Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Developments in BTB-WordNet

The paper reports on recent developments in Bulgarian BTB-WordNet (BTB-WN). This resource is viewed as playing a central role with respect to the integration and interlinking of various language resources such as: e-dictionaries (morphological, terminological, bilingual, orthographic, etymological and explanatory, etc., including editions from previous periods); corpora (coming from outside or being internal - like the corpus of definitions as well as the corpus of examples to synset meanings); ontologies (such as CIDOC-CRM, DBpedia, etc.); sources of world knowledge (such as information from the Bulgarian Encyclopedia, Wikipedia, etc.). The paper also gives information about a number of applications built on BTB-WN. These are: the Bulgaria-centered knowledge graph, the All about word application as well as some education-oriented exercises.
Reusing the Danish WordNet for a New Central Word Register for Danish - a Project Report

In this paper we report on a new Danish lexical initiative, the Central Word Register for Danish, (COR), which aims at providing an open-source, well curated and large-coverage lexicon for AI purposes. The semantic part of the lexicon (COR-S) relies to a large extent on the lexical-semantic information provided in the Danish wordnet, DanNet. However, we have taken the opportunity to evaluate and curate the wordnet information while compiling the new resource. Some information types have been simplified and more systematically curated. This is the case for the hyponymy relations, the ontological typing, and the sense inventory, i.e. the treatment of polysemy, including systematic polysemy.
Stable, circulation-preserving, simplicial fluids

Visual quality, low computational cost, and numerical stability are foremost goals in computer animation. An important ingredient in achieving these goals is the conservation of fundamental motion invariants. For example, rigid and deformable body simulation benefits greatly from the conservation of linear and angular momenta. In the case of fluids, however, none of the current techniques focuses on conserving invariants, and consequently, often introduce a visually disturbing numerical diffusion of vorticity. Just as important visually is the resolution of complex simulation domains. Doing so with regular (even if adaptive) grid techniques can be computationally delicate. In this article, we propose a novel technique for the simulation of fluid flows. It is designed to respect the defining differential properties, that is, the conservation of circulation along arbitrary loops as they are transported by the flow. Consequently, our method offers several new and desirable properties: Arbitrary simplicial meshes (triangles in 2D, tetrahedra in 3D) can be used to define the fluid domain; the computations involved in the update procedure are efficient due to discrete operators with small support; and it preserves discrete circulation, avoiding numerical diffusion of vorticity.
Genomic-inferred cross-selection metrics for multi-trait improvement in a recurrent selection breeding program

The major drawback to the implementation of genomic selection in a breeding program is the reduction of additive genetic variance in the long term, primarily due to the Bulmer effect. Increasing genetic gain and retaining additive genetic variance requires optimizing the trade-off between the two competing factors. Our approach integrated index selection in the genomic infer cross-selection (GCS) methods. With this strategy, we identified optimal crosses that simultaneously maximize progeny performance and maintain genetic variance for multiple traits. Using a stochastic simulated recurrent breeding program over a 40-year period, we evaluated different GCS metrics with other factors, such as the number of parents, crosses, and progenies per cross, that influence genetic gain in a breeding program. Across all breeding scenarios, the posterior mean-variance consistently enhances genetic gain when compared to other metrics such as the usefulness criterion, optimal haploid value, mean genomic estimated breeding value, and mean index selection value of the superior parents. In addition, we provide a detailed strategy to optimize the number of parents, crosses, and progenies per cross that maximizes short- and long-term genetic gain in a breeding program.
Extensive loss of forage diversity in social bees due to flower constancy and communication in simulated environments

Bees require a diverse diet for a healthy development. Many bee species show flower constancy, that is, they visit flowers of just one species during a foraging trip. Flower constancy is important for plant reproduction, but it could impair dietary diversity in bees, especially in biodiversity-depleted, human-modified landscapes. It is assumed that flower constancy does not lower dietary diversity in social bees, such as honey bees or bumble bees, because different colony members can specialise on different plant species. However, this has never been tested. We used computer simulations to investigate the effects of flower constancy on colony diet in plant species-rich and species-poor landscapes. We also explored if communication about food sources, which is used in many social bees, further reduces forage diversity. Our simulations reveal an extensive loss of forage diversity due to flower constancy in both plant species-rich and species-poor environments. Small colonies often discovered only 30-50% of all available plant species, thereby increasing the risk of nutritional deficiencies. Our simulation results could explain why bumble bees, which have small colony sizes, are less flower constant than honey bees and stingless bees, which have larger colony sizes. Remarkably, when colonies also communicated about food sources, Simpson’s diversity, which measures the evenness of flower visits, approached near zero in plant species-poor environments. Finally, we found that food source clustering, but not habitat fragmentation impaired dietary diversity. These findings can help in the design of landscapes that increase forage diversity and improve bee nutrition and health in human-modified landscapes.
The laminar pattern of proprioceptive activation in human primary motor cortex

