Miracle-dz/UniFAR-FTUs huggingface dataset:
Accounting for central place foraging constraints in habitat selection studies

Habitat selection studies contrast the actual space use with the expected use under the null hypothesis of no preference (hereafter neutral use). Neutral use is most often assimilated to the relative abundance of the different habitat types. This generates a considerable bias when studying habitat selection by foragers that perform numerous back and forth to a central place (CP). Indeed, the increased space use close to the CP with respect to distant places reflects a mechanical effect rather than a true preference for the closest habitats. Yet, correctly estimating habitat selection by CP foragers is of paramount importance for a better understanding of their ecology and efficiency of conservation actions. We show that (1) including the distance to the CP as a covariate in unconditional Resource Selection Functions (RSFs), as did in several studies, is quite inefficient to correct for the bias. Bias can be eliminated only by contrasting the actual use distribution to an appropriate neutral distribution that takes the CP forager behavior into account. (2) The need to specify such an appropriate neutral use distribution can be bypassed by relying on a conditional RSF, where the neutral use is assessed locally without reference to the CP.
Species-wide genomics of kākāpō provides transformational tools to accelerate recovery

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

The root systems of most plant species are aided by the soil foraging capacities of symbiotic Arbuscular Mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here are the most contiguous and highest-quality nuclear and mitochondrial genome assemblies of an arbuscular mycorrhizal fungus to date, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of Rhizophagus irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalogue of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While symbiotic nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle. Highlights Assembly of 32 highly contiguous chromosomal scaffolds for R. irregularis, with 23 complete and gapless Gene annotation based on short- and long-read RNA-Seq data from different developmental stages Complete annotation set including mitochondrial genes, DNA methylome, small RNAome, repetitive/transposable elements, functional annotation Identification of a burst of lineage-restricted genetic innovation in the Glomeromycotina subphylum
Spin-glass theory for pedestrians

In these notes the main theoretical concepts and techniques in the field of mean-field spin glasses are reviewed in a compact and pedagogical way, for the benefit of the graduate and undergraduate student. One particular spin-glass model is analysed (the p-spin spherical model) by using three different approaches: thermodynamics, covering pure states, overlaps, overlap distribution, replica symmetry breaking, and the static transition; dynamics, covering the generating functional method, generalized Langevin equation, equations for the correlation and the response, the mode coupling approximation, and the dynamical transition; and finally complexity, covering the mean-field (Thouless–Anderson–Palmer) free energy, metastable states, entropy crisis, threshold energy, and saddles. Particular attention has been paid to the mutual consistency of the results obtained from the different methods.
Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure

Cardiac fibrosis is causally linked to heart failure pathogenesis and adverse clinical outcomes. However, the precise fibroblast populations that drive fibrosis in the human heart and the mechanisms that govern their emergence remain incompletely defined. Here, we performed Cellular Indexing of Transcriptomes and Epitomes by sequencing (CITE-seq) in 22 explanted human hearts from healthy donors, acute myocardial infarction (MI), and chronic ischemic and non-ischemic cardiomyopathy patients. We identified a fibroblast trajectory marked by fibroblast activator protein (FAP) and periostin (POSTN) expression that was independent of myofibroblasts, peaked early after MI, remained elevated in chronic heart failure, and displayed a transcriptional signature consistent with fibrotic activity. We assessed the applicability of cardiac fibrosis models and demonstrated that mouse MI, angiotensin II/phenylephrine infusion, and pressure overload models were superior compared to cultured human heart and dermal fibroblasts in recapitulating cardiac fibroblast diversity including pathogenic cell states. Ligand-receptor analysis and spatial transcriptomics predicted interactions between macrophages, T cells, and fibroblasts within spatially defined niches. CCR2+ monocyte and macrophage states were the dominant source of ligands targeting fibroblasts. Inhibition of IL-1β signaling to cardiac fibroblasts was sufficient to suppress fibrosis, emergence, and maturation of FAP+POSTN+ fibroblasts. Herein, we identify a human fibroblast trajectory marked by FAP and POSTN expression that is associated with cardiac fibrosis and identify macrophage-fibroblast crosstalk mediated by IL-1β signaling as a key regulator of pathologic fibroblast differentiation and fibrosis.
Taste receptor T1R3 in nasal cilia detects Staphylococcus aureus D-amino acids to increase apical glucose uptake and enhance innate immunity

