalytic activity, etc. Mining the genome sequences for SSRs showed that 191,657 SSRs were identified with a frequency of one SSR per 4.23 kb and 103,656 SSR primer pairs were designed. Furthermore, 14, 502 EST-SSRs were also indentified using the available RNA-seq data in the NCBI. A subset of 150 SSRs (genomic and EST-SSRs) was randomly selected for validation and genetic diversity analysis. The genotypes could be easily distinguished using these SSR markers and the ‘Chiang Mai wild lotus’ was obviously differentiated from the other Chinese accessions. This study provides considerable amounts of genomic resources and markers for the quantitative trait locus (QTL) identification and molecular selection of the species, which could have a potential role in various applications in sacred lotus breeding. PMID:26606530

  8. Molecular replacement.

    PubMed

    Toth, Eric A

    2007-01-01

    As more protein structures are solved, the likelihood that current structural investigations will involve proteins for which there exists no homologous structure continually decreases. The extraction of phase information from diffraction experiments is one of several great barriers that crystallographers must overcome on the path to structure solution. One means to overcome this obstacle, the technique of molecular replacement, uses the structural similarity between proteins with similar sequences to give a good first estimate of the phases for the diffraction data of the protein of interest. The programs that execute this technique currently come in many flavors, from traditional Patterson-based methods, to stochastic searches in greater than three dimensions, to maximum likelihood-enhanced molecular replacement, each possessing unique advantages that can shake loose a recalcitrant solution. As crystallographers aim to solve larger macromolecular complexes that more faithfully depict the actors in cellular events, having existing phase information for parts of those biological machines will reinforce the technological advancements in data collection and structure solution that have already produced mammoth structures like the ribosome, yielding an ever-clearer picture of the inner workings of biology. PMID:17172763

  9. Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei.

    PubMed Central

    Linning, R; Lin, D; Lee, N; Abdennadher, M; Gaudet, D; Thomas, P; Mills, D; Kronstad, J W; Bakkeren, G

    2004-01-01

    Race-cultivar specialization during the interaction of the basidiomycete smut pathogen Ustilago hordei with its barley host was described in the 1940s. Subsequent genetic analyses revealed the presence of dominant avirulence genes in the pathogen that conform to the gene-for-gene theory. This pathosystem therefore presents an opportunity for the molecular genetic characterization of fungal genes controlling avirulence. We performed a cross between U. hordei strains to obtain 54 progeny segregating for three dominant avirulence genes on three differential barley cultivars. Bulked segregant analysis was used to identify RAPD and AFLP markers tightly linked to the avirulence gene UhAvr1. The UhAvr1 gene is located in an area containing repetitive DNA and this region is undetectable in cosmid libraries prepared from the avirulent parental strain. PCR and hybridization probes developed from the linked markers were therefore used to identify cosmid clones from the virulent (Uhavr1) parent. By walking on Uhavr1-linked cosmid clones, a nonrepetitive, nearby probe was found that recognized five overlapping BAC clones spanning 170 kb from the UhAvr1 parent. A contig of the clones in the UhAvr1 region was constructed and selected probes were used for RFLP analysis of the segregating population. This approach genetically defined an approximately 80-kb region that carries the UhAvr1 gene and provided cloned sequences for subsequent genetic analysis. UhAvr1 represents the first avirulence gene cloned from a basidiomycete plant pathogen. PMID:15020410

  10. Primate molecular divergence dates.

    PubMed

    Steiper, Michael E; Young, Nathan M

    2006-11-01

    With genomic data, alignments can be assembled that greatly increase the number of informative sites for analysis of molecular divergence dates. Here, we present an estimate of the molecular divergence dates for all of the major primate groups. These date estimates are based on a Bayesian analysis of approximately 59.8 kbp of genomic data from 13 primates and 6 mammalian outgroups, using a range of paleontologically supported calibration estimates. Results support a Cretaceous last common ancestor of extant primates (approximately 77 mya), an Eocene divergence between platyrrhine and catarrhine primates (approximately 43 mya), an Oligocene origin of apes and Old World monkeys (approximately 31 mya), and an early Miocene (approximately 18 mya) divergence of Asian and African great apes. These dates are examined in the context of other molecular clock studies. PMID:16815047

  11. Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. II. Experiment

    PubMed Central

    Choi, Jang-Hwan; Maier, Andreas; Keil, Andreas; Pal, Saikat; McWalter, Emily J.; Beaupré, Gary S.; Gold, Garry E.; Fahrig, Rebecca

    2014-01-01

    Purpose: A C-arm CT system has been shown to be capable of scanning a single cadaver leg under loaded conditions by virtue of its highly flexible acquisition trajectories. In Part I of this study, using the 4D XCAT-based numerical simulation, the authors predicted that the involuntary motion in the lower body of subjects in weight-bearing positions would seriously degrade image quality and the authors suggested three motion compensation methods by which the reconstructions could be corrected to provide diagnostic image quality. Here, the authors demonstrate that a flat-panel angiography system is appropriate for scanning both legs of subjects in vivo under weight-bearing conditions and further evaluate the three motion-correction algorithms using in vivo data. Methods: The geometry of a C-arm CT system for a horizontal scan trajectory was calibrated using the PDS-2 phantom. The authors acquired images of two healthy volunteers while lying supine on a table, standing, and squatting at several knee flexion angles. In order to identify the involuntary motion of the lower body, nine 1-mm-diameter tantalum fiducial markers were attached around the knee. The static mean marker position in 3D, a reference for motion compensation, was estimated by back-projecting detected markers in multiple projections using calibrated projection matrices and identifying the intersection points in 3D of the back-projected rays. Motion was corrected using three different methods (described in detail previously): (1) 2D projection shifting, (2) 2D deformable projection warping, and (3) 3D rigid body warping. For quantitative image quality analysis, SSIM indices for the three methods were compared using the supine data as a ground truth. Results: A 2D Euclidean distance-based metric of subjects’ motion ranged from 0.85 mm (±0.49 mm) to 3.82 mm (±2.91 mm) (corresponding to 2.76 to 12.41 pixels) resulting in severe motion artifacts in 3D reconstructions. Shifting in 2D, 2D warping, and 3D

  12. Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. II. Experiment

    SciTech Connect

    Choi, Jang-Hwan; Maier, Andreas; Keil, Andreas; McWalter, Emily J.; Gold, Garry E.; Fahrig, Rebecca; Pal, Saikat; Beaupré, Gary S.

    2014-06-15

    Purpose: A C-arm CT system has been shown to be capable of scanning a single cadaver leg under loaded conditions by virtue of its highly flexible acquisition trajectories. In Part I of this study, using the 4D XCAT-based numerical simulation, the authors predicted that the involuntary motion in the lower body of subjects in weight-bearing positions would seriously degrade image quality and the authors suggested three motion compensation methods by which the reconstructions could be corrected to provide diagnostic image quality. Here, the authors demonstrate that a flat-panel angiography system is appropriate for scanning both legs of subjectsin vivo under weight-bearing conditions and further evaluate the three motion-correction algorithms using in vivo data. Methods: The geometry of a C-arm CT system for a horizontal scan trajectory was calibrated using the PDS-2 phantom. The authors acquired images of two healthy volunteers while lying supine on a table, standing, and squatting at several knee flexion angles. In order to identify the involuntary motion of the lower body, nine 1-mm-diameter tantalum fiducial markers were attached around the knee. The static mean marker position in 3D, a reference for motion compensation, was estimated by back-projecting detected markers in multiple projections using calibrated projection matrices and identifying the intersection points in 3D of the back-projected rays. Motion was corrected using three different methods (described in detail previously): (1) 2D projection shifting, (2) 2D deformable projection warping, and (3) 3D rigid body warping. For quantitative image quality analysis, SSIM indices for the three methods were compared using the supine data as a ground truth. Results: A 2D Euclidean distance-based metric of subjects’ motion ranged from 0.85 mm (±0.49 mm) to 3.82 mm (±2.91 mm) (corresponding to 2.76 to 12.41 pixels) resulting in severe motion artifacts in 3D reconstructions. Shifting in 2D, 2D warping, and 3D

  13. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  14. Estimating Eggs

    ERIC Educational Resources Information Center

    Lindsay, Margaret; Scott, Amanda

    2005-01-01

    The authors discuss mass as one of the three fundamental measurements (the others being length and time), noting that estimation of mass is little taught and assessed in primary schools. This article briefly explores the reasons for this in terms of culture, practice, and the difficulty of assessing estimation of mass. An activity using the…

  15. Temperature estimators in computer simulation

    NASA Astrophysics Data System (ADS)

    Jara, César; González-Cataldo, Felipe; Davis, Sergio; Gutiérrez, Gonzalo

    2016-05-01

    Temperature is a key physical quantity that is used to describe equilibrium between two bodies in thermal contact. In computer simulations, the temperature is usually estimated by means of the equipartition theorem, as an average over the kinetic energy. However, recent studies have shown that the temperature can be estimated using only the particles positions, which has been called configurational temperature. Through classical molecular dynamics simulations of 108-argon-atoms system, we compare the performance of four different temperature estimators: the usual kinetic temperature and three configurational temperatures, Our results show that the different estimators converge to the same value, but their fluctuations are different.

  16. Molecular Plasmonics.

    PubMed

    Wilson, Andrew J; Willets, Katherine A

    2016-06-12

    In this review, we survey recent advances in the field of molecular plasmonics beyond the traditional sensing modality. Molecular plasmonics is explored in the context of the complex interaction between plasmon resonances and molecules and the ability of molecules to support plasmons self-consistently. First, spectroscopic changes induced by the interaction between molecular and plasmonic resonances are discussed, followed by examples of how tuning molecular properties leads to active molecular plasmonic systems. Next, the role of the position and polarizability of a molecular adsorbate on surface-enhanced Raman scattering signals is examined experimentally and theoretically. Finally, we introduce recent research focused on using molecules as plasmonic materials. Each of these examples is intended to highlight the role of molecules as integral components in coupled molecule-plasmon systems, as well as to show the diversity of applications in molecular plasmonics. PMID:27049633

  17. Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles

    PubMed Central

    Cortés, Camilo; Unzueta, Luis; de los Reyes-Guzmán, Ana; Ruiz, Oscar E.; Flórez, Julián

    2016-01-01

    In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR. PMID:27403044

  18. Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles.

    PubMed

    Cortés, Camilo; Unzueta, Luis; de Los Reyes-Guzmán, Ana; Ruiz, Oscar E; Flórez, Julián

    2016-01-01

    In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR. PMID:27403044

  19. Attitude Estimation or Quaternion Estimation?

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis

    2003-01-01

    The attitude of spacecraft is represented by a 3x3 orthogonal matrix with unity determinant, which belongs to the three-dimensional special orthogonal group SO(3). The fact that all three-parameter representations of SO(3) are singular or discontinuous for certain attitudes has led to the use of higher-dimensional nonsingular parameterizations, especially the four-component quaternion. In attitude estimation, we are faced with the alternatives of using an attitude representation that is either singular or redundant. Estimation procedures fall into three broad classes. The first estimates a three-dimensional representation of attitude deviations from a reference attitude parameterized by a higher-dimensional nonsingular parameterization. The deviations from the reference are assumed to be small enough to avoid any singularity or discontinuity of the three-dimensional parameterization. The second class, which estimates a higher-dimensional representation subject to enough constraints to leave only three degrees of freedom, is difficult to formulate and apply consistently. The third class estimates a representation of SO(3) with more than three dimensions, treating the parameters as independent. We refer to the most common member of this class as quaternion estimation, to contrast it with attitude estimation. We analyze the first and third of these approaches in the context of an extended Kalman filter with simplified kinematics and measurement models.

  20. Molecular dynamics

    SciTech Connect

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  1. Estimating risk.

    PubMed

    2016-07-01

    A free mobile phone app has been launched providing nurses and other hospital clinicians with a simple way to identify high-risk surgical patients. The app is a phone version of the Surgical Outcome Risk Tool (SORT), originally developed for online use with computers by researchers from the National Confidential Enquiry into Patient Outcome and Death and the University College London Hospital Surgical Outcomes Research Centre. SORT uses information about patients' health and planned surgical procedures to estimate the risk of death within 30 days of an operation. The percentages are only estimates, taking into account the general risks of the procedures and some information about patients, and should not be confused with patient-specific estimates in individual cases. PMID:27369709

  2. Estimation Destinations.

    ERIC Educational Resources Information Center

    Threewit, Fran

    This book leads students through a journey of hands-on investigations of skill-based estimation. The 30 lessons in the book are grouped into four units: Holding Hands, The Real Scoop, Container Calculations, and Estimeasurements. In each unit children work with unique, real materials intended to build an awareness of number, quantity, and…

  3. Molecular motors

    NASA Astrophysics Data System (ADS)

    Allemand, Jean François Desbiolles, Pierre

    2015-10-01

    How do we move? More precisely, what are the molecular mechanisms that can explain that our muscles, made of very small components can move at a osopic scale? To answer these questions we must introduce molecular motors. Those motors are proteins, or small protein assemblies that, in our cells, transform chemical energy into mechanical work. Then, like we could do for a oscopic motor, used in a car or in a fan, we are going to study the basic behavior of these molecular machines, present what are their energy sources, calculate their power, their yield. If molecular motors are crucial for our oscopic movements, we are going to see that they are also essential to cellular transport and that considering the activity of some enzymes as molecular motors bring some interesting new insights on their activity.

  4. Molecular Descriptors

    NASA Astrophysics Data System (ADS)

    Consonni, Viviana; Todeschini, Roberto

    In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

  5. Molecular Haeckel.

    PubMed

    Elinson, Richard P; Kezmoh, Lorren

    2010-07-01

    More than a century ago, Ernst Haeckel created embryo drawings to illustrate the morphological similarity of vertebrate early embryos. These drawings have been both widely presented and frequently criticized. At the same time that the idea of morphological similarity was recently attacked, there has been a growing realization of molecular similarities in the development of tissues and organs. We have surveyed genes expressed in vertebrate embryos, and we have used them to construct drawings that we call Molecular Haeckels. The Molecular Haeckels emphasize that, based on gene expression, there is a greater similarity among vertebrate embryos than even Haeckel might have imagined. PMID:20549737

  6. Computationally Designed Molecularly Imprinted Materials

    NASA Astrophysics Data System (ADS)

    Pavel, Dumitru; Lagowski, Jolanta; Faid, Karim

    2004-03-01

    Molecular dynamics simulations were carried out for different molecular systems in order to predict the binding affinities, binding energies, binding distances and the active site groups between the simulated molecular systems and different bio-ligands (theophylline and its derivatives), which have been designed and minimized using molecular simulation techniques. The first simulated molecular systems consisted of a ligand and functional monomer, such as methacrylic acid and its derivatives. For each pair of molecular systems, (10 monomers with a ligand and 10 monomers without a ligand) a total energy difference was calculated in order to estimate the binding energy between a ligand and the corresponding monomers. The analysis of the simulated functional monomers with ligands indicates that the functional group of monomers interacting with ligands tends to be either COOH or CH2=CH. The distances between the ligand and monomer, in the most stable cases as indicated above, are between 2.0-4.5 Å. The second simulated molecular systems consisted of a ligand and a polymer. The polymers were obtained from monomers that were simulated above. And similar to monomer study, for each pair of molecular systems, (polymer with a ligand and polymer without a ligand) a total energy difference was calculated in order to estimate the binding energy between ligand and the corresponding polymer. The binding distance between the active site of a polymer and a ligand will also be discussed.

  7. Estimates of missing heritability for complex traits in Brown Swiss cattle

    PubMed Central

    2014-01-01

    Background Genomic selection estimates genetic merit based on dense SNP (single nucleotide polymorphism) genotypes and phenotypes. This requires that SNPs explain a large fraction of the genetic variance. The objectives of this work were: (1) to estimate the fraction of genetic variance explained by dense genome-wide markers using 54 K SNP chip genotyping, and (2) to evaluate the effect of alternative marker-based relationship matrices and corrections for the base population on the fraction of the genetic variance explained by markers. Methods Two alternative marker-based relationship matrices were estimated using 35 706 SNPs on 1086 dairy bulls. Both pedigree- and marker-based relationship matrices were fitted simultaneously or separately in an animal model to estimate the fraction of variance not explained by the markers, i.e. the fraction explained by the pedigree. The phenotypes considered in the analysis were the deregressed estimated breeding values (dEBV) for milk, fat and protein yield and for somatic cell score (SCS). Results When dEBV were not sufficiently accurate (50 or 70%), the estimated fraction of the genetic variance explained by the markers was around 65% for yield traits and 45% for SCS. Scaling marker genotypes with locus-specific frequencies of heterozygotes slightly increased the variance explained by markers, compared with scaling with the average frequency of heterozygotes across loci. The estimated fraction of the genetic variance explained by the markers using separately both relationships matrices followed the same trends but the results were underestimated. With less accurate dEBV estimates, the fraction of the genetic variance explained by markers was underestimated, which is probably an artifact due to the dEBV being estimated by a pedigree-based animal model. Conclusions When using only highly accurate dEBV, the proportion of the genetic variance explained by the Illumina 54 K SNP chip was approximately 80% for Brown Swiss cattle

  8. Molecular printing

    PubMed Central

    Braunschweig, Adam B.; Huo, Fengwei; Mirkin, Chad A.

    2014-01-01

    Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography and soft lithography. Both are characterized by material and substrate flexibility, but dip-pen nanolithography has unlimited pattern design whereas soft lithography has limited pattern flexibility but is low in cost and has high throughput. Advances in DPN tip arrays and inking methods have increased the throughput and enabled applications such as multiplexed arrays. A new approach to molecular printing, polymer-pen lithography, achieves low-cost, high-throughput and pattern flexibility. This Perspective discusses the evolution and future directions of molecular printing. PMID:21378889

  9. Molecular Astrophysics

    NASA Astrophysics Data System (ADS)

    Hartquist, T. W.

    2005-07-01

    Part I. Molecular Clouds and the Distribution of Molecules in the Milky Way and Other Galaxies: 1. Molecular clouds in the Milky Way P. Friberg and A. Hjalmarson; 2. Molecules in galaxies L. Blitz; Part II. Diffuse Molecular Clouds: 3. Diffuse cloud chemistry E. F. Van Dishoeck; 4. Observations of velocity and density structure in diffuse clouds W. D. Langer; 5. Shock chemistry in diffuse clouds T. W. Hartquist, D. R. Flower and G. Pineau des Forets; Part III. Quiescent Dense Clouds: 6. Chemical modelling of quiescent dense interstellar clouds T. J. Millar; 7. Interstellar grain chemistry V. Buch; 8. Large molecules and small grains in astrophysics S. H. Lepp; Part IV. Studies of Molecular Processes: 9. Molecular photoabsorption processes K. P. Kirby; 10. Interstellar ion chemistry: laboratory studies D. Smith, N. G. Adams and E. E. Ferguson; 11. Theoretical considerations on some collisional processes D. R. Bates; 12. Collisional excitation processes E. Roueff; 13. Neutral reactions at Low and High Temperatures M. M. Graff; Part V. Atomic Species in Dense Clouds: 14. Observations of atomic species in dense clouds G. J. Melnick; 15. Ultraviolet radiation in molecular clouds W. G. Roberge; 16. Cosmic ray induced photodissociation and photoionization of interstellar molecules R. Gredel; 17. Chemistry in the molecular cloud Barnard 5 S. B. Charnley and D. A. Williams; 18. Molecular cloud structure, motions, and evolution P. C. Myers; Part VI. H in Regions of Massive Star Formation: 19. Infrared observations of line emission from molecular hydrogen T. R. Geballe; 20. Shocks in dense molecular clouds D. F. Chernoff and C. F. McKee; 21. Dissociative shocks D. A. Neufeld; 22. Infrared molecular hydrogen emission from interstellar photodissociation regions A. Sternberg; Part VII. Molecules Near Stars and in Stellar Ejecta: 23. Masers J. M. Moran; 24. Chemistry in the circumstellar envelopes around mass-losing red giants M. Jura; 25. Atoms and molecules in supernova 1987a R

  10. Molecular Spintronics using Molecular Nanomagnets

    NASA Astrophysics Data System (ADS)

    Wernsdorfer, Wolfgang

    2009-03-01

    A revolution in electronics is in view, with the contemporary evolution of two novel disciplines, spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets [1], which combine the classic macroscale properties of a magnet with the quantum properties of a nanoscale entity. The resulting field, molecular spintronics aims at manipulating spins and charges in electronic devices containing one or more molecules. In this context, we want to fabricate, characterize and study molecular devices (molecular spin-transistor, molecular spin-valve and spin filter, molecular double-dot devices, carbon nanotube nano-SQUIDs, etc.) in order to read and manipulate the spin states of the molecule and to perform basic quantum operations. The talk will discuss this--still largely unexplored--field and present our the first important results [2,3].[4pt] [1] L. Bogani & W. Wernsdorfer, Nature Mat. 7, 179 (2008).[0pt] [2] J.-P. Cleuziou, W. Wernsdorfer, V. Bouchiat, T. Ondarcuhu, M. Monthioux, Nature Nanotech. 1, 53-59 (2006).[0pt] [3] N. Roch, S. Florens, V. Bouchiat, W. Wernsdorfer, F. Balestro, Nature 453, 633 (2008).

  11. Spatial distribution of carbonaceous aerosol in the southeastern United States using molecular markers and carbon isotope data

    NASA Astrophysics Data System (ADS)

    Zheng, Mei; Ke, Lin; Edgerton, Eric S.; Schauer, James J.; Dong, Meiyu; Russell, Armistead G.

    2006-05-01

    Spatial variations of source contributions to fine organic carbon (OC) and fine particles in the southeastern United States were investigated using molecular marker-based chemical mass balance modeling (CMB-MM) and carbon isotope analysis. Nine primary emission sources were resolved with wood combustion (average 1.73 μg m-3, 23 ± 14% of measured OC) being the most dominant contributor to OC, followed by gasoline engine exhaust (0.45 μg m-3, 6.1 ± 6.2% of OC), diesel engine exhaust (0.43 μg m-3, 4.8 ± 4.1% of OC), and meat cooking (0.30 μg m-3, 4.1 ± 2.6% of OC). Measurable contributions from vegetative detritus, cigarette smoke, road dust, and natural gas exhaust were found. The impact of coke facilities was estimated for the first time in Birmingham, Alabama, and contributed 0.52 μg m-3 on average to fine OC. The unexplained OC accounted for 54 ± 26% of measured OC, possibly because of contributions from secondary OC, other unidentified primary sources and the possible positive artifact of OC. The urban excess of OC from diesel exhaust, gasoline exhaust and meat cooking can be seen from the results of the urban-rural pair in Alabama. Detailed chemical analysis revealed the wood burning episode at the rural site and an episode of secondary formation in the study region. The 14C analysis, a tool to study the relative contributions of contemporary and fossil carbon contents of fine particles, agreed well with the CMB-MM analysis. Both reflected a higher fossil fraction of carbon at urban sites especially in Birmingham, Alabama.

  12. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region.

    PubMed

    Dong, Lingli; Huo, Naxin; Wang, Yi; Deal, Karin; Luo, Ming-Cheng; Wang, Daowen; Anderson, Olin D; Gu, Yong Qiang

    2012-12-01

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A(u)A(u)) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A(m)A(m)), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A(u) genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A(u) genome. The difference in the compared region between A(u) and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A(u) than to A(m). The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A(u) sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat. PMID:23052831

  13. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  14. Molecular Electronics

    NASA Astrophysics Data System (ADS)

    Petty, Michael

    The prospects of using organic materials in electronics and optoelectronics applications have attracted scientists and technologists since the 1970s. This field has become known as molecular electronics. Some successes have already been achieved, for example the liquid-crystal display. Other products such as organic light-emitting displays, chemical sensors and plastic transistors are developing fast. There is also a keen interest in exploiting technologies at the molecular scale that might eventually replace silicon devices. This chapter provides some of the background physics and chemistry to the interdisciplinary subject of molecular electronics. A review of some of the possible application areas for organic materials is presented and some speculation is provided regarding future directions.

  15. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  16. WearDY: Wearable dynamics. A prototype for human whole-body force and motion estimation

    NASA Astrophysics Data System (ADS)

    Latella, Claudia; Kuppuswamy, Naveen; Nori, Francesco

    2016-06-01

    Motion capture is a powerful tool used in a large range of applications towards human movement analysis. Although it is a well-established technique, its main limitation is the lack of dynamic information such as forces and torques during the motion capture. In this paper, we present a novel approach for human wearable dynamic (WearDY) motion capture for the simultaneous estimation of whole-body forces along with the motion. Our conceptual framework encompasses traditional passive markers based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational framework for estimating dynamic quantities originally proposed in the domain of humanoid robot control. We present preliminary experimental analysis of our framework on subjects performing a two Degrees-of-Freedom bowing task and we estimate the motion and dynamic quantities. We discuss the implication of our proposal towards the design of a novel wearable force and motion capture suit and its applications.

  17. Molecular gastronomy

    NASA Astrophysics Data System (ADS)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  18. FORT Molecular Ecology Laboratory

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; Stevens, P.D.

    2011-01-01

    The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.

  19. The Application of Classification and Regression Trees for the Triage of Women for Referral to Colposcopy and the Estimation of Risk for Cervical Intraepithelial Neoplasia: A Study Based on 1625 Cases with Incomplete Data from Molecular Tests

    PubMed Central

    Pouliakis, Abraham; Karakitsou, Efrossyni; Chrelias, Charalampos; Pappas, Asimakis; Panayiotides, Ioannis; Valasoulis, George; Kyrgiou, Maria; Paraskevaidis, Evangelos; Karakitsos, Petros

    2015-01-01

    Objective. Nowadays numerous ancillary techniques detecting HPV DNA and mRNA compete with cytology; however no perfect test exists; in this study we evaluated classification and regression trees (CARTs) for the production of triage rules and estimate the risk for cervical intraepithelial neoplasia (CIN) in cases with ASCUS+ in cytology. Study Design. We used 1625 cases. In contrast to other approaches we used missing data to increase the data volume, obtain more accurate results, and simulate real conditions in the everyday practice of gynecologic clinics and laboratories. The proposed CART was based on the cytological result, HPV DNA typing, HPV mRNA detection based on NASBA and flow cytometry, p16 immunocytochemical expression, and finally age and parous status. Results. Algorithms useful for the triage of women were produced; gynecologists could apply these in conjunction with available examination results and conclude to an estimation of the risk for a woman to harbor CIN expressed as a probability. Conclusions. The most important test was the cytological examination; however the CART handled cases with inadequate cytological outcome and increased the diagnostic accuracy by exploiting the results of ancillary techniques even if there were inadequate missing data. The CART performance was better than any other single test involved in this study. PMID:26339651

  20. Molecular astrophysics

    NASA Astrophysics Data System (ADS)

    Herzberg, G.

    1989-01-01

    A brief history of Molecular Astrophysics is presented. The first molecules in space were identified in the 1920s in comets followed soon after by those in planetary atmospheres. The recent identification by MCKELLAR of the dimer of H 2, that is, (H 2) 2 in the atmosphere of Jupiter as well as the discovery, by DROSSART, MAILLARD, WATSON and others, of the H 3+ ion in the auroral zone of Jupiter are described. In this laboratory there is a continuing interest in interstellar molecules. Several molecules and molecular ions were observed by collaboration of laboratory spectroscopists and astronomers. Only the most recent ones are discussed. Also a few of the molecules not yet observed but likely to be observed are mentioned.

  1. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  2. Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When

  3. Molecular Mechanics

    PubMed Central

    Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

  4. Joint angle estimation with accelerometers for dynamic postural analysis.

    PubMed

    Ma, Jianting; Kharboutly, Haissam; Benali, Abderraouf; Benamar, Faïz; Bouzit, Mourad

    2015-10-15

    This paper presents a new accelerometer based method for estimating the posture of a subject standing on a dynamic perturbation platform. The induced perturbation is used to study the control mechanisms as well as the balance requirements that regulate the upright standing. These perturbations are translated into different intensity levels of speed and acceleration along longitudinal and lateral directions of motion. In our method, the human posture is modeled by a tridimensional, three-segment inverted pendulum which simultaneously takes into account both the anterior-posterior and medio-lateral strategies of hip and ankle. Four tri-axial accelerometers are used her, one accelerometer is placed on the platform, and the other three are attached to a human subject. Based on the results, the joint angle estimated compare closely to measurements from magnetic encoders placed on an articulated arm joint. The results were also comparable to those found when using a high-end optical motion capture system coupled with advanced biomechanical simulation software. This paper presents the comparisons of our accelerometer-based method with encoder and optical marker based method of the estimated joint angles under different dynamics perturbations. PMID:26338097

  5. Molecular thermometry of energetic materials

    SciTech Connect

    Fishbine, B.H.; Lippert, T.; Dick, J.J.

    1997-07-01

    When a solid object with a velocity <1 km/s strikes a solid high explosive, the increase in the bulk temperature of the explosive is usually too low to thermally initiate it. It is believed, however, that the energy in the stress or shock wave created by the impact can heat individual microscopic regions that ignite and cause detonation. Although many mechanisms have been suggested for how the impact energy creates these hot spots, there has been no real-time observation of their growth at early times because of their small dimensions (estimated to be 0.1--10 {micro}m), the short times required for their growth (estimated to be 0.5 {micro}s--1 ms), and because their temperatures are too low (estimated to be <2,000 K) for them to radiate much energy in the visible. One possible way to observe early hot-spot growth is to measure temperature-dependent changes in the optical properties--absorbance, diffuse reflection, Raman spectra--of either the components of the explosive or of molecules attached to them. This temperature measurement technique is called molecular thermometry. Molecular thermometers can respond to heating within a few picoseconds with spatial resolution that can, in principle, approach the diameter of a single molecule. Temperatures as high as 900 C have been measured by molecular thermometers in laser-pulse-heated polymers. The authors discuss the literature pertaining to molecular thermometry, the effect of stress on the optical properties of some molecules that may be used as thermometers, and experiments that have used molecular thermometry to probe, on the picosecond time scale, shock excitation of the vibrational modes of molecules of energetic material. The authors also suggest ways to use molecular thermometers to observe hot-spot formation in PBX9501, a plastic-bonded explosive, subjected to impact.

  6. Water in dense molecular clouds

    NASA Technical Reports Server (NTRS)

    Wannier, P. G.; Kuiper, T. B. H.; Frerking, M. A.; Gulkis, S.; Pickett, H. M.; Wilson, W. J.; Pagani, L.; Lecacheux, A.; Encrenaz, P.

    1991-01-01

    The G.P. Kuiper Airborne Observatory (KAO) was used to make initial observations of the half-millimeter ground-state transition of water in seven giant molecular clouds and in two late-type stars. No significant detections were made, and the resulting upper limits are significantly below those expected from other, indirect observations and from several theoretical models. The implied interstellar H2O/CO abundance is less than 0.003 in the cores of three giant molecular clouds. This value is less than expected from cloud chemistry models and also than estimates based on HDO and H3O(+) observations.