The primary motor cortex (M1) has traditionally been viewed as a motor output generator. However, its vital role in proprioceptive somatosensation is increasingly being recognized. Yet, our understanding of proprioceptive somatosensation in M1 at the laminar scale is limited, largely due to methodological challenges. Empirical findings in primates and rodents suggest a pronounced role of superficial cortical layers, but the involvement of deep layers has yet to be examined in humans. Submillimeter resolution fMRI has emerged in recent years, paving the way for the study of layer-dependent activity in humans (laminar fMRI). In the present study, laminar fMRI was employed to investigate the laminar pattern of proprioceptive somatosensation on M1 deep layer activation using passive finger movements as proprioceptive stimulation. Significant M1 deep layer activation was observed in response to proprioceptive stimulation across 10 healthy subjects using vascular space occupancy (VASO) at 7T. For further validation, two additional subjects were scanned using a balanced steady-state free precession (bSSFP) sequence with ultrahigh (0.3 mm) in-plane resolution, yielding converging results. These results were interpreted in the light of previous laminar fMRI studies and the active inference account of motor control. We suggest that a considerable proportion of M1 deep layer activation is due to proprioceptive influence and that deep layers of M1 constitute a key component in proprioceptive circuits.
Distribution of dinoflagellates at Jakarta Bay, Taman Jaya, Banten, and Benoa Bay, Bali : A report of an incider of fish poisoning at Eastern Nusa Tenggara

“Red tide” is the name given to the phenomenon of red discolouration of marine and estuarine waters caused by a bloom of single-celled plants. The colour of the water can range from blood red to orange or brown in daylight and is often visible as phosphorescence at night (Carey 1983). Harmful red tides cause severe damage to local fishery resources, especially cultured oysters, mussels, and fish. Some of the dinoflagellates associated with the red discolouration in coastal waters have been identified as Noctiluca miliaris, Gymnodinium, Cochlodinium, Ceratium, Prorocentrum, Per­ idinium, and Goriyaulax. Steidinger (1979) (as cited by Estudillo 1984) reported in her taxonomic account of toxic dinoflagellates that there are less than 20 dinoflagellate species known or thought to produce toxins. Unprecedented red tides have occurred all over the world, such as in Korean waters (Park 1982; Lee and Huh 1983). Park noted that the red tide in Jinhae Bay, Korea, due to Gymnodinium type 65, occurred during the period July to September 1981. Lee noted that the red tide at Jindon Bay, caused by Ceratium furca, occurred in August 1980. In Harima Nada, Japan, the main cause of red tides was Chatonella antiqua (Hada) Ono in 1977, 1978, and 1979. In each case the red tide was associated with mass fish mortality (Okaichi et al. 1981). In the Philippines, the main cause of a red tide was Pyrodinium bahamense var. compressa. Paralytic shellfish poisoning (PSP) was reported for the first time in late June to early September 1983 in Maqueda Bay of Western Samar (Estudillo 1984). In Hong Kong, red tides have been caused by Gymnodinium in clear water and Trichodesmium in offshore waters (Lam 1984). In Papua New Guinea, the major causative organism of red tides was Pyrodinium bahamense var. compressa (Maclean 1984). In some Indonesian waters, phytoplankton populations generally consist of diatoms and dinoflagellates; diatoms are dominant, whereas dinoflagellates are very rare. Under certain conditions, however, unprecedented blooms, such as Noctiluca have occurred. Praseno and Adnan (1978) reported on a bloom of Noctiluca in May 1976 in Jakarta Bay. At that time the abundance of Noctiluca was 2x 103 cells/ L. This paper deals with an incident of fish poisoning in East Nusa Tenggara in November 1983 and the distribution of dinoflagellates in Jakarta Bay, Taman Jaya, and Benoa Bay.
Biophysical modeling identifies an optimal hybrid amoeboid-mesenchymal phenotype for maximal T cell migration speeds

