Scalable Similarity Search for Molecular Descriptors

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solutions for more general integer vectors are in their infancy. In this paper we present a time- and space- efficient index for the problem that we call the succinct intervals-splitting tree algorithm for molecular descriptors (SITAd). Our approach extends efficient methods for binary-vector databases, and uses ideas from succinct data structures. Our experiments, on a large database of over 40 million compounds, show SITAd significantly outperforms alternative approaches in practice.Comment: To be appeared in the Proceedings of SISAP'1

Signatures of pulsars in the light curves of newly formed supernova remnants

We explore the effect of pulsars, in particular those born with millisecond periods, on their surrounding supernova ejectas. While they spin down, fast-spinning pulsars release their tremendous rotational energy in the form of a relativistic magnetized wind that can affect the dynamics and luminosity of the supernova. We estimate the thermal and non-thermal radiations expected from these specific objects, concentrating at times a few years after the onset of the explosion. We find that the bolometric light curves present a high luminosity plateau (that can reach 10^(43)–10^(44) erg s^(−1)) over a few years. An equally bright TeV gamma-ray emission, and a milder X-ray peak (of the order of 10^(40)–10^(42) erg s^(−1)) could also appear a few months to a few years after the explosion, as the pulsar wind nebula emerges, depending on the injection parameters. The observations of these signatures by following the emission of a large number of supernovae could have important implications for the understanding of core-collapse supernovae and reveal the nature of the remnant compact object

Stress, coping and job satisfaction in UK academics during the COVID-19 pandemic

Objectives. The occurrence of work-related stress is high among UK academics. This is associated with increased risk of ill-health, reduced productivity, and lower job satisfaction. These might have been exacerbated by the coronavirus disease (COVID-19) pandemic. Social support and coping strategies have the potential to ameliorate the impact of stress but have been less explored in academics; these were explored in a cross-sectional study. Methods. Fifty academic staff were recruited via links posted on social media and through snowballing sample technique. The survey included key demographics such as age, gender, relationship status, educational attainment, known to have relationship with work-related stress. Other measures include perceived stress, social support, coping strategies and job satisfaction. Results. Moderate stress was found in UK academics. Greater impact of COVID-19 and greater use of avoidance coping were significant predictors of higher stress. Conclusion. Encouraging the use of adaptive coping strategies such as problem solving, through staff training could help to reduce stress. Future longitudinal research should examine stress and coping in academics, establishing causation, while accounting for confounders such as contract type, teaching hours, and class sizes. Stress-management interventions should account for pandemic-related stressors including high workload and isolation, as academics continue to engage in hybrid/remote working. Implication. It is important that universities put in place support systems to reduce the level of stress in academics. This could be through training and education in the use of adaptive coping strategies, such as planning and problem solving as well as support from co-workers and management; which are associated with positive psychological wellbeing

Kinetics of the DNA polymerase \u3ci\u3epyrococcus kodakaraensis\u3c/i\u3e

The polymerase chain reaction is one of the most important reactions in molecular biology. Single stranded DNA is copied in a complex series of steps, at the core of which lies the action of the DNA polymerase. At each nucleotide along the template, the polymerase screens the dNTP pool until it finds the complementary dNTP. The insertion of each dNMP is a balance between high fidelity and rapid elongation. In this study the kinetics of the β type polymerase pyrococcus kodakaraensis (KOD) is analyzed. The kinetics is influenced by reaction conditions such as the dNTP pool composition and temperature. In a previous study by Viljoen et al. [2005, A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection. Computational Biology and Chemistry 29, 101–110], a macroscopic kinetics expression of the polymerase chain reaction has been derived. The model contains four parameters that are intrinsic to a specific polymerase. The experiments to measure the temperature- dependence of the parameters for KOD DNA polymerase are reported. The results indicate that the optimal temperature for an equimolar dNTP pool is 72.5 °C and the optimum temperature shifts to lower temperatures when the dNTP pool composition is biased

Positive psychology of Malaysian students: impacts of engagement, motivation, self-compassion and wellbeing on mental health

Malaysia plays a key role in education of the Asia Pacific, expanding its scholarly output rapidly. However, mental health of Malaysian students is challenging, and their help-seeking is low because of stigma. This study explored the relationships between mental health and positive psychological constructs (academic engagement, motivation, self-compassion, and wellbeing), and evaluated the relative contribution of each positive psychological construct to mental health in Malaysian students. An opportunity sample of 153 students completed the measures regarding these constructs. Correlation, regression, and mediation analyses were conducted. Engagement, amotivation, self-compassion, and wellbeing were associated with, and predicted large variance in mental health. Self-compassion was the strongest independent predictor of mental health among all the positive psychological constructs. Findings can imply the strong links between mental health and positive psychology, especially selfcompassion. Moreover, intervention studies to examine the effects of self-compassion training on mental health of Malaysian students appear to be warranted.N/