  7. Ovarian cancer: emerging molecular-targeted therapies

    PubMed Central

    Sourbier, Carole

    2012-01-01

    With about 22,000 new cases estimated in 2012 in the US and 15,500 related deaths, ovarian cancer is a heterogeneous and aggressive disease. Even though most of patients are sensitive to chemotherapy treatment following surgery, recurring disease is almost always lethal, and only about 30% of the women affected will be cured. Thanks to a better understanding of the molecular mechanisms underlying ovarian cancer malignancy, new therapeutic options with molecular-targeted agents have become available. This review discusses the rationale behind molecular-targeted therapies and examines how newly identified molecular targets may enhance personalized therapies for ovarian cancer patients. PMID:22807625

  8. Estimating potential evapotranspiration with improved radiation estimation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potential evapotranspiration (PET) is of great importance to estimation of surface energy budget and water balance calculation. The accurate estimation of PET will facilitate efficient irrigation scheduling, drainage design, and other agricultural and meteorological applications. However, accuracy o...

  9. Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

    PubMed Central

    Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

    2014-01-01

    Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

  10. Molecular markers and cotton genetic improvement: current status and future prospects.

    PubMed

    Malik, Waqas; Ashraf, Javaria; Iqbal, Muhammad Zaffar; Khan, Asif Ali; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Ahmad, Muhammad Qadir; Abbasi, Ghulam Hasan

    2014-01-01

    Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

  11. Ensemble estimators for multivariate entropy estimation

    PubMed Central

    Sricharan, Kumar; Wei, Dennis; Hero, Alfred O.

    2015-01-01

    The problem of estimation of density functionals like entropy and mutual information has received much attention in the statistics and information theory communities. A large class of estimators of functionals of the probability density suffer from the curse of dimensionality, wherein the mean squared error (MSE) decays increasingly slowly as a function of the sample size T as the dimension d of the samples increases. In particular, the rate is often glacially slow of order O(T−γ/d), where γ > 0 is a rate parameter. Examples of such estimators include kernel density estimators, k-nearest neighbor (k-NN) density estimators, k-NN entropy estimators, intrinsic dimension estimators and other examples. In this paper, we propose a weighted affine combination of an ensemble of such estimators, where optimal weights can be chosen such that the weighted estimator converges at a much faster dimension invariant rate of O(T−1). Furthermore, we show that these optimal weights can be determined by solving a convex optimization problem which can be performed offline and does not require training data. We illustrate the superior performance of our weighted estimator for two important applications: (i) estimating the Panter-Dite distortion-rate factor and (ii) estimating the Shannon entropy for testing the probability distribution of a random sample. PMID:25897177

  12. SURFACE VOLUME ESTIMATES FOR INFILTRATION PARAMETER ESTIMATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Volume balance calculations used in surface irrigation engineering analysis require estimates of surface storage. These calculations are often performed by estimating upstream depth with a normal depth formula. That assumption can result in significant volume estimation errors when upstream flow d...

  13. Molecular morphology of cyanobacterial phycobilisomes

    SciTech Connect

    Siegelman, H.W.; Kycia, J.H.

    1982-09-01

    Phycobilisomes were isolated from several cyanobacteria following cell lysis with Triton X-100. They were purified by phosphate precipitation and hydrophobic-interaction chromatography. Their phycobiliprotein compositions were quantitatively determined by application of sets of simultaneous absorbance equations to gel chromatographic separations of the chromoproteins. Phycobilisomes purified from several cyanobacteria had characteristic elution times on agarose gel chromatography. Combining electron microscope observations of phycobilisome structure, phycobiliprotein composition, and agarose gel chromatography estimates of molecular weight permitted the calculation of many details of phycobilisome molecular structure. Complementary chromatic adaptation resulted in a change of phycobilisome composition and structure. The polypeptide compositions of phycobilisomes were examined by sodium dodecyl sulfate-agarose gel chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The phycobilisomes were composed of phycobilipeptides derived from the constituent phycobiliproteins. Higher molecular-weight phycobilipeptide aggregates were also observed. The dominant forces responsible for the maintenance of phycobilisome structure are concluded to be hydropohobic interactions.

  14. Price and cost estimation

    NASA Technical Reports Server (NTRS)

    Stewart, R. D.

    1979-01-01

    Price and Cost Estimating Program (PACE II) was developed to prepare man-hour and material cost estimates. Versatile and flexible tool significantly reduces computation time and errors and reduces typing and reproduction time involved in preparation of cost estimates.

  15. Estimation of intermolecular interactions in polymer networks

    SciTech Connect

    Subrananian, P.R.; Galiatsatos, V.

    1993-12-31

    Strain-birefringence measurements have been used to estimate intermolecular interactions in polymer networks. The intensity of the interaction has been quantified through a theoretical scheme recently proposed by Erman. The results show that these interactions diminish with decreasing molecular weight between cross-links and decreasing cross-link functionality.

  16. Implicit solvent methods for free energy estimation

    PubMed Central

    Decherchi, Sergio; Masetti, Matteo; Vyalov, Ivan; Rocchia, Walter

    2014-01-01

    Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described. PMID:25193298

  17. ESTIMATION OF PHYSIOCHEMICAL PROPERTIES OF ORGANIC COMPOUNDS BY SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  18. Estimating avian population size using Bowden's estimator

    USGS Publications Warehouse

    Diefenbach, D.R.

    2009-01-01

    Avian researchers often uniquely mark birds, and multiple estimators could be used to estimate population size using individually identified birds. However, most estimators of population size require that all sightings of marked birds be uniquely identified, and many assume homogeneous detection probabilities. Bowden's estimator can incorporate sightings of marked birds that are not uniquely identified and relax assumptions required of other estimators. I used computer simulation to evaluate the performance of Bowden's estimator for situations likely to be encountered in bird studies. When the assumptions of the estimator were met, abundance and variance estimates and confidence-interval coverage were accurate. However, precision was poor for small population sizes (N ??? 50) unless a large percentage of the population was marked (>75%) and multiple (???8) sighting surveys were conducted. If additional birds are marked after sighting surveys begin, it is important to initially mark a large proportion of the population (pm ??? 0.5 if N ??? 100 or pm > 0.1 if N ??? 250) and minimize sightings in which birds are not uniquely identified; otherwise, most population estimates will be overestimated by >10%. Bowden's estimator can be useful for avian studies because birds can be resighted multiple times during a single survey, not all sightings of marked birds have to uniquely identify individuals, detection probabilities among birds can vary, and the complete study area does not have to be surveyed. I provide computer code for use with pilot data to design mark-resight surveys to meet desired precision for abundance estimates. ?? 2009 by The American Ornithologists' Union. All rights reserved.

  19. The molecular matching problem

    NASA Technical Reports Server (NTRS)

    Kincaid, Rex K.

    1993-01-01

    Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

  20. Biogeographic calibrations for the molecular clock

    PubMed Central

    Ho, Simon Y. W.; Tong, K. Jun; Foster, Charles S. P.; Ritchie, Andrew M.; Lo, Nathan; Crisp, Michael D.

    2015-01-01

    Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses. PMID:26333662

  1. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus

    PubMed Central

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus. PMID:26068192

  2. Direct Density Derivative Estimation.

    PubMed

    Sasaki, Hiroaki; Noh, Yung-Kyun; Niu, Gang; Sugiyama, Masashi

    2016-06-01

    Estimating the derivatives of probability density functions is an essential step in statistical data analysis. A naive approach to estimate the derivatives is to first perform density estimation and then compute its derivatives. However, this approach can be unreliable because a good density estimator does not necessarily mean a good density derivative estimator. To cope with this problem, in this letter, we propose a novel method that directly estimates density derivatives without going through density estimation. The proposed method provides computationally efficient estimation for the derivatives of any order on multidimensional data with a hyperparameter tuning method and achieves the optimal parametric convergence rate. We further discuss an extension of the proposed method by applying regularized multitask learning and a general framework for density derivative estimation based on Bregman divergences. Applications of the proposed method to nonparametric Kullback-Leibler divergence approximation and bandwidth matrix selection in kernel density estimation are also explored. PMID:27140943

  3. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

    PubMed Central

    2014-01-01

    Background Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation. PMID:25103329

  4. IMRT boost dose planning on dominant intraprostatic lesions: Gold marker-based three-dimensional fusion of CT with dynamic contrast-enhanced and {sup 1}H-spectroscopic MRI

    SciTech Connect

    Lin, Emile N.J.T. van . E-mail: E.vanLin@rther.umcn.nl; Fuetterer, Jurgen J.; Heijmink, Stijn W.T.P.J.; Vight, Lisette P. van der; Hoffmann, Aswin L.; Kollenburg, Peter van; Huisman, Henk Jan J.; Scheenen, Tom W.J.; Witjes, J. Alfred; Leer, Jan Willem; Barentsz, Jelle O.; Visser, Andries G.

    2006-05-01

    , and a feasible mechanism for treatment implementation has to be studied to extend these preliminary tumor control and toxicity estimates.

  5. Aircraft parameter estimation

    NASA Technical Reports Server (NTRS)

    Iliff, Kenneth W.

    1987-01-01

    The aircraft parameter estimation problem is used to illustrate the utility of parameter estimation, which applies to many engineering and scientific fields. Maximum likelihood estimation has been used to extract stability and control derivatives from flight data for many years. This paper presents some of the basic concepts of aircraft parameter estimation and briefly surveys the literature in the field. The maximum likelihood estimator is discussed, and the basic concepts of minimization and estimation are examined for a simple simulated aircraft example. The cost functions that are to be minimized during estimation are defined and discussed. Graphic representations of the cost functions are given to illustrate the minimization process. Finally, the basic concepts are generalized, and estimation from flight data is discussed. Some of the major conclusions for the simulated example are also developed for the analysis of flight data from the F-14, highly maneuverable aircraft technology (HiMAT), and space shuttle vehicles.

  6. Molecular implementation of molecular shift register memories

    NASA Technical Reports Server (NTRS)

    Beratan, David N. (Inventor); Onuchic, Jose N. (Inventor)

    1991-01-01

    An electronic shift register memory (20) at the molecular level is described. The memory elements are based on a chain of electron transfer molecules (22) and the information is shifted by photoinduced (26) electron transfer reactions. Thus, multi-step sequences of charge transfer reactions are used to move charge with high efficiency down a molecular chain. The device integrates compositions of the invention onto a VLSI substrate (36), providing an example of a molecular electronic device which may be fabricated. Three energy level schemes, molecular implementation of these schemes, optical excitation strategies, charge amplification strategies, and error correction strategies are described.

  7. Information geometric density estimation

    NASA Astrophysics Data System (ADS)

    Sun, Ke; Marchand-Maillet, Stéphane

    2015-01-01

    We investigate kernel density estimation where the kernel function varies from point to point. Density estimation in the input space means to find a set of coordinates on a statistical manifold. This novel perspective helps to combine efforts from information geometry and machine learning to spawn a family of density estimators. We present example models with simulations. We discuss the principle and theory of such density estimation.

  8. Thermoelectric efficiency of molecular junctions

    NASA Astrophysics Data System (ADS)

    Perroni, C. A.; Ninno, D.; Cataudella, V.

    2016-09-01

    Focus of the review is on experimental set-ups and theoretical proposals aimed to enhance thermoelectric performances of molecular junctions. In addition to charge conductance, the thermoelectric parameter commonly measured in these systems is the thermopower, which is typically rather low. We review recent experimental outcomes relative to several junction configurations used to optimize the thermopower. On the other hand, theoretical calculations provide estimations of all the thermoelectric parameters in the linear and non-linear regime, in particular of the thermoelectric figure of merit and efficiency, completing our knowledge of molecular thermoelectricity. For this reason, the review will mainly focus on theoretical studies analyzing the role of not only electronic, but also of the vibrational degrees of freedom. Theoretical results about thermoelectric phenomena in the coherent regime are reviewed focusing on interference effects which play a significant role in enhancing the figure of merit. Moreover, we review theoretical studies including the effects of molecular many-body interactions, such as electron–vibration couplings, which typically tend to reduce the efficiency. Since a fine tuning of many parameters and coupling strengths is required to optimize the thermoelectric conversion in molecular junctions, new theoretically proposed set-ups are discussed in the conclusions.

  9. Thermoelectric efficiency of molecular junctions.

    PubMed

    Perroni, C A; Ninno, D; Cataudella, V

    2016-09-21

    Focus of the review is on experimental set-ups and theoretical proposals aimed to enhance thermoelectric performances of molecular junctions. In addition to charge conductance, the thermoelectric parameter commonly measured in these systems is the thermopower, which is typically rather low. We review recent experimental outcomes relative to several junction configurations used to optimize the thermopower. On the other hand, theoretical calculations provide estimations of all the thermoelectric parameters in the linear and non-linear regime, in particular of the thermoelectric figure of merit and efficiency, completing our knowledge of molecular thermoelectricity. For this reason, the review will mainly focus on theoretical studies analyzing the role of not only electronic, but also of the vibrational degrees of freedom. Theoretical results about thermoelectric phenomena in the coherent regime are reviewed focusing on interference effects which play a significant role in enhancing the figure of merit. Moreover, we review theoretical studies including the effects of molecular many-body interactions, such as electron-vibration couplings, which typically tend to reduce the efficiency. Since a fine tuning of many parameters and coupling strengths is required to optimize the thermoelectric conversion in molecular junctions, new theoretically proposed set-ups are discussed in the conclusions. PMID:27420149

  10. ESTIMATING IRRIGATION COSTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Having accurate estimates of the cost of irrigation is important when making irrigation decisions. Estimates of fixed costs are critical for investment decisions. Operating cost estimates can assist in decisions regarding additional irrigations. This fact sheet examines the costs associated with ...

  11. Price Estimation Guidelines

    NASA Technical Reports Server (NTRS)

    Chamberlain, R. G.; Aster, R. W.; Firnett, P. J.; Miller, M. A.

    1985-01-01

    Improved Price Estimation Guidelines, IPEG4, program provides comparatively simple, yet relatively accurate estimate of price of manufactured product. IPEG4 processes user supplied input data to determine estimate of price per unit of production. Input data include equipment cost, space required, labor cost, materials and supplies cost, utility expenses, and production volume on industry wide or process wide basis.

  12. Dating Phylogenies with Hybrid Local Molecular Clocks

    PubMed Central

    Aris-Brosou, Stéphane

    2007-01-01

    Background Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods). However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. Principal Findings A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. Conclusions It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks. PMID:17849008

  13. Interstellar clouds and molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Jura, M.

    1977-01-01

    Data obtained from the Copernicus Orbiting Astronomical Observatory, launched in 1972 and still obtaining information, are used in a discussion of the interstellar medium. The Copernicus instruments have facilitated direct estimates for the density and temperature of individual interstellar clouds, and improved the ability to determine where along the line of sight a cloud lies with respect to background stars. The physical characteristics of hydrogen molecules are considered, with attention to the formation and destruction of interstellar hydrogen. The differences between 'thin' clouds, in which molecular hydrogen is optically thin, and 'thick' clouds are examined. Several features of the interstellar medium are described.

  14. Progress in molecular SIMS

    SciTech Connect

    Borman, S.

    1987-04-15

    A review of sputtering and molecular ion emission is presented. New derivatization techniques have produced lower detection limits for molecular secondary ion mass spectrometry (SIMS). Spectra of representative organic compounds are presented.

  15. Molecular electronics: Observation of molecular rectification

    SciTech Connect

    Waldeck, D.H.; Beratan, D.N. )

    1993-07-30

    The authors review some experiments in molecular rectification and their implication for commercial uses of molecular electronic devices. Two of the cases involve rectification by single molecules which consist of an electron donor on one side, an electron acceptor on the other side, and a bridge in between, coupled to electrodes. The third case involves rectification at a graphite electrode derivatized with a Cu phthalocyanine derivative, and probed with a Pt/Ir scanning tunneling microscope tip. Some potential applications of molecular devices are in high-density memory storage of holographic memory devices, neural networks, cellular automata, and chemical and biochemical sensors.

  16. Estimating Prices of Products

    NASA Technical Reports Server (NTRS)

    Aster, R. W.; Chamberlain, R. G.; Zendejas, S. C.; Lee, T. S.; Malhotra, S.

    1986-01-01

    Company-wide or process-wide production simulated. Price Estimation Guidelines (IPEG) program provides simple, accurate estimates of prices of manufactured products. Simplification of SAMIS allows analyst with limited time and computing resources to perform greater number of sensitivity studies. Although developed for photovoltaic industry, readily adaptable to standard assembly-line type of manufacturing industry. IPEG program estimates annual production price per unit. IPEG/PC program written in TURBO PASCAL.

  17. Estimating Airline Operating Costs

    NASA Technical Reports Server (NTRS)

    Maddalon, D. V.

    1978-01-01

    The factors affecting commercial aircraft operating and delay costs were used to develop an airline operating cost model which includes a method for estimating the labor and material costs of individual airframe maintenance systems. The model permits estimates of aircraft related costs, i.e., aircraft service, landing fees, flight attendants, and control fees. A method for estimating the costs of certain types of airline delay is also described.

  18. Molecular Research in Aquaculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular research and biotechnology have long been fields of study with applications useful to aquaculture and other animal sciences. Molecular Research in Aquaculture looks to provide an understanding of molecular research and its applications to the aquaculture industry in a format that allows in...

  19. Molecular Graphics and Chemistry.

    ERIC Educational Resources Information Center

    Weber, Jacques; And Others

    1992-01-01

    Explains molecular graphics, i.e., the application of computer graphics techniques to investigate molecular structure, function, and interaction. Structural models and molecular surfaces are discussed, and a theoretical model that can be used for the evaluation of intermolecular interaction energies for organometallics is described. (45…

  20. Ligand Affinities Estimated by Quantum Chemical Calculations.

    PubMed

    Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

    2010-05-11

    We present quantum chemical estimates of ligand-binding affinities performed, for the first time, at a level of theory for which there is a hope that dispersion and polarization effects are properly accounted for (MP2/cc-pVTZ) and at the same time effects of solvation, entropy, and sampling are included. We have studied the binding of seven biotin analogues to the avidin tetramer. The calculations have been performed by the recently developed PMISP approach (polarizable multipole interactions with supermolecular pairs), which treats electrostatic interactions by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions (dispersion, exchange repulsion, etc.) by explicit quantum chemical calculations, using a fragmentation approach, except for long-range interactions that are treated by standard molecular-mechanics Lennard-Jones terms. In order to include effects of sampling, 10 snapshots from a molecular dynamics simulation are studied for each biotin analogue. Solvation energies are estimated by the polarized continuum model (PCM), coupled to the multipole-polarizability model. Entropy effects are estimated from vibrational frequencies, calculated at the molecular mechanics level. We encounter several problems, not previously discussed, illustrating that we are first to apply such a method. For example, the PCM model is, in the present implementation, questionable for large molecules, owing to the use of a surface definition that gives numerous small cavities in a protein. PMID:26615702

  1. Reservoir Temperature Estimator

    SciTech Connect

    Palmer, Carl D.

    2014-12-08

    The Reservoir Temperature Estimator (RTEst) is a program that can be used to estimate deep geothermal reservoir temperature and chemical parameters such as CO2 fugacity based on the water chemistry of shallower, cooler reservoir fluids. This code uses the plugin features provided in The Geochemist’s Workbench (Bethke and Yeakel, 2011) and interfaces with the model-independent parameter estimation code Pest (Doherty, 2005) to provide for optimization of the estimated parameters based on the minimization of the weighted sum of squares of a set of saturation indexes from a user-provided mineral assemblage.

  2. Updated Conceptual Cost Estimating

    NASA Technical Reports Server (NTRS)

    Brown, J. A.

    1987-01-01

    16-page report discusses development and use of NASA TR-1508, the Kennedy Space Center Aerospace Construction Price Book for preparing conceptual, budget, funding, cost-estimating, and preliminary cost-engineering reports. Updated annually from 1974 through 1985 with actual bid prices and government estimates. Includes labor and material quantities and prices with contractor and subcontractor markups for buildings, facilities, and systems at Kennedy Space Center. While data pertains to aerospace facilities, format and cost-estimating techniques guide estimation of costs in other construction applications.

  3. Reservoir Temperature Estimator

    Energy Science and Technology Software Center (ESTSC)

    2014-12-08

    The Reservoir Temperature Estimator (RTEst) is a program that can be used to estimate deep geothermal reservoir temperature and chemical parameters such as CO2 fugacity based on the water chemistry of shallower, cooler reservoir fluids. This code uses the plugin features provided in The Geochemist’s Workbench (Bethke and Yeakel, 2011) and interfaces with the model-independent parameter estimation code Pest (Doherty, 2005) to provide for optimization of the estimated parameters based on the minimization of themore » weighted sum of squares of a set of saturation indexes from a user-provided mineral assemblage.« less

  4. Parameter estimating state reconstruction

    NASA Technical Reports Server (NTRS)

    George, E. B.

    1976-01-01

    Parameter estimation is considered for systems whose entire state cannot be measured. Linear observers are designed to recover the unmeasured states to a sufficient accuracy to permit the estimation process. There are three distinct dynamics that must be accommodated in the system design: the dynamics of the plant, the dynamics of the observer, and the system updating of the parameter estimation. The latter two are designed to minimize interaction of the involved systems. These techniques are extended to weakly nonlinear systems. The application to a simulation of a space shuttle POGO system test is of particular interest. A nonlinear simulation of the system is developed, observers designed, and the parameters estimated.

  5. Signal analysis of behavioral and molecular cycles

    PubMed Central

    Levine, Joel D; Funes, Pablo; Dowse, Harold B; Hall, Jeffrey C

    2002-01-01

    Background Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. Results We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. Conclusion Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed. PMID:11825337

  6. Engineering molecular machines

    NASA Astrophysics Data System (ADS)

    Erman, Burak

    2016-04-01

    Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

  7. Estimating Health Services Requirements

    NASA Technical Reports Server (NTRS)

    Alexander, H. M.

    1985-01-01

    In computer program NOROCA populations statistics from National Center for Health Statistics used with computational procedure to estimate health service utilization rates, physician demands (by specialty) and hospital bed demands (by type of service). Computational procedure applicable to health service area of any size and even used to estimate statewide demands for health services.

  8. Conceptual Cost Estimating

    NASA Technical Reports Server (NTRS)

    Brown, J. A.

    1983-01-01

    Kennedy Space Center data aid in efficient construction-cost managment. Report discusses development and use of NASA TR-1508, Kennedy Space Center Aerospace Construction price book for preparing conceptual budget, funding cost estimating, and preliminary cost engineering reports. Report based on actual bid prices and Government estimates.

  9. Estimating mutual information.

    PubMed

    Kraskov, Alexander; Stögbauer, Harald; Grassberger, Peter

    2004-06-01

    We present two classes of improved estimators for mutual information M(X,Y), from samples of random points distributed according to some joint probability density mu(x,y). In contrast to conventional estimators based on binnings, they are based on entropy estimates from k -nearest neighbor distances. This means that they are data efficient (with k=1 we resolve structures down to the smallest possible scales), adaptive (the resolution is higher where data are more numerous), and have minimal bias. Indeed, the bias of the underlying entropy estimates is mainly due to nonuniformity of the density at the smallest resolved scale, giving typically systematic errors which scale as functions of k/N for N points. Numerically, we find that both families become exact for independent distributions, i.e. the estimator M(X,Y) vanishes (up to statistical fluctuations) if mu(x,y)=mu(x)mu(y). This holds for all tested marginal distributions and for all dimensions of x and y. In addition, we give estimators for redundancies between more than two random variables. We compare our algorithms in detail with existing algorithms. Finally, we demonstrate the usefulness of our estimators for assessing the actual independence of components obtained from independent component analysis (ICA), for improving ICA, and for estimating the reliability of blind source separation. PMID:15244698

  10. Fano factor estimation.

    PubMed

    Rajdl, Kamil; Lansky, Petr

    2014-02-01

    Fano factor is one of the most widely used measures of variability of spike trains. Its standard estimator is the ratio of sample variance to sample mean of spike counts observed in a time window and the quality of the estimator strongly depends on the length of the window. We investigate this dependence under the assumption that the spike train behaves as an equilibrium renewal process. It is shown what characteristics of the spike train have large effect on the estimator bias. Namely, the effect of refractory period is analytically evaluated. Next, we create an approximate asymptotic formula for the mean square error of the estimator, which can also be used to find minimum of the error in estimation from single spike trains. The accuracy of the Fano factor estimator is compared with the accuracy of the estimator based on the squared coefficient of variation. All the results are illustrated for spike trains with gamma and inverse Gaussian probability distributions of interspike intervals. Finally, we discuss possibilities of how to select a suitable observation window for the Fano factor estimation. PMID:24245675

  11. Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers

    PubMed Central

    Wongsawad, Pheravut; Peerapornpisal, Yuwadee

    2014-01-01

    Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters. PMID:25313288

  12. Estimation and uncertainty of reversible Markov models

    NASA Astrophysics Data System (ADS)

    Trendelkamp-Schroer, Benjamin; Wu, Hao; Paul, Fabian; Noé, Frank

    2015-11-01

    Reversibility is a key concept in Markov models and master-equation models of molecular kinetics. The analysis and interpretation of the transition matrix encoding the kinetic properties of the model rely heavily on the reversibility property. The estimation of a reversible transition matrix from simulation data is, therefore, crucial to the successful application of the previously developed theory. In this work, we discuss methods for the maximum likelihood estimation of transition matrices from finite simulation data and present a new algorithm for the estimation if reversibility with respect to a given stationary vector is desired. We also develop new methods for the Bayesian posterior inference of reversible transition matrices with and without given stationary vector taking into account the need for a suitable prior distribution preserving the meta-stable features of the observed process during posterior inference. All algorithms here are implemented in the PyEMMA software — http://pyemma.org — as of version 2.0.

  13. Estimating Torque Imparted on Spacecraft Using Telemetry

    NASA Technical Reports Server (NTRS)

    Lee, Allan Y.; Wang, Eric K.; Macala, Glenn A.

    2013-01-01

    There have been a number of missions with spacecraft flying by planetary moons with atmospheres; there will be future missions with similar flybys. When a spacecraft such as Cassini flies by a moon with an atmosphere, the spacecraft will experience an atmospheric torque. This torque could be used to determine the density of the atmosphere. This is because the relation between the atmospheric torque vector and the atmosphere density could be established analytically using the mass properties of the spacecraft, known drag coefficient of objects in free-molecular flow, and the spacecraft velocity relative to the moon. The density estimated in this way could be used to check results measured by science instruments. Since the proposed methodology could estimate disturbance torque as small as 0.02 N-m, it could also be used to estimate disturbance torque imparted on the spacecraft during high-altitude flybys.

  14. Trapping cold molecular hydrogen.

    PubMed

    Seiler, Ch; Hogan, S D; Merkt, F

    2011-11-14

    Translationally cold H(2) molecules excited to non-penetrating |M(J)| = 3 Rydberg states of principal quantum number in the range 21-37 have been decelerated and trapped using time-dependent inhomogeneous electric fields. The |M(J)| = 3 Rydberg states were prepared from the X (1)Σ(+)(u)(v = 0, J = 0) ground state using a resonant three-photon excitation sequence via the B (1)Σ(+)(u)(v = 3, J = 1) and I (1)Π(g) (v = 0, J = 2) intermediate states and circularly polarized laser radiation. The circular polarization of the vacuum ultraviolet radiation used for the B ← X transition was generated by resonance-enhanced four-wave mixing in xenon and the degree of circular polarization was determined to be 96%. To analyse the deceleration and trapping experiments, the Stark effect in Rydberg states of molecular hydrogen was calculated using a matrix diagonalization procedure similar to that presented by Yamakita et al., J. Chem. Phys., 2004, 121, 1419. Particular attention was given to the prediction of zero-field positions of low-l states and of avoided crossings between Rydberg-Stark states with different values of |M(J)|. The calculated Stark maps and probabilities for diabatic traversal of the avoided crossings were used as input to Monte-Carlo particle-trajectory simulations. These simulations provide a quantitatively satisfactory description of the experimental data and demonstrate that particle loss caused by adiabatic traversals of avoided crossings between adjacent |M(J)| = 3 Stark states of H(2) is small at principal quantum numbers beyond n = 25. The main source of trap losses was found to be from collisional processes. Predissociation following the absorption of blackbody radiation is estimated to be the second most important trap-loss mechanism at room temperature, and trap loss by spontaneous emission is negligible under our experimental conditions. PMID:21818497

  15. Estimating cell populations

    NASA Technical Reports Server (NTRS)

    White, B. S.; Castleman, K. R.

    1981-01-01

    An important step in the diagnosis of a cervical cytology specimen is estimating the proportions of the various cell types present. This is usually done with a cell classifier, the error rates of which can be expressed as a confusion matrix. We show how to use the confusion matrix to obtain an unbiased estimate of the desired proportions. We show that the mean square error of this estimate depends on a 'befuddlement matrix' derived from the confusion matrix, and how this, in turn, leads to a figure of merit for cell classifiers. Finally, we work out the two-class problem in detail and present examples to illustrate the theory.

  16. Pore Velocity Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

    Devary, J. L.; Doctor, P. G.

    1982-08-01

    Geostatistical data analysis techniques were used to stochastically model the spatial variability of groundwater pore velocity in a potential waste repository site. Kriging algorithms were applied to Hanford Reservation data to estimate hydraulic conductivities, hydraulic head gradients, and pore velocities. A first-order Taylor series expansion for pore velocity was used to statistically combine hydraulic conductivity, hydraulic head gradient, and effective porosity surfaces and uncertainties to characterize the pore velocity uncertainty. Use of these techniques permits the estimation of pore velocity uncertainties when pore velocity measurements do not exist. Large pore velocity estimation uncertainties were found to be located in the region where the hydraulic head gradient relative uncertainty was maximal.

  17. Trawsfynydd Plutonium Estimate

    SciTech Connect

    Reid, Bruce D.; Gerlach, David C.; Heasler, Patrick G.; Livingston, J.

    2009-11-20

    Report serves to document an estimate of the cumulative plutonium production of the Trawsfynydd Unit II reactor (Traws II) over its operating life made using the Graphite Isotope Ratio Method (GIRM). The estimate of the plutonium production in Traws II provided in this report has been generated under blind conditions. In other words, the estimate ofthe Traws II plutonium production has been generated without the knowledge of the plutonium production declared by the reactor operator (Nuclear Electric). The objective of this report is to demonstrate that the GIRM can be employed to serve as an accurate tool to verify weapons materials production declarations.

  18. Estimating airline operating costs

    NASA Technical Reports Server (NTRS)

    Maddalon, D. V.

    1978-01-01

    A review was made of the factors affecting commercial aircraft operating and delay costs. From this work, an airline operating cost model was developed which includes a method for estimating the labor and material costs of individual airframe maintenance systems. The model, similar in some respects to the standard Air Transport Association of America (ATA) Direct Operating Cost Model, permits estimates of aircraft-related costs not now included in the standard ATA model (e.g., aircraft service, landing fees, flight attendants, and control fees). A study of the cost of aircraft delay was also made and a method for estimating the cost of certain types of airline delay is described.