Bitter (T2R) and sweet/umami (T1R) taste receptors serve chemosensory roles throughout the body. In airway cilia, T2Rs detect bacterial metabolites to stimulate bactericidal nitric oxide. T1Rs in solitary chemosensory cells detect glucose in airway surface liquid (ASL) and bacterial D-stereoisomer amino acids to regulate antimicrobial peptides. Using differentiated air-liquid interface cultures of primary nasal cells, we show that the T1R3 receptor is also expressed in human and mouse nasal cell cilia. D-amino acids produced at low mM concentrations by Staphylococcus aureus activate T1R3 to decrease ASL glucose and increase apical glucose uptake by increasing GLUT2 and GLUT10 expression through a β-arrestin pathway. Our data suggests that T1R3 localized to cilia functions as an immune detector for D-amino acids to reduce ASL glucose and potentially limit bacterial growth. Given that glucose protected S. aureus against bactericidal NO produced during T2R activation, the reduced ASL glucose with T1R3 activation may also sensitize bacteria to other innate defenses. HIGHLIGHTS Nasal motile cilia express the T1R3 subunit of the sweet taste receptor S. aureus D-amino acids activate cilia T1R3 to enhance mucosal glucose uptake Reduced airway surface liquid glucose likely reduces S. aureus growth Reduced airway glucose also sensitizes S. aureus to epithelial NO production
Mode of inhibition of RNase P by gambogic acid and juglone

The first step in transfer RNA (tRNA) maturation is the cleavage of the 5’ end of precursor transfer RNA (pre-tRNA) catalyzed by ribonuclease P (RNase P). RNase P is either a ribonucleoprotein (RNP) complex with a catalytic RNA subunit or a protein-only RNase P (PRORP). In most land plants, algae, and Euglenozoa, PRORP is a single-subunit enzyme. There are currently no inhibitors of protein-only RNase P that can be used as tools for studying the biological function of this enzyme. Therefore, we screened for compounds that inhibit the activity of a model PRORP from A. thaliana organelles (PRORP1) using a high throughput fluorescence polarization (FP) cleavage assay. Two compounds, gambogic acid and juglone (5-hydroxy-1,4-naphthalenedione) that inhibit PRORP1 in the 1 μM range were identified and analyzed. These compounds similarly inhibit human mtRNase P, a multi-subunit protein enzyme, and are 50-fold less potent against bacterial RNA-dependent RNase P. Biochemical measurements indicate that gambogic acid is a rapid-binding, uncompetitive inhibitor that targets the PRORP1-substrate complex while juglone acts as time-dependent inhibitor of PRORP1. X-ray crystal structures of PRORP1 in complex with juglone demonstrate the formation of a covalent complex with cysteine side chains on the surface of the protein. A model consistent with the kinetic data is that juglone binds to PRORP1 rapidly to form an inactive enzyme-inhibitor (EI) complex, and then undergoes a slow step to form an inactive covalent adduct with PRORP1. These inhibitors have the potential to be developed into tools to probe PRORP structure and function relationships.
Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains

Intergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins, also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously non-coding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome of S. cerevisiae harbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum, regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step towards understanding its evolutionary importance.
Insights into H2O2-induced signaling in Jurkat cells from analysis of gene expression

Hydrogen peroxide (H2O2) is a ubiquitous oxidant produced in a regulated manner by various enzymes in mammalian cells. H2O2 reversibly oxidises thiol groups of cysteine residues to mediate intracellular signalling. Whilst examples of H2O2 dependent signalling have been reported, the exact molecular mechanism(s) of signalling and the pathways affected are not well understood. Here, the transcriptomic response of Jurkat T cells to H2O2 was investigated to determine global effects on gene expression. With a low H2O2 concentration (10 μM) that did not induced an oxidative stress response or cell death, extensive changes in gene expression occurred after 4 hours (6803 differentially expressed genes). Of the genes with greater then 2-fold change in expression, 85% were upregulated suggesting that in a physiological setting H2O2 predominantly activates gene expression. Pathway analysis identified gene expression signatures associated with FOXO and NTRK signalling. These signatures were associated with an overlapping set of transcriptional regulators. Overall, our results provide a snapshot of gene expression changes in response to H2O2, which, along with further studies, will lead to new insights into the specific pathways that are activated in response to endogenous production of H2O2, and the molecular mechanisms of H2O2 signalling.
Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system

