Exploring chemical compound space with a graph-based recommender system

With the availability of extensive databases of inorganic materials, data-driven approaches leveraging machine learning have gained prominence in materials science research. In this study, we propose an innovative adaptation of data-driven concepts to the mapping and exploration of chemical compound space. Recommender systems, widely utilized for suggesting items to users, employ techniques such as collaborative filtering, which rely on bipartite graphs composed of users, items, and their interactions. Building upon the Open Quantum Materials Database (OQMD), we constructed a bipartite graph where elements from the periodic table and sites within crystal structures are treated as separate entities. The relationships between them, defined by the presence of ions at specific sites and weighted according to the thermodynamic stability of the respective compounds, allowed us to generate an embedding space that contains vector representations for each ion and each site. Through the correlation of ion-site occupancy with their respective distances within the embedding space, we explored new ion-site occupancies, facilitating the discovery of novel stable compounds. Moreover, the graph's embedding space enabled a comprehensive examination of chemical similarities among elements, and a detailed analysis of local geometries of sites. To demonstrate the effectiveness and robustness of our method, we conducted a historical evaluation using different versions of the OQMD and recommended new compounds with Kagome lattices, showcasing the applicability of our approach to practical materials design

Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae

<p>Abstract</p> <p>Background</p> <p><it>Mycoplasma hyopneumoniae </it>is a highly infectious swine pathogen and is the causative agent of enzootic pneumonia (EP). Following the previous report of a proteomic survey of the pathogenic 7448 strain of swine pathogen, <it>Mycoplasma hyopneumoniae</it>, we performed comparative protein profiling of three <it>M. hyopneumoniae </it>strains, namely the non-pathogenic J strain and the two pathogenic strains 7448 and 7422.</p> <p>Results</p> <p>In 2DE comparisons, we were able to identify differences in expression levels for 67 proteins, including the overexpression of some cytoadherence-related proteins only in the pathogenic strains. 2DE immunoblot analyses allowed the identification of differential proteolytic cleavage patterns of the P97 adhesin in the three strains. For more comprehensive protein profiling, an LC-MS/MS strategy was used. Overall, 35% of the <it>M. hyopneumoniae </it>genome coding capacity was covered. Partially overlapping profiles of identified proteins were observed in the strains with 81 proteins identified only in one strain and 54 proteins identified in two strains. Abundance analysis of proteins detected in more than one strain demonstrates the relative overexpression of 64 proteins, including the P97 adhesin in the pathogenic strains.</p> <p>Conclusions</p> <p>Our results indicate the physiological differences between the non-pathogenic strain, with its non-infective proliferate lifestyle, and the pathogenic strains, with its constitutive expression of adhesins, which would render the bacterium competent for adhesion and infection prior to host contact.</p

Ação de prolil-leucil-gliclnamida (PLG) na via nigroestriatal do rato

In order to study the nigrostriatal pathway, we obtained the rotatory behavior model in male Wistar rats by electrolytic lesion of the left lateral hypothalamic region. Animals thus lesioned displayed rotations toward the same side of lesion when apomorphine was administered, a result in disagreement with what has been obtained in the model with 6-hydroxydopamine lesion. The administration of PLG alone was not followed by rotatory behavior but when the compound was administered in low doses (0.25 to 1mg/kg) simultaneously with apomorphine to animals previously submitted to REM sleep deprivation, a significant increase in the number of rotations was observed in comparison with controls and groups receiving higher doses of PLG. These results indicate that PLG may act as, a modulator on dopamine receptors in the striatum.No intuito de estudar a via nigroestriatal, produzimos uma lesão na região hipotalâmica lateral de ratos Wistar. Os animais passavam a apresentar comportamento rotatório para o mesmo lado da lesão. A administração isolada do PLG não induziu o comportamento rotatório. Entretanto, com doses baixas do composto, concomitantemente à administração de apomorfina em animais previamente submetidos à privação de sono REM, observou-se aumento no número de rotações auando comparado ao grupo controle e aos grupos aue receberam doses altas de PLG. Estes achados sugerem que o PLG age como um modulador sobre os receptores dopaminérgicos do estriado.Escola Paulista de Medicina Department of Neurology and Neurosurgery Division of Extrapyramidal Diseases InvestigationEscola Paulista de Medicina Department of Neurology and Neurosurgery Head of the Division - Division of Extrapyramidal Diseases InvestigationUNIFESP, EPM, Department of Neurology and Neurosurgery Division of Extrapyramidal Diseases InvestigationEscola Paulista de Medicina Department of Neurology and Neurosurgery Head of the Division - Division of Extrapyramidal Diseases InvestigationSciEL

Transcriptome analysis of Taenia solium cysticerci using Open reading Frame ESTS (ORESTES)

<p>Abstract</p> <p>Background</p> <p>Human infection by the pork tapeworm <it>Taenia solium </it>affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form.</p> <p>Results</p> <p>Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development.</p> <p>Conclusion</p> <p>The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed.</p

CONTROLAB MUFA: a multi-level fusion architecture for intelligent navigation of a telerobot

This paper proposes a MUlti-level Fusion Architecture (MUFA) for controlling the navigation of a tele-commanded Autonomous Guided Vehicle (AGV). The architecture combines ideas derived from the fundamental concepts of sensor fusion and distributed intelligence. The focus of the work is the development of an intelligent navigation system for a tricycle drive AGV with the ability to move autonomously within any office enviromnent, following instructions issued by client stations connected to the office network and reacting accordingly to different situations found in the real world. The modules which integrate the MUFA architecture are discussed and results of some simulation experiments are presented

A simplified curcumin targets the membrane of Bacillus subtilis

Abstract Curcumin is the main constituent of turmeric, a seasoning popularized around the world with Indian cuisine. Among the benefits attributed to curcumin are anti‐inflammatory, antimicrobial, antitumoral, and chemopreventive effects. Besides, curcumin inhibits the growth of the gram‐positive bacterium Bacillus subtilis. The anti‐B. subtilis action happens by interference with the division protein FtsZ, an ancestral tubulin widespread in Bacteria. FtsZ forms protofilaments in a GTP‐dependent manner, with the concomitant recruitment of essential factors to operate cell division. By stimulating the GTPase activity of FtsZ, curcumin destabilizes its function. Recently, curcumin was shown to promote membrane permeabilization in B. subtilis. Here, we used molecular simplification to dissect the functionalities of curcumin. A simplified form, in which a monocarbonyl group substituted the β‐diketone moiety, showed antibacterial action against gram‐positive and gram‐negative bacteria of clinical interest. The simplified curcumin also disrupted the divisional septum of B. subtilis; however, subsequent biochemical analysis did not support a direct action on FtsZ. Our results suggest that the simplified curcumin exerted its function mainly through membrane permeabilization, with disruption of the membrane potential necessary for FtsZ intra‐cellular localization. Finally, we show here experimental evidence for the requirement of the β‐diketone group of curcumin for its interaction with FtsZ