  19. DISPERSION OF MAGNETIC FIELDS IN MOLECULAR CLOUDS. I

    SciTech Connect

    Hildebrand, Roger H.; Kirby, Larry; Dotson, Jessie L.; Houde, Martin; Vaillancourt, John E.

    2009-05-01

    We describe a method for determining the dispersion of magnetic field vectors about large-scale fields in turbulent molecular clouds. The method is designed to avoid inaccurate estimates of magnetohydrodynamic or turbulent dispersion-and help avoiding inaccurate estimates of field strengths-due to a large-scale, nonturbulent field structure when using the well known method of Chandrasekhar and Fermi. Our method also provides accurate, independent estimates of the turbulent to large-scale magnetic field strength ratio. We discuss applications to the molecular clouds OMC-1, M17, and DR21(Main)

  20. Standardized molecular typing.

    PubMed

    Müller, F M; Lischewski, A; Harmsen, D; Hacker, J

    1999-01-01

    Molecular typing methods are useful tools in molecular mycology. The results of these biotyping procedures may help to identify pathogenic strains in order to detect sources of nosocomial infection and for the investigation of epidemiological relationships. With respect to the facultative pathogen, Candida albicans, various methods such as pulse-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), DNA fingerprinting methods and hybridization with repetitive DNA elements have been described as useful tools in molecular epidemiology. The previously described hybridization method with the Candida albicans specific CARE-2 probe and subsequent rehybridization with a molecular size marker is a standardized reproducible typing method for comparison of results obtained in different laboratories. In a larger epidemiological study conducted at the University Hospital of Würzburg analysing clinical C. albicans isolates, we were able to describe relationships between sequential patient isolates. These findings demonstrate that standardized molecular typing methods are a powerful tool in molecular mycology studies. PMID:10865907

  1. Estimation of food consumption

    SciTech Connect

    Callaway, J.M. Jr.

    1992-04-01

    The research reported in this document was conducted as a part of the Hanford Environmental Dose Reconstruction (HEDR) Project. The objective of the HEDR Project is to estimate the radiation doses that people could have received from operations at the Hanford Site. Information required to estimate these doses includes estimates of the amounts of potentially contaminated foods that individuals in the region consumed during the study period. In that general framework, the objective of the Food Consumption Task was to develop a capability to provide information about the parameters of the distribution(s) of daily food consumption for representative groups in the population for selected years during the study period. This report describes the methods and data used to estimate food consumption and presents the results developed for Phase I of the HEDR Project.

  2. Multidimensional synthetic estimation filter

    NASA Technical Reports Server (NTRS)

    Monroe, Stanley E., Jr.; Juday, Richard D.

    1990-01-01

    The synthetic estimation filter (SEF) crafts an affine variation into its response to a changing parameter (e.g. scale or rotation). Sets of such filters are used in an estimation correlator to reduce the number of filters required for a given tracking accuracy. By overspecifying the system (one more SEF than parameters to be tracked), the ratio of correlation responses between filters forms a robust estimator into the spanned domain of the parameters. Previous results dealt with a laboratory correlator which could track a single parameter. This paper explores the SEF and the estimator's extension to more dimensions. A 2D example is given in which a reduction of filters from 25 to 3 is demonstrated to span a 4-degree square portion of pose space.

  3. Cost-Estimation Program

    NASA Technical Reports Server (NTRS)

    Cox, Brian

    1995-01-01

    COSTIT computer program estimates cost of electronic design by reading item-list file and file containing cost for each item. Accuracy of cost estimate based on accuracy of cost-list file. Written by use of AWK utility for Sun4-series computers running SunOS 4.x and IBM PC-series and compatible computers running MS-DOS. The Sun version (NPO-19587). PC version (NPO-19157).

  4. Capital cost estimate

    NASA Technical Reports Server (NTRS)

    1975-01-01

    The capital cost estimate for the nuclear process heat source (NPHS) plant was made by: (1) using costs from the current commercial HTGR for electricity production as a base for items that are essentially the same and (2) development of new estimates for modified or new equipment that is specifically for the process heat application. Results are given in tabular form and cover the total investment required for each process temperature studied.

  5. Efficient Bayesian Phase Estimation

    NASA Astrophysics Data System (ADS)

    Wiebe, Nathan; Granade, Chris

    2016-07-01

    We introduce a new method called rejection filtering that we use to perform adaptive Bayesian phase estimation. Our approach has several advantages: it is classically efficient, easy to implement, achieves Heisenberg limited scaling, resists depolarizing noise, tracks time-dependent eigenstates, recovers from failures, and can be run on a field programmable gate array. It also outperforms existing iterative phase estimation algorithms such as Kitaev's method.

  6. Efficient Bayesian Phase Estimation.

    PubMed

    Wiebe, Nathan; Granade, Chris

    2016-07-01

    We introduce a new method called rejection filtering that we use to perform adaptive Bayesian phase estimation. Our approach has several advantages: it is classically efficient, easy to implement, achieves Heisenberg limited scaling, resists depolarizing noise, tracks time-dependent eigenstates, recovers from failures, and can be run on a field programmable gate array. It also outperforms existing iterative phase estimation algorithms such as Kitaev's method. PMID:27419551

  7. Maximal combustion temperature estimation

    NASA Astrophysics Data System (ADS)

    Golodova, E.; Shchepakina, E.

    2006-12-01

    This work is concerned with the phenomenon of delayed loss of stability and the estimation of the maximal temperature of safe combustion. Using the qualitative theory of singular perturbations and canard techniques we determine the maximal temperature on the trajectories located in the transition region between the slow combustion regime and the explosive one. This approach is used to estimate the maximal temperature of safe combustion in multi-phase combustion models.

  8. Atomic and molecular supernovae

    SciTech Connect

    Liu, W.

    1997-12-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  9. Atomic and molecular supernovae

    NASA Technical Reports Server (NTRS)

    Liu, Weihong

    1997-01-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  10. Estimating networks with jumps

    PubMed Central

    Kolar, Mladen; Xing, Eric P.

    2013-01-01

    We study the problem of estimating a temporally varying coefficient and varying structure (VCVS) graphical model underlying data collected over a period of time, such as social states of interacting individuals or microarray expression profiles of gene networks, as opposed to i.i.d. data from an invariant model widely considered in current literature of structural estimation. In particular, we consider the scenario in which the model evolves in a piece-wise constant fashion. We propose a procedure that estimates the structure of a graphical model by minimizing the temporally smoothed L1 penalized regression, which allows jointly estimating the partition boundaries of the VCVS model and the coefficient of the sparse precision matrix on each block of the partition. A highly scalable proximal gradient method is proposed to solve the resultant convex optimization problem; and the conditions for sparsistent estimation and the convergence rate of both the partition boundaries and the network structure are established for the first time for such estimators. PMID:25013533

  11. Nonparametric conditional estimation

    SciTech Connect

    Owen, A.B.

    1987-01-01

    Many nonparametric regression techniques (such as kernels, nearest neighbors, and smoothing splines) estimate the conditional mean of Y given X = chi by a weighted sum of observed Y values, where observations with X values near chi tend to have larger weights. In this report the weights are taken to represent a finite signed measure on the space of Y values. This measure is studied as an estimate of the conditional distribution of Y given X = chi. From estimates of the conditional distribution, estimates of conditional means, standard deviations, quantiles and other statistical functionals may be computed. Chapter 1 illustrates the computation of conditional quantiles and conditional survival probabilities on the Stanford Heart Transplant data. Chapter 2 contains a survey of nonparametric regression methods and introduces statistical metrics and von Mises' method for later use. Chapter 3 proves some consistency results. Chapter 4 provides conditions under which the suitably normalized errors in estimating the conditional distribution of Y have a Brownian limit. Using von Mises' method, asymptotic normality is obtained for nonparametric conditional estimates of compactly differentiable statistical functionals.

  12. Fatigue failure and molecular machine design.

    PubMed

    Hess, Henry; Dumont, Emmanuel L P

    2011-06-20

    Sophisticated molecular machines have evolved in nature, and the first synthetic molecular machines have been demonstrated. With our increasing understanding of individual operating cycles, the question of how operation can be sustained over many cycles comes to the forefront. In the design of macroscale machines, performance and lifetime are opposing goals. Similarly, the natural evolution of biological nanomachines, such as myosin motor proteins, is likely constrained by lifetime requirements. Rather than bond rupture at high forces, bond fatigue under repeated small stresses may limit the mechanical performance of molecular machines. Here, the effect of cyclic stresses using single and double bonds as simple examples are discussed. Additionally, it is demonstrated that an increase in lifetime requires a reduction in mechanical load and that molecular engineering design features, such as polyvalent bonds capable of rebinding, can extend the bond lifetime dramatically. A universal scaling law for the force output of motors is extrapolated to the molecular scale to estimate the design space for molecular machines. PMID:21574250

  13. Molecular Typing and Differentiation

    EPA Science Inventory

    In this chapter, general background and bench protocols are provided for a number of molecular typing techniques in common use today. Methods for the molecular typing and differentiation of microorganisms began to be widely adopted following the development of the polymerase chai...

  14. Molecular Beacons in Diagnostics

    PubMed Central

    Kramer, Fred Russell

    2012-01-01

    Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies. PMID:22619695

  15. Molecular biology of development

    SciTech Connect

    Davidson, E.H.; Firtel, R.A.

    1984-01-01

    This book is a compilation of papers presented at a symposium on the molecular biology of development. Topics discussed include: cytoplasmic localizations and pattern formations, gene expression during oogenesis and early development, developmental expression of gene families molecular aspects of plant development and transformation in whole organisms and cells.

  16. Spectral estimators in elastography.

    PubMed

    Konofagou, E E; Varghese, T; Ophir, J

    2000-03-01

    Like velocity, strain induces a time delay and a time scaling to the received signal. Elastography typically uses time delay techniques to indirectly (i.e. via the displacement estimate) measure tissue strain induced by an applied compression, and considers time scaling as a source of distortion. More recently, we have shown that the time scaling factor can also be spectrally estimated and used as a direct measure of strain. Strain causes a Doppler-like frequency shift and a change in bandwidth of the bandpass power spectrum of the echo signal. Two frequency shift strain estimators are described that have been proven to be more robust but less precise when compared to time delay estimators, both in simulations and experiments. The increased robustness is due to the insensitivity of the spectral techniques to phase decorrelation noise. In this paper we discuss and compare the theoretical and experimental findings obtained with traditional time delay estimators and with the newly proposed spectral methods. PMID:10829698

  17. Estimation of soil sorption coefficients using QSARs

    SciTech Connect

    Doucette, W.J.

    1994-12-31

    Sorption coefficients quantitatively describe the extent to which an organic chemical distributes itself between an environmental solid and the aqueous phase that it is contact with at equilibrium. Because of the difficulty and expense associated with measuring sorption coefficients, estimated values are often used in place of site specific, experimental values for fate modeling. Most reported methods for estimating the sorption of organic chemicals onto environmental solids are based on observation that for many organic chemicals, and in particular neutral hydrophobic organics, sorption is directly proportional to the quantity of organic matter associated with the solid. Normalizing soil or sediment specific sorption coefficients to the organic carbon content of the sorbent yields a new ``constant``, Koc, that is considered unique property of the organic chemical being sorbed. Values of Koc are then typically estimated from correlations between Koc and various descriptors of hydrophobicity such as octanol/water partition coefficients (Kow), aqueous solubility (S), molecular connectivity indices (MCIs) and retention times or capacity factors generated by reverse phase high performance liquid chromatography (RP-HPLC). Group contribution methods have also been described. While the so-called ``Koc approach`` for estimating sorption coefficients is most appropriate for neutral, hydrophobic organic chemicals on environmental solids containing a significant amount of organic matter, it has been applied to a wide variety of chemical and soil types. This presentation will focus on a discussion of the Koc approach, its applicability and limitations. A comparison of several widely used methods for estimating Koc will be presented.

  18. Molecular dynamics modelling of solidification in metals

    SciTech Connect

    Boercker, D.B.; Belak, J.; Glosli, J.

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  19. Local likelihood estimation

    SciTech Connect

    Tibshirani, R.J.

    1984-12-01

    In this work, we extend the idea of local averaging to likelihood-based regression models. One application is in the class of generalized linear models (Nelder and Wedderburn (1972). We enlarge this class by replacing the covariate form chi..beta.. with an unspecified smooth function s(chi). This function is estimated from the data by a technique we call Local Likelihood Estimation - a type of local averaging. Multiple covariates are incorporated through a forward stepwise algorithm. In a number of real data examples, the local likelihood technique proves to be effective in uncovering non-linear dependencies. Finally, we give some asymptotic results for local likelihood estimates and provide some methods for inference.

  20. Optimal firing rate estimation

    NASA Technical Reports Server (NTRS)

    Paulin, M. G.; Hoffman, L. F.

    2001-01-01

    We define a measure for evaluating the quality of a predictive model of the behavior of a spiking neuron. This measure, information gain per spike (Is), indicates how much more information is provided by the model than if the prediction were made by specifying the neuron's average firing rate over the same time period. We apply a maximum Is criterion to optimize the performance of Gaussian smoothing filters for estimating neural firing rates. With data from bullfrog vestibular semicircular canal neurons and data from simulated integrate-and-fire neurons, the optimal bandwidth for firing rate estimation is typically similar to the average firing rate. Precise timing and average rate models are limiting cases that perform poorly. We estimate that bullfrog semicircular canal sensory neurons transmit in the order of 1 bit of stimulus-related information per spike.

  1. Thermodynamic estimation: Ionic materials

    SciTech Connect

    Glasser, Leslie

    2013-10-15

    Thermodynamics establishes equilibrium relations among thermodynamic parameters (“properties”) and delineates the effects of variation of the thermodynamic functions (typically temperature and pressure) on those parameters. However, classical thermodynamics does not provide values for the necessary thermodynamic properties, which must be established by extra-thermodynamic means such as experiment, theoretical calculation, or empirical estimation. While many values may be found in the numerous collected tables in the literature, these are necessarily incomplete because either the experimental measurements have not been made or the materials may be hypothetical. The current paper presents a number of simple and relible estimation methods for thermodynamic properties, principally for ionic materials. The results may also be used as a check for obvious errors in published values. The estimation methods described are typically based on addition of properties of individual ions, or sums of properties of neutral ion groups (such as “double” salts, in the Simple Salt Approximation), or based upon correlations such as with formula unit volumes (Volume-Based Thermodynamics). - Graphical abstract: Thermodynamic properties of ionic materials may be readily estimated by summation of the properties of individual ions, by summation of the properties of ‘double salts’, and by correlation with formula volume. Such estimates may fill gaps in the literature, and may also be used as checks of published values. This simplicity arises from exploitation of the fact that repulsive energy terms are of short range and very similar across materials, while coulombic interactions provide a very large component of the attractive energy in ionic systems. Display Omitted - Highlights: • Estimation methods for thermodynamic properties of ionic materials are introduced. • Methods are based on summation of single ions, multiple salts, and correlations. • Heat capacity, entropy

  2. Parametric Hazard Function Estimation.

    Energy Science and Technology Software Center (ESTSC)

    1999-09-13

    Version 00 Phaze performs statistical inference calculations on a hazard function (also called a failure rate or intensity function) based on reported failure times of components that are repaired and restored to service. Three parametric models are allowed: the exponential, linear, and Weibull hazard models. The inference includes estimation (maximum likelihood estimators and confidence regions) of the parameters and of the hazard function itself, testing of hypotheses such as increasing failure rate, and checking ofmore » the model assumptions.« less

  3. Virtual Screening Using Molecular Simulations

    PubMed Central

    Yang, Tianyi; Wu, Johnny C.; Yan, Chunli; Wang, Yuanfeng; Luo, Ray; Gonzales, Michael B.; Dalby, Kevin N.; Ren, Pengyu

    2011-01-01

    Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) Surface Area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range 0.56~0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data while the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery. PMID:21491494

  4. New approaches to molecular diagnosis.

    PubMed

    Korf, Bruce R; Rehm, Heidi L

    2013-04-10

    Advances in understanding the molecular basis of rare and common disorders, as well as in the technology of DNA analysis, are rapidly changing the landscape of molecular genetic and genomic testing. High-resolution molecular cytogenetic analysis can now detect deletions or duplications of DNA of a few hundred thousand nucleotides, well below the resolution of the light microscope. Diagnostic testing for "single-gene" disorders can be done by targeted analysis for specific mutations, by sequencing a specific gene to scan for mutations, or by analyzing multiple genes in which mutation may lead to a similar phenotype. The advent of massively parallel next-generation sequencing facilitates the analysis of multiple genes and now is being used to sequence the coding regions of the genome (the exome) for clinical testing. Exome sequencing requires bioinformatic analysis of the thousands of variants that are identified to find one that is contributing to the pathology; there is also a possibility of incidental identification of other medically significant variants, which may complicate genetic counseling. DNA testing can also be used to identify variants that influence drug metabolism or interaction of a drug with its cellular target, allowing customization of choice of drug and dosage. Exome and genome sequencing are being applied to identify specific gene changes in cancer cells to guide therapy, to identify inherited cancer risk, and to estimate prognosis. Genomic testing may be used to identify risk factors for common disorders, although the clinical utility of such testing is unclear. Genetic and genomic tests may raise new ethical, legal, and social issues, some of which may be addressed by existing genetic nondiscrimination legislation, but which also must be addressed in the course of genetic counseling. The purpose of this article is to assist physicians in recognizing where new approaches to genetic and genomic testing may be applied clinically and in being aware

  5. Embedded Clusters in Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Lada, Charles J.; Lada, Elizabeth A.

    Stellar clusters are born embedded within giant molecular clouds (GMCs) and during their formation and early evolution are often only visible at infrared wavelengths, being heavily obscured by dust. Over the past 15 years advances in infrared detection capabilities have enabled the first systematic studies of embedded clusters in galactic molecular clouds. In this article we review the current state of empirical knowledge concerning these extremely young protocluster systems. From a survey of the literature we compile the first extensive catalog of galactic embedded clusters. We use the catalog to construct the mass function and estimate the birthrate for embedded clusters within 2 kpc of the sun. We find that the embedded cluster birthrate exceeds that of visible open clusters by an order of magnitude or more indicating a high infant mortality rate for protocluster systems. Less than 4-7% of embedded clusters survive emergence from molecular clouds to become bound clusters of Pleiades age. The vast majority (90%) of stars that form in embedded clusters form in rich clusters of 100 or more members with masses in excess of 50 M⊙. Moreover, observations of nearby cloud complexes indicate that embedded clusters account for a significant (70-90%) fraction of all stars formed in GMCs. We review the role of embedded clusters in investigating the nature of the initial mass function (IMF) that, in one nearby example, has been measured over the entire range of stellar and substellar mass, from OB stars to substellar objects near the deuterium burning limit. We also review the role embedded clusters play in the investigation of circumstellar disk evolution and the important constraints they provide for understanding the origin of planetary systems. Finally, we discuss current ideas concerning the origin and dynamical evolution of embedded clusters and the implications for the formation of bound open clusters.

  6. Marker detection evaluation by phantom and cadaver experiments for C-arm pose estimation pattern

    NASA Astrophysics Data System (ADS)

    Steger, Teena; Hoßbach, Martin; Wesarg, Stefan

    2013-03-01

    C-arm fluoroscopy is used for guidance during several clinical exams, e.g. in bronchoscopy to locate the bronchoscope inside the airways. Unfortunately, these images provide only 2D information. However, if the C-arm pose is known, it can be used to overlay the intrainterventional fluoroscopy images with 3D visualizations of airways, acquired from preinterventional CT images. Thus, the physician's view is enhanced and localization of the instrument at the correct position inside the bronchial tree is facilitated. We present a novel method for C-arm pose estimation introducing a marker-based pattern, which is placed on the patient table. The steel markers form a pattern, allowing to deduce the C-arm pose by use of the projective invariant cross-ratio. Simulations show that the C-arm pose estimation is reliable and accurate for translations inside an imaging area of 30 cm x 50 cm and rotations up to 30°. Mean error values are 0.33 mm in 3D space and 0.48 px in the 2D imaging plane. First tests on C-arm images resulted in similarly compelling accuracy values and high reliability in an imaging area of 30 cm x 42.5 cm. Even in the presence of interfering structures, tested both with anatomy phantoms and a turkey cadaver, high success rates over 90% and fully satisfying execution times below 4 sec for 1024 px × 1024 px images could be achieved.

  7. EDITORIAL: Molecular Imaging Technology

    NASA Astrophysics Data System (ADS)

    Asai, Keisuke; Okamoto, Koji

    2006-06-01

    'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

  8. Fragment oriented molecular shapes.

    PubMed

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  9. Shrinkage estimators for covariance matrices.

    PubMed

    Daniels, M J; Kass, R E

    2001-12-01

    Estimation of covariance matrices in small samples has been studied by many authors. Standard estimators, like the unstructured maximum likelihood estimator (ML) or restricted maximum likelihood (REML) estimator, can be very unstable with the smallest estimated eigenvalues being too small and the largest too big. A standard approach to more stably estimating the matrix in small samples is to compute the ML or REML estimator under some simple structure that involves estimation of fewer parameters, such as compound symmetry or independence. However, these estimators will not be consistent unless the hypothesized structure is correct. If interest focuses on estimation of regression coefficients with correlated (or longitudinal) data, a sandwich estimator of the covariance matrix may be used to provide standard errors for the estimated coefficients that are robust in the sense that they remain consistent under misspecification of the covariance structure. With large matrices, however, the inefficiency of the sandwich estimator becomes worrisome. We consider here two general shrinkage approaches to estimating the covariance matrix and regression coefficients. The first involves shrinking the eigenvalues of the unstructured ML or REML estimator. The second involves shrinking an unstructured estimator toward a structured estimator. For both cases, the data determine the amount of shrinkage. These estimators are consistent and give consistent and asymptotically efficient estimates for regression coefficients. Simulations show the improved operating characteristics of the shrinkage estimators of the covariance matrix and the regression coefficients in finite samples. The final estimator chosen includes a combination of both shrinkage approaches, i.e., shrinking the eigenvalues and then shrinking toward structure. We illustrate our approach on a sleep EEG study that requires estimation of a 24 x 24 covariance matrix and for which inferences on mean parameters critically

  10. Quantifying surface normal estimation

    NASA Astrophysics Data System (ADS)

    Reid, Robert B.; Oxley, Mark E.; Eismann, Michael T.; Goda, Matthew E.

    2006-05-01

    An inverse algorithm for surface normal estimation from thermal polarimetric imagery was developed and used to quantify the requirements on a priori information. Building on existing knowledge that calculates the degree of linear polarization (DOLP) and the angle of polarization (AOP) for a given surface normal in a forward model (from an object's characteristics to calculation of the DOLP and AOP), this research quantifies the impact of a priori information with the development of an inverse algorithm to estimate surface normals from thermal polarimetric emissions in long-wave infrared (LWIR). The inverse algorithm assumes a polarized infrared focal plane array capturing LWIR intensity images which are then converted to Stokes vectors. Next, the DOLP and AOP are calculated from the Stokes vectors. Last, the viewing angles, θ v, to the surface normals are estimated assuming perfect material information about the imaged scene. A sensitivity analysis is presented to quantitatively describe the a priori information's impact on the amount of error in the estimation of surface normals, and a bound is determined given perfect information about an object. Simulations explored the impact of surface roughness (σ) and the real component (n) of a dielectric's complex index of refraction across a range of viewing angles (θ v) for a given wavelength of observation.

  11. Estimating Cloud Cover

    ERIC Educational Resources Information Center

    Moseley, Christine

    2007-01-01

    The purpose of this activity was to help students understand the percentage of cloud cover and make more accurate cloud cover observations. Students estimated the percentage of cloud cover represented by simulated clouds and assigned a cloud cover classification to those simulations. (Contains 2 notes and 3 tables.)

  12. Bayesian Threshold Estimation

    ERIC Educational Resources Information Center

    Gustafson, S. C.; Costello, C. S.; Like, E. C.; Pierce, S. J.; Shenoy, K. N.

    2009-01-01

    Bayesian estimation of a threshold time (hereafter simply threshold) for the receipt of impulse signals is accomplished given the following: 1) data, consisting of the number of impulses received in a time interval from zero to one and the time of the largest time impulse; 2) a model, consisting of a uniform probability density of impulse time…

  13. Estimating Gender Wage Gaps

    ERIC Educational Resources Information Center

    McDonald, Judith A.; Thornton, Robert J.

    2011-01-01

    Course research projects that use easy-to-access real-world data and that generate findings with which undergraduate students can readily identify are hard to find. The authors describe a project that requires students to estimate the current female-male earnings gap for new college graduates. The project also enables students to see to what…

  14. Radiation risk estimation models

    SciTech Connect

    Hoel, D.G.

    1987-11-01

    Cancer risk models and their relationship to ionizing radiation are discussed. There are many model assumptions and risk factors that have a large quantitative impact on the cancer risk estimates. Other health end points such as mental retardation may be an even more serious risk than cancer for those with in utero exposures. 8 references.

  15. Estimating Delays In ASIC's

    NASA Technical Reports Server (NTRS)

    Burke, Gary; Nesheiwat, Jeffrey; Su, Ling

    1994-01-01

    Verification is important aspect of process of designing application-specific integrated circuit (ASIC). Design must not only be functionally accurate, but must also maintain correct timing. IFA, Intelligent Front Annotation program, assists in verifying timing of ASIC early in design process. This program speeds design-and-verification cycle by estimating delays before layouts completed. Written in C language.

  16. Estimating Large Numbers

    ERIC Educational Resources Information Center

    Landy, David; Silbert, Noah; Goldin, Aleah

    2013-01-01

    Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions…

  17. Traffic Flow Estimates.

    ERIC Educational Resources Information Center

    Hart, Vincent G.

    1981-01-01

    Two examples are given of ways traffic engineers estimate traffic flow. The first, Floating Car Method, involves some basic ideas and the notion of relative velocity. The second, Maximum Traffic Flow, is viewed to involve simple applications of calculus. The material provides insight into specialized applications of mathematics. (MP)

  18. Magnetomotive Molecular Nanoprobes

    PubMed Central

    John, Renu; Boppart, Stephen A.

    2012-01-01

    Tremendous developments in the field of biomedical imaging in the past two decades have resulted in the transformation of anatomical imaging to molecular-specific imaging. The main approaches towards imaging at a molecular level are the development of high resolution imaging modalities with high penetration depths and increased sensitivity, and the development of molecular probes with high specificity. The development of novel molecular contrast agents and their success in molecular optical imaging modalities have lead to the emergence of molecular optical imaging as a more versatile and capable technique for providing morphological, spatial, and functional information at the molecular level with high sensitivity and precision, compared to other imaging modalities. In this review, we discuss a new class of dynamic contrast agents called magnetomotive molecular nanoprobes for molecular-specific imaging. Magnetomotive agents are superparamagnetic nanoparticles, typically iron-oxide, that are physically displaced by the application of a small modulating external magnetic field. Dynamic phase-sensitive position measurements are performed using any high resolution imaging modality, including optical coherence tomography (OCT), ultrasonography, or magnetic resonance imaging (MRI). The dynamics of the magnetomotive agents can be used to extract the biomechanical tissue properties in which the nanoparticles are bound, and the agents can be used to deliver therapy via magnetomotive displacements to modulate or disrupt cell function, or hyperthermia to kill cells. These agents can be targeted via conjugation to antibodies, and in vivo targeted imaging has been shown in a carcinogen-induced rat mammary tumor model. The iron-oxide nanoparticles also exhibit negative T2 contrast in MRI, and modulations can produce ultrasound imaging contrast for multimodal imaging applications. PMID:21517766

  19. Estimating Thermoelectric Water Use

    NASA Astrophysics Data System (ADS)

    Hutson, S. S.

    2012-12-01

    In 2009, the Government Accountability Office recommended that the U.S. Geological Survey (USGS) and Department of Energy-Energy Information Administration, (DOE-EIA) jointly improve their thermoelectric water-use estimates. Since then, the annual mandatory reporting forms returned by powerplant operators to DOE-EIA have been revised twice to improve the water data. At the same time, the USGS began improving estimation of withdrawal and consumption. Because of the variation in amount and quality of water-use data across powerplants, the USGS adopted a hierarchy of methods for estimating water withdrawal and consumptive use for the approximately 1,300 water-using powerplants in the thermoelectric sector. About 800 of these powerplants have generation and cooling data, and the remaining 500 have generation data only, or sparse data. The preferred method is to accept DOE-EIA data following validation. This is the traditional USGS method and the best method if all operators follow best practices for measurement and reporting. However, in 2010, fewer than 200 powerplants reported thermodynamically realistic values of both withdrawal and consumption. Secondly, water use was estimated using linked heat and water budgets for the first group of 800 plants, and for some of the other 500 powerplants where data were sufficient for at least partial modeling using plant characteristics, electric generation, and fuel use. Thermodynamics, environmental conditions, and characteristics of the plant and cooling system constrain both the amount of heat discharged to the environment and the share of this heat that drives evaporation. Heat and water budgets were used to define reasonable estimates of withdrawal and consumption, including likely upper and lower thermodynamic limits. These results were used to validate the reported values at the 800 plants with water-use data, and reported values were replaced by budget estimates at most of these plants. Thirdly, at plants without valid

  20. Potential molecular wires and molecular alligator clips

    NASA Astrophysics Data System (ADS)

    Schumm, Jeffry S.; Pearson, Darren L.; Jones, LeRoy, II; Hara, Ryuichiro; Tour, James M.

    1996-12-01

    The synthesis of oligo(2-ethylphenylene-ethynylene)s, oligo(2-(0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s, and oligo(3-ethylthiophene-ethynylene)s is described via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, octamer and 16-mer of the oligo(3-ethylthiophene-ethynylene)s and oligo(2-0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s. The 16-mers are 100 Å and 128 Å long, respectively. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers versus the random coils of polystyrene. These differences become quite apparent at the octamer stage. The preparation of thiol-protected end groups is described. These may serve as molecular alligator clips for adhesion to gold surfaces. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

  1. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

    The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

  2. Molecularly Imprinted Membranes

    PubMed Central

    Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

    2012-01-01

    Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

  3. Estimating extragalactic Faraday rotation

    NASA Astrophysics Data System (ADS)

    Oppermann, N.; Junklewitz, H.; Greiner, M.; Enßlin, T. A.; Akahori, T.; Carretti, E.; Gaensler, B. M.; Goobar, A.; Harvey-Smith, L.; Johnston-Hollitt, M.; Pratley, L.; Schnitzeler, D. H. F. M.; Stil, J. M.; Vacca, V.

