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

Termination of Triangular Integer Loops is Decidable

We consider the problem whether termination of affine integer loops is decidable. Since Tiwari conjectured decidability in 2004, only special cases have been solved. We complement this work by proving decidability for the case that the update matrix is triangular.Comment: Full version (with proofs) of a paper published in the Proceedings of the 31st International Conference on Computer Aided Verification (CAV '19), New York, NY, USA, Lecture Notes in Computer Science, Springer-Verlag, 201

T-Bet and Eomes Regulate the Balance between the Effector/Central Memory T Cells versus Memory Stem Like T Cells

Memory T cells are composed of effector, central, and memory stem cells. Previous studies have implicated that both T-bet and Eomes are involved in the generation of effector and central memory CD8 T cells. The exact role of these transcription factors in shaping the memory T cell pool is not well understood, particularly with memory stem T cells. Here, we demonstrate that both T-bet or Eomes are required for elimination of established tumors by adoptively transferred CD8 T cells. We also examined the role of T-bet and Eomes in the generation of tumor-specific memory T cell subsets upon adoptive transfer. We showed that combined T-bet and Eomes deficiency resulted in a severe reduction in the number of effector/central memory T cells but an increase in the percentage of CD62LhighCD44low Sca-1+ T cells which were similar to the phenotype of memory stem T cells. Despite preserving large numbers of phenotypic memory stem T cells, the lack of both of T-bet and Eomes resulted in a profound defect in antitumor memory responses, suggesting T-bet and Eomes are crucial for the antitumor function of these memory T cells. Our study establishes that T-bet and Eomes cooperate to promote the phenotype of effector/central memory CD8 T cell versus that of memory stem like T cells. © 2013 Li et al

Nonmethane hydrocarbon measurements in the North Atlantic Flight Corridor during the Subsonic Assessment Ozone and Nitrogen Oxide Experiment

Mixing ratios of nonmethane hydrocarbons (NMHCs) were not enhanced in whole air samples collected within the North Atlantic Flight Corridor (NAFC) during the fall of 1997. The investigation was conducted aboard NASA's DC-8 research aircraft, as part of the Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX). NMHC enhancements were not detected within the general organized tracking system of the NAFC, nor during two tail chases of the DC-8's own exhaust. Because positive evidence of aircraft emissions was demonstrated by enhancements in both nitrogen oxides and condensation nuclei during SONEX, the NMHC results suggest that the commercial air traffic fleet operating in the North Atlantic region does not contribute at all or contributes negligibly to NMHCs in the NAFC. Copyright 2000 by the American Geophysical Union

Radially restricted linear energy transfer for high-energy protons: A new analytical approach

Radially restricted linear energy transfer (LET) is a basic physical parameter relevant to radiation biology and radiation protection. In this report a convenient method is presented for the analytical computation of this quantity without the need for complicated simulation. The method uses the energy-re-stricted LETL, as recently redefined in a 1993 ICRU draft document and supplements it by a relatively simple term that represents the energy of fast rays lost within distancer from the track core. The method provides a better fit than other models and is valid over the entire range of radial distance from track center to the maximum radial distance traveled by the most energetic secondary electrons.L r computed by this approach differs only a few percent from the values Contribution to the international symposium on heavy ions research: space, radiation protection and therapy, 21–24 March 1994, Sophia-Antipolis, Franc

Genetic steps to organ laterality in zebrafish.

