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

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/

Climate change anxiety among parents of school-aged children in the UK: Experience as a common predictor of cognitive-emotional and functional impairments

Climate change anxiety (CCA) is distress about climate change and its impacts on the environment and human health. CCA is manifested as cognitive-emotional impairment and functional impairment. CCA has been increasingly recognised in the mental health field, however, how to reduce CCA remains uninformed. Parents of school-aged children are vulnerable to CCA, due to parenting stress and worries for the future. We aimed to identify predictors of the CCA impairment, from experience of climate change, behavioural engagement, and number of children among parents of school-aged children. A convenience sample of 126 parents (82 mothers and 44 fathers) responded to an online survey. Multiple regression analyses were used. After controlling for age and gender, (a) experience of climate change (b=0.16, p< 0.01, 95%CI 0.06-0.27) and behavioural engagement (b=0.31, p<0.05, 95%CI 0.08-0.55) predicted cognitive-emotional impairment, and (b) experience of climate change predicted functional impairment (b=0.20, p<0.01, 95%CI 0.08-0.31). Experience of climate change was a common predictor. Cognitive re-appraisal and compassion practice may help alter the experiential aspect of climate change to mitigate CCA. Future research needs to evaluate the mechanism of climate change experience in order to effectively reduce CCA

Fast and easy blind deblurring using an inverse filter and PROBE

PROBE (Progressive Removal of Blur Residual) is a recursive framework for blind deblurring. Using the elementary modified inverse filter at its core, PROBE's experimental performance meets or exceeds the state of the art, both visually and quantitatively. Remarkably, PROBE lends itself to analysis that reveals its convergence properties. PROBE is motivated by recent ideas on progressive blind deblurring, but breaks away from previous research by its simplicity, speed, performance and potential for analysis. PROBE is neither a functional minimization approach, nor an open-loop sequential method (blur kernel estimation followed by non-blind deblurring). PROBE is a feedback scheme, deriving its unique strength from the closed-loop architecture rather than from the accuracy of its algorithmic components

Understanding how children are coping with climate change anxiety by exploring coping strategies and supportive interventions.

Climate change presents a significant threat to both the planet and human prosperity which impacts our physical health and mental well-being. There is an imminent requirement for significant global action. This means (a) our children have been born into unprecedented times and (b) as future adults, they will find themselves facing the major consequences of climate change. These can negatively affect their mental health and well-being. This paper reports the effect of climate anxiety on this population group through an exploration of coping strategies and supportive interventions. Empowering children to engage in climate action has been identified as a coping strategy. Whilst equipping them with knowledge and resources on climate change and providing safe spaces and experiences in nature are identified as supportive interventions. However, further empirical research evidence is needed to determine the next steps to address the extent of the impact of climate anxiety and prepare our children for the future

Ontological addiction theory: attachment to me, mine, and I

Background: Ontological addiction theory (OAT) is a novel metaphysical model of psychopathology and posits that human beings are prone to forming implausible beliefs concerning the way they think they exist, and that these beliefs can become addictive leading to functional impairments and mental illness. The theoretical underpinnings of OAT derive from the Buddhist philosophical perspective that all phenomena, including the self, do not manifest inherently or independently. Aims and methods: This paper outlines the theoretical foundations of OAT along with indicative supportive empirical evidence from studies evaluating meditation awareness training as well as studies investigating non-attachment, emptiness, compassion, and loving-kindness. Results: OAT provides a novel perspective on addiction, the factors that underlie mental illness, and how beliefs concerning selfhood are shaped and reified. Conclusion: In addition to continuing to test the underlying assumptions of OAT, future empirical research needs to determine how ontological addiction fits with extant theories of self, reality, and suffering, as well with more established models of addiction

Oligonucleotide−Oligospermine Conjugates (Zip Nucleic Acids): A Convenient Means of Finely Tuning Hybridization Temperatures

Synthesis of oligonucleotide probes and control of their hybridization temperature are key aspects of polymerase chain reaction (PCR)-based detection of genetic sequences. A straightforward means to approach the last goal is to decrease the repulsion between the polyanionic probe and target strands. To this end, we have developed a versatile automated synthesis of oligonucleotide−oligospermine derivatives that gave fast access to a large variety of compounds. Plots of their hybridization temperatures Tm vs overall charge provided a measure of the impact of interstrand phosphate repulsion (and of spermine-mediated attraction) on the main driving force of duplex formation, i.e., base pairing. It showed that stabilization brought about by excess cationic charges can be of larger absolute magnitude than interstrand repulsion, even in high salt media. Base sequence and conjugation site (3′ or 5′) hardly influenced the effect of spermine on Tm. In typical PCR probe conditions, the Tm increased linearly with the number of grafted spermines (e.g., 6.2 °C per spermine for a decanucleotide probe). The large data set of Tm vs number of spermines and oligonucleotide length allowed us to empirically derive a simple mathematical relation that is accurately predicting the Tm of any oligonucleotide−oligospermine derivative. Zip nucleic acids (ZNA) are thus providing an interesting alternative to locked nucleic acids (LNA) or minor groove binders (MGB) for raising the stability of 8−12-mer oligonucleotides up to ca. 70 °C, the level required for quantitative PCR experiments