Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Topology for the Discovery of New Broad-Spectrum Antibacterial Drugs

In this study, molecular topology was used to develop several discriminant equations capable of classifying compounds according to their antibacterial activity. Topological indices were used as structural descriptors and their relation to antibacterial activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four equations were constructed, named DF1, DF2, DF3, and DF4, all with good statistical parameters such as Fisher–Snedecor’s F (over 25 in all cases), Wilk’s lambda (below 0.36 in all cases) and percentage of correct classification (over 80% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. From the four discriminant functions, it can be extracted that the presence of sp3 carbons, ramifications, and secondary amine groups in a molecule enhance antibacterial activity, whereas the presence of 5-member rings, sp2 carbons, and sp2 oxygens hinder it. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of antibacterial activity.
Viral pandemic preparedness: A pluripotent stem cell‐based machine‐learning platform for simulating SARS‐CoV‐2 infection to enable drug discovery and repurposing

Infection with the SARS‐CoV‐2 virus has rapidly become a global pandemic for which we were not prepared. Several clinical trials using previously approved drugs and drug combinations are urgently under way to improve the current situation. A vaccine option has only recently become available, but worldwide distribution is still a challenge. It is imperative that, for future viral pandemic preparedness, we have a rapid screening technology for drug discovery and repurposing. The primary purpose of this research project was to evaluate the DeepNEU stem‐cell based platform by creating and validating computer simulations of artificial lung cells infected with SARS‐CoV‐2 to enable the rapid identification of antiviral therapeutic targets and drug repurposing. The data generated from this project indicate that (a) human alveolar type lung cells can be simulated by DeepNEU (v5.0), (b) these simulated cells can then be infected with simulated SARS‐CoV‐2 virus, (c) the unsupervised learning system performed well in all simulations based on available published wet lab data, and (d) the platform identified potentially effective anti‐SARS‐CoV2 combinations of known drugs for urgent clinical study. The data also suggest that DeepNEU can identify potential therapeutic targets for expedited vaccine development. We conclude that based on published data plus current DeepNEU results, continued development of the DeepNEU platform will improve our preparedness for and response to future viral outbreaks. This can be achieved through rapid identification of potential therapeutic options for clinical testing as soon as the viral genome has been confirmed.
The Light/Dark cycle disruption affects hepatic function both in metabolic parameters and tissue structure in a nocturnal desert rodent: Gerbillus tarabuli.

INTRODUCTION Biological rhythms, such as Light/Dark (LD) cycles, are an integral component of virtually all aspects of life. These rhythms are controlled in large part by circadian clocks, allowing the organism to adapt its internal rhythmic metabolism to changes in the external environment created by daily fluctuations in the LD cycle. Therefore, changes in the daily duration of the lighting could lead to adverse health consequences. The aim of the study was to investigate, in a nocturnal desert rodent, Gerbillus tarabuli, the effects of the LD cycle disruption on the structure of the hepatic tissue and the content of carbohydrate and lipid parameters as indicators of metabolic state. MATERIAL AND METHODS . The present study was conducted on two gerbil groups: control group was exposed to a standard lighting cycle (LD: 12:12), and the shifted group was subjected to a chronic disrupted LD cycle, alternating a standard cycle (LD: 12:12) with a modified cycle (LD: 20:4), i.e., the light phase of 24-h cycle was prolonged by 8 h on every second day during a period of 12 weeks. We used: (i) routine histology and histochemical staining for tissue analysis; (ii) immunohistochemistry (IHC) for MPO detection; (iii) biochemical methods for hepatic glycogen and lipids extraction and quantification. Blood metabolic parameters were assessed by enzymatic methods. RESULTS Our structural results indicate in the shifted group an alteration of tissue architecture, showing widely scattered inflammatory foci with many dilated sinusoids and prominent leukocyte infiltration with connective fibrotic extension. IHC revealed also increased hepatic myeloperoxidase (MPO) expression confirming neutrophils' presence. In parallel, the histochemical study revealed a strong depletion of hepatocytic glycogen and lipid inclusions; these observations were also supported by the measurements of glycogen and total lipids in extracted tissue indicating a reduction in liver content. These results were accompanied by a decrease in body weight relative to the reduction of food intake, as well as hyperglycemia and some alterations in serum lipid parameters (triglycerides and cholesterol) suggesting a metabolic disturbance. CONCLUSION We conclude that a phase difference between the endogenous activity rhythm of the species and the daily cycle of illumination has a strong impact on the liver morphology as well as on the metabolic activity of liver cells.
Inhibition of TRPV1 by SHP-1 in nociceptive primary sensory neurons is critical in PD-L1 analgesia