Prophages need to tightly control their lifestyle to either be maintained within the host genome or enter the lytic cycle. The SPβ prophage present in the genome of Bacillus subtilis 168 was recently shown to possess an arbitrium system defining its replication stage. Using an historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we analyzed a key component of the lysis-lysogeny decision system called YopR, which is critical for maintenance of lysogeny. Here, we demonstrate that the heat-sensitive SPβ c2 phenotype is due to a single nucleotide exchange in the yopR gene, rendering the encoded YopRG136E protein temperature sensitive. Structural characterization of YopR revealed that the protein is a DNA-binding protein with an overall fold like tyrosine recombinases. Biochemical and functional analyses indicate that YopR has lost the recombinase function and the G136E exchange impairs its higher order structure and DNA binding activity. We further show that the heat-inducible SPβ excision of the c2 mutant still depends on the serine recombinase SprA. Finally, an evolution experiment identified the YosL protein of unknown function as a novel component of the lysis-lysogeny management system, as the presence of yosL is crucial for the induction of the lytic cycle of SPβ.
Unique and Shared Proteome Responses of Rice Plants (Oryza sativa) to Individual Abiotic Stresses

Food safety of staple crops such as rice is of global concern and is at the top of the policy agenda worldwide. Abiotic stresses are one of the main limitations to optimizing yields for sustainability, food security and food safety. We analyzed proteome changes in Oryza sativa ssp. Nipponbare in response to three adverse abiotic treatments, including three levels of drought (mild, moderate, and severe), soil salinization, and non-optimal temperatures. All treatments had modest, negative effects on plant growth, enabling us to identify proteins that were common to all stresses, or unique to one. More than 75% of the total of differentially abundant proteins in response to abiotic stresses were specific to individual stresses, while fewer than 5% of stress-induced proteins were shared across all abiotic constraints. Stress-specific and non-specific stress-responsive proteins identified were categorized in terms of core biological processes, molecular functions, and cellular localization. Data Access All data have also been submitted to the PRIDE data repository, and will be available with project identifier PXD037280.
Tmem117 in AVP neurons regulates the counterregulatory response to hypoglycemia

The counterregulatory response to hypoglycemia (CRR), which ensures a sufficient glucose supply to the brain, is an essential survival function. It is orchestrated by incompletely characterized glucose-sensing neurons, which trigger a coordinated autonomous and hormonal response that restores normoglycemia. Here, we investigated the role of hypothalamic Tmem117, identified in a genetic screen as a regulator of CRR. We show that Tmem117 is expressed in vasopressin magnocellular neurons of the hypothalamus. Tmem117 inactivation in these neurons increases hypoglycemia-induced vasopressin secretion leading to higher glucagon secretion, an estrus cycle phase-dependent effect in female mice. Ex vivo electrophysiological analysis, in-situ hybridization and in vivo calcium imaging reveal that Tmem117 inactivation does not affect the glucose-sensing properties of vasopressin neurons but increases ER-stress, ROS production and intracellular calcium levels accompanied by increased AVP production and secretion. Thus, Tmem117 in vasopressin neurons is a physiological regulator of glucagon secretion and highlight the role of these neurons in the coordinated response to hypoglycemia.
Residence time analysis on cerebral aneurysms treated with coils using planar-laser-induced fluorescence and computational fluid dynamics

Biofidelic numerical models have been developed such as the coil-resolved model to study hemodynamics in the treated aneurysm. In this model, the geometry of the coils is recreated from high-resolution tomography scans of a phantom aneurysm treated with coils. However, this model hasn’t been validated. The purpose of this work is to validate the coil-resolved model. To achieve this, we used the planar-laser induced fluorescence technique on phantom aneurysm treated with coils and measured the residence time and the evolution of rhodamine concentration during the washout. We run passive scalar simulations with the coil-resolved model and measured the evolution of concentration over time. The comparison of the numerical and the experimental results shows that the coil-resolved model reproduces the hemodynamics of the experimental setup. Therefore it can be used as a reference to study hemodynamics in the treated aneurysm or to validate porous media models developed for treatment outcomes prediction.
Workﬂow for processing digitized documents at the United Nations

