Inferring Implicit 3D Representations from Human Figures on Pictorial Maps

In this work, we present an automated workflow to bring human figures, one of the most frequently appearing entities on pictorial maps, to the third dimension. Our workflow is based on training data and neural networks for single-view 3D reconstruction of real humans from photos. We first let a network consisting of fully connected layers estimate the depth coordinate of 2D pose points. The gained 3D pose points are inputted together with 2D masks of body parts into a deep implicit surface network to infer 3D signed distance fields (SDFs). By assembling all body parts, we derive 2D depth images and body part masks of the whole figure for different views, which are fed into a fully convolutional network to predict UV images. These UV images and the texture for the given perspective are inserted into a generative network to inpaint the textures for the other views. The textures are enhanced by a cartoonization network and facial details are resynthesized by an autoencoder. Finally, the generated textures are assigned to the inferred body parts in a ray marcher. We test our workflow with 12 pictorial human figures after having validated several network configurations. The created 3D models look generally promising, especially when considering the challenges of silhouette-based 3D recovery and real-time rendering of the implicit SDFs. Further improvement is needed to reduce gaps between the body parts and to add pictorial details to the textures. Overall, the constructed figures may be used for animation and storytelling in digital 3D maps.Comment: to be published in 'Cartography and Geographic Information Science

The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems

In Rosaceae species, two gametophytic self-incompatibility (GSI) mechanisms are described, the Prunus self-recognition system and the Maleae (Malus/Pyrus/Sorbus) non-self- recognition system. In both systems the pistil component is a S-RNase gene, but from two distinct phylogenetic lineages. The pollen component, always a F-box gene(s), in the case of Prunus is a single gene, and in Maleae there are multiple genes. Previously, the Rosa S-locus was mapped on chromosome 3, and three putative S-RNase genes were identified in the R. chinensis ‘Old Blush’ genome. Here, we show that these genes do not belong to the S-locus region. Using R. chinensis and R. multiflora genomes and a phylogenetic approach, we identified the S-RNase gene, that belongs to the Prunus S-lineage. Expression patterns support this gene as being the S-pistil. This gene is here also identified in R. moschata, R. arvensis, and R. minutifolia low coverage genomes, allowing the identification of positively selected amino acid sites, and thus, further supporting this gene as the S-RNase. Furthermore, genotype–phenotype association experiments also support this gene as the S-RNase. For the S-pollen GSI component we find evidence for multiple F-box genes, that show the expected expression pattern, and evidence for diversifying selection at the F-box genes within an S-haplotype. Thus, Rosa has a non-self-recognition system, like in Maleae species, despite the S-pistil gene belonging to the Prunus S-RNase lineage. These findings are discussed in the context of the Rosaceae GSI evolution. Knowledge on the Rosa S-locus has practical implications since genes controlling floral and other ornamental traits are in linkage disequilibrium with the S-locus.This work was financed by the National Funds through FCT—Fundação para a Ciência e a Tecnologia, I.P., under the project UIDB/04293/2020, and the Centre National de la Recherche Scientifique (CNRS)

The validation of a home food inventory

<p>Abstract</p> <p>Background</p> <p>Home food inventories provide an efficient method for assessing home food availability; however, few are validated. The present study's aim was to develop and validate a home food inventory that is easily completed by research participants in their homes and includes a comprehensive range of both healthful and less healthful foods that are associated with obesity.</p> <p>Methods</p> <p>A home food inventory (HFI) was developed and tested with two samples. Sample 1 included 51 adult participants and six trained research staff who independently completed the HFI in participants' homes. Sample 2 included 342 families in which parents completed the HFI and the Diet History Questionnaire (DHQ) and students completed three 24-hour dietary recall interviews. HFI items assessed 13 major food categories as well as two categories assessing ready-access to foods in the kitchen and the refrigerator. An obesogenic household food availability score was also created. To assess criterion validity, participants' and research staffs' assessment of home food availability were compared (staff = gold standard). Criterion validity was evaluated with kappa, sensitivity, and specificity. Construct validity was assessed with correlations of five HFI major food category scores with servings of the same foods and associated nutrients from the DHQ and dietary recalls.</p> <p>Results</p> <p>Kappa statistics for all 13 major food categories and the two ready-access categories ranged from 0.61 to 0.83, indicating substantial agreement. Sensitivity ranged from 0.69 to 0.89, and specificity ranged from 0.86 to 0.95. Spearman correlations between staff and participant major food category scores ranged from 0.71 to 0.97. Correlations between the HFI scores and food group servings and nutrients on the DHQ (parents) were all significant (p < .05) while about half of associations between the HFI and dietary recall interviews (adolescents) were significant (p < .05). The obesogenic home food availability score was significantly associated (p < .05) with energy intake of both parents and adolescents.</p> <p>Conclusion</p> <p>This new home food inventory is valid, participant-friendly, and may be useful for community-based behavioral nutrition and obesity prevention research. The inventory builds on previous measures by including a wide range of healthful and less healthful foods rather than foods targeted for a specific intervention.</p