Non-variable cosmologically distant gamma-ray emitters as an imprint of propagation of ultra-high-energy protons

The acceleration cites of ultra-high-energy (UHE) protons can be traced by the footprint left by these particles propagating through cosmic microwave background (CMB) radiation. Secondary electrons produced in extended region of several tens of Mpc emit their energy via synchrotron radiation predominantly in the initial direction of the parent protons. It forms a non-variable and compact (almost point-like) source of high energy gamma rays. The importance of this effect is increased for cosmologically distant objects; because of severe energy losses, UHE protons cannot achieve us even in the case of extremely weak intergalactic magnetic fields. Moreover, at high redshifts the energy conversion from protons to secondary particles becomes significantly more effective due to the denser and more energetic CMB in the past. This increases the chances of UHE cosmic rays to be traced by the secondary synchrotron gamma radiation. We discuss the energy budget and the redshift dependence of the efficiency of energy transfer from UHE protons to synchrotron radiation. The angular and spectral distributions of radiation in the gamma- and X-ray energy bands are calculated and discussed in the context of their detectability by Fermi LAT and Chandra observatories

Cosmic Rays at the highest energies

After a century of observations, we still do not know the origin of cosmic rays. I will review the current state of cosmic ray observations at the highest energies, and their implications for proposed acceleration models and secondary astroparticle fluxes. Possible sources have narrowed down with the confirmation of a GZK-like spectral feature. The anisotropy observed by the Pierre Auger Observatory may signal the dawn of particle astronomy raising hopes for high energy neutrino observations. However, composition related measurements point to a different interpretation. A clear resolution of this mystery calls for much larger statistics than the reach of current observatories.Comment: 8 pages, 4 figures, in the Proceedings of TAUP 201

Ultra High Energy Cosmic Rays: The disappointing model

We develop a model for explaining the data of Pierre Auger Observatory (Auger) for Ultra High Energy Cosmic Rays (UHECR), in particular, the mass composition being steadily heavier with increasing energy from 3 EeV to 35 EeV. The model is based on the proton-dominated composition in the energy range (1 - 3) EeV observed in both Auger and HiRes experiments. Assuming extragalactic origin of this component, we argue that it must disappear at higher energies due to a low maximum energy of acceleration, E_p^{\max} \sim (4 - 10) EeV. Under an assumption of rigidity acceleration mechanism, the maximum acceleration energy for a nucleus with the charge number Z is ZE_p^{\max}, and the highest energy in the spectrum, reached by Iron, does not exceed (100 - 200) EeV. The growth of atomic weight with energy, observed in Auger, is provided by the rigidity mechanism of acceleration, since at each energy E=ZE_p^{\max} the contribution of nuclei with Z' < Z vanishes. The described model has disappointing consequences for future observations in UHECR: Since average energies per nucleon for all nuclei are less than (2 - 4) EeV, (i) pion photo-production on CMB photons in extragalactic space is absent; (ii) GZK cutoff in the spectrum does not exist; (iii) cosmogenic neutrinos produced on CMBR are absent; (iv) fluxes of cosmogenic neutrinos produced on infrared - optical background radiation are too low for registration by existing detectors and projects. Due to nuclei deflection in galactic magnetic fields, the correlation with nearby sources is absent even at highest energies.Comment: Essentially revised version as published in Astropart. Physics 10 pages, 6 figure

Restricting UHECRs and cosmogenic neutrinos with Fermi-LAT

Ultrahigh energy cosmic ray (UHECR) protons interacting with the cosmic microwave background (CMB) produce UHE electrons and gamma-rays that in turn initiate electromagnetic cascades on CMB and infrared photons. As a result, a background of diffuse isotropic gamma radiation is accumulated in the energy range E\lsim 100 GeV. The Fermi-LAT collaboration has recently reported a measurement of the extragalactic diffuse background finding it less intense and softer than previously measured by EGRET. We show that this new result constrains UHECR models and the flux of cosmogenic neutrinos. In particular, it excludes models with cosmogenic neutrino fluxes detectable by existing neutrino experiments, while next-generation detectors as e.g. JEM-EUSO can observe neutrinos only for extreme parameters.Comment: 7 pages, 6 eps figures; v2: minor changes, v3: final version, added discussion of EGMF influenc