Recently programmed death-ligand 1 (PD-L1) receptor PD-1 was found in dorsal root ganglion (DRG) neurons, and PD-L1 activates PD-1 to inhibit inflammatory and neuropathic pain by modulating neuronal excitability. However, the downstream signaling of PD-1 in sensory neurons remains unclear. Here, we show that PD-L1 activated Src homology 2 domain-containing tyrosine phosphatase-1 (SHP-1) to downregulate transient receptor potential vanilloid 1 (TRPV1) in DRG neurons and inhibit bone cancer pain in mice. Local injection of PD-L1 produced analgesia. PD-1 in DRG neurons colocalized with TRPV1 and SHP-1. PD-L1 induced the phosphorylation of SHP-1 in DRG TRPV1 neurons and inhibited TRPV1 currents. Loss of TRPV1 in mice abolished bone cancer–induced thermal hyperalgesia and PD-L1 analgesia. Conditioned deletion of SHP-1 in NaV1.8+ neurons aggravated bone cancer pain and diminished the inhibition of PD-L1 on TRPV1 currents and pain. Together, our findings suggest that PD-L1/PD-1 signaling suppresses bone cancer pain via inhibition of TRPV1 activity. Our results also suggest that SHP-1 in sensory neurons is an endogenous pain inhibitor and delays the development of bone cancer pain via suppressing TRPV1 function.
Sur l’impact des contraintes structurelles pour l’analyse en dépendances profondes fondée sur les graphes (On the impact of structural constraints for graph-based deep dependency parsing)

Les algorithmes existants pour l’analyse en dépendances profondes fondée sur les graphes capables de garantir la connexité des structures produites ne couvrent pas les corpus du français. Nous proposons un nouvel algorithme qui couvre l’ensemble des structures possibles. Nous nous évaluons sur les corpus français FTB et Sequoia et observons un compromis entre la production de structures valides et la qualité des analyses.
Potential distribution and invasiveness of recently naturalised alien plants under climate change

i Acknowledgements . iii Publications . v Table of contents . ix List of Tables . xv List of Figures . xix CHAPTER 1 INTRODUCTION . 1 1.1 Biological invasions . 2 1.1.
When Information Improves Information Security (Short Paper)

This paper presents a formal, quantitative evaluation of the impact of bounded-rational security decision-making subject to limited information and externalities. We investigate a mixed economy of an individual rational expert and several na¨ıve near-sighted agents. We further model three canonical types of negative externalities (weakest-link, best shot and total effort), and study the impact of two information regimes on the threat level agents are facing.
Research , development and innovation management in the energy sector

This study aimed to observe trends in the literature on research, development, and innovation management in the energy sector, using performance assessment systems. The paper presented a bibliometric analysis of 40 studies on the subject. These materials come from ScienceDirect, Scopus and the Institute of Electrical and Electronics Engineers (IEEE) databases from 2006 to 2016. The results showed an increasing trend in the number of publications on the theme, showing the scientific community’s interest in the subject. In addition, it was verified that the predominant language used to write the publications was English, the country that most published articles in the area was Brazil and most of the articles were produced through collaboration between researchers. It was found that the journal with the greatest number of publications on the subject was the Procedia – Social and Behavioral Sciences, while the Expert Systems with Applications journal presented the article with the greatest number of citations. This analysis allowed us to identify important points of the research and its future directions, in addition to enabling a better understanding of the world trend of the subject approached.
Expressão gênica em larga escala de raizes de Coffea arabica L.

The use of new large-scale sequencing technologies is an innovative strategy in coffee biotechnology, identifying and characterizing genomic components involved in nitrogen (N) starvation. Coffee plants were grown under N starvation and roots were used for construction of cDNA libraries and sequencing using GS-FLX Titanium Roche platform. We obtained 809 517 reads, assembled in 34,654 contigs. Using this data, we expect to identify and characterize genes involved in transport and nitrogen metabolism in coffee plants.
Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode

(K247002 and K247003) from different localities to ational nagro­ Biodiversity center, rural agricultural administration(rDa), as genetic resources for vegetative clones, be­cause chrysanthemum can easily be propagated by cut­ting.as the national agricultural Genome center project, rural agricultural administration (rDa), the genome of
Isolation and characterization of the promoter of SEPALLATA1-like gene from Platanus acerifolia