Geosciences Roadmap for Research Infrastructures 2025–2028 by the Swiss Geosciences Community

This community roadmap presents an integrative approach including the most urgent infrastructure requests for the future development of geosciences in Switzerland. It recommends to strengthen the multidisciplinary nature of the geosciences by putting all activities under the roof of the Integrated Swiss Geosciences supported by four specific research infrastructure pillars. The roadmap represents the view of the Swiss scientific community in the field of geosciences and is a formal element of the process to elaborate the Swiss Roadmap for Research Infrastructures 2023. This bottom-up contribution to the identification and selection of important national and international research infrastructures has been coordinated by the Swiss Academy of Sciences (SCNAT) on a mandate by the State Secretariat for Education, Research and Innovation (SERI).ISSN:2297-1564ISSN:2297-157

On Robustness Computation and Optimization in BIOCHAM-4

Long version with appendicesInternational audienceBIOCHAM-4 is a tool for modeling, analyzing and synthesizing biochemical reaction networks with respect to some formal, yet possibly imprecise, specification of their behavior. We focus here on one new capability of this tool to optimize the robustness of a parametric model with respect to a specification of its dynamics in quantitative temporal logic. More precisely, we present two complementary notions of robustness: the statistical notion of model robustness to parameter perturbations, defined as its mean functionality, and a metric notion of formula satisfaction robustness, defined as the penetration depth in the validity domain of the temporal logic constraints. We show how the formula robustness can be used in BIOCHAM-4 with no extra cost as an objective function in the parameter optimization procedure, to actually improve the model robustness. We illustrate these unique features with a classical example of the hybrid systems community and provide some performance figures on a model of MAPK signalling with 37 parameters

The MYST-Containing Protein Chameau Is Required for Proper Sensory Organ Specification during Drosophila Thorax Morphogenesis

The adult thorax of Drosophila melanogaster is covered by a stereotyped pattern of mechanosensory bristles called macrochaetes. Here, we report that the MYST containing protein Chameau (Chm) contributes to the establishment of this pattern in the most dorsal part of the thorax. Chm mutant pupae present extra-dorsocentral (DC) and scutellar (SC) macrochaetes, but a normal number of the other macrochaetes. We provide evidences that chm restricts the singling out of sensory organ precursors from proneural clusters and genetically interacts with transcriptional regulators involved in the regulation of achaete and scute in the DC and SC proneural cluster. This function of chm likely relies on chromatin structure regulation since a protein with a mutation in the conserved catalytic site fails to rescue the formation of supernumerary DC and SC bristles in chm mutant flies. This is further supported by the finding that mutations in genes encoding chromatin modifiers and remodeling factors, including Polycomb group (PcG) and Trithorax group (TrxG) members, dominantly modulate the penetrance of chm extra bristle phenotype. These data support a critical role for chromatin structure modulation in the establishment of the stereotyped sensory bristle pattern in the fly thorax

NF-κB/Rel-Mediated Regulation of the Neural Fate in Drosophila

Two distinct roles are described for Dorsal, Dif and Relish, the three NF-κB/Rel proteins of Drosophila, in the development of the peripheral nervous system. First, these factors regulate transcription of scute during the singling out of sensory organ precursors from clusters of cells expressing the proneural genes achaete and scute. This effect is possibly mediated through binding sites for NF-κB/Rel proteins in a regulatory module of the scute gene required for maintenance of scute expression in precursors as well as repression in cells surrounding precursors. Second, genetic evidence suggests that the receptor Toll-8, Relish, Dif and Dorsal, and the caspase Dredd pathway are active over the entire imaginal disc epithelium, but Toll-8 expression is excluded from sensory organ precursors. Relish promotes rapid turnover of transcripts of the target genes scute and asense through an indirect, post-transcriptional mechanism. We propose that this buffering of gene expression levels serves to keep the neuro-epithelium constantly poised for neurogenesis