Despite recent experimental progress characterizing the mechanics of cell migration, our understanding of the mechanisms governing how cells move rapidly through the body remains limited. To effectively limit the growth of tumors, antitumoral T cells need to rapidly migrate to find and kill cancer cells. To understand what sets the upper limit on cell speed, we developed a new hybrid stochastic-mean field model of bleb-based cell motility to guide T cell engineering approaches to enhance T cell movement in tumor environments. We first examined the potential for adhesion-free bleb-based migration and show that cells only inefficiently migrate in the absence of adhesion-based forces, i.e., cell swimming. High-to-low cortical contractility oscillations, where a high cortical contractility phase characterized by multiple bleb nucleation events is followed by an intracellular pressure buildup recovery phase at low cortical tensions, results in modest net cell motion. However, our model suggests that cells can employ a hybrid bleb- and adhesion-based migration mechanism for rapid cell motility and identifies conditions for optimality. The model provides a momentum-conserving mechanism underlying rapid single-cell migration and identifies factors that can be used as design criteria for engineering T cell therapies that move better in mechanically complex environments.
Behavioral Syndromes in Paper Wasps: links between social and non-social personality in Polistes fuscatus

Although much work has focused on non-social personality traits such as activity, exploration, and neophobia, there is a growing appreciation that social personality traits play an important role in group dynamics, disease transmission, and fitness, and that social personality traits may be linked to non-social personality traits. These relationships are important because behavioral syndromes, defined here as correlated behavioral phenotypes, can constrain evolutionary responses. However, the strength and direction of relationships between social and non-social personality traits remain unclear. In this project, we examine social and non-social personality traits, and the relationships between them, in the paper wasp Polistes fuscatus. With a novel assay we identify five personality traits, two non-social (exploration and activity) and three social (aggression, affiliation, and antennation) personality traits. We also find that social and non-social personality traits are phenotypically linked. We find a positive correlation between aggression and activity (rs = 0.33) and a negative correlation between affiliation and activity (rs = - 0.35). We also find a positive correlation between exploration and activity. Our work is an important step in understanding how phenotypic linkage between social and non-social behaviors may influence behavioral evolution. As a burgeoning model system for the study of genetic and neurobiological mechanisms of social behavior, Polistes fuscatus has potential to add to this work through exploring the causes and consequences of individual behavioral variation.
BatCRISPRi: Bacillus titratable CRISPRi for dynamic control in Bacillus subtilis

The discovery of new genes regulating essential biological processes has become increasingly important, and CRISPRi has emerged as a powerful tool for achieving this goal. This method has been used in many model organisms to decrease the expression of specific genes and assess their impact on phenotype. Pooled CRISPRi libraries in bacteria have been particularly useful in discovering new regulators of growth, division, and other biological processes. However, these libraries rely on the induction of dCas9 via an inducible promoter, which can be problematic due to promoter leakiness. This is a widespread phenomenon of any inducible promoter that can result in the unwanted downregulation of genes and the emergence of genetic suppressors when essential genes are knocked down. To overcome this issue, we have developed a novel strategy that eliminates dCas9 leakiness and enables reversible knockdown control using the rapamycin-dependent degron system in Bacillus subtilis. This degron system causes rapid degradation of dCas9, resulting in an almost instant reset of the system. Our results demonstrate that it is possible to achieve zero CRISPRi activity in the uninduced state and full activity in the induced state. This improved CRISPRi system will enable researchers to investigate phenotypic changes more effectively while reducing the undesirable effects of leaky expression and noise in their phenotypic data. Moreover, a rapid degradation system could serve as a tool for dynamic perturbation before compensation mechanisms or stress responses kick in. Finally, this approach can be adapted to other organisms and other promoter-inducible systems, potentially opening up strategies for tighter control of gene expression.
Human lncRNAs harbor conserved modules embedded in different sequence contexts

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human lncRNA exons and identified 340 pairs of exons with high sequence and/or secondary structure similarity but embedded in a dissimilar sequence context. We grouped these pairs in 106 clusters based on their reciprocal similarities. These shared modules are highly conserved between humans and the four great ape species, display evidence of purifying selection and likely arose as a result of recent segmental duplications. Our analysis contributes to the understanding of the mechanisms driving the evolution of the non-coding genome and suggests additional strategies towards deciphering the functional complexity of this class of molecules. Author summary The Human genome includes more than 18,000 genes coding for RNAs that are not translated into proteins, called long non-coding RNAs (lncRNA). Mounting evolutionary and experimental evidence shows that a large amount of these RNAs have a specific function, mainly as regulators of a diverse set of biological processes. Here we set out to investigate whether these genes have a modular organization similar to that of protein-coding genes. Accordingly, we compared the sequence of all the exonic regions of human lncRNAs and identified 106 clusters of non-repetitive exonic modules shared between this class of genes. These modules display evidence of purifying selection, are highly conserved between humans and the four great ape species, and may represent distinct functional units that have been shuffled among multiple lncRNA genes, in a manner similar to the exon-shuffling process that is observed in the coding genome.
Cryo-EM structure of the Spo11 core complex bound to DNA