    2015-03-01

    Observations of Faraday rotation for extragalactic sources probe magnetic fields both inside and outside the Milky Way. Building on our earlier estimate of the Galactic contribution, we set out to estimate the extragalactic contributions. We discuss the problems involved; in particular, we point out that taking the difference between the observed values and the Galactic foreground reconstruction is not a good estimate for the extragalactic contributions. We point out a degeneracy between the contributions to the observed values due to extragalactic magnetic fields and observational noise and comment on the dangers of over-interpreting an estimate without taking into account its uncertainty information. To overcome these difficulties, we develop an extended reconstruction algorithm based on the assumption that the observational uncertainties are accurately described for a subset of the data, which can overcome the degeneracy with the extragalactic contributions. We present a probabilistic derivation of the algorithm and demonstrate its performance using a simulation, yielding a high quality reconstruction of the Galactic Faraday rotation foreground, a precise estimate of the typical extragalactic contribution, and a well-defined probabilistic description of the extragalactic contribution for each data point. We then apply this reconstruction technique to a catalog of Faraday rotation observations for extragalactic sources. The analysis is done for several different scenarios, for which we consider the error bars of different subsets of the data to accurately describe the observational uncertainties. By comparing the results, we argue that a split that singles out only data near the Galactic poles is the most robust approach. We find that the dispersion of extragalactic contributions to observed Faraday depths is most likely lower than 7 rad/m2, in agreement with earlier results, and that the extragalactic contribution to an individual data point is poorly

  4. Resistive molecular memories: influence of molecular parameters on the electrical bistability.

    PubMed

    Di Motta, Simone; Di Donato, Eugenio; Negri, Fabrizia; Orlandi, Giorgio; Fazzi, Daniele; Castiglioni, Chiara

    2009-05-13

    The electrical bistability behavior of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) along with two additional benzoquinone derivatives (TCQ and TCN) and pentacene (PNT) is investigated by computing intra- and intermolecular charge transfer parameters and by comparing the efficiency of bulk charge transport and charge injection at the electrode/organic interface in the presence of neutral and charged molecular species. The bulk charge transport is modeled assuming a charge hopping regime and by computing hopping rates and mobilities. Molecular dynamics simulations are carried out to estimate the effect of thermal disorder on charge transfer integrals. The efficiency of the interface transport is estimated by comparing the electron affinities of benzoquinone derivatives and the ionization potential of pentacene with the work function of commonly employed electrodes. It is shown that the observed memory effect can be rationalized in terms of an interplay of the two transport mechanisms by showing that the OFF state is dominated by interface limited phenomena and the ON state may be determined also by bulk transport limited phenomena. While the contribution of collective effects cannot be ruled out for the macroscopic memory phenomenon, we show that, at a molecular level, sizable intramolecular reorganization energies are fundamental for the efficiency of the device, provided their magnitude does not hamper the charge transport across the device. It is suggested that control over molecular parameters might be exploited to design more efficient resistive molecular memories. PMID:19374415

  5. FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION.

    PubMed

    Bajaj, Chandrajit; Zhao, Wenqi

    2010-01-20

    The total free energy of a molecule includes the classical molecular mechanical energy (which is understood as the free energy in vacuum) and the solvation energy which is caused by the change of the environment of the molecule (solute) from vacuum to solvent. The solvation energy is important to the study of the inter-molecular interactions. In this paper we develop a fast surface-based generalized Born method to compute the electrostatic solvation energy along with the energy derivatives for the solvation forces. The most time-consuming computation is the evaluation of the surface integrals over an algebraic spline molecular surface (ASMS) and the fast computation is achieved by the use of the nonequispaced fast Fourier transform (NFFT) algorithm. The main results of this paper involve (a) an efficient sampling of quadrature points over the molecular surface by using nonlinear patches, (b) fast linear time estimation of energy and inter-molecular forces, (c) error analysis, and (d) efficient implementation combining fast pairwise summation and the continuum integration using nonlinear patches. PMID:20200598

  6. Molecular Epidemiology of Tuberculosis: Current Insights

    PubMed Central

    Mathema, Barun; Kurepina, Natalia E.; Bifani, Pablo J.; Kreiswirth, Barry N.

    2006-01-01

    Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB. PMID:17041139

  7. Statistical Analysis of Molecular Signal Recording

    PubMed Central

    Glaser, Joshua I.; Moffitt, Jeffrey R.; Tyo, Keith; Boyden, Edward S.; Church, George; Kording, Konrad P.

    2013-01-01

    A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales. PMID:23874187

  8. An alternative covariance estimator to investigate genetic heterogeneity in populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic predictions and GWAS have used mixed models for identification of associations and trait predictions. In both cases, the covariance between individuals for performance is estimated using molecular markers. Mixed model properties indicate that the use of the data for prediction is optimal if ...

  9. [Molecular diagnosis of mycobacteria].

    PubMed

    Kessler, Harald H

    2003-01-01

    Tuberculosis is one of the leading infectious diseases in the world. Using conventional methods, the isolation, identification, and drug susceptibility testing of Mycobacterium tuberculosis and other clinically important mycobacteria can take several weeks. During the past several years, molecular methods have been developed for direct detection, species identification, and drug susceptibility testing of mycobacteria. These methods can potentially reduce the diagnostic time from weeks to hours. For direct detection of Mycobacterium tuberculosis from clinical specimens, several molecular assays are commercially available today. They have been shown useful for the routine diagnostic laboratory. DNA probes and polymerase chain reaction-based sequencing have been widely used to identify mycobacterial species. Molecular methods have also been applied for the detection of mutations that confer drug resistance in mycobacteria. All in all, the future of clinical mycobacteriology appears to be heading toward direct detection, species identification and drug resistance determination using molecular methods. PMID:13677254

  10. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  11. Molecular photoionization dynamics

    SciTech Connect

    Dehmer, Joseph L.

    1982-05-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)

  12. Appendix II. Molecular Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The study of crop evolution, origins, and conservation entails the assessment of genetic variability with and between populations and species at different genetic, evolutionary, and taxonomic hierarchical levels. Molecular biology has greatly increased the amount of data and computational intensity...

  13. Are there molecular signatures?

    SciTech Connect

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  14. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  15. Ontologies for molecular biology.

    PubMed

    Schulze-Kremer, S

    1998-01-01

    Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning. A prominent example is the concept "gene" which is used with different semantics by major international genomic databases. Ontologies are one means to provide a semantic repository to systematically order relevant concepts in molecular biology and to bridge the different notions in various databases by explicitly specifying the meaning of and relation between the fundamental concepts in an application domain. Here, the upper level and a database branch of a prospective ontology for molecular biology (OMB) is presented and compared to other ontologies with respect to suitability for molecular biology (http:/(/)igd.rz-berlin.mpg.de/approximately www/oe/mbo.html). PMID:9697223

  16. Atomic & Molecular Interactions

    SciTech Connect

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  17. Estimating the mass of mutagens in indeterminate mixtures

    SciTech Connect

    Schaeffer, D.J.; Kerster, H.W.

    1985-10-01

    A method is shown for estimating the quantity (mass) of genotoxic compounds in complex mixtures without prior identification of components. This method uses fractiles of the probability distribution of responses from the assay of interest and dose-response of the mixture. The method depends upon the assumption of additivity, on average, in the interaction of mutagens and on lognormality of the distribution of mutagen molecular weights. Mass estimates are necessary for hazard characterization, risk estimation, and risk assessment. The method is illustrated using Ames assay results from a coke plant wastewater.

  18. J-adaptive estimation with estimated noise statistics

    NASA Technical Reports Server (NTRS)

    Jazwinski, A. H.; Hipkins, C.

    1973-01-01

    The J-adaptive sequential estimator is extended to include simultaneous estimation of the noise statistics in a model for system dynamics. This extension completely automates the estimator, eliminating the requirement of an analyst in the loop. Simulations in satellite orbit determination demonstrate the efficacy of the sequential estimation algorithm.

  19. THE DARK MOLECULAR GAS

    SciTech Connect

    Wolfire, Mark G.; Hollenbach, David; McKee, Christopher F. E-mail: dhollenbach@seti.or

    2010-06-20

    The mass of molecular gas in an interstellar cloud is often measured using line emission from low rotational levels of CO, which are sensitive to the CO mass, and then scaling to the assumed molecular hydrogen H{sub 2} mass. However, a significant H{sub 2} mass may lie outside the CO region, in the outer regions of the molecular cloud where the gas-phase carbon resides in C or C{sup +}. Here, H{sub 2} self-shields or is shielded by dust from UV photodissociation, whereas CO is photodissociated. This H{sub 2} gas is 'dark' in molecular transitions because of the absence of CO and other trace molecules, and because H{sub 2} emits so weakly at temperatures 10 K molecular component. This component has been indirectly observed through other tracers of mass such as gamma rays produced in cosmic-ray collisions with the gas and far-infrared/submillimeter wavelength dust continuum radiation. In this paper, we theoretically model this dark mass and find that the fraction of the molecular mass in this dark component is remarkably constant ({approx}0.3 for average visual extinction through the cloud A-bar{sub V{approx_equal}}8) and insensitive to the incident ultraviolet radiation field strength, the internal density distribution, and the mass of the molecular cloud as long as A-bar{sub V}, or equivalently, the product of the average hydrogen nucleus column and the metallicity through the cloud, is constant. We also find that the dark mass fraction increases with decreasing A-bar{sub V}, since relatively more molecular H{sub 2} material lies outside the CO region in this case.

  20. Molecular Electronic Shift Registers

    NASA Technical Reports Server (NTRS)

    Beratan, David N.; Onuchic, Jose N.

    1990-01-01

    Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

  1. Introductory molecular genetics

    SciTech Connect

    Edwards-Moulds, J.

    1986-01-01

    This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.

  2. Workshop on Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Cummings, Michael P.

    2004-01-01

    Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

  3. Molecular classification of gliomas.

    PubMed

    Masui, Kenta; Mischel, Paul S; Reifenberger, Guido

    2016-01-01

    The identification of distinct genetic and epigenetic profiles in different types of gliomas has revealed novel diagnostic, prognostic, and predictive molecular biomarkers for refinement of glioma classification and improved prediction of therapy response and outcome. Therefore, the new (2016) World Health Organization (WHO) classification of tumors of the central nervous system breaks with the traditional principle of diagnosis based on histologic criteria only and incorporates molecular markers. This will involve a multilayered approach combining histologic features and molecular information in an "integrated diagnosis". We review the current state of diagnostic molecular markers for gliomas, focusing on isocitrate dehydrogenase 1 or 2 (IDH1/IDH2) gene mutation, α-thalassemia/mental retardation syndrome X-linked (ATRX) gene mutation, 1p/19q co-deletion and telomerase reverse transcriptase (TERT) promoter mutation in adult tumors, as well as v-raf murine sarcoma viral oncogene homolog B1 (BRAF) and H3 histone family 3A (H3F3A) aberrations in pediatric gliomas. We also outline prognostic and predictive molecular markers, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, and discuss the potential clinical relevance of biologic glioblastoma subtypes defined by integration of multiomics data. Commonly used methods for individual marker detection as well as novel large-scale DNA methylation profiling and next-generation sequencing approaches are discussed. Finally, we illustrate how advances in molecular diagnostics affect novel strategies of targeted therapy, thereby raising new challenges and identifying new leads for personalized treatment of glioma patients. PMID:26948350

  4. Magnetic nanoparticle temperature estimation

    SciTech Connect

    Weaver, John B.; Rauwerdink, Adam M.; Hansen, Eric W.

    2009-05-15

    The authors present a method of measuring the temperature of magnetic nanoparticles that can be adapted to provide in vivo temperature maps. Many of the minimally invasive therapies that promise to reduce health care costs and improve patient outcomes heat tissue to very specific temperatures to be effective. Measurements are required because physiological cooling, primarily blood flow, makes the temperature difficult to predict a priori. The ratio of the fifth and third harmonics of the magnetization generated by magnetic nanoparticles in a sinusoidal field is used to generate a calibration curve and to subsequently estimate the temperature. The calibration curve is obtained by varying the amplitude of the sinusoidal field. The temperature can then be estimated from any subsequent measurement of the ratio. The accuracy was 0.3 deg. K between 20 and 50 deg. C using the current apparatus and half-second measurements. The method is independent of nanoparticle concentration and nanoparticle size distribution.

  5. Power spectral estimation algorithms

    NASA Technical Reports Server (NTRS)

    Bhatia, Manjit S.

    1989-01-01

    Algorithms to estimate the power spectrum using Maximum Entropy Methods were developed. These algorithms were coded in FORTRAN 77 and were implemented on the VAX 780. The important considerations in this analysis are: (1) resolution, i.e., how close in frequency two spectral components can be spaced and still be identified; (2) dynamic range, i.e., how small a spectral peak can be, relative to the largest, and still be observed in the spectra; and (3) variance, i.e., how accurate the estimate of the spectra is to the actual spectra. The application of the algorithms based on Maximum Entropy Methods to a variety of data shows that these criteria are met quite well. Additional work in this direction would help confirm the findings. All of the software developed was turned over to the technical monitor. A copy of a typical program is included. Some of the actual data and graphs used on this data are also included.

  6. Chernobyl source term estimation

    SciTech Connect

    Gudiksen, P.H.; Harvey, T.F.; Lange, R.

    1990-09-01

    The Chernobyl source term available for long-range transport was estimated by integration of radiological measurements with atmospheric dispersion modeling and by reactor core radionuclide inventory estimation in conjunction with WASH-1400 release fractions associated with specific chemical groups. The model simulations revealed that the radioactive cloud became segmented during the first day, with the lower section heading toward Scandinavia and the upper part heading in a southeasterly direction with subsequent transport across Asia to Japan, the North Pacific, and the west coast of North America. By optimizing the agreement between the observed cloud arrival times and duration of peak concentrations measured over Europe, Japan, Kuwait, and the US with the model predicted concentrations, it was possible to derive source term estimates for those radionuclides measured in airborne radioactivity. This was extended to radionuclides that were largely unmeasured in the environment by performing a reactor core radionuclide inventory analysis to obtain release fractions for the various chemical transport groups. These analyses indicated that essentially all of the noble gases, 60% of the radioiodines, 40% of the radiocesium, 10% of the tellurium and about 1% or less of the more refractory elements were released. These estimates are in excellent agreement with those obtained on the basis of worldwide deposition measurements. The Chernobyl source term was several orders of magnitude greater than those associated with the Windscale and TMI reactor accidents. However, the {sup 137}Cs from the Chernobyl event is about 6% of that released by the US and USSR atmospheric nuclear weapon tests, while the {sup 131}I and {sup 90}Sr released by the Chernobyl accident was only about 0.1% of that released by the weapon tests. 13 refs., 2 figs., 7 tabs.

  7. Optimal Centroid Position Estimation

    SciTech Connect

    Candy, J V; McClay, W A; Awwal, A S; Ferguson, S W

    2004-07-23

    The alignment of high energy laser beams for potential fusion experiments demand high precision and accuracy by the underlying positioning algorithms. This paper discusses the feasibility of employing online optimal position estimators in the form of model-based processors to achieve the desired results. Here we discuss the modeling, development, implementation and processing of model-based processors applied to both simulated and actual beam line data.

  8. Estimating Dark Matter Distributions

    NASA Astrophysics Data System (ADS)

    Wang, Xiao; Woodroofe, Michael; Walker, Matthew G.; Mateo, Mario; Olszewski, Edward

    2005-06-01

    Thanks to instrumental advances, new, very large kinematic data sets for nearby dwarf spheroidal (dSph) galaxies are on the horizon. A key aim of these data sets is to help determine the distribution of dark matter in these galaxies. Past analyses have generally relied on specific dynamical models or highly restrictive dynamical assumptions. We describe a new, nonparametric analysis of the kinematics of nearby dSph galaxies designed to take full advantage of the future large data sets. The method takes as input the projected positions and radial velocities of stars known to be members of the galaxies but does not use any parametric dynamical model or the assumption that the mass distribution follows that of the visible matter. The problem of estimating the radial mass distribution M(r) (the mass within the true radius r) is converted into a problem of estimating a regression function nonparametrically. From the Jeans equation we show that the unknown regression function is subject to fundamental shape restrictions, which we exploit in our analysis using statistical techniques borrowed from isotonic estimation and spline smoothing. Simulations indicate that M(r) can be estimated to within a factor of 2 or better with samples as small as 1000 stars over almost the entire radial range sampled by the kinematic data. The technique is applied to a sample of 181 stars in the Fornax dSph galaxy. We show that the galaxy contains a significant, extended dark halo some 10 times more massive than its baryonic component. Although applied here to dSph kinematics, this approach can be used in the analysis of any kinematically hot stellar system in which the radial velocity field is discretely sampled.

  9. Molecular characterization of Opisthorchis noverca (Digenea: Opisthorchiidae) based on nuclear ribosomal ITS2 and mitochondrial COI genes.

    PubMed

    Sahu, R; Biswal, D K; Roy, B; Tandon, V

    2016-09-01

    Opisthorchiasis is a public health problem in South-East Asian countries and Eastern Europe. The infection implicates mainly two species of Opisthorchis, namely O. viverrini and O. felineus, that occur mostly in fish-eating mammals and humans, although there are rare reports of human cases involving two other species, O. noverca and O. guayaquilensis. Opisthorchis noverca has been reported frequently in dogs and pigs from the Indian subcontinent, with rare reports from cattle and human subjects. With a view to supplementing morphology-based identification of this species, the present study aimed to provide molecular characterization of O. noverca, using rDNA internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase I (mt COI) markers so as to determine its genetic correlation with other species of Opisthorchiidae, and also to generate a taxon-specific molecular marker based on the ITS2 region. The phylogenetic relationship between O. noverca and other species of the genus was determined using molecular sequence data. To strengthen the result, secondary structure sequence analyses of ITS2 with hemi-compensatory base changes (hCBCs), and amino acid sequence analyses, were also evaluated. Our results confirm that O. noverca is a distinct and valid species. PMID:26467395

  10. Bayesian Error Estimation Functionals

    NASA Astrophysics Data System (ADS)

    Jacobsen, Karsten W.

    The challenge of approximating the exchange-correlation functional in Density Functional Theory (DFT) has led to the development of numerous different approximations of varying accuracy on different calculated properties. There is therefore a need for reliable estimation of prediction errors within the different approximation schemes to DFT. The Bayesian Error Estimation Functionals (BEEF) have been developed with this in mind. The functionals are constructed by fitting to experimental and high-quality computational databases for molecules and solids including chemisorption and van der Waals systems. This leads to reasonably accurate general-purpose functionals with particual focus on surface science. The fitting procedure involves considerations on how to combine different types of data, and applies Tikhonov regularization and bootstrap cross validation. The methodology has been applied to construct GGA and metaGGA functionals with and without inclusion of long-ranged van der Waals contributions. The error estimation is made possible by the generation of not only a single functional but through the construction of a probability distribution of functionals represented by a functional ensemble. The use of the functional ensemble is illustrated on compound heat of formation and by investigations of the reliability of calculated catalytic ammonia synthesis rates.

  11. Estimating Distances from Parallaxes

    NASA Astrophysics Data System (ADS)

    Bailer-Jones, Coryn A. L.

    2015-10-01

    Astrometric surveys such as Gaia and LSST will measure parallaxes for hundreds of millions of stars. Yet they will not measure a single distance. Rather, a distance must be estimated from a parallax. In this didactic article, I show that doing this is not trivial once the fractional parallax error is larger than about 20%, which will be the case for about 80% of stars in the Gaia catalog. Estimating distances is an inference problem in which the use of prior assumptions is unavoidable. I investigate the properties and performance of various priors and examine their implications. A supposed uninformative uniform prior in distance is shown to give very poor distance estimates (large bias and variance). Any prior with a sharp cut-off at some distance has similar problems. The choice of prior depends on the information one has available—and is willing to use—concerning, e.g., the survey and the Galaxy. I demonstrate that a simple prior which decreases asymptotically to zero at infinite distance has good performance, accommodates nonpositive parallaxes, and does not require a bias correction.

  12. An Improved Fst Estimator

    PubMed Central

    Chen, Guanjie; Yuan, Ao; Shriner, Daniel; Tekola-Ayele, Fasil; Zhou, Jie; Bentley, Amy R.; Zhou, Yanxun; Wang, Chuntao; Newport, Melanie J.; Adeyemo, Adebowale; Rotimi, Charles N.

    2015-01-01

    The fixation index Fst plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (F^st1), Weir and Cockerham (F^st2), and Hudson et al. (F^st3) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator F^stm using F^st1 and F^st2. We tested F^stm in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that F^stm has smaller bias than F^st2 for small sample sizes and smaller bias than F^st1 for large sample sizes. Also, F^stm has smaller variance than F^st2 for small Fst values and smaller variance than F^st1 for large Fst values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate Fst. PMID:26317214

  13. ESTIMATION OF PHYSICAL PROPERTIES AND CHEMICAL REACTIVITY PARAMETERS OF ORGANIC COMPOUNDS

    EPA Science Inventory

    The computer program SPARC (Sparc Performs Automated Reasoning in Chemistry)has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms ...

  14. Nanotechnology Review: Molecular Electronics to Molecular Motors

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  15. Injury Risk Estimation Expertise

    PubMed Central

    Petushek, Erich J.; Ward, Paul; Cokely, Edward T.; Myer, Gregory D.

    2015-01-01

    Background: Simple observational assessment of movement is a potentially low-cost method for anterior cruciate ligament (ACL) injury screening and prevention. Although many individuals utilize some form of observational assessment of movement, there are currently no substantial data on group skill differences in observational screening of ACL injury risk. Purpose/Hypothesis: The purpose of this study was to compare various groups’ abilities to visually assess ACL injury risk as well as the associated strategies and ACL knowledge levels. The hypothesis was that sports medicine professionals would perform better than coaches and exercise science academics/students and that these subgroups would all perform better than parents and other general population members. Study Design: Cross-sectional study; Level of evidence, 3. Methods: A total of 428 individuals, including physicians, physical therapists, athletic trainers, strength and conditioning coaches, exercise science researchers/students, athletes, parents, and members of the general public participated in the study. Participants completed the ACL Injury Risk Estimation Quiz (ACL-IQ) and answered questions related to assessment strategy and ACL knowledge. Results: Strength and conditioning coaches, athletic trainers, physical therapists, and exercise science students exhibited consistently superior ACL injury risk estimation ability (+2 SD) as compared with sport coaches, parents of athletes, and members of the general public. The performance of a substantial number of individuals in the exercise sciences/sports medicines (approximately 40%) was similar to or exceeded clinical instrument-based biomechanical assessment methods (eg, ACL nomogram). Parents, sport coaches, and the general public had lower ACL-IQ, likely due to their lower ACL knowledge and to rating the importance of knee/thigh motion lower and weight and jump height higher. Conclusion: Substantial cross-professional/group differences in visual ACL

  16. Estimating Divergence Times and Substitution Rates in Rhizobia.

    PubMed

    Chriki-Adeeb, Rim; Chriki, Ali

    2016-01-01

    Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes. PMID:27168719

  17. Estimating Divergence Times and Substitution Rates in Rhizobia

    PubMed Central

    Chriki-Adeeb, Rim; Chriki, Ali

    2016-01-01

    Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth–death, birth–death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes. PMID:27168719

  18. Estimation for bilinear stochastic systems

    NASA Technical Reports Server (NTRS)

    Willsky, A. S.; Marcus, S. I.

    1974-01-01

    Three techniques for the solution of bilinear estimation problems are presented. First, finite dimensional optimal nonlinear estimators are presented for certain bilinear systems evolving on solvable and nilpotent lie groups. Then the use of harmonic analysis for estimation problems evolving on spheres and other compact manifolds is investigated. Finally, an approximate estimation technique utilizing cumulants is discussed.

  19. Artificial Molecular Machines.

    PubMed

    Balzani; Credi; Raymo; Stoddart

    2000-10-01

    The miniaturization of components used in the construction of working devices is being pursued currently by the large-downward (top-down) fabrication. This approach, however, which obliges solid-state physicists and electronic engineers to manipulate progressively smaller and smaller pieces of matter, has its intrinsic limitations. An alternative approach is a small-upward (bottom-up) one, starting from the smallest compositions of matter that have distinct shapes and unique properties-namely molecules. In the context of this particular challenge, chemists have been extending the concept of a macroscopic machine to the molecular level. A molecular-level machine can be defined as an assembly of a distinct number of molecular components that are designed to perform machinelike movements (output) as a result of an appropriate external stimulation (input). In common with their macroscopic counterparts, a molecular machine is characterized by 1) the kind of energy input supplied to make it work, 2) the nature of the movements of its component parts, 3) the way in which its operation can be monitored and controlled, 4) the ability to make it repeat its operation in a cyclic fashion, 5) the timescale needed to complete a full cycle of movements, and 6) the purpose of its operation. Undoubtedly, the best energy inputs to make molecular machines work are photons or electrons. Indeed, with appropriately chosen photochemically and electrochemically driven reactions, it is possible to design and synthesize molecular machines that do work. Moreover, the dramatic increase in our fundamental understanding of self-assembly and self-organizational processes in chemical synthesis has aided and abetted the construction of artificial molecular machines through the development of new methods of noncovalent synthesis and the emergence of supramolecular assistance to covalent synthesis as a uniquely powerful synthetic tool. The aim of this review is to present a unified view of the field

  20. Los Alamos PC estimating system

    SciTech Connect

    Stutz, R.A.; Lemon, G.D.

    1987-01-01

    The Los Alamos Cost Estimating System (QUEST) is being converted to run on IBM personal computers. This very extensive estimating system is capable of supporting cost estimators from many different and varied fields. QUEST does not dictate any fixed method for estimating. QUEST supports many styles and levels of detail estimating. QUEST can be used with or without data bases. This system allows the estimator to provide reports based on levels of detail defined by combining work breakdown structures. QUEST provides a set of tools for doing any type of estimate without forcing the estimator to use any given method. The level of detail in the estimate can be mixed based on the amount of information known about different parts of the project. The system can support many different data bases simultaneously. Estimators can modify any cost in any data base.

  1. Hybrid estimation technique for predicting butene concentration in polyethylene reactor

    NASA Astrophysics Data System (ADS)

    Mohd Ali, Jarinah; Hussain, M. A.

    2016-03-01

    A component of artificial intelligence (AI), which is fuzzy logic, is combined with the so-called conventional sliding mode observer (SMO) to establish a hybrid type estimator to predict the butene concentration in the polyethylene production reactor. Butene or co-monomer concentration is another significant parameter in the polymerization process since it will affect the molecular weight distribution of the polymer produced. The hybrid estimator offers straightforward formulation of SMO and its combination with the fuzzy logic rules. The error resulted from the SMO estimation will be manipulated using the fuzzy rules to enhance the performance, thus improved on the convergence rate. This hybrid estimation is able to estimate the butene concentration satisfactorily despite the present of noise in the process.

  2. ESTIM: A parameter estimation computer program: Final report

    SciTech Connect

    Hills, R.G.

    1987-08-01

    The computer code, ESTIM, enables subroutine versions of existing simulation codes to be used to estimate model parameters. Nonlinear least squares techniques are used to find the parameter values that result in a best fit between measurements made in the simulation domain and the simulation code's prediction of these measurements. ESTIM utilizes the non-linear least square code DQED (Hanson and Krogh (1982)) to handle the optimization aspects of the estimation problem. In addition to providing weighted least squares estimates, ESTIM provides a propagation of variance analysis. A subroutine version of COYOTE (Gartling (1982)) is provided. The use of ESTIM with COYOTE allows one to estimate the thermal property model parameters that result in the best agreement (in a least squares sense) between internal temperature measurements and COYOTE's predictions of these internal temperature measurements. We demonstrate the use of ESTIM through several example problems which utilize the subroutine version of COYOTE.

  3. DockingShop: A Tool for Interactive Molecular Docking

    SciTech Connect

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  4. Giant Molecular Magnetocapacitance

    SciTech Connect

    Wu, Yuning; Zhang, Xiaoguang; Cheng, Hai-Ping

    2013-01-01

    Capacitance of a nanoscale system is usually thought of having two contributions, a classical electrostatic contribution and a quantum contribution dependent on the density of states and/or molecular orbitals close to the Fermi energy. In this letter we demonstrate that in molecular nano-magnets and other magnetic nanoscale systems, the quantum part of the capacitance becomes spin-dependent, and is tunable by an external magnetic field. This molecular magnetocapacitance can be realized using single molecule nano-magnets and/or other nano-structures that have antiferromagnetic ground states. As a proof of principle, first-principles calculation of the nano-magnet [Mn3O(sao)3(O2CMe)(H2O)(py)3] shows that the charging energy of the high-spin state is 260 meV lower than that of the low-spin state, yielding a 6% difference in capacitance. A magnetic field of ~40T can switch the spin state, thus changing the molecular capacitance. A smaller switching field may be achieved using nanostructures with a larger moment. Molecular magnetocapacitance may lead to revolutionary device designs, e.g., by exploiting the Coulomb blockade magnetoresistance whereby a small change in capacitance can lead to a huge change in resistance.

  5. Estimation of Lung Ventilation

    NASA Astrophysics Data System (ADS)

    Ding, Kai; Cao, Kunlin; Du, Kaifang; Amelon, Ryan; Christensen, Gary E.; Raghavan, Madhavan; Reinhardt, Joseph M.

    Since the primary function of the lung is gas exchange, ventilation can be interpreted as an index of lung function in addition to perfusion. Injury and disease processes can alter lung function on a global and/or a local level. MDCT can be used to acquire multiple static breath-hold CT images of the lung taken at different lung volumes, or with proper respiratory control, 4DCT images of the lung reconstructed at different respiratory phases. Image registration can be applied to this data to estimate a deformation field that transforms the lung from one volume configuration to the other. This deformation field can be analyzed to estimate local lung tissue expansion, calculate voxel-by-voxel intensity change, and make biomechanical measurements. The physiologic significance of the registration-based measures of respiratory function can be established by comparing to more conventional measurements, such as nuclear medicine or contrast wash-in/wash-out studies with CT or MR. An important emerging application of these methods is the detection of pulmonary function change in subjects undergoing radiation therapy (RT) for lung cancer. During RT, treatment is commonly limited to sub-therapeutic doses due to unintended toxicity to normal lung tissue. Measurement of pulmonary function may be useful as a planning tool during RT planning, may be useful for tracking the progression of toxicity to nearby normal tissue during RT, and can be used to evaluate the effectiveness of a treatment post-therapy. This chapter reviews the basic measures to estimate regional ventilation from image registration of CT images, the comparison of them to the existing golden standard and the application in radiation therapy.

  6. Estimating turbine limit load

    NASA Technical Reports Server (NTRS)

    Glassman, Arthur J.

    1993-01-01

    A method for estimating turbine limit-load pressure ratio from turbine map information is presented and demonstrated. It is based on a mean line analysis at the last-rotor exit. The required map information includes choke flow rate at all speeds as well as pressure ratio and efficiency at the onset of choke at design speed. One- and two-stage turbines are analyzed to compare the results with those from a more rigorous off-design flow analysis and to show the sensitivities of the computed limit-load pressure ratios to changes in the key assumptions.

