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

A new dataset of global irrigation areas from 2001 to 2015

About 40% of global crop production takes place on irrigated land, which accounts for approximately 20% of the global farmland. The great majority of freshwater consumption by human societies is associated with irrigation, which contributes to a major modification of the global water cycle by enhancing evapotranspiration and reducing surface and groundwater runoff. In many regions of the world irrigation contributes to streamflow and groundwater depletion, soil salinization, cooler microclimate conditions, and altered land-atmosphere interactions. Despite the important role played by irrigation in food security, water cycle, soil productivity, and near-surface atmospheric conditions, its global extent remains poorly quantified. To date global maps of irrigated land are often based on estimates from circa year 2000. Here we apply artificial intelligence methods based on machine learning algorithms to satellite remote sensing and monthly climate data to map the spatial extent of irrigated areas between 2001 and 2015. We provide global annual maps of irrigated land at ≈9km resolution for the 2001-2015 and we make this dataset available online

Niche differentiation mechanisms among canopy frugivores and zoochoric trees in the northeastern extreme of the Amazon

Frugivores and zoocoric trees represent an important proportion of tropical rainforest biodiversity. As niche differences favor species coexistence, we aimed to evaluate morphological and temporal niche segregation mechanisms among zoochoric trees and canopy frugivores in a tropical rainforest in the northeastern extreme of the Brazilian Amazon. We tested the effects of fruit morphology, tree size, frugivore body size and time of day on fruit consumption. We recorded the frugivore species that fed on 72 trees (44 species, 22 genera) and whether these frugivores swallowed the seeds. We monitored trees only once from 07:00 to 17:00 h between January and September 2017. We observed fruit consumption in 20 of the 72 trees. Seventy-three frugivore individuals from 22 species visited the trees. Heavier fruits were consumed by larger frugivores, while seed size was inversely correlated with frugivore size. Narrower fruits and fruits with smaller seeds had greater probability of having their seeds ingested, and larger frugivores were more prone to ingest seeds. Trees bearing fruits with smaller seeds were visited by a greater number of frugivores. Taxonomic groups differed in the time of arrival at fruiting trees. None of the evaluated variables (fruit weight and size, and seed size) affected the richness of frugivores that visited the trees. We concluded that, in the studied forest, fruit morphology (weight, size and seed size) is a niche segregation mechanism among zoochoric trees, while body size and time of day are niche segregation mechanisms among frugivores.info:eu-repo/semantics/publishedVersio

Understanding the Influence of Diverse Non‐Volatile Media on Rheological Properties of Thermophilic Biological Sludge and Evaluation of Its Thixotropic Behaviour

In this study, the rheological properties of thermophilic biological sludge (TBS) have been investigated evaluating the influence of non‐volatile solids (NVS). Calcium carbonate, sand, and sodium bentonite were separately added to the sludge to evaluate the effect of concentration and type of NVS. Results show that TBS consistency coefficient significantly enhanced increasing sodium bentonite concentration. On the contrary, calcium carbonate and sand showed relatively small influence on the rheological properties of TBS. Thixotropic behaviour of TBS has also been investigated and is more pronounced at higher shear rate (1000 s−1). Double exponential fitting model was the best choice to represent thixotropic behaviour in case of low (100 s−1) and high shear rate (1000 s−1), while a single‐exponential model represents the best option in case of medium shear rate (400 s−1)

Telomeric Trans-Silencing: An Epigenetic Repression Combining RNA Silencing and Heterochromatin Formation

The study of P-element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequence or TAS) has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located in euchromatin. TSE shows variegation among egg chambers in ovaries when silencing is incomplete. Here, we report that TSE displays an epigenetic transmission through meiosis, which involves an extrachromosomal maternally transmitted factor. We show that this silencing is highly sensitive to mutations affecting both heterochromatin formation (Su(var)205 encoding Heterochromatin Protein 1 and Su(var)3–7) and the repeat-associated small interfering RNA (or rasiRNA) silencing pathway (aubergine, homeless, armitage, and piwi). In contrast, TSE is not sensitive to mutations affecting r2d2, which is involved in the small interfering RNA (or siRNA) silencing pathway, nor is it sensitive to a mutation in loquacious, which is involved in the micro RNA (or miRNA) silencing pathway. These results, taken together with the recent discovery of TAS homologous small RNAs associated to PIWI proteins, support the proposition that TSE involves a repeat-associated small interfering RNA pathway linked to heterochromatin formation, which was co-opted by the P element to establish repression of its own transposition after its recent invasion of the D. melanogaster genome. Therefore, the study of TSE provides insight into the genetic properties of a germline-specific small RNA silencing pathway

Prediction of Hydrate and Solvate Formation Using Statistical Models

Novel, knowledge based models for the prediction of hydrate and solvate formation are introduced, which require only the molecular formula as input. A data set of more than 19 000 organic, nonionic, and nonpolymeric molecules was extracted from the Cambridge Structural Database. Molecules that formed solvates were compared with those that did not using molecular descriptors and statistical methods, which allowed the identification of chemical properties that contribute to solvate formation. The study was conducted for five types of solvates: ethanol, methanol, dichloromethane, chloroform, and water solvates. The identified properties were all related to the size and branching of the molecules and to the hydrogen bonding ability of the molecules. The corresponding molecular descriptors were used to fit logistic regression models to predict the probability of any given molecule to form a solvate. The established models were able to predict the behavior of ∼80% of the data correctly using only two descriptors in the predictive model