The DNA double-strand breaks that initiate meiotic recombination are formed by topoisomerase relative Spo11, supported by conserved auxiliary factors. Because high-resolution structural data are lacking, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-EM structures at up to 3.3 Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104, and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3’-OH and first 5’ overhanging nucleotide, definitively establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.
DeLoop: a deep learning model for chromatin loop prediction from sparse ATAC-seq data

Deciphering gene regulation and understanding the functional implications of disease-associated non-coding variants require the identification of cell-type-specific 3D chromatin interactions. Current chromosome conformation capture technologies fall short in resolution when handling limited cell inputs. To address this limitation, we introduce DeLoop, a deep learning model designed to predict CTCF-mediated chromatin loops from sparse ATAC-seq data by leveraging multitask learning techniques and attention mechanisms. Our model utilizes ATAC-seq data and DNA sequence features, showcasing superior performance compared to existing state-of-the-art models, particularly under low read depth conditions, enabling accurate chromatin loop inference when sufficient cells are infeasible. In addition, generalizing across cell types, DeLoop proves effective in de novo prediction tasks and its potential for predicting functional interactions.
Social avoidance of mice in pain in naturalistic conditions

Pain and social behavior are subject to reciprocal modulation. Both humans and rodents experience emotional contagion from afflicted conspecifics, and may act to relieve the afflicted state of these. Little has been done to investigate the motivation of such prosocial behavior in rodents in naturalistic conditions. Here, we analyzed social interactions in mice group-housed in a seminatural environment (SNE). Social buffering reduced nocifensive behavior in formalin-injected mice. These mice were also both socially withdrawn and avoided by other mice. These findings appear counter to those showing empathy in mouse pain models. It is possible that in naturalistic conditions, healthy mice simply avoid individuals in pain and the cost associated with emotional contagion. Interestingly, behaviors involving direct body contact were not different between saline– and formalin-treated mice, and thus may carry a prosocial, altruistic component. These findings unveil new patterns of social modulation by pain in a naturalistic laboratory setting holding high translational value. Teaser In a new, ethological assay, mice in pain are socially withdrawn and avoided by others, challenging findings of empathy in rodent models.
Atmospheric Boundary Layer Response to Mesoscale SST Anomalies in the Kuroshio Extension

Abstract The atmospheric boundary layer (ABL) response to mesoscale eddies in sea surface temperature (SST) in the Kuroshio Extension was investigated using a high-resolution (T213L30) atmospheric general circulation model. A control run was performed first by integrating the model for 40 days, driven by the satellite-derived, eddy-resolving SST during January 2006. The spatial pattern of surface wind anomalies—that is, a deviation from large-scale winds—reveals a positive correlation with the spatial pattern of mesoscale SST anomalies. The momentum budget analysis of the anomalous zonal wind was performed to investigate the formation of the ABL response. The most dominant term was the pressure gradient force; the advection term was comparable but in the opposite sense. Vertical mixing acts to weaken the anomalous zonal wind near the surface; however, the downward (upward) vertical turbulent flux anomalies were dominant near the ABL top over the warm (cold) SST anomalies, suggesting that the vertical mixi.
Classificação de imagens de sensoriamento remoto baseada em textura por redes neurais

This paper describes a method for classification of remote sensing images integrating the importance of texture with the eficiency of the artificial neural networks. The classification process consists of applying Gabor filters followed by neural network classification. This classification is based on a multi-layer perceptron neural network with backpropagation algorythm. Some results of experiments with synthetic and remote sensing images are presented and discussed.
An insight into the variation of the antioxidative and antibacterial activity of extracts from populations of the subalpine and montane lichen Cetraria islandica

Lichens are supra-organismal symbiotic systems found in most environments. Environmental factors, such as temperature, altitude, precipitation, UV irradiation, or pathogens, significantly influence the physiology of lichens, and thus their secondary metabolism. The thalli of the same lichen species from different environments exhibit variation in the production of secondary metabolites and protective pigments. We selected two populations of the lichen Cetraria islandica from habitats differing in altitude, temperature, and precipitation. Then we compared their antioxidative and antibacterial activity. The lichen thalli were divided into two parts: the upper parts were exposed to light and the lower parts hidden from extensive radiation. The results show that the thalli from harsh alpine environments have higher 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging activity suggesting better tolerance to oxidative stress. On the other hand, the individuals from milder montane environments generally produce more secondary metabolites, leading to increased antibacterial activity of the extracts. The extracts of C. islandica containing fumarprotocetraric and paraconic acids exhibit inhibitory effects against gram-positive bacteria (e.g. Staphylococcus aureus) and some lower activity against gram-negative bacteria (e.g. Escherichia coli).