  7. Temperature estimation with ultrasound

    NASA Astrophysics Data System (ADS)

    Daniels, Matthew

    Hepatocelluar carcinoma is the fastest growing type of cancer in the United States. In addition, the survival rate after one year is approximately zero without treatment. In many instances, patients with hepatocelluar carcinoma may not be suitable candidates for the primary treatment options, i.e. surgical resection or liver transplantation. This has led to the development of minimally invasive therapies focused on destroying hepatocelluar by thermal or chemical methods. The focus of this dissertation is on the development of ultrasound-based image-guided monitoring options for minimally invasive therapies such as radiofrequency ablation. Ultrasound-based temperature imaging relies on relating the gradient of locally estimated tissue displacements to a temperature change. First, a realistic Finite Element Analysis/ultrasound simulation of ablation was developed. This allowed evaluation of the ability of ultrasound-based temperature estimation algorithms to track temperatures for three different ablation scenarios in the liver. It was found that 2-Dimensional block matching and a 6 second time step was able to accurately track the temperature over a 12 minute ablation procedure. Next, a tissue-mimicking phantom was constructed to determine the accuracy of the temperature estimation method by comparing estimated temperatures to that measured using invasive fiber-optic temperature probes. The 2-Dimensional block matching was able to track the temperature accurately over the entire 8 minute heating procedure in the tissue-mimicking phantom. Finally, two separate in-vivo experiments were performed. The first experiment examined the ability of our algorithm to track frame-to-frame displacements when external motion due to respiration and the cardiac cycle were considered. It was determined that a frame rate between 13 frames per second and 33 frames per second was sufficient to track frame-to-frame displacements between respiratory cycles. The second experiment examined

  8. On Schmidt's Vm estimator and other estimators of luminosity functions

    NASA Technical Reports Server (NTRS)

    Felten, J. E.

    1976-01-01

    Schmidt's (1968) estimator, sometimes used to calculate the luminosity function from a complete sample of observed objects, can be generalized naively to the case in which the maximum distance for detection is a function of the direction. Though unbiased, this estimator then does not have minimum variance and, in some cases, is inferior to the classical estimator. The classical estimator, however, is biased when the magnitude boxes are not infinitesimal. A generalization of Schmidt's estimator is proposed which is unbiased and usually superior to both Schmidt's and the classical estimator. Variance formulas and numerical examples are given. The results can be used in combining several catalogs.

  9. Electronic structure and conformation of polymers from cluster molecular orbital and molecular mechanics calculations: Polyimide

    SciTech Connect

    Kafafi, S.A. ); LaFemina, J.P. ); Nauss, J.L. )

    1990-11-21

    Full geometry optimizations using molecular mechanics and the quantum chemical AM1 method have been carried out to determine the minimum energy conformation of pyromellitic dianhydride-oxydianiline polyimide (PMDA-ODA PI). The phenyl-imide twist angle for this compound was determined to be {approximately}30. These computations also provided a quantitative determination of the energy gap (7 eV), electron affinity ({minus}2 eV), and ionization potential (8.97 eV). Computations on the PMDA-ODA PI radical anion provided an estimate of the hopping barrier for an electron to hop from one chain to another (3.2 eV), the mechanism believed responsible for photoconduction. Moreover, the use of qualitative molecular orbital theory (QMOT) arguments provided an interpretation of these results in a simple molecular orbital framework.

  10. Applications of Molecular Imaging

    PubMed Central

    Galbán, Craig; Galbán, Stefanie; Van Dort, Marcian; Luker, Gary D.; Bhojani, Mahaveer S.; Rehemtualla, Alnawaz; Ross, Brian D.

    2015-01-01

    Today molecular imaging technologies play a central role in clinical oncology. The use of imaging techniques in early cancer detection, treatment response and new therapy development is steadily growing and has already significantly impacted clinical management of cancer. In this chapter we will overview three different molecular imaging technologies used for the understanding of disease biomarkers, drug development, or monitoring therapeutic outcome. They are (1) optical imaging (bioluminescence and fluorescence imaging) (2) magnetic resonance imaging (MRI), and (3) nuclear imaging (e.g, single photon emission computed tomography (SPECT) and positron emission tomography (PET)). We will review the use of molecular reporters of biological processes (e.g. apoptosis and protein kinase activity) for high throughput drug screening and new cancer therapies, diffusion MRI as a biomarker for early treatment response and PET and SPECT radioligands in oncology. PMID:21075334

  11. Stueckelberg and Molecular Physics

    NASA Astrophysics Data System (ADS)

    Lacki, Jan

    The first period of E. C. G. Stueckelberg's scientific career was marked by important contributions he made to molecular physics.1 After publishing his thesis in 1927 in Basel [1] Stueckelberg joined the prestigious Palmer Physical Laboratory in Princeton where he worked under the guidance of Karl Taylor Compton, brother of Arthur Holly Compton. Stueckelberg owed this position devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3 to a recommendation by A. Sommerfeld.2 In this stimulating environment, he devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3

  12. Molecular psychiatry of zebrafish.

    PubMed

    Stewart, A M; Ullmann, J F P; Norton, W H J; Parker, M O; Brennan, C H; Gerlai, R; Kalueff, A V

    2015-02-01

    Due to their well-characterized neural development and high genetic homology to mammals, zebrafish (Danio rerio) have emerged as a powerful model organism in the field of biological psychiatry. Here, we discuss the molecular psychiatry of zebrafish, and its implications for translational neuroscience research and modeling central nervous system (CNS) disorders. In particular, we outline recent genetic and technological developments allowing for in vivo examinations, high-throughput screening and whole-brain analyses in larval and adult zebrafish. We also summarize the application of these molecular techniques to the understanding of neuropsychiatric disease, outlining the potential of zebrafish for modeling complex brain disorders, including attention-deficit/hyperactivity disorder (ADHD), aggression, post-traumatic stress and substance abuse. Critically evaluating the advantages and limitations of larval and adult fish tests, we suggest that zebrafish models become a rapidly emerging new field in modern molecular psychiatry research. PMID:25349164

  13. Porous Organic Molecular Materials

    SciTech Connect

    Tian, Jian; Thallapally, Praveen K.; McGrail, B. Peter

    2012-01-01

    Most nanoporous materials with molecular-scale pores are extended frameworks composed of directional covalent or coordination bonding, such as porous metal-organic frameworks and organic network polymers. By contrast, nanoporous materials comprised of discrete organic molecules, between which there are only weak non-covalent interactions, are seldom encountered. Indeed, most organic molecules pack efficiently in the solid state to minimize the void volume, leading to non-porous materials. In recent years, a significant number of nanoporous organic molecular materials, which may be either crystalline or amorphous, have been confirmed by the studies of gas adsorption and they are surveyed in this Highlight. In addition, the possible advantages of porous organic molecular materials over porous networks are discussed.

  14. Estimating sparse precision matrices

    NASA Astrophysics Data System (ADS)

    Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross

    2016-08-01

    We apply a method recently introduced to the statistical literature to directly estimate the precision matrix from an ensemble of samples drawn from a corresponding Gaussian distribution. Motivated by the observation that cosmological precision matrices are often approximately sparse, the method allows one to exploit this sparsity of the precision matrix to more quickly converge to an asymptotic 1/sqrt{N_sim} rate while simultaneously providing an error model for all of the terms. Such an estimate can be used as the starting point for further regularization efforts which can improve upon the 1/sqrt{N_sim} limit above, and incorporating such additional steps is straightforward within this framework. We demonstrate the technique with toy models and with an example motivated by large-scale structure two-point analysis, showing significant improvements in the rate of convergence. For the large-scale structure example, we find errors on the precision matrix which are factors of 5 smaller than for the sample precision matrix for thousands of simulations or, alternatively, convergence to the same error level with more than an order of magnitude fewer simulations.

  15. Automated Estimating System

    Energy Science and Technology Software Center (ESTSC)

    1996-04-15

    AES6.1 is a PC software package developed to aid in the preparation and reporting of cost estimates. AES6.1 provides an easy means for entering and updating the detailed cost, schedule information, project work breakdown structure, and escalation information contained in a typical project cost estimate through the use of menus and formatted input screens. AES6.1 combines this information to calculate both unescalated and escalated cost for a project which can be reported at varying levelsmore » of detail. Following are the major modifications to AES6.0f: Contingency update was modified to provide greater flexibility for user updates, Schedule Update was modified to provide user ability to schedule Bills of Material at the WBS/Participant/Cost Code level, Schedule Plot was modified to graphically show schedule by WBS/Participant/Cost Code, All Fiscal Year reporting has been modified to use the new schedule format, The Schedule 1-B-7, Cost Schedule, and the WBS/Participant reprorts were modified to determine Phase of Work from the B/M Cost Code, Utility program was modified to allow selection by cost code and update cost code in the Global Schedule update, Generic summary and line item download were added to the utility program, and an option was added to all reports which allows the user to indicate where overhead is to be reported (bottom line or in body of report)« less

  16. Parameter estimation through ignorance.

    PubMed

    Du, Hailiang; Smith, Leonard A

    2012-07-01

    Dynamical modeling lies at the heart of our understanding of physical systems. Its role in science is deeper than mere operational forecasting, in that it allows us to evaluate the adequacy of the mathematical structure of our models. Despite the importance of model parameters, there is no general method of parameter estimation outside linear systems. A relatively simple method of parameter estimation for nonlinear systems is introduced, based on variations in the accuracy of probability forecasts. It is illustrated on the logistic map, the Henon map, and the 12-dimensional Lorenz96 flow, and its ability to outperform linear least squares in these systems is explored at various noise levels and sampling rates. As expected, it is more effective when the forecast error distributions are non-Gaussian. The method selects parameter values by minimizing a proper, local skill score for continuous probability forecasts as a function of the parameter values. This approach is easier to implement in practice than alternative nonlinear methods based on the geometry of attractors or the ability of the model to shadow the observations. Direct measures of inadequacy in the model, the "implied ignorance," and the information deficit are introduced. PMID:23005513

  17. Estimating sparse precision matrices

    NASA Astrophysics Data System (ADS)

    Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross

    2016-05-01

    We apply a method recently introduced to the statistical literature to directly estimate the precision matrix from an ensemble of samples drawn from a corresponding Gaussian distribution. Motivated by the observation that cosmological precision matrices are often approximately sparse, the method allows one to exploit this sparsity of the precision matrix to more quickly converge to an asymptotic 1/√{N_sim} rate while simultaneously providing an error model for all of the terms. Such an estimate can be used as the starting point for further regularization efforts which can improve upon the 1/√{N_sim} limit above, and incorporating such additional steps is straightforward within this framework. We demonstrate the technique with toy models and with an example motivated by large-scale structure two-point analysis, showing significant improvements in the rate of convergence. For the large-scale structure example we find errors on the precision matrix which are factors of 5 smaller than for the sample precision matrix for thousands of simulations or, alternatively, convergence to the same error level with more than an order of magnitude fewer simulations.

  18. Estimating sparse precision matrices

    NASA Astrophysics Data System (ADS)

    Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross

    2016-08-01

    We apply a method recently introduced to the statistical literature to directly estimate the precision matrix from an ensemble of samples drawn from a corresponding Gaussian distribution. Motivated by the observation that cosmological precision matrices are often approximately sparse, the method allows one to exploit this sparsity of the precision matrix to more quickly converge to an asymptotic 1/√{N_sim} rate while simultaneously providing an error model for all of the terms. Such an estimate can be used as the starting point for further regularization efforts which can improve upon the 1/√{N_sim} limit above, and incorporating such additional steps is straightforward within this framework. We demonstrate the technique with toy models and with an example motivated by large-scale structure two-point analysis, showing significant improvements in the rate of convergence. For the large-scale structure example, we find errors on the precision matrix which are factors of 5 smaller than for the sample precision matrix for thousands of simulations or, alternatively, convergence to the same error level with more than an order of magnitude fewer simulations.

  19. Phenological Parameters Estimation Tool

    NASA Technical Reports Server (NTRS)

    McKellip, Rodney D.; Ross, Kenton W.; Spruce, Joseph P.; Smoot, James C.; Ryan, Robert E.; Gasser, Gerald E.; Prados, Donald L.; Vaughan, Ronald D.

    2010-01-01

    The Phenological Parameters Estimation Tool (PPET) is a set of algorithms implemented in MATLAB that estimates key vegetative phenological parameters. For a given year, the PPET software package takes in temporally processed vegetation index data (3D spatio-temporal arrays) generated by the time series product tool (TSPT) and outputs spatial grids (2D arrays) of vegetation phenological parameters. As a precursor to PPET, the TSPT uses quality information for each pixel of each date to remove bad or suspect data, and then interpolates and digitally fills data voids in the time series to produce a continuous, smoothed vegetation index product. During processing, the TSPT displays NDVI (Normalized Difference Vegetation Index) time series plots and images from the temporally processed pixels. Both the TSPT and PPET currently use moderate resolution imaging spectroradiometer (MODIS) satellite multispectral data as a default, but each software package is modifiable and could be used with any high-temporal-rate remote sensing data collection system that is capable of producing vegetation indices. Raw MODIS data from the Aqua and Terra satellites is processed using the TSPT to generate a filtered time series data product. The PPET then uses the TSPT output to generate phenological parameters for desired locations. PPET output data tiles are mosaicked into a Conterminous United States (CONUS) data layer using ERDAS IMAGINE, or equivalent software package. Mosaics of the vegetation phenology data products are then reprojected to the desired map projection using ERDAS IMAGINE

  20. Semimajor Axis Estimation Strategies

    NASA Technical Reports Server (NTRS)

    How, Jonathan P.; Alfriend, Kyle T.; Breger, Louis; Mitchell, Megan

    2004-01-01

    This paper extends previous analysis on the impact of sensing noise for the navigation and control aspects of formation flying spacecraft. We analyze the use of Carrier-phase Differential GPS (CDGPS) in relative navigation filters, with a particular focus on the filter correlation coefficient. This work was motivated by previous publications which suggested that a "good" navigation filter would have a strong correlation (i.e., coefficient near -1) to reduce the semimajor axis (SMA) error, and therefore, the overall fuel use. However, practical experience with CDGPS-based filters has shown this strong correlation seldom occurs (typical correlations approx. -0.1), even when the estimation accuracies are very good. We derive an analytic estimate of the filter correlation coefficient and demonstrate that, for the process and sensor noises levels expected with CDGPS, the expected value will be very low. It is also demonstrated that this correlation can be improved by increasing the time step of the discrete Kalman filter, but since the balance condition is not satisfied, the SMA error also increases. These observations are verified with several linear simulations. The combination of these simulations and analysis provide new insights on the crucial role of the process noise in determining the semimajor axis knowledge.

  1. Molecular Rotors as Switches

    PubMed Central

    Xue, Mei; Wang, Kang L.

    2012-01-01

    The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene) monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V) revealed a temperature-dependent negative differential resistance (NDR) associated with the device. The analysis of the device I–V characteristics suggests the source of the

  2. Molecular subgroups of medulloblastoma

    PubMed Central

    Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

    2014-01-01

    Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

  3. Molecular Umbrella Transport

    PubMed Central

    Mehiri, Mohamed; Chen, Wen-Hua; Janout, Vaclav; Regen, Steven L.

    2009-01-01

    The ability of a series of molecular umbrellas, derived from cholic acid, L-lysine, spermidine and Cascade Blue, to cross fluid liposomal membranes made from 1-palmitoyl-2-oleyol-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) (95/5, mol/mol) has been determined. In sharp contrast to the clasic “size/lipophilicity” rule of membrane transport, those molecular umbrellas that were larger in size and less lipophilic crossed these liposomal membranes more readily. The likely origin for this unusual behavior is briefly discussed. PMID:19140686

  4. Circumstellar radio molecular lines

    NASA Technical Reports Server (NTRS)

    NGUYEN-QUANG-RIEU

    1987-01-01

    Radio molecular lines appear to be useful probes into the stellar environment. Silicon oxide masers provide information on the physical conditions in the immediate vicinity of the stellar photosphere. Valuable information on the physics operating in the envelope of IRC + 10216 was recently obtained by high sensitivity observations and detailed theoretical analyses. Infrared speckle interferometry in the molecular lines and in the continuum is helpful in the investigation of the inner region of the envelope. These techniques are discussed in terms of late-type star mass loss.

  5. Synthetic mechanochemical molecular swimmer.

    PubMed

    Golestanian, Ramin

    2010-07-01

    A minimal design for a molecular swimmer is proposed that is based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net charges through catalyzed chemical reactions involving ionic components. The mechanochemical cycle is designed such that the resulting conformational changes would be sufficient for achieving low Reynolds number propulsion. The system is analyzed within the recently developed framework of stochastic swimmers to take account of the noisy environment at the molecular scale. The swimming velocity of the device is found to depend on the concentration of the fuel molecule according to the Michaelis-Menten rule in enzymatic reactions. PMID:20867483

  6. Molecular Pathology Informatics.

    PubMed

    Roy, Somak

    2015-06-01

    Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing. PMID:26065793

  7. Substructured multibody molecular dynamics.

    SciTech Connect

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  8. Molecular Engineering of DNA: Molecular Beacons

    PubMed Central

    Tang, Zhiwen; Yang, Chaoyong James; Kim, Youngmi; Fang, Xiaohong; Li, Wei; Wu, Yanrong; Medley, Colin D.; Cao, Zehui; Li, Jun; Colon, Patrick; Lin, Hui

    2009-01-01

    Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein–DNA interaction studies, and protein recognition. PMID:19065690

  9. Earthquake Loss Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

    Frolova, Nina; Bonnin, Jean; Larionov, Valery; Ugarov, Aleksander

    2013-04-01

    The paper addresses the reliability issues of strong earthquakes loss assessment following strong earthquakes with worldwide Systems' application in emergency mode. Timely and correct action just after an event can result in significant benefits in saving lives. In this case the information about possible damage and expected number of casualties is very critical for taking decision about search, rescue operations and offering humanitarian assistance. Such rough information may be provided by, first of all, global systems, in emergency mode. The experience of earthquakes disasters in different earthquake-prone countries shows that the officials who are in charge of emergency response at national and international levels are often lacking prompt and reliable information on the disaster scope. Uncertainties on the parameters used in the estimation process are numerous and large: knowledge about physical phenomena and uncertainties on the parameters used to describe them; global adequacy of modeling techniques to the actual physical phenomena; actual distribution of population at risk at the very time of the shaking (with respect to immediate threat: buildings or the like); knowledge about the source of shaking, etc. Needless to be a sharp specialist to understand, for example, that the way a given building responds to a given shaking obeys mechanical laws which are poorly known (if not out of the reach of engineers for a large portion of the building stock); if a carefully engineered modern building is approximately predictable, this is far not the case for older buildings which make up the bulk of inhabited buildings. The way population, inside the buildings at the time of shaking, is affected by the physical damage caused to the buildings is not precisely known, by far. The paper analyzes the influence of uncertainties in strong event parameters determination by Alert Seismological Surveys, of simulation models used at all stages from, estimating shaking intensity

  10. A molecular palaeobiological exploration of arthropod terrestrialization.

    PubMed

    Lozano-Fernandez, Jesus; Carton, Robert; Tanner, Alastair R; Puttick, Mark N; Blaxter, Mark; Vinther, Jakob; Olesen, Jørgen; Giribet, Gonzalo; Edgecombe, Gregory D; Pisani, Davide

    2016-07-19

    Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325830

  11. Atomic and Molecular Adsorption on Re(0001)

    SciTech Connect

    Hahn, Konstanze; Mavrikakis, Manos

    2014-02-01

    Using periodic, self-consistent density functional theory calculations, the adsorption of several atomic (H, S, N, O and C) and molecular (CO2, N2, NH3, HCN, CO and NO) species and molecular fragments (NH2, NH, CN, CNH2, HNO, NOH, CH3, CH2, CH and OH) on the (0001) facet of rhenium at a coverage of 0.25 ML has been studied. Preferred binding sites with their corresponding binding energy and deformation energy of the surface, as well as an estimated diffusion barrier of each species have been determined. Atomic species and molecular fragments tend to bind to threefold sites, whereas molecular species tend to bind to top sites. The binding strength, with respect to the corresponding gas phase species and in increasing order for all species studied, is: CO2 < N2 < NH3 < CO < CH3 < HCN < NO < H < NH2 < OH < CH2 < CNH2 < CN < HNO < NH < NOH < S < N < O < CH < C. The vibrational frequencies of all species in their most energetically favorable adsorbed configuration have been calculated. Finally, the thermochemistry of adsorption and decomposition of NO, NO + H, NH3, N2, CO2, CO and CH4 on Re(0001) has been analyzed.

  12. Self-correcting maps of molecular pathways.

    PubMed

    Rzhetsky, Andrey; Zheng, Tian; Weinreb, Chani

    2006-01-01

    Reliable and comprehensive maps of molecular pathways are indispensable for guiding complex biomedical experiments. Such maps are typically assembled from myriads of disparate research reports and are replete with inconsistencies due to variations in experimental conditions and/or errors. It is often an intractable task to manually verify internal consistency over a large collection of experimental statements. To automate large-scale reconciliation efforts, we propose a random-arcs-and-nodes model where both nodes (tissue-specific states of biological molecules) and arcs (interactions between them) are represented with random variables. We show how to obtain a non-contradictory model of a molecular network by computing the joint distribution for arc and node variables, and then apply our methodology to a realistic network, generating a set of experimentally testable hypotheses. This network, derived from an automated analysis of over 3,000 full-text research articles, includes genes that have been hypothetically linked to four neurological disorders: Alzheimer's disease, autism, bipolar disorder, and schizophrenia. We estimated that approximately 10% of the published molecular interactions are logically incompatible. Our approach can be directly applied to an array of diverse problems including those encountered in molecular biology, ecology, economics, politics, and sociology. PMID:17183692

  13. A molecular palaeobiological exploration of arthropod terrestrialization

    PubMed Central

    Carton, Robert; Edgecombe, Gregory D.

    2016-01-01

    Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325830

  14. Precipitation Estimates for Hydroelectricity

    NASA Technical Reports Server (NTRS)

    Tapiador, Francisco J.; Hou, Arthur Y.; de Castro, Manuel; Checa, Ramiro; Cuartero, Fernando; Barros, Ana P.

    2011-01-01

    Hydroelectric plants require precise and timely estimates of rain, snow and other hydrometeors for operations. However, it is far from being a trivial task to measure and predict precipitation. This paper presents the linkages between precipitation science and hydroelectricity, and in doing so it provides insight into current research directions that are relevant for this renewable energy. Methods described include radars, disdrometers, satellites and numerical models. Two recent advances that have the potential of being highly beneficial for hydropower operations are featured: the Global Precipitation Measuring (GPM) mission, which represents an important leap forward in precipitation observations from space, and high performance computing (HPC) and grid technology, that allows building ensembles of numerical weather and climate models.

  15. Electric propulsion cost estimation

    NASA Technical Reports Server (NTRS)

    Palaszewski, B. A.

    1985-01-01

    A parametric cost model for mercury ion propulsion modules is presented. A detailed work breakdown structure is included. Cost estimating relationships were developed for the individual subsystems and the nonhardware items (systems engineering, software, etc.). Solar array and power processor unit (PPU) costs are the significant cost drivers. Simplification of both of these subsystems through applications of advanced technology (lightweight solar arrays and high-efficiency, self-radiating PPUs) can reduce costs. Comparison of the performance and cost of several chemical propulsion systems with the Hg ion module are also presented. For outer-planet missions, advanced solar electric propulsion (ASEP) trip times and O2/H2 propulsion trip times are comparable. A three-year trip time savings over the baselined NTO/MMH propulsion system is possible with ASEP.

  16. Directly estimating nonclassicality.

    PubMed

    Mari, A; Kieling, K; Nielsen, B Melholt; Polzik, E S; Eisert, J

    2011-01-01

    We establish a method of directly measuring and estimating nonclassicality--operationally defined in terms of the distinguishability of a given state from one with a positive Wigner function. It allows us to certify nonclassicality, based on possibly much fewer measurement settings than necessary for obtaining complete tomographic knowledge, and is at the same time equipped with a full certificate. We find that even from measuring two conjugate variables alone, one may infer the nonclassicality of quantum mechanical modes. This method also provides a practical tool to eventually certify such features in mechanical degrees of freedom in opto-mechanics. The proof of the result is based on Bochner's theorem characterizing classical and quantum characteristic functions and on semidefinite programming. In this joint theoretical-experimental work we present data from experimental optical Fock state preparation. PMID:21231723

  17. Bayesian sperm competition estimates.

    PubMed Central

    Jones, Beatrix; Clark, Andrew G

    2003-01-01

    We introduce a Bayesian method for estimating parameters for a model of multiple mating and sperm displacement from genotype counts of brood-structured data. The model is initially targeted for Drosophila melanogaster, but is easily adapted to other organisms. The method is appropriate for use with field studies where the number of mates and the genotypes of the mates cannot be controlled, but where unlinked markers have been collected for a set of females and a sample of their offspring. Advantages over previous approaches include full use of multilocus information and the ability to cope appropriately with missing data and ambiguities about which alleles are maternally vs. paternally inherited. The advantages of including X-linked markers are also demonstrated. PMID:12663555

  18. Estimating earthquake potential

    USGS Publications Warehouse

    Page, R.A.

    1980-01-01

    The hazards to life and property from earthquakes can be minimized in three ways. First, structures can be designed and built to resist the effects of earthquakes. Second, the location of structures and human activities can be chosen to avoid or to limit the use of areas known to be subject to serious earthquake hazards. Third, preparations for an earthquake in response to a prediction or warning can reduce the loss of life and damage to property as well as promote a rapid recovery from the disaster. The success of the first two strategies, earthquake engineering and land use planning, depends on being able to reliably estimate the earthquake potential. The key considerations in defining the potential of a region are the location, size, and character of future earthquakes and frequency of their occurrence. Both historic seismicity of the region and the geologic record are considered in evaluating earthquake potential. 

  19. Estimating many variances

    SciTech Connect

    Robbins, H.

    1981-01-01

    Suppose that an unknown random parameter theta with distribution function G is such that given theta, an observable random variable x has conditional probability density f(x / theta) of known form. If a function t = t(x) is used to estimate theta, then the expected squared error with respect to the random variation of both theta and x is: E(t-theta)/sup 2/ = ..integral.. ..integral..(t(x)-theta)/sup 2/ f(x parallel theta)dx dG(theta). For fixed G we can seek to minimize this equation within any desired class of functions t, such as the class of all linear functions A + Bx, or the class of al Borel functions whatsoever.

  20. Estimating Bias Error Distributions

    NASA Technical Reports Server (NTRS)

    Liu, Tian-Shu; Finley, Tom D.

    2001-01-01

    This paper formulates the general methodology for estimating the bias error distribution of a device in a measuring domain from less accurate measurements when a minimal number of standard values (typically two values) are available. A new perspective is that the bias error distribution can be found as a solution of an intrinsic functional equation in a domain. Based on this theory, the scaling- and translation-based methods for determining the bias error distribution arc developed. These methods are virtually applicable to any device as long as the bias error distribution of the device can be sufficiently described by a power series (a polynomial) or a Fourier series in a domain. These methods have been validated through computational simulations and laboratory calibration experiments for a number of different devices.

  1. Remote remanence estimation (RRE)

    NASA Astrophysics Data System (ADS)

    Pratt, David A.; McKenzie, K. Blair; White, Tony S.

    2014-09-01

    The remote determination of magnetic remanence in rocks is a method that has largely been ignored because of the ambiguity associated with the estimation of both the Koenigsberger ratio and remanent magnetisation direction. Our research shows that the resultant magnetisation direction can be derived directly through inversion of magnetic data for an isolated magnetic anomaly from a compact magnetic source. The resultant magnetisation direction is a property of the target magnetic rocks and a robust inversion parameter. The departure angle of the resultant magnetisation vector from that of the inducing magnetic field is an important indicator of the existence of remanent magnetisation and the inversion process can detect departures that are not easily detected by visual inspection. This departure angle is called the apparent resultant rotation angle or ARRA. The induced field vector, remanent magnetisation vector and resultant magnetisation vector lie on the plane of a great circle. We find the intersection of the transformed polar wander vector trace with the great circle plane to obtain one or more possible solutions for the remanent magnetisation vector. Geological deduction will normally allow us to reduce the ambiguity for multiple solutions to obtain the most likely remanent magnetisation direction. Once the remanent magnetisation direction is established, it is then possible to determine the Koenigsberger ratio and magnetic susceptibility for the target. We illustrate the methodology using survey data over the Black Hill Norite which also has extensive palaeomagnetic data available for comparison with the inversion results. We then apply the remote remanence estimation (RRE) method to a systematic study of a large number of intrusive pipes in the Thomson Orogen, New South Wales. The corrected magnetic susceptibility and remanence properties, spatial distribution and underlying uncertainties are evaluated for their potential use by diamond explorers. The

  2. Biophysics of molecular gastronomy.

    PubMed

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. PMID:25815978

  3. [Ortho-molecular nutrition].

    PubMed

    Martínez Bradshaw, Alejandro

    2005-03-01

    Ortho-molecular nutrition contemplates the deficiency of certain nutrients, not their deprivation, as the generator of short-term and long-term pathologies. By means of supplying these nutrients, an organism recovers. This method consists in building up an organism's functions by following the guides and indications provided by the organism itself. PMID:15871343

  4. Molecular Adsorber Coating

    NASA Technical Reports Server (NTRS)

    Straka, Sharon; Peters, Wanda; Hasegawa, Mark; Hedgeland, Randy; Petro, John; Novo-Gradac, Kevin; Wong, Alfred; Triolo, Jack; Miller, Cory

    2011-01-01

    A document discusses a zeolite-based sprayable molecular adsorber coating that has been developed to alleviate the size and weight issues of current ceramic puck-based technology, while providing a configuration that more projects can use to protect against degradation from outgassed materials within a spacecraft, particularly contamination-sensitive instruments. This coating system demonstrates five times the adsorption capacity of previously developed adsorber coating slurries. The molecular adsorber formulation was developed and refined, and a procedure for spray application was developed. Samples were spray-coated and tested for capacity, thermal optical/radiative properties, coating adhesion, and thermal cycling. Work performed during this study indicates that the molecular adsorber formulation can be applied to aluminum, stainless steel, or other metal substrates that can accept silicate-based coatings. The coating can also function as a thermal- control coating. This adsorber will dramatically reduce the mass and volume restrictions, and is less expensive than the currently used molecular adsorber puck design.

  5. Atomic and Molecular Physics

    NASA Technical Reports Server (NTRS)

    Bhatia, Anand K.

    2005-01-01

    A symposium on atomic and molecular physics was held on November 18, 2005 at Goddard Space Flight Center. There were a number of talks through the day on various topics such as threshold law of ionization, scattering of electrons from atoms and molecules, muonic physics, positron physics, Rydberg states etc. The conference was attended by a number of physicists from all over the world.

  6. Molecular Detection of Sarcocystis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When people eat undercooked beef or pork containing viable Sarcocystis hominis or Sarcocystis suihominis, they can contract acute gastro-intestinal infections that culminate, about two weeks later, with the excretion of parasites infectious for cattle or swine, respectively. Molecular methods can p...

