Viewpoints: A high-performance high-dimensional exploratory data analysis tool

Scientific data sets continue to increase in both size and complexity. In the past, dedicated graphics systems at supercomputing centers were required to visualize large data sets, but as the price of commodity graphics hardware has dropped and its capability has increased, it is now possible, in principle, to view large complex data sets on a single workstation. To do this in practice, an investigator will need software that is written to take advantage of the relevant graphics hardware. The Viewpoints visualization package described herein is an example of such software. Viewpoints is an interactive tool for exploratory visual analysis of large, high-dimensional (multivariate) data. It leverages the capabilities of modern graphics boards (GPUs) to run on a single workstation or laptop. Viewpoints is minimalist: it attempts to do a small set of useful things very well (or at least very quickly) in comparison with similar packages today. Its basic feature set includes linked scatter plots with brushing, dynamic histograms, normalization and outlier detection/removal. Viewpoints was originally designed for astrophysicists, but it has since been used in a variety of fields that range from astronomy, quantum chemistry, fluid dynamics, machine learning, bioinformatics, and finance to information technology server log mining. In this article, we describe the Viewpoints package and show examples of its usage.Comment: 18 pages, 3 figures, PASP in press, this version corresponds more closely to that to be publishe

Can Self-Organizing Maps accurately predict photometric redshifts?

We present an unsupervised machine learning approach that can be employed for estimating photometric redshifts. The proposed method is based on a vector quantization approach called Self--Organizing Mapping (SOM). A variety of photometrically derived input values were utilized from the Sloan Digital Sky Survey's Main Galaxy Sample, Luminous Red Galaxy, and Quasar samples along with the PHAT0 data set from the PHoto-z Accuracy Testing project. Regression results obtained with this new approach were evaluated in terms of root mean square error (RMSE) to estimate the accuracy of the photometric redshift estimates. The results demonstrate competitive RMSE and outlier percentages when compared with several other popular approaches such as Artificial Neural Networks and Gaussian Process Regression. SOM RMSE--results (using $\Delta$z=z$_{phot}$--z$_{spec}$) for the Main Galaxy Sample are 0.023, for the Luminous Red Galaxy sample 0.027, Quasars are 0.418, and PHAT0 synthetic data are 0.022. The results demonstrate that there are non--unique solutions for estimating SOM RMSEs. Further research is needed in order to find more robust estimation techniques using SOMs, but the results herein are a positive indication of their capabilities when compared with other well-known methods.Comment: 5 pages, 3 figures, submitted to PAS

Stabilization of LFT systems

The problem of parametrizing all stabilizing controllers for general linear fractional transformation (LFT) systems is studied. The LFT systems can be variously interpreted as multidimensional systems or uncertain systems, and the controller is allowed to have the same dependence on the frequency/uncertainty structure as the plant. For multidimensional systems, this means that the controller is allowed dynamic feedback, while the uncertain system case can be given a gain scheduling interpretation. Both mu and Q stability are considered, although the latter is emphasized. In both cases, the output feedback problem is reduced by a separation argument to two simpler problems, involving the dual problems of full information and full control. For Q stability, these problems can be characterized completely in terms of linear matrix inequalities. In the standard 1D system case with no uncertainty, the results in the present work reduce to the standard parametrization of D.C. Youla, H.A. Jabr and J.J. Bongiorno (1976), although the development appears to be much simpler, and does not require coprime factorizations

Ocular Phenotype Associated with DYRK1A Variants

Dual-specificity tyrosine phosphorylation-regulated kinase 1A or DYRK1A, contributes to central nervous system development in a dose-sensitive manner. Triallelic DYRK1A is implicated in the neuropathology of Down syndrome, whereas haploinsufficiency causes the rare DYRK1A-related intellectual disability syndrome (also known as mental retardation 7). It is characterised by intellectual disability, autism spectrum disorder and microcephaly with a typical facial gestalt. Preclinical studies elucidate a role for DYRK1A in eye development and case studies have reported associated ocular pathology. In this study families of the DYRK1A Syndrome International Association were asked to self-report any co-existing ocular abnormalities. Twenty-six patients responded but only 14 had molecular confirmation of a DYRK1A pathogenic variant. A further nineteen patients from the UK Genomics England 100,000 Genomes Project were identified and combined with 112 patients reported in the literature for further analysis. Ninety out of 145 patients (62.1%) with heterozygous DYRK1A variants revealed ocular features, these ranged from optic nerve hypoplasia (13%, 12/90), refractive error (35.6%, 32/90) and strabismus (21.1%, 19/90). Patients with DYRK1A variants should be referred to ophthalmology as part of their management care pathway to prevent amblyopia in children and reduce visual comorbidity, which may further impact on learning, behaviour, and quality of life

Brief Note: Growth of Pisidium Casertanum (Poli) in West Central Ohio

Author Institution: Department of Biology, University of Dayto

Life Cycle of a Torrenticolous Hawaiian Chironomid (Telmatogeton Torrenticola): Stream Flow and Microhabitat Effects