London plane (Platanus acerifolia Wild.) is a famous landscape plant because of its numerous desirable traits except the abundant pollens and seed hairs, which not only pollute the environment but also affect human health. To resolve these problems, we herein isolated and functionally analyzed the promoter of PlacSEP1.1, an orthologous gene of Arabidopsis SEPALLATA1, and investigated the potential usability for cell ablation strategies to engineer reproductive sterility in plants. A 2130 bp 5' upstream region of PlacSEP1.1 was isolated and termed pPlacSEP1.1. Putative motif detections show that there were several types of motifs in pPlacSEP1.1 including core promoter elements, tissue-specific expression regulatory elements, and some negative regulatory elements. β-Glucuronidase histochemical and quantitative assay showed that pPlacSEP1.1 of all deletions was active in all detected tissues except the shortest deletion D5 in roots. In order to test whether pPlacSEP1.1 could be used for London plane sterility breeding with a cytotoxic gene Barnase, the pPlacSEP1.1::Barnase and pPlacSEP1.1::Barnase-mic35S-Barstar vectors were constructed and transformed into tobacco. The pPlacSEP1.1::Barnase transgenic tobacco showed serious defects with respect to vegetative development and died within a couple of weeks after transplantation. On the other hand, most pPlacSEP1.1::Barnase-mic35S-Barstar transgenic tobacco showed normal vegetative growth and inflorescence, and flower development prevented phenotype.
The Impact of Alternative Audiovisual Products on the Socialization of the Sexual-Affective Desires of Teenagers

In the theories of communication and information, the way in which many audiovisual products have linked violence to sexual-affective relationships has been analyzed, especially using quantitative methodologies. The way in which such audiovisual products, which are a key socializing agent for teenagers, have an influence on teenagers’ sexual-affective relationships has also been analyzed. However, alternative audiovisual products also exist; such products mostly link attraction to egalitarian and nonviolent relationships. The present study aims at contributing to overcoming the attraction to violence that some audiovisual products might generate, therefore preventing gender violence among teenagers. With this purpose, this article provides a way of analyzing the impact that alternative audiovisual products have on teenagers’ sexual-affective desires using communicative methodology.
The Dialogic Public Policy: A Successful Case

This article presents the concept of dialogic public policies using a case study of the Integrated Plan for the Roma People in Catalonia. For centuries, the Roma people have been considered one of the most socially excluded and discriminated groups across Europe. Several public policies have been promoted to achieve greater social inclusion and reverse this situation. In this context, from 2001 onward, the dialogic public policies began to be developed, which indicated the beginning of the Integrated Plan for the Roma People in Catalonia. The egalitarian dialogue between the Roma people and the scientific community started with the WORKALO project. This research funded by the V Framework Research Programme of the European Commission that generated a political impact and prompted unanimous recognition of the Roma people on the part of the European Parliament and some of the parliaments of the member states. The dialogic public policies had two defining points: they had to be made using an egalitarian dialogue with the Roma people, and they had to base themselves on actions indicated by the scientific evidence to provide the best possible results.
Deep learning methods for fingerprint-based indoor positioning: a review

ABSTRACT Outdoor positioning systems based on the Global Navigation Satellite System have several shortcomings that have deemed their use for indoor positioning impractical. Location fingerprinting, which utilizes machine learning, has emerged as a viable method and solution for indoor positioning due to its simple concept and accurate performance. In the past, shallow learning algorithms were traditionally used in location fingerprinting. Recently, the research community started utilizing deep learning methods for fingerprinting after witnessing the great success and superiority these methods have over traditional/shallow machine learning algorithms. This paper provides a comprehensive review of deep learning methods in indoor positioning. First, the advantages and disadvantages of various fingerprint types for indoor positioning are discussed. The solutions proposed in the literature are then analyzed, categorized, and compared against various performance evaluation metrics. Since data is key in fingerprinting, a detailed review of publicly available indoor positioning datasets is presented. While incorporating deep learning into fingerprinting has resulted in significant improvements, doing so, has also introduced new challenges. These challenges along with the common implementation pitfalls are discussed. Finally, the paper is concluded with some remarks as well as future research trends.
The chemodynamics of prograde and retrograde Milky Way stars

Context. The accretion history of the Milky Way is still unknown, despite the recent discovery of stellar systems that stand out in terms of their energy-angular momentum space, such as Gaia-Enceladus-Sausage. In particular, it is still unclear how these groups are linked and to what extent they are well-mixed. Aims. We investigate the similarities and differences in the properties between the prograde and retrograde (counter-rotating) stars and set those results in context by using the properties of Gaia-Enceladus-Sausage, Thamnos/Sequoia, and other suggested accreted populations. Methods. We used the stellar metallicities of the major large spectroscopic surveys (APOGEE, Gaia-ESO, GALAH, LAMOST, RAVE, SEGUE) in combination with astrometric and photometric data from Gaia’s second data-release. We investigated the presence of radial and vertical metallicity gradients as well as the possible correlations between the azimuthal velocity, vϕ, and metallicity, [M/H], as qualitative indicators of the presence of mixed populations. Results. We find that a handful of super metal-rich stars exist on retrograde orbits at various distances from the Galactic center and the Galactic plane. We also find that the counter-rotating stars appear to be a well-mixed population, exhibiting radial and vertical metallicity gradients on the order of ∼ − 0.04 dex kpc−1 and −0.06 dex kpc−1, respectively, with little (if any) variation when different regions of the Galaxy are probed. The prograde stars show a vϕ − [M/H] relation that flattens – and, perhaps, even reverses as a function of distance from the plane. Retrograde samples selected to roughly probe Thamnos and Gaia-Enceladus-Sausage appear to be different populations yet they also appear to be quite linked, as they follow the same trend in terms of the eccentricity versus metallicity space.
HTR-Flor++: A Handwritten Text Recognition System Based on a Pipeline of Optical and Language Models