All internal organs are asymmetric along the left-right axis. Here we report a genetic screen to discover mutations which perturb organ laterality. Our particular focus is upon whether, and how, organs are linked to each other as they achieve their laterally asymmetric positions. We generated mutations by ENU mutagenesis and examined F3 progeny using a cocktail of probes that reveal early primordia of heart, gut, liver and pancreas. From the 750 genomes examined, we isolated seven recessive mutations which affect the earliest left-right positioning of one or all of the organs. None of these mutations caused discernable defects elsewhere in the embryo at the stages examined. This is in contrast to those mutations we reported previously (Chen et al., 1997) which, along with left-right abnormalities, cause marked perturbation in gastrulation, body form or midline structures. We find that the mutations can be classified on the basis of whether they perturb relationships among organ laterality. In Class 1 mutations, none of the organs manifest any left-right asymmetry. The heart does not jog to the left and normally leftpredominant BMP4 in the early heart tube remains symmetric. The gut tends to remain midline. There frequently is a remarkable bilateral duplication of liver and pancreas. Embryos with Class 2 mutations have organotypic asymmetry but, in any given embryo, organ positions can be normal, reversed or randomized. Class 3 reveals a hitherto unsuspected gene that selectively affects laterality of heart. We find that visceral organ positions are predicted by the direction of the preceding cardiac jog. We interpret this as suggesting that normally there is linkage between cardiac and visceral organ laterality. Class 1 mutations, we suggest, effectively remove the global laterality signals, with the consequence that organ positions are effectively symmetrical. Embryos with Class 2 mutations do manifest linkage among organs, but it may be reversed, suggesting that the global signals may be present but incorrectly orientated in some of the embryos. That laterality decisions of organs may be independently perturbed, as in the Class 3 mutation, indicates that there are distinctive pathways for reception and organotypic interpretation of the global signals

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

Designing hollow nano gold golf balls.

Hollow/porous nanoparticles, including nanocarriers, nanoshells, and mesoporous materials have applications in catalysis, photonics, biosensing, and delivery of theranostic agents. Using a hierarchical template synthesis scheme, we have synthesized a nanocarrier mimicking a golf ball, consisting of (i) solid silica core with a pitted gold surface and (ii) a hollow/porous gold shell without silica. The template consisted of 100 nm polystyrene beads attached to a larger silica core. Selective gold plating of the core followed by removal of the polystyrene beads produced a golf ball-like nanostructure with 100 nm pits. Dissolution of the silica core produced a hollow/porous golf ball-like nanostructure

Multi-response optimization of face milling performance considering tool path strategies in machining of Al-2024

It is hypothesized that the orientation of tool maneuvering in the milling process defines the quality of machining. In that respect, here, the influence of different path strategies of the tool in face milling is investigated, and subsequently, the best strategy is identified following systematic optimization. The surface roughness, material removal rate and cutting time are considered as key responses, whereas the cutting speed, feed rate and depth of cut were considered as inputs (quantitative factors) beside the tool path strategy (qualitative factor) for the material Al 2024 with a torus end mill. The experimental plan, i.e., 27 runs were determined by using the Taguchi design approach. In addition, the analysis of variance is conducted to statistically identify the effects of parameters. The optimal values of process parameters have been evaluated based on Taguchi-grey relational analysis, and the reliability of this analysis has been verified with the confirmation test. It was found that the tool path strategy has a significant influence on the end outcomes of face milling. As such, the surface topography respective to different cutter path strategies and the optimal cutting strategy is discussed in detail

Fast image reconstruction for near-field terahertz imaging with multistatic non-uniform sparse arrays

Conference paper presented at Radar Sensor Technology XXVII, Orlando, FL, USA, 30 April - 5 May, 2023.In this paper, first, the structure of a linear sparse periodic array for two-dimensional scanning is described. Then, based on its characteristics, an algorithm is presented for fast image reconstruction of the scene in a near-field (NF) multistatic terahertz imaging scenario. Although the basis of this algorithm is developed in the Fourier domain, it is compatible with the non-uniform structure of the array and also takes into account the phase deviations caused by multistatic imaging in NF. The performance of the proposed approach is evaluated with numerical data obtained from electromagnetic simulations in FEKO as well as experimental data. The results are discussed in terms of computational time on the central processing unit and graphics processing unit as well as the quality of the reconstructed image.Leverhulme Trust under Research Leadership Award RL-2019-019. The work of Shaoqing Hu is funded by Brunel University London under Research Development Fund LBG194 and 2022/2023 Brunel Research Initiative and Enterprise Fund 12455