An intelligent position-specific training system for mission operations

Marshall Space Flight Center's (MSFC's) payload ground controller training program provides very good generic training; however, ground controller position-specific training can be improved by including position-specific training systems in the training program. This report explains why MSFC needs to improve payload ground controller position-specific training. The report describes a generic syllabus for position-specific training systems, a range of system designs for position-specific training systems, and a generic development process for developing position-specific training systems. The report also describes a position-specific training system prototype that was developed for the crew interface coordinator payload operations control center ground controller position. The report concludes that MSFC can improve the payload ground controller training program by incorporating position-specific training systems for each ground controller position; however, MSFC should not develop position-specific training systems unless payload ground controller position experts will be available to participate in the development process

Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSIC

Position-Specific Hydrogen Isotope Equilibrium in Propane

Intramolecular isotope distributions can constrain source attribution, mechanisms of formation and destruction, and temperature-time histories of molecules. In this study, we explore the D/H fractionation between central (-CH_2-) and terminal (-CH_3) positions of propane (C_3H_8)- a percent level component of natural gases. The temperature dependenceof position-specific D/H fractionation of propane could potentially work as a geo-thermometer for natural gas systems, and a forensic identifier of specific thermogenic sources of atmospheric or aquatic emissions. Moreover, kinetically controlled departures from temperature dependent equilibrium might constrain mechanisms of thermogenic production, or provide indicators of biological or photochemical destruction. We developed a method to measure position-specific D/H differences of propane with high-resolution gas source mass spectrometry. We performed laboratory exchange experiments to study the exchange ratesfor both terminal and central positions, and used catalysts to drive the hydrogen isotopedistribution of propane to thermodynamic equilibrium. Experimental results demonstrate that D/H exchange between propane and water happens easily in the presence of either Pd catalyst or Ni catalyst. Exchange rates are similar between the two positions catalyzed by Pd. However, the central position exchanges 2.2 times faster than the terminal position in the presence of Ni catalyst. At 200 °C in the presence of Pd catalyst, the e-folding time of propane-water exchange is 20 days and of homogeneous exchange (i.e., equilibrium between central and terminal positions) is 28 min. An equilibrated (bracketed and time-invariant) intramolecular hydrogen isotope distribution was attained for propane at three temperatures, 30 °C, 100 °C and 200 °C; these data serve as an initial experimental calibration of a new position-specific thermometer with a temperature sensitivity of 0.25‰ per °C at 100 °C. We use this calibration to test the validity of prior published theoretical predictions. Comparison of data with models suggest the most sophisticated of these discrepant models (Webb and Miller, 2014) is most accurate; this conclusion implies that there is a combined experimental and theoretical foundation for an ‘absolute reference frame’ for position-specific H isotope analysis of propane, following principles previously used for clumped isotope analysis of CO_2, CH_4 and O_2 (Eiler and Schauble, 2004; Yeung et al., 2014; Stolper et al., 2014)

Position-specific induction of ectopic limbs in non-regenerating blastemas on axolotl forelimbs.

Ectopic retinoic acid (RA) has been hypothesized to reprogram the positional identity of cells in developing and regenerating limbs to a single positional value corresponding to the posterior-ventral-proximal (PVPr) position on the limb. We tested this hypothesis by using RA to reprogram the information of blastema cells that were induced to form at different positions around the limb circumference. We observed that RA treatment of blastemas in anterior and dorsal locations, but not posterior and ventral locations, resulted in the induction of complete ectopic limbs. These position-specific differences in limb induction are probably due to differences in the positional disparity between the RA-reprogrammed blastema cells and the cells at the periphery of the wound. These observations are consistent with the hypothesis that RA treatment reprograms the information in blastema cells to the PVPr position on the limb, since anterior and dorsal positions have the largest disparity and posterior and ventral have the smallest disparity from the PVPr identity

Development of an advanced on-line position-specific stable carbon isotope system and application to methyl tert-butyl ether

We present an advanced system for on-line position-specific carbon isotope analysis. The main limitation of on-line intramolecular isotope ratio measurements has been that optimal pyrolytic fragments are obtained mostly at temperatures where the analyte has not completely reacted. As a result of undetermined isotopic fractionation, the isotopic signatures of the pyrolysis products are not strictly equal to these of the equivalent moieties in the parent molecule. We designed a pyrolytic unit in which both temperature and reaction time are variable parameters, enabling determination of the enrichment factor of the pyrolysis at optimal temperature by construction of a Rayleigh plot. In the case of methyl tert-butyl ether (MTBE) presented here, a 'pre-pyrolysis' fractionation of MTBE leading to a depletion of 0.9 parts per thousand was discovered and the enrichment factor of the optimal pyrolysis reaction was determined at -1.7 parts per thousand. Absolute delta C-13 values of two functional groups of MTBE - the methoxy group and the 2-methylpropane group - could be determined with 95% confidence intervals of 0.4 parts per thousand and 0.5 parts per thousand, respectively

Causality in Dense Matter

The possibility of non-causal signal propagation is examined for various theories of dense matter. This investigation requires a discussion of definitions of causality, together with interpretations of spacetime position. Specific examples are used to illustrate the satisfaction or violation of causality in realistic calculations.Comment: 24 pages; 1 PostScript figure; uses revte

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Genome position specific priors for genomic prediction

<p>Abstract</p> <p>Background</p> <p>The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed.</p> <p>Results</p> <p>Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P<0.05) using the Hotelling Williams t-test for protein- and fat yield.</p> <p>Conclusion</p> <p>For some traits the method might be advantageous compared to pooling of reference data for distantly related populations, but further investigation is needed to confirm the results. For closely related populations the method does not perform better than pooling reference data. However, it does give an increased accuracy compared to analysis based on only one reference population, without an increased computational burden. The approach described here provides a general setup for inclusion of location specific priors: the approach could be used to include biological information in genomic predictions.</p

Positive emotion broadens attention focus through decreased position-specific spatial encoding in early visual cortex: evidence from ERPs

Recent evidence has suggested that not only stimulus-specific attributes or top-down expectations can modulate attention selection processes, but also the actual mood state of the participant. In this study, we tested the prediction that the induction of positive mood can dynamically influence attention allocation and, in turn, modulate early stimulus sensory processing in primary visual cortex (V1). High-density visual event-related potentials (ERPs) were recorded while participants performed a demanding task at fixation and were presented with peripheral irrelevant visual textures, whose position was systematically varied in the upper visual field (close, medium, or far relative to fixation). Either a neutral or a positive mood was reliably induced and maintained throughout the experimental session. The ERP results showed that the earliest retinotopic component following stimulus onset (C1) strongly varied in topography as a function of the position of the peripheral distractor, in agreement with a near-far spatial gradient. However, this effect was altered for participants in a positive relative to a neutral mood. On the contrary, positive mood did not modulate attention allocation for the central (task-relevant) stimuli, as reflected by the P300 component. We ran a control behavioral experiment confirming that positive emotion selectively impaired attention allocation to the peripheral distractors. These results suggest a mood-dependent tuning of position-specific encoding in V1 rapidly following stimulus onset. We discuss these results against the dominant broaden-and-build theory