Offline Handwritten Text Recognition (HTR) is a task that offers a challenge in computer vision, where images are the only source of information. In fact, several approaches to optical models have been developed, such as through of Hidden Markov Model (HMM) or recurrent Bidirectional/Multidimensional layers. The current state-of-the-art consists of combined deep learning techniques, the Convolutional Recurrent Neural Networks (CRNN), in which recurrent layers still suffer from vanishing gradient problem when processing very long texts. In a way, high-performance models generally have millions of trainable parameters and a high computational cost. However, recently a new optical model architecture, Gated-CNN, demonstrated improvements to complement CRNN modeling. Thus, in this work, we present a new small architecture for HTR (based on Gated-CNN) integrated with two steps of language model at the character and word levels, respectively. Therefore, we used 9 state-of-the-art approaches and validated the results using the IAM public dataset. Finally, the proposed model surpasses the results obtained by different approaches in the literature, reaching recognition rates of CER 2.7% and WER 5.6%, which means an improvement of 13% over the best results on IAM dataset.
Trophic level analysis of organisms from Changjiang estuary and adjacent waters of southern Yellow Sea in spring with stable isotope technology

Stable isotope technique is increasingly used in ecological studies.The isotopic ratio of nitrogen has successfully been used to calculate trophic levels of organisms in food web studies.By detecting the nitrogen stable isotope ratio,the present study investigated the tropic levels,spatial and temporal difference of organisms from Changjiang Estuary and adjacent waters of southern Yellow Sea on April 2005.The results showed that:the trophic levels of organisms in Changjiang Estuary were 3.19-5.11,concentrating in the range of 3.70-4.65;those of southern Yellow Sea were 2.46-4.88,concentrating in the range of 3.90-4.40. Considering the effect of stable isotope baseline indicator on the trophic levels of organisms in different systems,the trophic levels of 55% organisms in Changjiang Estuary were larger,with the variations being 0.01-0.63,concentrating in the range of 0.01-0.06 with the percentage of 30% in total organism quantity and the trophic levels of 40% organisms in Changjian Estuary were smaller,with the variations being 0.02-0.74,concentrating in the range of 0-0.21 with the percentage of 30% in total organism quantity compared with those of organisms in southern Yellow Sea.The range of the absolute variation value of trophic levels in the two ocean areas calculated in the study was close to that calculated with stomach content analysis method.We compared the trophic levels of the same organisms in Changjiang Estuary or adjacent waters of southern Yellow Sea,which were calculated with stomach content analysis method and stable isotope technique respectively,and found that the absolute variation value of trophic level of nine fish species calculated with the two methods in Changjiang Estuary was 0.01-1.21,and that of eleven fish species in southern Yellow Sea was 0.08-1.26,indicting the absolute variation values in the two ocean aeras was close to each other.Results showed that temporal and spatial differences in organisms'trophic level exists between the two ocean areas,and the differences varied in different organisms,and also confirmed the results calculated with stable isotope technique and with stomach content analysis are close to each other.
Complexity growth for topological black holes by holographic method

We consider the growth of the action for black hole spacetime with a fundamental string. Our interest is to find the difference of the behavior between black holes with three different topologies in the scenario of complexity-action conjecture. These black holes have positive, negative and zero curvatures. We would like to calculate the action growth of these systems with a probe fundamental string according to the complexity-action conjecture. We find that for the case where the black holes have the toroidal horizon structure this probe string behaves very differently from the other two cases.
Will it Blend? 2

Color is a phenomenon that depends heavily on human perception, however not all people perceive color the same way. In the human-computer interaction ﬁeld, when it comes to represent more complex data, color blending became an alternative comparing to other similar techniques. However, there are some aspects about color blending that haven’t been studied before. Our main goal is to study the inﬂuence of the Brightness component on color blending, while testing the users’ perception on diﬀerent color blending techniques. In order to do so, a testing interface was created to study if given two initial colors, users can perceive the Brightness of the mixed color between the two. In our study, we have focused on the analysis of the results obtained from the user study. We have found that, overall, intermediate values of Brightness were the ones users perceived better, and also that adjacent color blends are better perceived than equidistant blends in the HSV circle.