Variation of Molecular Line Ratios and Cloud Properties in the Arp 299 Galaxy Merger

High resolution observations of 12CO (2.''3), 13CO (3.''9), and HCN (5.''4) J=1--0 in the galaxy merger Arp 299 (IC 694 and NGC 3690) show the line ratios vary dramatically across the system. The 12CO/13CO ratio is unusually large, 60 +- 15, at the IC 694 nucleus, where 12CO emission is very strong, and much smaller, 10 +- 3, in the southern extended disk of that galaxy. Elsewhere, the 12CO/13CO line ratio is 5-20, typical of spiral galaxies. The line ratio variation in the overlap between the two galaxies is smaller, ranging from 10 +- 3 in the east to 20 +- 4 in the west. The 12CO/HCN line ratio also varies across Arp 299, although to a lesser degree. HCN emission is bright towards each galaxy nucleus and in the extranuclear region of active star formation; it was not detected in the IC 694 disk, or the eastern part of the overlap region, leading to lower limits of 25 and 20 respectively. By contrast, at the nuclei of IC 694 and NGC 3690 the ratios are 9 +- 1 and 14 +- 3 respectively. In the western part of the overlap region it is 11 +- 3.Comment: 16 pages, 4 postscript figures, to appear in ApJ Letter

Rapid DNA extraction from Neurospora crassa.

A rapid method for DNA extraction is described

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn \alpha-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical Review Letter

Geometric deep learning

The goal of these course notes is to describe the main mathematical ideas behind geometric deep learning and to provide implementation details for several applications in shape analysis and synthesis, computer vision and computer graphics. The text in the course materials is primarily based on previously published work. With these notes we gather and provide a clear picture of the key concepts and techniques that fall under the umbrella of geometric deep learning, and illustrate the applications they enable. We also aim to provide practical implementation details for the methods presented in these works, as well as suggest further readings and extensions of these ideas

Assessing the coherence in biological and environmental drivers of young sea bass abundance across important estuarine nursery areas of the northern European sea bass stock

Year class strength is an important determinant of fish population size, but the drivers are often unknown. The northern stock of European sea bass (Dicentrarchus labrax) is an important target species for both commercial and recreational fisheries. Scientific assessments showed a rapid decline in spawning stock biomass from 2010-18 attributed to a combination of fishing mortality and poor year class strength. Recruitment to the adult stock is linked to the abundance and temporal dynamics of young bass in estuarine nursery areas, but little is known about the relative importance of environmental and biological drivers on the survival of these young life stages. In this study, we use Generalised Linear Models to attempt to identify important local environmental (sea surface temperature and river flow) and biological (chlorophyll-a concentration and predator abundance) drivers of young sea bass abundance. We focus on seven British and Irish estuarine areas that are important to the northern stock of European sea bass. In four English estuarine areas there were good model fits to the abundance of young sea bass, but predictors differed amongst these suggesting that drivers of abundance may differ among individual nursery areas. This was further demonstrated by poor fits of models generated for English estuaries to interannual patterns of abundance in the Irish nursery areas tested. The differences found in the most important abundance drivers amongst areas highlight the complex and differing dynamics between estuaries. If the number of young bass that eventually join the adult stock is dependent on survivors from a diverse set of unique nursery area conditions, then endeavours to incorporate this knowledge into fisheries management should be further explored

The Single-Particle Structure of Neutron-Rich Nuclei of Astrophysical Interest at the Ornl Hribf

The rapid nuetron-capture process (r process) produces roughly half of the elements heavier than iron. The path and abundances produced are uncertain, however, because of the lack of nuclear strucure information on important neutron-rich nuclei. We are studying nuclei on or near the r-process path via single-nucleon transfer reactions on neutron-rich radioactive beams at ORNL's Holifield Radioactive Ion Beam Facility (HRIBF). Owing to the difficulties in studying these reactions in inverse kinematics, a variety of experimental approaches are being developed. We present the experimental methods and initial results.Comment: Proceedings of the Third International Conference on Fission and Properties of Neutron-Rich Nucle

"Just old age" - a qualitative investigation of owner and veterinary professional experiences of and attitudes to ageing in dogs in the UK.

ObjectivesMany UK dogs live into old age, but owners may not recognise or report age-associated signs of disease which lead to negative welfare. This study investigated dog owner and veterinary professional experiences and attitudes towards ageing in dogs, how health care is offered, barriers to its delivery, and some best-practice solutions.Materials and methodsIn-depth semi-structured interviews were conducted with 15 owners of 21 dogs (aged 8 to 17 years mean: 13) and 11 veterinary professional (eight veterinary surgeons, two nurses and one physiotherapist). Open-text responses from 61 dog owner were collected using an online survey. Transcripts and survey responses were inductively coded into themes.ResultsFour themes were constructed: "just old age", barriers to care, trust in veterinary surgeons, and tools to improve health care. Age-related changes were mostly perceived as "just old age" by dog owner. Many dogs were no longer vaccinated and did not attend check-ups unless owners identified a problem. The greatest barriers to health care were finances (dog owner), owner awareness, willingness to act and consultation time (veterinary professional). Trust in veterinary professional was more likely when dog owner experienced continuity, prioritisation of care, clear communication and an accessible, knowledgeable and empathic veterinary professional. Participants suggested that senior health care and communication between dog owner and veterinary professional could be improved through questionnaires, and evidence-based online information.Clinical significanceOpportunities to educate owners on which clinical signs represent healthy or pathological ageing are being missed. Resources should be developed to guide on best-practice discussions in consultations, encourage more owners to recognise clinical signs and to seek and trust veterinary advice

Discovering the New Standard Model: Fundamental Symmetries and Neutrinos

This White Paper describes recent progress and future opportunities in the area of fundamental symmetries and neutrinos.Comment: Report of the Fundamental Symmetries and Neutrinos Workshop, August 10-11, 2012, Chicago, I

Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information