  7. Molecular contributions to conservation

    USGS Publications Warehouse

    Haig, Susan M.

    1998-01-01

    Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

  8. Molecular ion photofragment spectroscopy

    SciTech Connect

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  9. Caroviologens: Towards molecular wires

    NASA Astrophysics Data System (ADS)

    Blanchard-Desce, M.; Arrhenius, T. S.; Dvolaïtzky, M.; Kugimiya, S.-I.; Lazrak, T.; Lehn, J.-M.

    1992-07-01

    Bispyridinium conjugated polyenes of different lengths and charges have been synthesized. Since they combine the features of carotenoids and of viologens, they have been termed caroviologens. Such molecules, possessing an extended conjugated chain fitted with polar electroactive endgroups, and having a length sufficient to span a lipid membrane could function as transmembrane electron channels, i.e., as molecular wires.

  10. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  11. Making Molecular Borromean Rings

    ERIC Educational Resources Information Center

    Pentecost, Cari D.; Tangchaivang, Nichol; Cantrill, Stuart J.; Chichak, Kelly S.; Peters, Andrea J.; Stoddart, Fraser J.

    2007-01-01

    A procedure that requires seven 4-hour blocks of time to allow undergraduate students to prepare the molecular Borromean rings (BRs) on a gram-scale in 90% yield is described. The experiment would serve as a nice capstone project to culminate any comprehensive organic laboratory course and expose students to fundamental concepts, symmetry point…

  12. Gymnastics of molecular chaperones.

    PubMed

    Mayer, Matthias P

    2010-08-13

    Molecular chaperones assist folding processes and conformational changes in many proteins. In order to do so, they progress through complex conformational cycles themselves. In this review, I discuss the diverse conformational dynamics of the ATP-dependent chaperones of the Hsp60, Hsp70, Hsp90, and Hsp100 families. PMID:20705236

  13. Molecular Stiffness of Selectins*

    PubMed Central

    Sarangapani, Krishna K.; Marshall, Bryan T.; McEver, Rodger P.; Zhu, Cheng

    2011-01-01

    During inflammation, selectin-ligand interactions provide forces for circulating leukocytes to adhere to vascular surfaces, which stretch the interacting molecules, suggesting that mechanical properties may be pertinent to their biological function. From mechanical measurements with atomic force microscopy, we analyzed the molecular characteristics of selectins complexed with ligands and antibodies. Respective stiffness of L-, E-, and P-selectins (4.2, 1.4, and 0.85 piconewton/nm) correlated inversely with the number (2, 6, and 9) of consensus repeats in the selectin structures that acted as springs in series to dominate their compliance. After reconstitution into a lipid bilayer, purified membrane P-selectin remained a dimer, capable of forming dimeric bonds with P-selectin glycoprotein ligand (PSGL)-1, endoglycan-Ig, and a dimeric form of a glycosulfopeptide modeled after the N terminus of PSGL-1. By comparison, purified membrane L- and E-selectin formed only monomeric bonds under identical conditions. Ligands and antibodies were much less stretchable than selectins. The length of endoglycan-Ig was found to be 51 ± 12 nm. These results provide a comprehensive characterization of the molecular stiffness of selectins and illustrate how mechanical measurements can be utilized for molecular analysis, e.g. evaluating the multimericity of selectins and determining the molecular length of endoglycan. PMID:21216951

  14. Soybean Molecular Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A history of the various DNA marker types used in the assessment of molecular genetic diversity in soybean [Glycine max (L.) Merr.] is followed by a description of a number of studies on the assessment of genetic diversity. These studies include a review of reports on 1) the quantification and comp...

  15. Reading the Molecular Clock.

    ERIC Educational Resources Information Center

    McKean, Kevin

    1983-01-01

    Suggesting that the evolutionary record may be written in proteins and genes, discusses research in which species are compared by immunology, DNA, and radioimmunoassay. Molecular studies show that DNA from humans and chimps is 98 percent identical, a degree of similarity usually occurring only among animals of the same genus. (JN)

  16. Unbound star-forming molecular clouds

    NASA Astrophysics Data System (ADS)

    Ward, Rachel L.; Wadsley, James; Sills, Alison

    2014-03-01

    We explore whether observed molecular clouds could include a substantial population of unbound clouds. Using simulations which include only turbulence and gravity, we are able to match observed relations and naturally reproduce the observed scatter in the cloud size-linewidth coefficient, at fixed surface density. We identify the source of this scatter as a spread in the intrinsic virial parameter. Thus, these observational trends do not require that clouds exist in a state of dynamical equilibrium. We demonstrate that cloud virial parameters can be accurately determined observationally with an appropriate size estimator. All our simulated clouds eventually form collapsing cores, regardless of whether the cloud is bound overall. This supports the idea that molecular clouds do not have to be bound to form stars or to have observed properties like those of nearby low-mass clouds.

  17. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  18. Energy pooling upconversion in organic molecular systems.

    PubMed

    LaCount, Michael D; Weingarten, Daniel; Hu, Nan; Shaheen, Sean E; van de Lagemaat, Jao; Rumbles, Garry; Walba, David M; Lusk, Mark T

    2015-04-30

    A combination of molecular quantum electrodynamics, perturbation theory, and ab initio calculations was used to create a computational methodology capable of estimating the rate of three-body singlet upconversion in organic molecular assemblies. The approach was applied to quantify the conditions under which such relaxation rates, known as energy pooling, become meaningful for two test systems, stilbene-fluorescein and hexabenzocoronene-oligothiophene. Both exhibit low intramolecular conversion, but intermolecular configurations exist in which pooling efficiency is at least 90% when placed in competition with more conventional relaxation pathways. For stilbene-fluorescein, the results are consistent with data generated in an earlier experimental investigation. Exercising these model systems facilitated the development of a set of design rules for the optimization of energy pooling. PMID:25793313

  19. Age at first reproduction explains rate variation in the strepsirrhine molecular clock

    PubMed Central

    Tsantes, C.; Steiper, M. E.

    2009-01-01

    Although the molecular clock hypothesis posits that the rate of molecular change is constant over time, there is evidence that rates vary among lineages. Some of the strongest evidence for variable molecular rates comes from the primates; e.g., the “hominoid slowdown.” These rate differences are hypothesized to correlate with certain species attributes, such as generation time and body size. Here, we examine rates of molecular change in the strepsirrhine suborder of primates and test whether body size or age at first reproduction (a proxy for generation time) explains patterns of rate variation better than a null model where the molecular clock is independent of these factors. To examine these models, we analyzed DNA sequences from four pairs of recently diverged strepsirrhine sister taxa to estimate molecular rates by using sign tests, likelihood ratio tests, and regression analyses. Our analysis does not support a model where body weight or age at first reproduction strongly influences rates of molecular evolution across mitochondrial and nuclear sites. Instead, our analysis supports a model where age at first reproduction influences neutral evolution in the nuclear genome. This study supports the generation time hypothesis for rate variation in the nuclear molecular clock. Molecular clock variation due to generation time may help to resolve the discordance between molecular and paleontological estimates for divergence date estimates in primate evolution. PMID:19841267

  20. Strategies for Estimating Discrete Quantities.

    ERIC Educational Resources Information Center

    Crites, Terry W.

    1993-01-01

    Describes the benchmark and decomposition-recomposition estimation strategies and presents five techniques to develop students' estimation ability. Suggests situations involving quantities of candy and popcorn in which the teacher can model those strategies for the students. (MDH)

  1. Localization of deformable tumors from short-arc projections using Bayesian estimation

    SciTech Connect

    Hoegele, W.; Zygmanski, P.; Dobler, B.; Kroiss, M.; Koelbl, O.; Loeschel, R.

    2012-12-15

    Purpose: The authors present a stochastic framework for radiotherapy patient positioning directly utilizing radiographic projections. This framework is developed to be robust against anatomical nonrigid deformations and to cope with challenging imaging scenarios, involving only a few cone beam CT projections from short arcs. Methods: Specifically, a Bayesian estimator (BE) is explicitly derived for the given scanning geometry. This estimator is compared to reference methods such as chamfer matching (CM) and the minimization of the median absolute error adapted as tools of robust image processing and statistics. In order to show the performance of the stochastic short-arc patient positioning method, a CIRS IMRT thorax phantom study is presented with movable markers and the utilization of an Elekta Synergy{sup Registered-Sign} XVI system. Furthermore, a clinical prostate CBCT scan of a Varian{sup Registered-Sign} On-Board Imager{sup Registered-Sign} system is utilized to investigate the robustness of the method for large variations of image quality (anterior-posterior vs lateral views). Results: The results show that the BE shifts reduce the initial setup error of up to 3 cm down to 3 mm at maximum for an imaging arc as short as 10 Degree-Sign while CM achieves residual errors of 7 mm at maximum only for arcs longer than 40 Degree-Sign . Furthermore, the BE can compensate robustly for low image qualities using several low quality projections simultaneously. Conclusions: In conclusion, an estimation method for marker-based patient positioning for short imaging arcs is presented and shown to be robust and accurate for deformable anatomies.

  2. [Future prospects of molecular epidemiology in tuberculosis].

    PubMed

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    Before the availability of high-resolution genotyping tools in 1990s, there was a prevailing dogma of little genomic sequence diversity in Mycobacterium tuberculosis. Due to the low levels of genetic variation, it was assumed that M. tuberculosis exhibit very little phenotypic variation in immunologic and virulence factors. The fingerprinting method based on restriction fragment length polymorphisms (RFLP) of IS6110 insertion sequences had unveiled the underestimation of the sequence variation in M. tuberculosis and the importance of strain-to-strain variation for understanding pathogenesis, immune mechanisms, bacterial evolution, and host adaptation. This method became a gold standard for strain differentiation in the molecular epidemiological study. It had lead to a profusion of studies in molecular epidemiology such as the detection of unsuspected transmission, the estimation of the extent of recent transmission, the identification of laboratory cross-contamination, the identification of outbreaks, and distinction between reinfection and relapse. This, in 1990s, is the opening of the molecular epidemiology of tuberculosis. After the completion of genome project of the M. tuberculosis laboratory strain H37Rv, some of the clinical isolates were completely sequenced. This prompted the in silico genome comparison and identified various genomic markers which can give a unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis population. Of them, variable numbers of tandem repeats (VNTR) was found as the most promising PCR-based method which can provide adequate discrimination of M. tuberculosis strains in many cases, including the estimation of M. tuberculosis transmission and the identification of genetic lineages. PCR-based VNTR analysis is easy, rapid, and highly specific and can generate portable digit-based data, unlike the analog information obtained from IS6110 RFLP which is labor intensive. In this regards, investigators can

  3. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  4. Estimating concurrence via entanglement witnesses

    SciTech Connect

    Jurkowski, Jacek; Chruscinski, Dariusz

    2010-05-15

    We show that each entanglement witness detecting a given bipartite entangled state provides an estimation of its concurrence. We illustrate our result with several well-known examples of entanglement witnesses and compare the corresponding estimation of concurrence with other estimations provided by the trace norm of partial transposition and realignment.

  5. Bibliography for aircraft parameter estimation

    NASA Technical Reports Server (NTRS)

    Iliff, Kenneth W.; Maine, Richard E.

    1986-01-01

    An extensive bibliography in the field of aircraft parameter estimation has been compiled. This list contains definitive works related to most aircraft parameter estimation approaches. Theoretical studies as well as practical applications are included. Many of these publications are pertinent to subjects peripherally related to parameter estimation, such as aircraft maneuver design or instrumentation considerations.

  6. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

    PubMed

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

    Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. PMID:21271625

  7. Determination of Molecular Size and Avogadro's Number: A Student Experiment

    ERIC Educational Resources Information Center

    Alexandrakis, George C.

    1978-01-01

    Describes an experiment for estimating molecular size and Avogadro's number. Uses the diffusion length of iodine in air at 100 degrees Celsius as a function of time, and the change in volume of a small quantity of carbon dioxide as it goes from the solid to the gaseous state. (GA)

  8. CULTURE-INDEPENDENT MOLECULAR METHODS FOR FECAL SOURCE IDENTIFICATION

    EPA Science Inventory

    Fecal contamination is widespread in the waterways of the United States. Both to correct the problem, and to estimate public health risk, it is necessary to identify the source of the contamination. Several culture-independent molecular methods for fecal source identification hav...

  9. Some Stereochemical Principles from Polymers: Molecular Symmetry and Molecular Flexibility

    ERIC Educational Resources Information Center

    Price, Charles C.

    1973-01-01

    Discusses the use of the properties of polyethylene, polypropylene, polyisobutylene, and their three epoxides to illustrate the relationships of entropy to molecular properties and the concepts of molecular chirality, geometry, and flexibility. (CC)

  10. TRACING TURBULENT AMBIPOLAR DIFFUSION IN MOLECULAR CLOUDS

    SciTech Connect

    Li Huabai; Houde, Martin; Lai Shihping; Sridharan, T. K.

    2010-08-01

    Though flux freezing is a good approximation frequently assumed for molecular clouds, ambipolar diffusion (AD) is inevitable at certain scales. The scale at which AD sets in can be a crucial parameter for turbulence and the star formation process. However, both observation and simulation of AD are very challenging and our knowledge of it is very limited. We recently proposed that the difference between ion and neutral velocity spectra is a signature of turbulent AD and can be used to estimate the AD scales and magnetic field strengths. Here, we present observational evidence showing that this difference between the velocity dispersions from coexistent ions and neutrals is indeed correlated with magnetic field strength.

  11. Gate engineered performance of single molecular transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.

    2016-05-01

    The operation, performance and electrostatics of multigated Single Molecular Transistor (SMT) devices are investigated using first-principles based density functional theory calculations for planar (pentacene) and non-planar (sucrose) molecules as islands. It has been found that the incorporation of larger numbers of gates allows enhanced electrostatic control in the SMT operation which has been quantified from the energy calculations and estimation of the gate capacitances. The effect of multiple gates is more dominant for a non-planar molecule than a planar molecule within an SMT which indicates the usefulness of such multi-gate architectures for future nanoelectronic devices.

  12. Mean thermospheric density estimation derived from satellite constellations

    NASA Astrophysics Data System (ADS)

    Li, Alan; Close, Sigrid

    2015-10-01

    This paper defines a method to estimate the mean neutral density of the thermosphere given many satellites of the same form factor travelling in similar regions of space. A priori information to the estimation scheme include ranging measurements and a general knowledge of the onboard ADACS, although precise measurements are not required for the latter. The estimation procedure seeks to utilize order statistics to estimate the probability of the minimum drag coefficient achievable, and amalgamating all measurements across multiple time periods allows estimation of the probability density of the ballistic factor itself. The model does not depend on prior models of the atmosphere; instead we require estimation of the minimum achievable drag coefficient which is based upon physics models of simple shapes in free molecular flow. From the statistics of the minimum, error statistics on the estimated atmospheric density can be calculated. Barring measurement errors from the ranging procedure itself, it is shown that with a constellation of 10 satellites, we can achieve a standard deviation of roughly 4% on the estimated mean neutral density. As more satellites are added to the constellation, the result converges towards the lower limit of the achievable drag coefficient, and accuracy becomes limited by the quality of the ranging measurements and the probability of the accommodation coefficient. Comparisons are made to existing atmospheric models such as NRLMSISE-00 and JB2006.

  13. Estimating Relatedness Between Individuals in General Populations With a Focus on Their Use in Conservation Programs

    PubMed Central

    Oliehoek, Pieter A.; Windig, Jack J.; van Arendonk, Johan A. M.; Bijma, Piter

    2006-01-01

    Relatedness estimators are widely used in genetic studies, but effects of population structure on performance of estimators, criteria to evaluate estimators, and benefits of using such estimators in conservation programs have to date received little attention. In this article we present new estimators, based on the relationship between coancestry and molecular similarity between individuals, and compare them with existing estimators using Monte Carlo simulation of populations, either panmictic or structured. Estimators were evaluated using statistical criteria and a diversity criterion that minimized relatedness. Results show that ranking of estimators depends on the population structure. An existing estimator based on two-gene and four-gene coefficients of identity performs best in panmictic populations, whereas a new estimator based on coancestry performs best in structured populations. The number of marker alleles and loci did not affect ranking of estimators. Statistical criteria were insufficient to evaluate estimators for their use in conservation programs. The regression coefficient of pedigree relatedness on estimated relatedness (β2) was substantially lower than unity for all estimators, causing overestimation of the diversity conserved. A simple correction to achieve β2 = 1 improves both existing and new estimators. Using relatedness estimates with correction considerably increased diversity in structured populations, but did not do so or even decreased diversity in panmictic populations. PMID:16510792

  14. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    PubMed

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  15. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

    PubMed Central

    Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  16. Estimate exchanger vibration

    SciTech Connect

    Nieh, C.D.; Zengyan, H.

    1986-04-01

    Based on the classical beam theory, a simple method for calculating the natural frequency of unequally spanned tubes is presented. The method is suitable for various boundary conditions. Accuracy of the calculations is sufficient for practical applications. This method will help designers and operators estimate the vibration of tubular exchangers. In general, there are three reasons why a tube vibrates in cross flow: vortex shedding, fluid elasticity and turbulent buffeting. No matter which is the cause, the basic reason is that the frequency of exciting force is approximately the same as or equal to the natural frequency of the tube. To prevent the heat exchanger from vibrating, it is necessary to select correctly the shell-side fluid velocity so that the frequency of exciting force is different from the natural frequency of the tube, or to vary the natural frequency of the heat exchanger tube. So precisely determining the natural frequency of the heat exchanger, especially its foundational frequency under various supporting conditions, is of significance.

  17. Tree Topology Estimation.

    PubMed

    Estrada, Rolando; Tomasi, Carlo; Schmidler, Scott C; Farsiu, Sina

    2015-08-01

    Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree - what connects to what - from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar graph, and the inverse problem of reconstructing the topology of the tree from that of the graph is ill-posed. We regularize this problem with a generative, parametric tree-growth model. Under this model, reconstruction is possible in linear time if one knows the direction of each edge in the graph - which edge endpoint is closer to the root of the tree - but becomes NP-hard if the directions are not known. For the latter case, we present a heuristic search algorithm to estimate the most likely topology of a rooted, three-dimensional tree from a single two-dimensional image. Experimental results on retinal vessel, plant root, and synthetic tree data sets show that our methodology is both accurate and efficient. PMID:26353004

  18. TRAC performance estimates

    NASA Technical Reports Server (NTRS)

    Everett, L.

    1992-01-01

    This report documents the performance characteristics of a Targeting Reflective Alignment Concept (TRAC) sensor. The performance will be documented for both short and long ranges. For long ranges, the sensor is used without the flat mirror attached to the target. To better understand the capabilities of the TRAC based sensors, an engineering model is required. The model can be used to better design the system for a particular application. This is necessary because there are many interrelated design variables in application. These include lense parameters, camera, and target configuration. The report presents first an analytical development of the performance, and second an experimental verification of the equations. In the analytical presentation it is assumed that the best vision resolution is a single pixel element. The experimental results suggest however that the resolution is better than 1 pixel. Hence the analytical results should be considered worst case conditions. The report also discusses advantages and limitations of the TRAC sensor in light of the performance estimates. Finally the report discusses potential improvements.

  19. Tree Topology Estimation

    PubMed Central

    Estrada, Rolando; Tomasi, Carlo; Schmidler, Scott C.; Farsiu, Sina

    2015-01-01

    Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree—what connects to what—from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar graph, and the inverse problem of reconstructing the topology of the tree from that of the graph is ill-posed. We regularize this problem with a generative, parametric tree-growth model. Under this model, reconstruction is possible in linear time if one knows the direction of each edge in the graph—which edge endpoint is closer to the root of the tree—but becomes NP-hard if the directions are not known. For the latter case, we present a heuristic search algorithm to estimate the most likely topology of a rooted, three-dimensional tree from a single two-dimensional image. Experimental results on retinal vessel, plant root, and synthetic tree datasets show that our methodology is both accurate and efficient. PMID:26353004

  20. Uveal melanoma: estimating prognosis.

    PubMed

    Kaliki, Swathi; Shields, Carol L; Shields, Jerry A

    2015-02-01

    Uveal melanoma is the most common primary malignant tumor of the eye in adults, predominantly found in Caucasians. Local tumor control of uveal melanoma is excellent, yet this malignancy is associated with relatively high mortality secondary to metastasis. Various clinical, histopathological, cytogenetic features and gene expression features help in estimating the prognosis of uveal melanoma. The clinical features associated with poor prognosis in patients with uveal melanoma include older age at presentation, male gender, larger tumor basal diameter and thickness, ciliary body location, diffuse tumor configuration, association with ocular/oculodermal melanocytosis, extraocular tumor extension, and advanced tumor staging by American Joint Committee on Cancer classification. Histopathological features suggestive of poor prognosis include epithelioid cell type, high mitotic activity, higher values of mean diameter of ten largest nucleoli, higher microvascular density, extravascular matrix patterns, tumor-infiltrating lymphocytes, tumor-infiltrating macrophages, higher expression of insulin-like growth factor-1 receptor, and higher expression of human leukocyte antigen Class I and II. Monosomy 3, 1p loss, 6q loss, and 8q and those classified as Class II by gene expression are predictive of poor prognosis of uveal melanoma. In this review, we discuss the prognostic factors of uveal melanoma. A database search was performed on PubMed, using the terms "uvea," "iris," "ciliary body," "choroid," "melanoma," "uveal melanoma" and "prognosis," "metastasis," "genetic testing," "gene expression profiling." Relevant English language articles were extracted, reviewed, and referenced appropriately. PMID:25827538

  1. Filament L1482 in the California molecular cloud

    NASA Astrophysics Data System (ADS)

    Li, D. L.; Esimbek, J.; Zhou, J. J.; Lou, Y.-Q.; Wu, G.; Tang, X. D.; He, Y. X.

    2014-07-01

    Aims: The process of gravitational fragmentation in the L1482 molecular filament of the California molecular cloud is studied by combining several complementary observations and physical estimates. We investigate the kinematic and dynamical states of this molecular filament and physical properties of several dozens of dense molecular clumps embedded therein. Methods: We present and compare molecular line emission observations of the J = 2-1 and J = 3-2 transitions of 12CO in this molecular complex, using the Kölner Observatorium für Sub-Millimeter Astronomie (KOSMA) 3-m telescope. These observations are complemented with archival data observations and analyses of the 13CO J = 1-0 emission obtained at the Purple Mountain Observatory (PMO) 13.7-m radio telescope at Delingha Station in QingHai Province of west China, as well as infrared emission maps from the Herschel Space Telescope online archive, obtained with the SPIRE and PACS cameras. Comparison of these complementary datasets allows for a comprehensive multiwavelength analysis of the L1482 molecular filament. Results: We have identified 23 clumps along the molecular filament L1482 in the California molecular cloud. For these molecular clumps, we were able to estimate column and number densities, masses, and radii. The masses of these clumps range from ~6.8 to 62.8 M⊙ with an average value of 24.7-16.2+31.1 M⊙. Eleven of the identified molecular clumps appear to be associated with protostars and are thus referred to as protostellar clumps. Protostellar clumps and the remaining starless clumps of our sample appear to have similar temperatures and linewidths, yet on average, the protostellar clumps appear to be slightly more massive than the latter. All these molecular clumps show supersonic nonthermal gas motions. While surprisingly similar in mass and size to the much better known Orion molecular cloud, the formation rate of high-mass stars appears to be suppressed in the California molecular cloud

  2. Direct volume estimation without segmentation

    NASA Astrophysics Data System (ADS)

    Zhen, X.; Wang, Z.; Islam, A.; Bhaduri, M.; Chan, I.; Li, S.

    2015-03-01

    Volume estimation plays an important role in clinical diagnosis. For example, cardiac ventricular volumes including left ventricle (LV) and right ventricle (RV) are important clinical indicators of cardiac functions. Accurate and automatic estimation of the ventricular volumes is essential to the assessment of cardiac functions and diagnosis of heart diseases. Conventional methods are dependent on an intermediate segmentation step which is obtained either manually or automatically. However, manual segmentation is extremely time-consuming, subjective and highly non-reproducible; automatic segmentation is still challenging, computationally expensive, and completely unsolved for the RV. Towards accurate and efficient direct volume estimation, our group has been researching on learning based methods without segmentation by leveraging state-of-the-art machine learning techniques. Our direct estimation methods remove the accessional step of segmentation and can naturally deal with various volume estimation tasks. Moreover, they are extremely flexible to be used for volume estimation of either joint bi-ventricles (LV and RV) or individual LV/RV. We comparatively study the performance of direct methods on cardiac ventricular volume estimation by comparing with segmentation based methods. Experimental results show that direct estimation methods provide more accurate estimation of cardiac ventricular volumes than segmentation based methods. This indicates that direct estimation methods not only provide a convenient and mature clinical tool for cardiac volume estimation but also enables diagnosis of cardiac diseases to be conducted in a more efficient and reliable way.

  3. Molecular symmetry with quaternions.

    PubMed

    Fritzer, H P

    2001-09-01

    A new and relatively simple version of the quaternion calculus is offered which is especially suitable for applications in molecular symmetry and structure. After introducing the real quaternion algebra and its classical matrix representation in the group SO(4) the relations with vectors in 3-space and the connection with the rotation group SO(3) through automorphism properties of the algebra are discussed. The correlation of the unit quaternions with both the Cayley-Klein and the Euler parameters through the group SU(2) is presented. Besides rotations the extension of quaternions to other important symmetry operations, reflections and the spatial inversion, is given. Finally, the power of the quaternion calculus for molecular symmetry problems is revealed by treating some examples applied to icosahedral symmetry. PMID:11666072

  4. Carbyne: The Molecular Approach.

    PubMed

    Tykwinski, Rik R

    2015-12-01

    For the last 60+ years, the synthesis and study of cumulenes and polyynes have been the focus of a small, but dedicated, group of researchers. Many of the remarkable electronic, optical, and structural properties of cumulenes and polyynes had already been identified in the earliest reports. The molecular lengths achievable by the initial syntheses were, unfortunately, somewhat limited by synthetic methods available. For the past 15 years, we have worked toward expanding on the synthesis of cumulenes and polyynes through the development of new methods and stabilization motifs. As new compounds have become available, homologous series of cumulenes and polyynes have then been examined as a function of molecular length. While we are not yet there, we would like to eventually provide a general description of the sp-carbon allotrope carbyne, and this account presents some of our efforts toward this goal. PMID:26200096

  5. An Artificial Molecular Transporter

    PubMed Central

    Schäfer, Christian; Ragazzon, Giulio; Colasson, Benoit; La Rosa, Marcello; Silvi, Serena

    2015-01-01

    Abstract The transport of substrates is one of the main tasks of biomolecular machines in living organisms. We report a synthetic small‐molecule system designed to catch, displace, and release molecular cargo in solution under external control. The system consists of a bistable rotaxane that behaves as an acid–base controlled molecular shuttle, whose ring component bears a tether ending with a nitrile group. The latter can be coordinated to a ruthenium complex that acts as the load, and dissociated upon irradiation with visible light. The cargo loading/unloading and ring transfer/return processes are reversible and can be controlled independently. The robust coordination bond ensures that the cargo remains attached to the device while the transport takes place. PMID:27308223

  6. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  7. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  8. Welding Molecular Crystals.

    PubMed

    Adolf, Cyril R R; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2015-12-16

    Both for fundamental and applied sciences, the design of complex molecular systems in the crystalline phase with strict control of order and periodicity at both microscopic and macroscopic levels is of prime importance for development of new solid-state materials and devices. The design and fabrication of complex crystalline systems as networks of crystals displaying task-specific properties is a step toward smart materials. Here we report on isostructural and almost isometric molecular crystals of different colors, their use for fabrication of core-shell crystals, and their welding by 3D epitaxial growth into networks of crystals as single-crystalline entities. Welding of crystals by self-assembly processes into macroscopic networks of crystals is a powerful strategy for the design of hierarchically organized periodic complex architectures composed of different subdomains displaying targeted characteristics. Crystal welding may be regarded as a first step toward the design of new hierarchically organized complex crystalline systems. PMID:26581391

  9. An artificial molecular pump.

    PubMed

    Cheng, Chuyang; McGonigal, Paul R; Schneebeli, Severin T; Li, Hao; Vermeulen, Nicolaas A; Ke, Chenfeng; Stoddart, J Fraser

    2015-06-01

    Carrier proteins consume fuel in order to pump ions or molecules across cell membranes, creating concentration gradients. Their control over diffusion pathways, effected entirely through noncovalent bonding interactions, has inspired chemists to devise artificial systems that mimic their function. Here, we report a wholly artificial compound that acts on small molecules to create a gradient in their local concentration. It does so by using redox energy and precisely organized noncovalent bonding interactions to pump positively charged rings from solution and ensnare them around an oligomethylene chain, as part of a kinetically trapped entanglement. A redox-active viologen unit at the heart of a dumbbell-shaped molecular pump plays a dual role, first attracting and then repelling the rings during redox cycling, thereby enacting a flashing energy ratchet mechanism with a minimalistic design. Our artificial molecular pump performs work repetitively for two cycles of operation and drives rings away from equilibrium toward a higher local concentration. PMID:25984834

  10. Superposition State Molecular Dynamics.

    PubMed

    Venkatnathan, Arun; Voth, Gregory A

    2005-01-01

    The ergodic sampling of rough energy landscapes is crucial for understanding phenomena like protein folding, peptide aggregation, polymer dynamics, and the glass transition. These rough energy landscapes are characterized by the presence of many local minima separated by high energy barriers, where Molecular Dynamics (MD) fails to satisfy ergodicity. To enhance ergodic behavior, we have developed the Superposition State Molecular Dynamics (SSMD) method, which uses a superposition of energy states to obtain an effective potential for the MD simulation. In turn, the dynamics on this effective potential can be used to sample the configurational free energy of the real potential. The effectiveness of the SSMD method for a one-dimensional rough potential energy landscape is presented as a test case. PMID:26641113

  11. An artificial molecular pump

    NASA Astrophysics Data System (ADS)

    Cheng, Chuyang; McGonigal, Paul R.; Schneebeli, Severin T.; Li, Hao; Vermeulen, Nicolaas A.; Ke, Chenfeng; Stoddart, J. Fraser

    2015-06-01

    Carrier proteins consume fuel in order to pump ions or molecules across cell membranes, creating concentration gradients. Their control over diffusion pathways, effected entirely through noncovalent bonding interactions, has inspired chemists to devise artificial systems that mimic their function. Here, we report a wholly artificial compound that acts on small molecules to create a gradient in their local concentration. It does so by using redox energy and precisely organized noncovalent bonding interactions to pump positively charged rings from solution and ensnare them around an oligomethylene chain, as part of a kinetically trapped entanglement. A redox-active viologen unit at the heart of a dumbbell-shaped molecular pump plays a dual role, first attracting and then repelling the rings during redox cycling, thereby enacting a flashing energy ratchet mechanism with a minimalistic design. Our artificial molecular pump performs work repetitively for two cycles of operation and drives rings away from equilibrium toward a higher local concentration.

