689 research outputs found
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
MMT, Npeoc-protected spermine, a valuable synthon for the solid phase synthesis of oligonucleotide oligospermine conjugates via guanidine linkers
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/
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
The optical depth of the Universe to ultrahigh energy cosmic ray scattering in the magnetized large scale structure
This paper provides an analytical description of the transport of ultrahigh
energy cosmic rays in an inhomogeneously magnetized intergalactic medium. This
latter is modeled as a collection of magnetized scattering centers such as
radio cocoons, magnetized galactic winds, clusters or magnetized filaments of
large scale structure, with negligible magnetic fields in between. Magnetic
deflection is no longer a continuous process, it is rather dominated by
scattering events. We study the interaction between high energy cosmic rays and
the scattering agents. We then compute the optical depth of the Universe to
cosmic ray scattering and discuss the phenomological consequences for various
source scenarios. For typical parameters of the scattering centers, the optical
depth is greater than unity at 5x10^{19}eV, but the total angular deflection is
smaller than unity. One important consequence of this scenario is the
possibility that the last scattering center encountered by a cosmic ray be
mistaken with the source of this cosmic ray. In particular, we suggest that
part of the correlation recently reported by the Pierre Auger Observatory may
be affected by such delusion: this experiment may be observing in part the last
scattering surface of ultrahigh energy cosmic rays rather than their source
population. Since the optical depth falls rapidly with increasing energy, one
should probe the arrival directions of the highest energy events beyond
10^{20}eV on an event by event basis to circumvent this effect.Comment: version to appear in PRD; substantial improvements: extended
introduction, sections added on angular images and on direction dependent
effects with sky maps of optical depth, enlarged discussion of Auger results
(conclusions unchanged); 27 pages, 9 figure
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
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