In this study we documented the instar densities and life cycle of Telmatogeton torrenticola Terry (Chironomidae : Telmatogetoninae) from Kinihapai Stream, Maui, Hawaii. Greatest larval densities of this midge are found on substrates of high velocity, shallow flows of cascades, and splash zones of waterfalls, with lower densities in riffles. In the summer of 1994 we compared the effects of two microhabitats (termed optimal and suboptimal) on inter-instar density and relative abundance. In a second year (1995), we evaluated the effect of long-term reduced stream flow on these variables only in optimal microhabitats. A significant reduction in stream flow from 1994 to 1995 was correlated with a similar reduction in larval densities that precluded larval colonization of suboptimal habitats in 1995, thereby preventing sampling in this microhabitat during that summer. Depth of optimal habitats of 1995 were significantly shallower than both habitats of 1994, with suboptimal habitats of 1994 the deepest. Total larval density was significantly higher in 1994 optimal habitats, while 1994 suboptimal and 1995 optimal habitats were statistically similar. Individual instar densities showed variable differences among habitats and years, with the first three instars always highest in 1994 optimal habitats. All instars and pupae were collected on most sampling dates in both years ; however, pupae were only collected on a two dates in suboptimal habitats of 1994. Based on larval size frequency histograms, T. torrenticola has a multivoltine, asynchronous life cycle, with continuous reproduction, which is variable among microhabitats characterized by different flow velocity and depth, and between years of differing stream discharge. Reduced stream flow during the summer of 1995 had effects of reducing densities and changing life cycle features similar to those found in 1994 (a year of higher stream flow) suboptimal habitats

X-ray Over-Luminous Elliptical Galaxies: A New Class of Mass Concentrations in the Universe?

We detect four isolated, X-ray over-luminous (Lx>2e43 [h/0.5]**-2 erg/s) elliptical galaxies (OLEGs) in our 160 square degree ROSAT PSPC survey. The extent of their X-ray emission, total X-ray luminosity, total mass, and mass of the hot gas in these systems correspond to poor clusters, and the optical luminosity of the central galaxies (M_R<-22.5 + 5 lg h) is comparable to that of cluster cDs. However, there are no detectable fainter galaxy concentrations around the central elliptical. The mass-to-light ratio within the radius of detectable X-ray emission is in the range 250-450 Msun/Lsun, which is 2-3 times higher than typically found in clusters or groups. These objects can be the result of galaxy merging within a group. However, their high M/L values are difficult to explain in this scenario. OLEGs must have been undisturbed for a very long time, which makes them the ultimate examples of systmes in hydrostatic equilibrium. The number density of OLEGs is n=2.4(+3.1-1.2}x10**-7 (h/0.5)**-3 Mpc**-3 at the 90% confidence. They comprise 20% of all clusters and groups of comparable X-ray luminosity, and nearly all galaxies brighter than M_R=-22.5. The estimated contirubution of OLEGs to the total mass density in the Universe is close to that of T>7 keV clusters.Comment: 4 pages, 2 figures, uses emulateapj.sty, submitted to ApJ Letter

Development and preliminary testing of the psychosocial adjustment to hereditary diseases scale

Background: The presence of Lynch syndrome (LS) can bring a lifetime of uncertainty to an entire family as members adjust to living with a high lifetime cancer risk. The research base on how individuals and families adjust to genetic-linked diseases following predictive genetic testing has increased our understanding of short-term impacts but gaps continue to exist in knowledge of important factors that facilitate or impede long-term adjustment. The failure of existing scales to detect psychosocial adjustment challenges in this population has led researchers to question the adequate sensitivity of these instruments. Furthermore, we have limited insight into the role of the family in promoting adjustment. Methods: The purpose of this study was to develop and initially validate the Psychosocial Adjustment to Hereditary Diseases (PAHD) scale. This scale consists of two subscales, the Burden of Knowing (BK) and Family Connectedness (FC). Items for the two subscales were generated from a qualitative data base and tested in a sample of 243 participants from families with LS. Results: The Multitrait/Multi-Item Analysis Program-Revised (MAP-R) was used to evaluate the psychometric properties of the PAHD. The findings support the convergent and discriminant validity of the subscales. Construct validity was confirmed by factor analysis and Cronbach’s alpha supported a strong internal consistency for BK (0.83) and FC (0.84). Conclusion: Preliminary testing suggests that the PAHD is a psychometrically sound scale capable of assessing psychosocial adjustment. We conclude that the PAHD may be a valuable monitoring tool to identify individuals and families who may require therapeutic interventions

Insulation of a synthetic hydrogen metabolism circuit in bacteria

<p>Abstract</p> <p>Background</p> <p>The engineering of metabolism holds tremendous promise for the production of desirable metabolites, particularly alternative fuels and other highly reduced molecules. Engineering approaches must redirect the transfer of chemical reducing equivalents, preventing these electrons from being lost to general cellular metabolism. This is especially the case for high energy electrons stored in iron-sulfur clusters within proteins, which are readily transferred when two such clusters are brought in close proximity. Iron sulfur proteins therefore require mechanisms to ensure interaction between proper partners, analogous to many signal transduction proteins. While there has been progress in the isolation of engineered metabolic pathways in recent years, the design of insulated electron metabolism circuits <it>in vivo </it>has not been pursued.</p> <p>Results</p> <p>Here we show that a synthetic hydrogen-producing electron transfer circuit in <it>Escherichia coli </it>can be insulated from existing cellular metabolism via multiple approaches, in many cases improving the function of the pathway. Our circuit is composed of heterologously expressed [Fe-Fe]-hydrogenase, ferredoxin, and pyruvate-ferredoxin oxidoreductase (PFOR), allowing the production of hydrogen gas to be coupled to the breakdown of glucose. We show that this synthetic pathway can be insulated through the deletion of competing reactions, rational engineering of protein interaction surfaces, direct protein fusion of interacting partners, and co-localization of pathway components on heterologous protein scaffolds.</p> <p>Conclusions</p> <p>Through the construction and characterization of a synthetic metabolic circuit <it>in vivo</it>, we demonstrate a novel system that allows for predictable engineering of an insulated electron transfer pathway. The development of this system demonstrates working principles for the optimization of engineered pathways for alternative energy production, as well as for understanding how electron transfer between proteins is controlled.</p