  12. Molecular psychiatry of zebrafish

    PubMed Central

    Stewart, Adam Michael; Ullmann, Jeremy F.P.; Norton, William H.J.; Brennan, Caroline H.; Parker, Matthew O.; Gerlai, Robert; Kalueff, Allan V.

    2014-01-01

    Due to their well-characterized neural development and high genetic homology to mammals, zebrafish (Danio rerio) have emerged as a powerful model organism in the field of biological psychiatry. Here, we discuss the molecular psychiatry of zebrafish, and its implications for translational neuroscience research and modeling CNS disorders. In particular, we outline recent genetic and technological developments allowing for in-vivo examinations, high-throughput screening and whole-brain analyses in larval and adult zebrafish. We also summarize the application of these molecular techniques to the understanding of neuropsychiatric disease, outlining the potential of zebrafish for modeling complex brain disorders, including attention-deficit/hyperactivity disorder (ADHD), aggression, post-traumatic stress and substance abuse. Critically evaluating the advantages and limitations of larval and adult fish tests, we suggest that zebrafish models become a rapidly emerging new field in modern biological psychiatry research. PMID:25349164

  13. Wholly Synthetic Molecular Machines.

    PubMed

    Cheng, Chuyang; Stoddart, J Fraser

    2016-06-17

    The past quarter of a century has witnessed an increasing engagement on the part of physicists and chemists in the design and synthesis of molecular machines de novo. This minireview traces the development of artificial molecular machines from their prototypes in the form of shuttles and switches to their emergence as motors and pumps where supplies of energy in the form of chemical fuel, electrochemical potential and light activation become a minimum requirement for them to function away from equilibrium. The challenge facing this rapidly growing community of scientists and engineers today is one of putting wholly synthetic molecules to work, both individually and as collections. Here, we highlight some of the recent conceptual and practical advances relating to the operation of wholly synthetic rotary and linear motors. PMID:26833859

  14. Molecular pathways in dystonia

    PubMed Central

    Bragg, D. Cristopher; Armata, Ioanna A.; Nery, Flavia C.; Breakefield, Xandra O.; Sharma, Nutan

    2011-01-01

    The hereditary dystonias comprise a set of diseases defined by a common constellation of motor deficits. These disorders are most likely associated with different molecular etiologies, many of which have yet to be elucidated. Here we discuss recent advances in three forms of hereditary dystonia, DYT1, DYT6 and DYT16, which share a similar clinical picture: onset in childhood or adolescence, progressive spread of symptoms with generalized involvement of body regions and a steady state affliction without treatment. Unlike DYT1, the genes responsible for DYT6 and DYT16 have only recently been identified, with relatively little information about the function of the encoded proteins. Nevertheless, recent data suggest that these proteins may fit together within interacting pathways involved in dopaminergic signaling, transcriptional regulation, and cellular stress responses. This review focuses on these molecular pathways, highlighting potential common themes among these dystonias which may serve as areas for future research. PMID:21134457

  15. Molecular water pumps.

    PubMed

    Zeuthen, T

    2000-01-01

    There is good evidence that cotransporters of the symport type behave as molecular water pumps, in which a water flux is coupled to the substrate fluxes. The free energy stored in the substrate gradients is utilized, by a mechanism within the protein, for the transport of water. Accordingly, the water flux is secondary active and can proceed uphill against the water chemical potential difference. The effect has been recognized in all symports studied so far (Table 1). It has been studied in details for the K+/Cl- cotransporter in the choroid plexus epithelium, the H+/lactate cotransporter in the retinal pigment epithelium, the intestinal Na+/glucose cotransporter (SGLT1) and the renal Na+/dicarboxylate cotransporter both expressed in Xenopus oocytes. The generality of the phenomenon among symports with widely different primary structures suggests that the property of molecular water pumps derives from a pattern of conformational changes common for this type of membrane proteins. Most of the data on molecular water pumps are derived from fluxes initiated by rapid changes in the composition of the external solution. There was no experimental evidence for unstirred layers in such experiments, in accordance with theoretical evaluations. Even the experimental introduction of unstirred layers did not lead to any measurable water fluxes. The majority of the experimental data supports a molecular model where water is cotransported: A well defined number of water molecules act as a substrate on equal footing with the non-aqueous substrates. The ratio of any two of the fluxes is constant, given by the properties of the protein, and is independent of the driving forces or other external parameters. The detailed mechanism behind the molecular water pumps is as yet unknown. It is, however, possible to combine well established phenomena for enzymes into a working model. For example, uptake and release of water is associated with conformational changes during enzymatic action; a

  16. Bayesian phylogenetic estimation of fossil ages.

    PubMed

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  17. Bayesian phylogenetic estimation of fossil ages

    PubMed Central

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  18. Theoretical molecular studies of astrophysical interest

    NASA Technical Reports Server (NTRS)

    Flynn, George

    1991-01-01

    When work under this grant began in 1974 there was a great need for state-to-state collisional excitation rates for interstellar molecules observed by radio astronomers. These were required to interpret observed line intensities in terms of local temperatures and densities, but, owing to lack of experimental or theoretical values, estimates then being used for this purpose ranged over several orders of magnitude. A problem of particular interest was collisional excitation of formaldehyde; Townes and Cheung had suggested that the relative size of different state-to-state rates (propensity rules) was responsible for the anomalous absorption observed for this species. We believed that numerical molecular scattering techniques (in particular the close coupling or coupled channel method) could be used to obtain accurate results, and that these would be computationally feasible since only a few molecular rotational levels are populated at the low temperatures thought to prevail in the observed regions. Such calculations also require detailed knowledge of the intermolecular forces, but we thought that those could also be obtained with sufficient accuracy by theoretical (quantum chemical) techniques. Others, notably Roy Gordon at Harvard, had made progress in solving the molecular scattering equations, generally using semi-empirical intermolecular potentials. Work done under this grant generalized Gordon's scattering code, and introduced the use of theoretical interaction potentials obtained by solving the molecular Schroedinger equation. Earlier work had considered only the excitation of a diatomic molecule by collisions with an atom, and we extended the formalism to include excitation of more general molecular rotors (e.g., H2CO, NH2, and H2O) and also collisions of two rotors (e.g., H2-H2).

  19. Molecular Dynamics of Acetylcholinesterase

    SciTech Connect

    Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy

    2002-06-01

    Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.

  20. Functional Molecular Ecological Networks

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  1. Primer on molecular genetics

    SciTech Connect

    Not Available

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  2. MOLSCAT: MOLecular SCATtering

    NASA Astrophysics Data System (ADS)

    Hutson, Jeremy M.; Green, Sheldon

    2012-06-01

    MOLSCAT is a FORTRAN code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem and was developed to obtain collision rates for molecules in the interstellar gas which are needed to understand microwave and infrared astronomical observations. The code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided.

  3. Functional molecular ecological networks.

    PubMed

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on "species" richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO(2) enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO(2) and ambient CO(2) (aCO(2)) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO(2) and aCO(2), at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO(2) dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  4. Moving beyond molecular mechanisms

    PubMed Central

    2015-01-01

    A major goal in cell biology is to bridge the gap in our understanding of how molecular mechanisms contribute to cell and organismal physiology. Approaches well established in the physical sciences could be instrumental in achieving this goal. A better integration of the physical sciences with cell biology will therefore be an important step in our quest to decipher how cells work together to construct a living organism. PMID:25601400

  5. Open boundary molecular dynamics

    NASA Astrophysics Data System (ADS)

    Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.

    2015-09-01

    This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.

  6. Communication: Molecular gears.

    PubMed

    Burnell, E Elliott; de Lange, Cornelis A; Meerts, W Leo

    2016-09-01

    The (1)H nuclear magnetic resonance spectrum of hexamethylbenzene orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy. The spectrum contains over 350 000 lines with many overlapping transitions, from which four independent direct dipolar couplings are obtained. The rotations of the six methyl groups appear to be correlated due to mutual steric hindrance. Adjacent methyl groups show counter-rotating or geared motion. Hexamethylbenzene thus behaves as a molecular hexagonal gear. PMID:27608981

  7. Molecular opacities for exoplanets.

    PubMed

    Bernath, Peter F

    2014-04-28

    Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy. PMID:24664921

  8. Molecular-beam scattering

    SciTech Connect

    Vernon, M.F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N/sub 2/ from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HCl ..-->.. NaCl + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2/sup 2/P/sub 3/2/) and Na(3/sup 2/P/sub 3/2/) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  9. Graphs in molecular biology

    PubMed Central

    Huber, Wolfgang; Carey, Vincent J; Long, Li; Falcon, Seth; Gentleman, Robert

    2007-01-01

    Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network. PMID:17903289

  10. Molecular opacities for exoplanets

    PubMed Central

    Bernath, Peter F.

    2014-01-01

    Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy. PMID:24664921

  11. Conceptual Considerations in Molecular Science

    ERIC Educational Resources Information Center

    Sawyer, Donald T.

    2005-01-01

    There are significant misconceptions within the chemical community and molecular science, particularly in the undergraduate curriculum and the associated textbooks. Some of the misconceptions are described, which give poor basis to understand molecular bonding and structure, and reaction mechanisms.

  12. Digitotalar dysmorphism: Molecular elucidation.

    PubMed

    Vorster, Anna Alvera; Beighton, Peter; Ramesar, Rajkumar Sewcharan

    2016-01-01

    Dominantly inherited digitotalar dysmorphism (DTD), which is characterised by flexion contractures of digits and 'rocker-bottom' feet due to a vertical talus, was first described in a South African family of European stock in 1972. We review the clinical manifestations and document the molecular basis for DTD in this prototype family. This family was restudied in 1995 and 2006 and biological specimens were obtained for molecular studies. Since the distal arthrogryposes (DAs) are genetically heterogeneous, an unbiased approach to mutation identification was undertaken through whole-exome next-generation sequencing of DNA from a single DTD-affected female. Venous blood specimens were obtained for DNA banking and subsequent molecular studies. Analysis of the nine genes that had previously been shown to cause DAs revealed a pathogenic mutation in exon nine of TNNT3. The presence of the p.(Arg63His) missense mutation at position 63 of TNNT3 was confirmed through direct cycle sequencing of genomic DNA in six affected family members for whom DNA had been archived. PMID:26915936

  13. Molecular Neuropathology of Gliomas

    PubMed Central

    Riemenschneider, Markus J.; Reifenberger, Guido

    2009-01-01

    Gliomas are the most common primary human brain tumors. They comprise a heterogeneous group of benign and malignant neoplasms that are histologically classified according to the World Health Organization (WHO) classification of tumors of the nervous system. Over the past 20 years the cytogenetic and molecular genetic alterations associated with glioma formation and progression have been intensely studied and genetic profiles as additional aids to the definition of brain tumors have been incorporated in the WHO classification. In fact, first steps have been undertaken in supplementing classical histopathological diagnosis by the use of molecular tests, such as MGMT promoter hypermethylation in glioblastomas or detection of losses of chromosome arms 1p and 19q in oligodendroglial tumors. The tremendous progress that has been made in the use of array-based profiling techniques will likely contribute to a further molecular refinement of glioma classification and lead to the identification of glioma core pathways that can be specifically targeted by more individualized glioma therapies. PMID:19333441

  14. Molecular basis of alcoholism.

    PubMed

    Most, Dana; Ferguson, Laura; Harris, R Adron

    2014-01-01

    Acute alcohol intoxication causes cellular changes in the brain that last for hours, while chronic alcohol use induces widespread neuroadaptations in the nervous system that can last a lifetime. Chronic alcohol use and the progression into dependence involve the remodeling of synapses caused by changes in gene expression produced by alcohol. The progression of alcohol use, abuse, and dependence can be divided into stages, which include intoxication, withdrawal, and craving. Each stage is associated with specific changes in gene expression, cellular function, brain circuits, and ultimately behavior. What are the molecular mechanisms underlying the transition from recreational use (acute) to dependence (chronic)? What cellular adaptations result in drug memory retention, leading to the persistence of addictive behaviors, even after prolonged drug abstinence? Research into the neurobiology of alcoholism aims to answer these questions. This chapter will describe the molecular adaptations caused by alcohol use and dependence, and will outline key neurochemical participants in alcoholism at the molecular level, which are also potential targets for therapy. PMID:25307570

  15. Molecular biology of hearing

    PubMed Central

    Stöver, Timo; Diensthuber, Marc

    2012-01-01

    The inner ear is our most sensitive sensory organ and can be subdivided into three functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound, which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear houses the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In recent years there has been significant progress in research on the molecular basis of hearing. An increasing number of genes and proteins related to hearing are being identified and characterized. The growing knowledge of these genes contributes not only to greater appreciation of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss. PMID:22558056

  16. Molecular adsorption on graphene

    NASA Astrophysics Data System (ADS)

    Kong, Lingmei; Enders, Axel; Rahman, Talat S.; Dowben, Peter A.

    2014-11-01

    Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H2O, H2, O2, CO, NO2, NO, and NH3), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH2, An-CH3, An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene’s electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

  17. Molecular adsorption on graphene.

    PubMed

    Kong, Lingmei; Enders, Axel; Rahman, Talat S; Dowben, Peter A

    2014-11-01

    Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H(2)O, H(2), O(2), CO, NO(2), NO, and NH(3)), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH(2), An-CH(3), An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene's electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity. PMID:25287516

  18. Thermoelectricity in molecular junctions.

    PubMed

    Reddy, Pramod; Jang, Sung-Yeon; Segalman, Rachel A; Majumdar, Arun

    2007-03-16

    By trapping molecules between two gold electrodes with a temperature difference across them, the junction Seebeck coefficients of 1,4-benzenedithiol (BDT), 4,4'-dibenzenedithiol, and 4,4''-tribenzenedithiol in contact with gold were measured at room temperature to be +8.7 +/- 2.1 microvolts per kelvin (muV/K), +12.9 +/- 2.2 muV/K, and +14.2 +/- 3.2 muV/K, respectively (where the error is the full width half maximum of the statistical distributions). The positive sign unambiguously indicates p-type (hole) conduction in these heterojunctions, whereas the Au Fermi level position for Au-BDT-Au junctions was identified to be 1.2 eV above the highest occupied molecular orbital level of BDT. The ability to study thermoelectricity in molecular junctions provides the opportunity to address these fundamental unanswered questions about their electronic structure and to begin exploring molecular thermoelectric energy conversion. PMID:17303718

  19. Maximum-Likelihood Estimator of Clock Offset between Nanomachines in Bionanosensor Networks.

    PubMed

    Lin, Lin; Yang, Chengfeng; Ma, Maode

    2015-01-01

    Recent advances in nanotechnology, electronic technology and biology have enabled the development of bio-inspired nanoscale sensors. The cooperation among the bionanosensors in a network is envisioned to perform complex tasks. Clock synchronization is essential to establish diffusion-based distributed cooperation in the bionanosensor networks. This paper proposes a maximum-likelihood estimator of the clock offset for the clock synchronization among molecular bionanosensors. The unique properties of diffusion-based molecular communication are described. Based on the inverse Gaussian distribution of the molecular propagation delay, a two-way message exchange mechanism for clock synchronization is proposed. The maximum-likelihood estimator of the clock offset is derived. The convergence and the bias of the estimator are analyzed. The simulation results show that the proposed estimator is effective for the offset compensation required for clock synchronization. This work paves the way for the cooperation of nanomachines in diffusion-based bionanosensor networks. PMID:26690173

  20. Maximum-Likelihood Estimator of Clock Offset between Nanomachines in Bionanosensor Networks

    PubMed Central

    Lin, Lin; Yang, Chengfeng; Ma, Maode

    2015-01-01

    Recent advances in nanotechnology, electronic technology and biology have enabled the development of bio-inspired nanoscale sensors. The cooperation among the bionanosensors in a network is envisioned to perform complex tasks. Clock synchronization is essential to establish diffusion-based distributed cooperation in the bionanosensor networks. This paper proposes a maximum-likelihood estimator of the clock offset for the clock synchronization among molecular bionanosensors. The unique properties of diffusion-based molecular communication are described. Based on the inverse Gaussian distribution of the molecular propagation delay, a two-way message exchange mechanism for clock synchronization is proposed. The maximum-likelihood estimator of the clock offset is derived. The convergence and the bias of the estimator are analyzed. The simulation results show that the proposed estimator is effective for the offset compensation required for clock synchronization. This work paves the way for the cooperation of nanomachines in diffusion-based bionanosensor networks. PMID:26690173

  1. Consequences of Secondary Calibrations on Divergence Time Estimates.

    PubMed

    Schenk, John J

    2016-01-01

    Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates. PMID:26824760

  2. Consequences of Secondary Calibrations on Divergence Time Estimates

    PubMed Central

    Schenk, John J.

    2016-01-01

    Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates. PMID:26824760

  3. Uveal melanoma: Estimating prognosis

    PubMed Central

    Kaliki, Swathi; Shields, Carol L; Shields, Jerry A

    2015-01-01

    Uveal melanoma is the most common primary malignant tumor of the eye in adults, predominantly found in Caucasians. Local tumor control of uveal melanoma is excellent, yet this malignancy is associated with relatively high mortality secondary to metastasis. Various clinical, histopathological, cytogenetic features and gene expression features help in estimating the prognosis of uveal melanoma. The clinical features associated with poor prognosis in patients with uveal melanoma include older age at presentation, male gender, larger tumor basal diameter and thickness, ciliary body location, diffuse tumor configuration, association with ocular/oculodermal melanocytosis, extraocular tumor extension, and advanced tumor staging by American Joint Committee on Cancer classification. Histopathological features suggestive of poor prognosis include epithelioid cell type, high mitotic activity, higher values of mean diameter of ten largest nucleoli, higher microvascular density, extravascular matrix patterns, tumor-infiltrating lymphocytes, tumor-infiltrating macrophages, higher expression of insulin-like growth factor-1 receptor, and higher expression of human leukocyte antigen Class I and II. Monosomy 3, 1p loss, 6q loss, and 8q and those classified as Class II by gene expression are predictive of poor prognosis of uveal melanoma. In this review, we discuss the prognostic factors of uveal melanoma. A database search was performed on PubMed, using the terms “uvea,” “iris,” “ciliary body,” “choroid,” “melanoma,” “uveal melanoma” and “prognosis,” “metastasis,” “genetic testing,” “gene expression profiling.” Relevant English language articles were extracted, reviewed, and referenced appropriately. PMID:25827538

  4. Relating space radiation environments to risk estimates

    NASA Technical Reports Server (NTRS)

    Curtis, Stanley B.

    1993-01-01

    A number of considerations must go into the process of determining the risk of deleterious effects of space radiation to travelers. Among them are (1) determination of the components of the radiation environment (particle species, fluxes and energy spectra) which will encounter, (2) determination of the effects of shielding provided by the spacecraft and the bodies of the travelers which modify the incident particle spectra and mix of particles, and (3) determination of relevant biological effects of the radiation in the organs of interest. The latter can then lead to an estimation of risk from a given space scenario. Clearly, the process spans many scientific disciplines from solar and cosmic ray physics to radiation transport theeory to the multistage problem of the induction by radiation of initial lesions in living material and their evolution via physical, chemical, and biological processes at the molecular, cellular, and tissue levels to produce the end point of importance.

  5. Relating space radiation environments to risk estimates

    SciTech Connect

    Curtis, S.B. ||

    1993-12-31

    A number of considerations must go into the process of determining the risk of deleterious effects of space radiation to travelers. Among them are (1) determination of the components of the radiation environment (particle species, fluxes and energy spectra) which will encounter, (2) determination of the effects of shielding provided by the spacecraft and the bodies of the travelers which modify the incident particle spectra and mix of particles, and (3) determination of relevant biological effects of the radiation in the organs of interest. The latter can then lead to an estimation of risk from a given space scenario. Clearly, the process spans many scientific disciplines from solar and cosmic ray physics to radiation transport theeory to the multistage problem of the induction by radiation of initial lesions in living material and their evolution via physical, chemical, and biological processes at the molecular, cellular, and tissue levels to produce the end point of importance.

  6. Estimating the Cost to do a Cost Estimate

    NASA Technical Reports Server (NTRS)

    Remer, D. S.; Buchanan, H. R.

    1998-01-01

    This article provides a model for estimating the cost required to do a cost estimate. Overruns may lead to concellation of a project. In 1991, we completed a study on the cost of doing cost estimates for the class of projects normally encountered in the development and implementation of equipment at the network of tracking stations operated by the Jet Propulsion Laboratory (JPL) for NASA.

  7. On the massive star-forming capacity of molecular clouds

    NASA Technical Reports Server (NTRS)

    Franco, Jose; Shore, Steven N.; Tenorio-Tagle, Guillermo

    1994-01-01

    Assuming that photoionization is the self-limiting process for continued star formation, we estimate the maximum number of massive (OB) stars that can form within a molecular cloud. The most efficient cloud destruction mechanism in the early stages of H II region evolution is the evaporation of the cloud by stars located near the cloud boundary. The maximum number of OB stars is of order 1 per 10(exp 4) solar mass of average molecular gas, or 10 per 10(exp 4) solar mass of dense molecular gas. The resulting star-forming efficiencies within cloud complexes range from 2% to 16% depending on both the location of the stars in the cloud and the details of the initial mass function, with an overall value of about 5% for average molecular gas.

  8. Estimators for the Cauchy distribution

    SciTech Connect

    Hanson, K.M.; Wolf, D.R.

    1993-12-31

    We discuss the properties of various estimators of the central position of the Cauchy distribution. The performance of these estimators is evaluated for a set of simulated experiments. Estimators based on the maximum and mean of the posterior probability density function are empirically found to be well behaved when more than two measurements are available. On the contrary, because of the infinite variance of the Cauchy distribution, the average of the measured positions is an extremely poor estimator of the location of the source. However, the median of the measured positions is well behaved. The rms errors for the various estimators are compared to the Fisher-Cramer-Rao lower bound. We find that the square root of the variance of the posterior density function is predictive of the rms error in the mean posterior estimator.

  9. A maximum-likelihood estimation of pairwise relatedness for autopolyploids

    PubMed Central

    Huang, K; Guo, S T; Shattuck, M R; Chen, S T; Qi, X G; Zhang, P; Li, B G

    2015-01-01

    Relatedness between individuals is central to ecological genetics. Multiple methods are available to quantify relatedness from molecular data, including method-of-moment and maximum-likelihood estimators. We describe a maximum-likelihood estimator for autopolyploids, and quantify its statistical performance under a range of biologically relevant conditions. The statistical performances of five additional polyploid estimators of relatedness were also quantified under identical conditions. When comparing truncated estimators, the maximum-likelihood estimator exhibited lower root mean square error under some conditions and was more biased for non-relatives, especially when the number of alleles per loci was low. However, even under these conditions, this bias was reduced to be statistically insignificant with more robust genetic sampling. We also considered ambiguity in polyploid heterozygote genotyping and developed a weighting methodology for candidate genotypes. The statistical performances of three polyploid estimators under both ideal and actual conditions (including inbreeding and double reduction) were compared. The software package POLYRELATEDNESS is available to perform this estimation and supports a maximum ploidy of eight. PMID:25370210

  10. Supercooled liquid water Estimation Tool

    Energy Science and Technology Software Center (ESTSC)

    2012-05-04

    The Cloud Supercooled liquid water Estimation Tool (SEET) is a user driven Graphical User Interface (GUI) that estimates cloud supercooled liquid water (SLW) content in terms of vertical column and total mass from Moderate resolution Imaging Supercooled liquid water Estimation Tool Spectroradiometer (MODIS) spatially derived cloud products and realistic vertical cloud parameterizations that are user defined. It also contains functions for post-processing of the resulting data in tabular and graphical form.

  11. Randomized gap and amplitude estimation

    NASA Astrophysics Data System (ADS)

    Zintchenko, Ilia; Wiebe, Nathan

    2016-06-01

    We provide a method for estimating spectral gaps in low-dimensional systems. Unlike traditional phase estimation, our approach does not require ancillary qubits nor does it require well-characterized gates. Instead, it only requires the ability to perform approximate Haar random unitary operations, applying the unitary whose eigenspectrum is sought and performing measurements in the computational basis. We discuss application of these ideas to in-place amplitude estimation and quantum device calibration.

  12. Estimating the Modified Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles

    1995-01-01

    The third-difference approach to modified Allan variance (MVAR) leads to a tractable formula for a measure of MVAR estimator confidence, the equivalent degrees of freedom (edf), in the presence of power-law phase noise. The effect of estimation stride on edf is tabulated. A simple approximation for edf is given, and its errors are tabulated. A theorem allowing conservative estimates of edf in the presence of compound noise processes is given.

  13. Spring Small Grains Area Estimation

    NASA Technical Reports Server (NTRS)

    Palmer, W. F.; Mohler, R. J.

    1986-01-01

    SSG3 automatically estimates acreage of spring small grains from Landsat data. Report describes development and testing of a computerized technique for using Landsat multispectral scanner (MSS) data to estimate acreage of spring small grains (wheat, barley, and oats). Application of technique to analysis of four years of data from United States and Canada yielded estimates of accuracy comparable to those obtained through procedures that rely on trained analysis.

  14. Estimators of bottom reflectance spectra

    NASA Technical Reports Server (NTRS)

    Estep, L.; Holloway, J.

    1992-01-01

    Estimators of in situ bottom spectral reflectance are calculated from multi-station optical field data gathered with standard instrumentation from different sites. These spectra are then compared to reflectance spectra measured in the laboratory of the bottom sediments collected in the field for the stations at these different sites. The relative fit of the estimated spectral curves to those measured in the laboratory was measured. The most accurate absolute estimation was provided by the single scattering irradiance model.

  15. Efficient estimation of Weber's W.

    PubMed

    Piantadosi, Steven T

    2016-03-01

    Many studies rely on estimation of Weber ratios (W) in order to quantify the acuity an individual's approximate number system. This paper discusses several problems encountered in estimating W using the standard methods, most notably low power and inefficiency. Through simulation, this work shows that W can best be estimated in a Bayesian framework that uses an inverse (1/W) prior. This beneficially balances a bias/variance trade-off and, when used with MAP estimation is extremely simple to implement. Use of this scheme substantially improves statistical power in examining correlates of W. PMID:26122978

  16. Estimated Russian stockpile, September 1996

    SciTech Connect

    Norris, R.S.; Arkin, W.

    1996-09-01

    An estimate of the size and composition of the former Soviet nuclear stockpile, based on START I memorandum of understanding data, is provided. The estimate covers operational forces that are assumed to be in a ready condition available for use. Total warhead stockpiles are estimated at about 12,000. Strategic offensive warheads comprise 7500 of the total, strategic defense missiles are estimated at 1200, land-based nonstrategic bombers and fighters at 1600, and naval nonstrategic weapons at 1600. Subtotals are provided for weapons categories (missiles, bombers, etc.) and weapons launchers.

  17. Estimating the Cost of Doing a Cost Estimate

    NASA Technical Reports Server (NTRS)

    Remer, D. S.; Buchanan, H. R.

    1996-01-01

    This article provides a model for estimating the cost required to do a cost estimate...Our earlier work provided data for high technology projects. This article adds data from the construction industry which validates the model over a wider range of technology.

  18. Molecular proxies for paleoclimatology

    NASA Astrophysics Data System (ADS)

    Eglinton, Timothy I.; Eglinton, Geoffrey

    2008-10-01

    We summarize the applications of molecular proxies in paleoclimatology. Marine molecular records especially are proving to be of value but certain environmentally persistent compounds can also be measured in lake sediments, loess deposits and ice cores. The fundamentals of this approach are the molecular parameters, the compound abundances and carbon, hydrogen, nitrogen and oxygen isotopic contents which can be derived by the analysis of sediment extracts. These afford proxy measures which can be interpreted in terms of the conditions which control climate and also reflect its operation. We discuss two types of proxy; those of terrigenous and those of aquatic origin, and exemplify their application in the study of marine sediments through the medium of ten case studies based in the Atlantic, Mediterranean and Pacific Oceans, and in Antarctica. The studies are mainly for periods in the present, the Holocene and particularly the last glacial/interglacial, but they also include one study from the Cretaceous. The terrigenous proxies, which are measures of continental vegetation, are based on higher plant leaf wax compounds, i.e. long-chain (circa C 30) hydrocarbons, alcohols and acids. They register the relative contributions of C 3 vs. C 4 type plants to the vegetation in the source areas. The two marine proxies are measures of sea surface temperatures (SST). The longer established one, (U 37K') is based on the relative abundances of C 37 alkenones photosynthesized by unicellular algae, members of the Haptophyta. The newest proxy (TEX 86) is based on C 86 glycerol tetraethers (GDGTs) synthesized in the water column by some of the archaeal microbiota, the Crenarchaeota.

  19. VMD: visual molecular dynamics.

    PubMed

    Humphrey, W; Dalke, A; Schulten, K

    1996-02-01

    VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. PMID:8744570

  20. Dense circumnuclear molecular gas in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Green, C.-E.; Cunningham, M. R.; Green, J. A.; Dawson, J. R.; Jones, P. A.; López-Sánchez, Á. R.; Verdes-Montenegro, L.; Henkel, C.; Baan, W. A.; Martín, S.

    2016-04-01

    We present results from a study of the dense circumnuclear molecular gas of starburst galaxies. The study aims to investigate the interplay between starbursts, active galactic nuclei and molecular gas. We characterize the dense gas traced by HCN, HCO+ and HNC and examine its kinematics in the circumnuclear regions of nine starburst galaxies observed with the Australia Telescope Compact Array. We detect HCN (1-0) and HCO+ (1-0) in seven of the nine galaxies and HNC (1-0) in four. Approximately 7 arcsec resolution maps of the circumnuclear molecular gas are presented. The velocity-integrated intensity ratios, HCO+ (1-0)/HCN (1-0) and HNC (1-0)/HCN (1-0), are calculated. Using these integrated intensity ratios and spatial intensity ratio maps, we identify photon-dominated regions (PDRs) in NGC 1097, NGC 1365 and NGC 1808. We find no galaxy which shows the PDR signature in only one part of the observed nuclear region. We also observe unusually strong HNC emission in NGC 5236, but it is not strong enough to be consistent with X-ray-dominated region chemistry. Rotation curves are derived for five of the galaxies and dynamical mass estimates of the inner regions of three of the galaxies are made.

  1. Molecular ecological network analyses

    PubMed Central

    2012-01-01

    Background Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP

  2. Molecular Mediators of Angiogenesis

    PubMed Central

    Ucuzian, Areck A.; Gassman, Andrew A.; East, Andrea T.; Greisler, Howard P.