This work addresses the problem of the digitization of paper documents under the responsibility of the Archives and Records Management Service of the United Nations. Those collections are unique, reﬂecting the history of the organization since 1945, which motivates its digitization, to promote its easy access. So far, more than 10 million images and more than 5TB of data was created, a large part already available online, but there is still a long way ahead to either digitize what is still in paper and to have an automated workﬂow to process the digitized images and produce objects for convenient digital access. This thesis therefore aims to build an effective automated workﬂow to process those digitized images for optimal online publishing and search.
Breadth-First Pipeline Parallelism

We introduce Breadth-First Pipeline Parallelism, a novel training schedule which optimizes the combination of pipeline and data parallelism. Breadth-First Pipeline Parallelism lowers the training time, cost and memory usage by combining a high GPU utilization with a small batch size per GPU, and by making use of fully sharded data parallelism. Experimentally, we observed increases of up to 53% in training speed.
Modeling a Square Vibrating Plate

This report is inspired by the work of Ernst Florens Friedrich Chladni, who visualized the nodal lines on a vibrating plate under resonance. We have investigated two models to reproduce the modes of vibration on a square plate with free edges. Both of the models are solved analytically by separation of variables and numerically using an explicit finite difference method. The first model is based on the wave equation, which produces clear nodal patterns but the patterns are different from the experimental results. However, due to the simplicity of the model, we are able to test different techniques such as the eigenvector/eigenvalue approach, various forcing methods, and beats. The second model is based on elasticity theory which, unlike the wave equation model, involves the mechanical properties of the plate. Though the analytical solution of this model cannot be verified, we applied similar techniques used for the wave equation to estimate the resonant frequencies. The resulting nodal patterns are closer to those observed in the experiments. Related issues and possible future work are also discussed in this report.
Effect of molasses on growth and lipid profile of Dunaliella salina

This research aims to evaluate the effect of molasses as a source of organic carbon on the growth and lipid profile of Dunaliella salina cultivated under different light regimes to determine its strategy and potential use to produce biodiesel. Two sources of nutrients (F/2 medium, F/2; molasses, M) and two light conditions (12 h light: 12 h darkness, 12L:12D) conformed four treatments (F/2 12L:12D, F/2 D, M 12L:12D, and MD) that were investigated with three replicates each. The concentration of microalgae produced by the groups under light conditions was more than double that of those grown in darkness. The highest biomass produced (46.91 ± 6.47 g L) was obtained in the F/2 medium with 12L:12D treatment, while the lowest (18.99 ± 0.78 g L) was in the M 12L:12D group. Regardless of the culture conditions, the lipids were mainly composed of the C16:0 and C18 fatty acids. The use of molasses as a culture medium produced the highest amount of C18:1, regardless of the light regime. Molasses promoted the highest production of fatty acids methyl esters. Depending on the culture medium, D. salina cells showed different percentages of saturated (SFA), monounsaturated (MFA), and polyunsaturated (PUFA) fatty acids. The highest amount of saturated fatty acids was obtained in F/2 12L:12D. The highest amount of polyunsaturated fatty acids was presented in the mixotrophic culture (molasses and light). The cultures grown with molasses were rich in monounsaturated fatty acids. An inexpensive industrial by-product, Cane molasses could be a low-cost feedstock for biodiesel in cultivating D. salina.
Simulating Bruise and Defects on Mango images using Image-to-Image Translation Generative Adversarial Networks

A well-balanced dataset is essential for every computer vision task. However, the process of gathering data from various sources is laborious and time-consuming. The lack of samples and class imbalance will reduce the reliability of the CNN model in image classification and recognition tasks. In this research, we examine the use of Image-to-Image translation with conditional GAN for producing synthetic mango images with bruises. We introduce a conditional GAN for producing mango images with controlled surface defects, which is suited for dataset augmentation tasks within the fruit classification problem domain. The findings shows that our networks is able to generate mango images with bruises that are very close to the ground truth with FID value of 37.0