Structural Basis for Self-Renewal of Neural Progenitors in Cortical Neurogenesis

In mammalian brain development, neuroepithelial cells act as progenitors that produce self-renewing and differentiating cells. Recent technical advances in live imaging and gene manipulation now enable us to investigate how neural progenitors generate the 2 different types of cells with unprecedented accuracy and resolution, shedding new light on the roles of epithelial structure in cell fate decisions and also on the plasticity of neurogenesis

Socio-economic inequalities in physical activity practice among Italian children and adolescents: a cross-sectional study

Aim: The aim of the study was to evaluate whether socio-economic inequalities in the practice of physical activity existed among children and adolescents, using different indicators of socio-economic status (SES). Subjects and methods: Data were derived from the Italian National Health Interview Survey carried out in 2004–2005, which examined a large random sample of the Italian population using both an interviewer-administered and a self-compiled questionnaire. This study was based on a sample of 15,216 individuals aged 6–17 years. The practice of physical activity was measured on the basis of questions regarding frequency and intensity of activity during leisure time over the past 12 months. Parents’ educational and occupational level, as well as family’s availability of material resource, were used as indicators of SES. Multivariable logistic regression analyses were performed to estimate the contribution of each SES indicator to the practice of physical activity, adjusting for potential confounding factors. The results of the regression models are expressed as odds ratio (OR) with 95% confidence intervals (95% CI). Results: About 64% of children and adolescents in the sample declared that they participated in moderate or vigorous physical activity at least once a week. After adjustment for gender, age, parental attitudes towards physical activity and geographical area, the practice of physical activity increased with higher parental educational and occupational level and greater availability of material resources. Children and adolescents whose parents held a middle or high educational title were 80% more likely to practice moderate or vigorous physical activity than subjects whose parents had a lower level of education (OR = 1.80, 95% CI: 1.40–2.33), while subjects with unemployed parents had an odds of practicing moderate or vigorous physical activity 0.43 times that of those children whose parents belonged to the top job occupation category (administrative/professionals). Socio-economic differences were about the same when the practice of vigorous physical activity only was considered instead of that of moderate or vigorous physical activity. Conclusion: Interventions that promote the practice of physical activity, and especially those aimed at the wider physical and social environment, are strongly needed to contrast socio-economic differences in physical activity among children and adolescents

Transcriptional Regulation by CHIP/LDB Complexes

It is increasingly clear that transcription factors play versatile roles in turning genes “on” or “off” depending on cellular context via the various transcription complexes they form. This poses a major challenge in unraveling combinatorial transcription complex codes. Here we use the powerful genetics of Drosophila combined with microarray and bioinformatics analyses to tackle this challenge. The nuclear adaptor CHIP/LDB is a major developmental regulator capable of forming tissue-specific transcription complexes with various types of transcription factors and cofactors, making it a valuable model to study the intricacies of gene regulation. To date only few CHIP/LDB complexes target genes have been identified, and possible tissue-dependent crosstalk between these complexes has not been rigorously explored. SSDP proteins protect CHIP/LDB complexes from proteasome dependent degradation and are rate-limiting cofactors for these complexes. By using mutations in SSDP, we identified 189 down-stream targets of CHIP/LDB and show that these genes are enriched for the binding sites of APTEROUS (AP) and PANNIER (PNR), two well studied transcription factors associated with CHIP/LDB complexes. We performed extensive genetic screens and identified target genes that genetically interact with components of CHIP/LDB complexes in directing the development of the wings (28 genes) and thoracic bristles (23 genes). Moreover, by in vivo RNAi silencing we uncovered novel roles for two of the target genes, xbp1 and Gs-alpha, in early development of these structures. Taken together, our results suggest that loss of SSDP disrupts the normal balance between the CHIP-AP and the CHIP-PNR transcription complexes, resulting in down-regulation of CHIP-AP target genes and the concomitant up-regulation of CHIP-PNR target genes. Understanding the combinatorial nature of transcription complexes as presented here is crucial to the study of transcription regulation of gene batteries required for development