    2010-01-01

    Angiogenesis, or the formation of new blood vessels from the preexisting vasculature, is a key component in numerous physiologic and pathologic responses and has broad impact in many medical and surgical specialties. In this review, we discuss the key cellular steps which lead to the neovascularization of tissues, and highlight the main molecular mechanisms and mediators in this process. We include discussions on proteolytic enzymes, cell/matrix interactions, pertinent cell signaling pathways, and end with a survey of the mechanisms which lead to the stabilization and maturation of neovasculatures. PMID:20061852

  3. Molecular biology and reproduction.

    PubMed

    McDonough, P G

    1999-03-01

    Modern molecular biology has provided unique insights into the fundamental understanding of reproductive disorders and the detection of microorganisms. The remarkable advances in DNA diagnostics have been expedited by the development of polymerase chain reaction (PCR) and the ability to isolate DNA and RNA from many different sources such as blood, saliva, hair roots, microscopic slides, paraffin-embedded tissue sections, clinical swabs, and even cancellous bone. These technical advances have been bolstered by the development of an increasing number of effective screening techniques to scan genomic DNA for unknown point mutations. The continued development of technology will ultimately result in automated DNA (desoxyribonucleic acid) diagnosis for the practicing clinician. The continuing expansion of information concerning the human genome will place an increasing emphasis on bioinformatics and the use of computer software for analyzing DNA sequences. With the automation of DNA diagnosis and the use of small samples (500 nanograms), the direct examination of the DNA of a patient, fetus, or microorganism will emerge as a definitive means of establishing the presence of the specific genetic change that causes disease. A knowledge of the precise pathology at the molecular level has and will provide important insights into the biochemical basis for many human diseases. A firm knowledge of the DNA alterations in disease and expression patterns of specific genes will provide for more directed therapeutic strategies. The refinement of vector technology and nuclear transplantion techniques will provide the opportunity for directed gene therapy to the early human embryo. This presentation is designed to acquaint the reader with current techniques of testing at the DNA level, prototype mutations in the reproductive sciences, new concepts in the molecular mechanisms of disease that affect reproduction, and therapeutic opportunities for the future. It is hoped that future

  4. Molecular mechanisms of epilepsy

    PubMed Central

    Staley, Kevin

    2015-01-01

    Decades of experimental work have established an imbalance of excitation and inhibition as the leading mechanism of the transition from normal brain function to seizure. In epilepsy, these transitions are rare and abrupt. Transition processes incorporating positive feedback, such as activity-dependent disinhibition, could provide these unique timing features. A rapidly expanding array of genetic etiologies will help delineate the molecular mechanism(s). This delineation will entail quite a bit of cell biology. The genes discovered to date are currently more remarkable for their diversity than their similarities. PMID:25710839

  5. Estimating discharge measurement uncertainty using the interpolated variance estimator

    USGS Publications Warehouse

    Cohn, T.; Kiang, J.; Mason, R., Jr.

    2012-01-01

    Methods for quantifying the uncertainty in discharge measurements typically identify various sources of uncertainty and then estimate the uncertainty from each of these sources by applying the results of empirical or laboratory studies. If actual measurement conditions are not consistent with those encountered in the empirical or laboratory studies, these methods may give poor estimates of discharge uncertainty. This paper presents an alternative method for estimating discharge measurement uncertainty that uses statistical techniques and at-site observations. This Interpolated Variance Estimator (IVE) estimates uncertainty based on the data collected during the streamflow measurement and therefore reflects the conditions encountered at the site. The IVE has the additional advantage of capturing all sources of random uncertainty in the velocity and depth measurements. It can be applied to velocity-area discharge measurements that use a velocity meter to measure point velocities at multiple vertical sections in a channel cross section.

  6. Space Vehicle Pose Estimation via Optical Correlation and Nonlinear Estimation

    NASA Technical Reports Server (NTRS)

    Rakoczy, John; Herren, Kenneth

    2007-01-01

    A technique for 6-degree-of-freedom (6DOF) pose estimation of space vehicles is being developed. This technique draws upon recent developments in implementing optical correlation measurements in a nonlinear estimator, which relates the optical correlation measurements to the pose states (orientation and position). For the optical correlator, the use of both conjugate filters and binary, phase-only filters in the design of synthetic discriminant function (SDF) filters is explored. A static neural network is trained a priori and used as the nonlinear estimator. New commercial animation and image rendering software is exploited to design the SDF filters and to generate a large filter set with which to train the neural network. The technique is applied to pose estimation for rendezvous and docking of free-flying spacecraft and to terrestrial surface mobility systems for NASA's Vision for Space Exploration. Quantitative pose estimation performance will be reported. Advantages and disadvantages of the implementation of this technique are discussed.

  7. Space Vehicle Pose Estimation via Optical Correlation and Nonlinear Estimation

    NASA Technical Reports Server (NTRS)

    Rakoczy, John M.; Herren, Kenneth A.

    2008-01-01

    A technique for 6-degree-of-freedom (6DOF) pose estimation of space vehicles is being developed. This technique draws upon recent developments in implementing optical correlation measurements in a nonlinear estimator, which relates the optical correlation measurements to the pose states (orientation and position). For the optical correlator, the use of both conjugate filters and binary, phase-only filters in the design of synthetic discriminant function (SDF) filters is explored. A static neural network is trained a priori and used as the nonlinear estimator. New commercial animation and image rendering software is exploited to design the SDF filters and to generate a large filter set with which to train the neural network. The technique is applied to pose estimation for rendezvous and docking of free-flying spacecraft and to terrestrial surface mobility systems for NASA's Vision for Space Exploration. Quantitative pose estimation performance will be reported. Advantages and disadvantages of the implementation of this technique are discussed.

  8. Estimating statistical distributions using an integral identity

    NASA Astrophysics Data System (ADS)

    Zhang, Cheng; Ma, Jianpeng

    2012-05-01

    We present an identity for an unbiased estimate of a general statistical distribution. The identity computes the distribution density from dividing a histogram sum over a local window by a correction factor from a mean-force integral, and the mean force can be evaluated as a configuration average. We show that the optimal window size is roughly the inverse of the local mean-force fluctuation. The new identity offers a more robust and precise estimate than a previous one by Adib and Jarzynski [J. Chem. Phys. 122, 014114 (2005)], 10.1063/1.1829631. It also allows a straightforward generalization to an arbitrary ensemble and a joint distribution of multiple variables. Particularly we derive a mean-force enhanced version of the weighted histogram analysis method. The method can be used to improve distributions computed from molecular simulations. We illustrate the use in computing a potential energy distribution, a volume distribution in a constant-pressure ensemble, a radial distribution function, and a joint distribution of amino acid backbone dihedral angles.

  9. Ecotope-Based Entomological Surveillance and Molecular Xenomonitoring of Multidrug Resistant Malaria Parasites in Anopheles Vectors

    PubMed Central

    2014-01-01

    The emergence and spread of multidrug resistant (MDR) malaria caused by Plasmodium falciparum or Plasmodium vivax have become increasingly important in the Greater Mekong Subregion (GMS). MDR malaria is the heritable and hypermutable property of human malarial parasite populations that can decrease in vitro and in vivo susceptibility to proven antimalarial drugs as they exhibit dose-dependent drug resistance and delayed parasite clearance time in treated patients. MDR malaria risk situations reflect consequences of the national policy and strategy as this influences the ongoing national-level or subnational-level implementation of malaria control strategies in endemic GMS countries. Based on our experience along with current literature review, the design of ecotope-based entomological surveillance (EES) and molecular xenomonitoring of MDR falciparum and vivax malaria parasites in Anopheles vectors is proposed to monitor infection pockets in transmission control areas of forest and forest fringe-related malaria, so as to bridge malaria landscape ecology (ecotope and ecotone) and epidemiology. Malaria ecotope and ecotone are confined to a malaria transmission area geographically associated with the infestation of Anopheles vectors and particular environments to which human activities are related. This enables the EES to encompass mosquito collection and identification, salivary gland DNA extraction, Plasmodium- and species-specific identification, molecular marker-based PCR detection methods for putative drug resistance genes, and data management. The EES establishes strong evidence of Anopheles vectors carrying MDR P. vivax in infection pockets epidemiologically linked with other data obtained during which a course of follow-up treatment of the notified P. vivax patients receiving the first-line treatment was conducted. For regional and global perspectives, the EES would augment the epidemiological surveillance and monitoring of MDR falciparum and vivax malaria

  10. Estimation of Genomic Inbreeding Coefficients Using BovineSNP50 genotypes from U.S. Jersey Cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In dairy cattle, inbreeding coefficients have been estimated from pedigree information; however, recent advances in genotyping technology allow the calculation of inbreeding based on molecular pedigree information. Because strong selection and recurrent inbreeding have decreased genetic variation, ...

  11. Evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Sevenster, M.

    1993-01-01

    The evolution of interstellar molecular hydrogen was studied, with a special interest for the formation and evolution of molecular clouds and star formation within them, by a two-dimensional hydrodynamical simulation performed on a rectangular grid of physical sizes on the order of 100 pc. It is filled with an initial density of approx. 1 cm(exp -3), except for one cell (approx. 1 pc(exp 2)) at the center of the grid where an accretion core of 1-10(exp 3) solar masses is placed. The grid is co-moving with the gridcenter that is on a circular orbit around the Galactic center and that also is the guiding center of epicyclic approximation of orbits of the matter surrounding it. The initial radial velocity is zero; to account for differential rotation the initial tangential velocity (i.e. the movement around the galactic center) is proportional to the radial distance to the grid center. The rate is comparable to the rotation rate at the Local Standard of Rest. The influence of galactic rotation is noticed by spiral or elliptical forms, but on much longer time scales than self gravitation and cooling processes. Density and temperature are kept constant at the boundaries and no inflow is allowed along the tangential boundaries.

  12. The Molecular Atlas Project

    NASA Astrophysics Data System (ADS)

    Silverberg, Jesse; Yin, Peng

    The promise of super-resolution microscopy is a technology to discover new biological mechanisms that occur at smaller length scales then previously observable. However, with higher-resolution, we generally lose the larger spatial context of the image itself. The Molecular Atlas Project (MAP) directly asks how these competing interests between super-resolution imaging and broader spatially contextualized information can be reconciled. MAP enables us to acquire, visualize, explore, and annotate proteomic image data representing 7 orders of magnitude in length ranging from molecular (nm) to tissue (cm) scales. This multi-scale understanding is made possible by combining multiplexed DNA-PAINT, a DNA nanotechnology approach to super-resolution imaging, with ``big-data'' strategies for information management and image visualization. With these innovations combined, MAP enables us to explore cell-specific heterogeneity in ductal carcinoma for every cellin a cm-sized tissue section, analyze organoid growth for advances in high-throughput tissue-on-a-chip technology, and examine individual synapses for connectome mapping over extremely wide areas. Ultimately, MAP is a fundamentally new way to interact with multiscale biophysical data.

  13. Molecular Epidemiology of Amebiasis

    PubMed Central

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis. PMID:18571478

  14. Multiscale reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-12-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

  15. Multiscale reactive molecular dynamics

    PubMed Central

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-01-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062

  16. Towards graphyne molecular electronics.

    PubMed

    Li, Zhihai; Smeu, Manuel; Rives, Arnaud; Maraval, Valérie; Chauvin, Remi; Ratner, Mark A; Borguet, Eric

    2015-01-01

    α-Graphyne, a carbon-expanded version of graphene ('carbo-graphene') that was recently evidenced as an alternative zero-gap semiconductor, remains a theoretical material. Nevertheless, using specific synthesis methods, molecular units of α-graphyne ('carbo-benzene' macrocycles) can be inserted between two anilinyl (4-NH2-C6H4)-anchoring groups that allow these fragments to form molecular junctions between gold electrodes. Here, electrical measurements by the scanning tunnelling microscopy (STM) break junction technique and electron transport calculations are carried out on such a carbo-benzene, providing unprecedented single molecule conductance values: 106 nS through a 1.94-nm N-N distance, essentially 10 times the conductance of a shorter nanographenic hexabenzocoronene analogue. Deleting a C4 edge of the rigid C18 carbo-benzene circuit results in a flexible 'carbo-butadiene' molecule that has a conductance 40 times lower. Furthermore, carbo-benzene junctions exhibit field-effect transistor behaviour when an electrochemical gate potential is applied, opening the way for device applications. All the results are interpreted on the basis of theoretical calculations. PMID:25699991

  17. Towards graphyne molecular electronics

    NASA Astrophysics Data System (ADS)

    Li, Zhihai; Smeu, Manuel; Rives, Arnaud; Maraval, Valérie; Chauvin, Remi; Ratner, Mark A.; Borguet, Eric

    2015-02-01

    α-Graphyne, a carbon-expanded version of graphene (‘carbo-graphene’) that was recently evidenced as an alternative zero-gap semiconductor, remains a theoretical material. Nevertheless, using specific synthesis methods, molecular units of α-graphyne (‘carbo-benzene’ macrocycles) can be inserted between two anilinyl (4-NH2-C6H4)-anchoring groups that allow these fragments to form molecular junctions between gold electrodes. Here, electrical measurements by the scanning tunnelling microscopy (STM) break junction technique and electron transport calculations are carried out on such a carbo-benzene, providing unprecedented single molecule conductance values: 106 nS through a 1.94-nm N-N distance, essentially 10 times the conductance of a shorter nanographenic hexabenzocoronene analogue. Deleting a C4 edge of the rigid C18 carbo-benzene circuit results in a flexible ‘carbo-butadiene’ molecule that has a conductance 40 times lower. Furthermore, carbo-benzene junctions exhibit field-effect transistor behaviour when an electrochemical gate potential is applied, opening the way for device applications. All the results are interpreted on the basis of theoretical calculations.

  18. Molecular Comb Development

    SciTech Connect

    Ferrell, T.L.; Thundat, G.T.; Witkowski, C.E., III

    2007-07-17

    This CRADA was developed to enable ORNL to assist Protein Discovery, Inc. to develop a novel biomolecular separation system based on an ORNL patent application 'Photoelectrochemical Molecular Comb' by Thundat, Ferrell, and Brown. The Molecular Comb concept is based on creating light-induced charge carriers at a semiconductor-liquid interface, which is kept at a potential control such that a depletion layer is formed in the semiconductor. Focusing light from a low-power illumination source creates electron-hole pairs, which get separated in the depletion layer. The light-induced charge carriers reaching the surface attract oppositely charged biomolecules present in the solution. The solution is a buffer solution with very small concentrations of biomolecules. As the focused light is moved across the surface of the semiconductor-liquid interface, the accumulated biomolecules follow the light beam. A thin layer of gel or other similar material on the surface of the semiconductor can act as a sieving medium for separating the biomolecules according to their sizes.

  19. Methods in Molecular Biophysics

    NASA Astrophysics Data System (ADS)

    Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph

    2001-12-01

    Our knowledge of biological macromolecules and their interactions is based on the application of physical methods, ranging from classical thermodynamics to recently developed techniques for the detection and manipulation of single molecules. These methods, which include mass spectrometry, hydrodynamics, microscopy, diffraction and crystallography, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, are complementary; each has its specific advantages and limitations. Organised by method, this textbook provides descriptions and examples of applications for the key physical methods in modern biology. It is an invaluable resource for undergraduate and graduate students of molecular biophysics in science and medical schools, as well as research scientists looking for an introduction to techniques beyond their specialty. As appropriate for this interdisciplinary field, the book includes short asides to explain physics aspects to biologists and biology aspects to physicists. Comprehensive coverage and up-to-date treatment of the latest physical methods in modern biology Each method includes a brief historical introduction, theoretical principles, applications, advantages and limitations, and concludes with a checklist of key ideas Interdisciplinary and accessible to biologists, physicists, and those with medical backgrounds

  20. Photoinduced diffusion molecular transport

    NASA Astrophysics Data System (ADS)

    Rozenbaum, Viktor M.; Dekhtyar, Marina L.; Lin, Sheng Hsien; Trakhtenberg, Leonid I.

    2016-08-01

    We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).

  1. MOLECULAR VACUUM PUMP

    DOEpatents

    Eckberg, E.E.

    1960-09-27

    A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

  2. Molecular basis of vaccination.

    PubMed

    Del Giudice, G; Pizza, M; Rappuoli, R

    1998-02-01

    Vaccines represent the most cost-effective means to prevent infectious diseases. Most of the vaccines which are currently available were developed long before the era of molecular biology and biotechnology. They were obtained following empirical approaches leading to the inactivation or to the attenuation of microorganisms, without any knowledge neither of the mechanisms of pathogenesis of the disease they were expected to protect from, nor of the immune responses elicited by the infectious agents or by the vaccine itself. The past two decades have seen an impressive progress in the field of immunology and molecular biology, which have allowed a better understanding of the interactions occurring between microbes and their hosts. This basic knowledge has represented an impetus towards the generation of better vaccines and the development of new vaccines. In this monograph we briefly summarize some of the most important biotechnological approaches that are currently followed in the development of new vaccines, and provide details on an approach to vaccine development: the genetic detoxification of bacterial toxins. Such an approach has been particularly successful in the rational design of a new vaccine against pertussis, which has been shown to be extremely efficacious and safe. It has been applied to the construction of powerful mucosal adjuvants, for administration of vaccines at mucosal surfaces. PMID:9789264

  3. Estimation of resource and reserves

    NASA Astrophysics Data System (ADS)

    Adelman, M. A.; Houghton, J. C.; Kaufman, G.; Zimmerman, M.

    1982-03-01

    The economics of resource and reserve estimation are analyzed. The economic theory of natural resources and exhaustible resources are discussed. The measurement of already discovered deposits, undiscovered deposits, coal resource and reserve estimation, uranium, and a cumulative cost curve are also discussed.

  4. A method for estimating proportions

    NASA Technical Reports Server (NTRS)

    Guseman, L. F., Jr.; Marion, B. P.

    1975-01-01

    A proportion estimation procedure is presented which requires only on set of ground truth data for determining the error matrix. The error matrix is then used to determine an unbiased estimate. The error matrix is shown to be directly related to the probability of misclassifications, and is more diagonally dominant with the increase in the number of passes used.

  5. Reinforcing flood-risk estimation.

    PubMed

    Reed, Duncan W

    2002-07-15

    Flood-frequency estimation is inherently uncertain. The practitioner applies a combination of gauged data, scientific method and hydrological judgement to derive a flood-frequency curve for a particular site. The resulting estimate can be thought fully satisfactory only if it is broadly consistent with all that is reliably known about the flood-frequency behaviour of the river. The paper takes as its main theme the search for information to strengthen a flood-risk estimate made from peak flows alone. Extra information comes in many forms, including documentary and monumental records of historical floods, and palaeological markers. Meteorological information is also useful, although rainfall rarity is difficult to assess objectively and can be a notoriously unreliable indicator of flood rarity. On highly permeable catchments, groundwater levels present additional data. Other types of information are relevant to judging hydrological similarity when the flood-frequency estimate derives from data pooled across several catchments. After highlighting information sources, the paper explores a second theme: that of consistency in flood-risk estimates. Following publication of the Flood estimation handbook, studies of flood risk are now using digital catchment data. Automated calculation methods allow estimates by standard methods to be mapped basin-wide, revealing anomalies at special sites such as river confluences. Such mapping presents collateral information of a new character. Can this be used to achieve flood-risk estimates that are coherent throughout a river basin? PMID:12804255

  6. Estimating Bottleneck Bandwidth using TCP

    NASA Technical Reports Server (NTRS)

    Allman, Mark

    1998-01-01

    Various issues associated with estimating bottleneck bandwidth using TCP are presented in viewgraph form. Specific topics include: 1) Why TCP is wanted to estimate the bottleneck bandwidth; 2) Setting ssthresh to an appropriate value to reduce loss; 3) Possible packet-pair solutions; and 4) Preliminary results: ACTS and the Internet.

  7. The incredible shrinking covariance estimator

    NASA Astrophysics Data System (ADS)

    Theiler, James

    2012-05-01

    Covariance estimation is a key step in many target detection algorithms. To distinguish target from background requires that the background be well-characterized. This applies to targets ranging from the precisely known chemical signatures of gaseous plumes to the wholly unspecified signals that are sought by anomaly detectors. When the background is modelled by a (global or local) Gaussian or other elliptically contoured distribution (such as Laplacian or multivariate-t), a covariance matrix must be estimated. The standard sample covariance overfits the data, and when the training sample size is small, the target detection performance suffers. Shrinkage addresses the problem of overfitting that inevitably arises when a high-dimensional model is fit from a small dataset. In place of the (overfit) sample covariance matrix, a linear combination of that covariance with a fixed matrix is employed. The fixed matrix might be the identity, the diagonal elements of the sample covariance, or some other underfit estimator. The idea is that the combination of an overfit with an underfit estimator can lead to a well-fit estimator. The coefficient that does this combining, called the shrinkage parameter, is generally estimated by some kind of cross-validation approach, but direct cross-validation can be computationally expensive. This paper extends an approach suggested by Hoffbeck and Landgrebe, and presents efficient approximations of the leave-one-out cross-validation (LOOC) estimate of the shrinkage parameter used in estimating the covariance matrix from a limited sample of data.

  8. Quantity Estimation Of The Interactions

    SciTech Connect

    Gorana, Agim; Malkaj, Partizan; Muda, Valbona

    2007-04-23

    In this paper we present some considerations about quantity estimations, regarding the range of interaction and the conservations laws in various types of interactions. Our estimations are done under classical and quantum point of view and have to do with the interaction's carriers, the radius, the influence range and the intensity of interactions.

  9. PBXN-110 Burn Rate Estimate

    SciTech Connect

    Glascoe, E

    2008-08-11

    It is estimated that PBXN-110 will burn laminarly with a burn function of B = (0.6-1.3)*P{sup 1.0} (B is the burn rate in mm/s and P is pressure in MPa). This paper provides a brief discussion of how this burn behavior was estimated.

  10. Estimating the Polyserial Correlation Coefficient.

    ERIC Educational Resources Information Center

    Bedrick, Edward J.; Breslin, Frederick C.

    1996-01-01

    Simple noniterative estimators of the polyserial correlation coefficient are developed by exploiting a general relationship between the polyserial correlation and the point polyserial correlation to give extensions of the biserial estimators of K. Pearson (1909), H. E. Brogden (1949), and F. M. Lord (1963) to the multicategory setting. (SLD)

  11. Computer-Aided Reliability Estimation

    NASA Technical Reports Server (NTRS)

    Bavuso, S. J.; Stiffler, J. J.; Bryant, L. A.; Petersen, P. L.

    1986-01-01

    CARE III (Computer-Aided Reliability Estimation, Third Generation) helps estimate reliability of complex, redundant, fault-tolerant systems. Program specifically designed for evaluation of fault-tolerant avionics systems. However, CARE III general enough for use in evaluation of other systems as well.

  12. Correlation filters for orientation estimation

    NASA Technical Reports Server (NTRS)

    Kumar, B. V. K. Vijaya; Lee, Andrew J.; Connelly, James M.

    1988-01-01

    An important task in many vision applications is that of rapidly estimating the orientation of an object with respect to some frame of reference. Because of their speed and parallel processing capabilities, optical correlators should prove valuable in this application. This paper considers two algorithms for object orientation estimation based on optical correlations and presents some initial simulation results.

  13. Kalman estimation for SEDS measurements

    NASA Technical Reports Server (NTRS)

    Carrington, Connie K.

    1989-01-01

    The first on-orbit experiment of the Small Expendable Deployer System (SEDS) for tethered satellites will collect telemetry data for tethered length, rate of deployment, and tether tension. The post-flight analysis will use this data to reconstruct the deployment history and determine payload position and tether shape. Two Kalman estimator algorithms were written, and output using simulated measurement data was compared. Both estimators exhibited the same estimated state histories, indicating that numerical instability in the traditional algorithm was not the cause of filter divergence. Estimation of acceleration biases was added, which reduced the error but did not correct the divergence. An add-a-bead estimator that adds lumped masses as the tether is deployed was written, which provides a state model that matches the BEADSIM simulation providing the true measurements and states. This twenty-one bead estimator produced state histories similar to those of the two-bead estimator, indicating that the filter divergence was not caused by a reduced-order model. The noise models used to date are relatively simple and may be the source of estimator divergence. The investigation of colored noise models, cross-correlated measurement and process covariances, and noise-adaptive filter techniques is recommended.

  14. Robust and intelligent bearing estimation

    SciTech Connect

    Claassen, J.P.

    1998-07-01

    As the monitoring thresholds of global and regional networks are lowered, bearing estimates become more important to the processes which associate (sparse) detections and which locate events. Current methods of estimating bearings from observations by 3-component stations and arrays lack both accuracy and precision. Methods are required which will develop all the precision inherently available in the arrival, determine the measurability of the arrival, provide better estimates of the bias induced by the medium, permit estimates at lower SNRs, and provide physical insight into the effects of the medium on the estimates. Initial efforts have focused on 3-component stations since the precision is poorest there. An intelligent estimation process for 3-component stations has been developed and explored. The method, called SEE for Search, Estimate, and Evaluation, adaptively exploits all the inherent information in the arrival at every step of the process to achieve optimal results. In particular, the approach uses a consistent and robust mathematical framework to define the optimal time-frequency windows on which to make estimates, to make the bearing estimates themselves, and to withdraw metrics helpful in choosing the best estimate(s) or admitting that the bearing is immeasurable. The approach is conceptually superior to current methods, particular those which rely on real values signals. The method has been evaluated to a considerable extent in a seismically active region and has demonstrated remarkable utility by providing not only the best estimates possible but also insight into the physical processes affecting the estimates. It has been shown, for example, that the best frequency at which to make an estimate seldom corresponds to the frequency having the best detection SNR and sometimes the best time interval is not at the onset of the signal. The method is capable of measuring bearing dispersion, thereby withdrawing the bearing bias as a function of frequency

  15. Dense Molecular Gas in Centaurus A

    NASA Astrophysics Data System (ADS)

    Wild, Wolfgang; Eckart, Andreas

    1999-10-01

    Centaurus A (NGC 5128) is the closest radio galaxy, and its molecular interstellar medium has been studied extensively in recent years. However, these studies used mostly molecular lines tracing low to medium density gas (see e.g. Eckart et al. 1990. Wild et al. 1997). The amount and distribution of the dense component remained largely unknown. We present spectra of the HCN(1-0) emission - which traces dense (n(H2) > 104 cm-3) molecular gas - at the center and along the prominent dust lane at offset positions +/- 60" and +/- 100", as well as single CS(2-1) and CS(3-2) spectra, observed with the SEST on La Silla, Chile. At the central position, the integrated intensity ratio I(HCN)/I(CO) peaks at 0.064, and decreases to somewhat equal to 0.02 to 0.04 in the dust lane. Based on the line luminosity ratio L(HCN)/L(CO) we estimate that there is a significant amount of dense gas in Centaurus A. The fraction of dense molecular gas as well as the star formation efficiency LFIR/LCO towards the center of Cen A is comparable to ultra-luminous infrared galaxies, and falls in between the values for ULIRGs and normal galaxies for positions in the dust lane. Details will be published in Wild & Eckart (A&A, in prep.). Eckart et al. 1990, ApJ 363, 451 Rydbeck et al. 1993, Astr.Ap. (Letters) 270, L13. Wild, W., Eckart, A. & Wiklind, T. 1997, Astr.Ap. 322, 419.

  16. Coverage-adjusted entropy estimation.

    PubMed

    Vu, Vincent Q; Yu, Bin; Kass, Robert E

    2007-09-20

    Data on 'neural coding' have frequently been analyzed using information-theoretic measures. These formulations involve the fundamental and generally difficult statistical problem of estimating entropy. We review briefly several methods that have been advanced to estimate entropy and highlight a method, the coverage-adjusted entropy estimator (CAE), due to Chao and Shen that appeared recently in the environmental statistics literature. This method begins with the elementary Horvitz-Thompson estimator, developed for sampling from a finite population, and adjusts for the potential new species that have not yet been observed in the sample-these become the new patterns or 'words' in a spike train that have not yet been observed. The adjustment is due to I. J. Good, and is called the Good-Turing coverage estimate. We provide a new empirical regularization derivation of the coverage-adjusted probability estimator, which shrinks the maximum likelihood estimate. We prove that the CAE is consistent and first-order optimal, with rate O(P)(1/log n), in the class of distributions with finite entropy variance and that, within the class of distributions with finite qth moment of the log-likelihood, the Good-Turing coverage estimate and the total probability of unobserved words converge at rate O(P)(1/(log n)(q)). We then provide a simulation study of the estimator with standard distributions and examples from neuronal data, where observations are dependent. The results show that, with a minor modification, the CAE performs much better than the MLE and is better than the best upper bound estimator, due to Paninski, when the number of possible words m is unknown or infinite. PMID:17567838

  17. Space shuttle propulsion parameter estimation using optimal estimation techniques

    NASA Technical Reports Server (NTRS)

    1983-01-01

    The first twelve system state variables are presented with the necessary mathematical developments for incorporating them into the filter/smoother algorithm. Other state variables, i.e., aerodynamic coefficients can be easily incorporated into the estimation algorithm, representing uncertain parameters, but for initial checkout purposes are treated as known quantities. An approach for incorporating the NASA propulsion predictive model results into the optimal estimation algorithm was identified. This approach utilizes numerical derivatives and nominal predictions within the algorithm with global iterations of the algorithm. The iterative process is terminated when the quality of the estimates provided no longer significantly improves.

  18. RHEOLOGICAL PROPERTIES & MOLECULAR WEIGHT DISTRIBUTIONS OF FOUR PERFLUORINATED THERMOPLASTIC POLYMERS

    SciTech Connect

    Hoffman, D M; Shields, A L

    2009-02-24

    Dynamic viscosity measurements and molecular weight estimates have been made on four commercial, amorphous fluoropolymers with glass transitions (Tg) above 100 C: Teflon AF 1600, Hyflon AD 60, Cytop A and Cytop M. These polymers are of interest as binders for the insensitive high explosive 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) because of their high density and Tg above ambient, but within a suitable processing range of TATB. As part of this effort, the rheological properties and molecular weight distributions of these polymers were evaluated.

  19. Diffusion on (110) Surface of Molecular Crystal Pentaerythritol Tetranitrate

    SciTech Connect

    Wang, J; Golfinopoulos, T; Gee, R H; Huang, H

    2007-01-25

    Using classical molecular dynamics simulations, we investigate the diffusion mechanisms of admolecules on the (110) surface of molecular crystal pentaerythritol tetranitrate. Our results show that (1) admolecules are stable at off lattice sites, (2) admolecules diffuse along close-packed [1{bar 1}1] and [{bar 1}11] directions, and (3) admolecules detach from the surface at 350K and above. Based on the number of diffusion jumps as a function of temperature, we estimate the jump frequency to be v=1.14 x 10{sup 12} e{sup -0.08eV/kT} per second.

  20. W3 North: Far-infrared and radio molecular observations

    NASA Technical Reports Server (NTRS)

    Thronson, H. A., Jr.; Schwartz, P. R.; Smith, H. A.; Lada, C. J.; Glaccum, W.; Harper, D. A.

    1984-01-01

    The W3 North (G133.8 + 1.4) source is the northernmost member of a string of active star forming regions that marks the western boundary of the giant HII region W4. Far infrared and radio observations of molecular CO were made of the W3 star forming region. The W3 North object shows extended dust and gas emission which suggests a fairly advanced disruption of a molecular cloud. An estimate of the age of the embedded HII region is given, and emission maps of the W3 object are presented. The W3 North source may be the oldest object among the W3 complex of sources.