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Fleury, D.

Publications and source records attributed to Fleury, D..

6 recordsLinked to original sources

Video-Language Models as Flexible Social and Physical Reasoners

From an early age, humans are challenged with evaluating rich environments full of socially and physically grounded concepts. For example, we might be spectating a rapidly unfolding tennis match, anticipating ball trajectories based on players body cues and goals. In another scenario, we may engage with long storylines, juggling the mental states of characters with varying knowledge of an unfolding conflict. The complexity of this learning problem is notable as it can be multimodal, integrate information at varying timescales, and implicitly co-attend to social and physical scene properties for downstream reasoning. Large language-vision models like GPT4-V, LLaMA-3, which use vision-language embeddings, show skills in commonsense psychology and physics, though they only process single images. Models like CLIP and VisualBERT encode visual information in high-level cortical areas but do not inherently capture video-level representations. This paper introduces a novel video-language architecture that incorporates pooled video embeddings into LLMs by first extracting spatiotemporal embeddings and mapping them to the models decoder through a learnable linear layer. We enhance the model by training it with video-caption pairs from the ADEPT and AGENT datasets, aimed at quantifying "surprisal" in physical and psychological contexts. Finally, we design separate voxel wise encoding models for videos involving physics and psychology using the hidden states and logits from the LLMs last layer and pre-projected CLIP embeddings. We find that hidden state activations can remarkably explain high variance (R^2 up to [~]70%) across dorsal physics regions and highly distributed, ventral social vision areas. Notably, for models trained to only encode physically surprising stimuli, the hidden states and pre-projected CLIP embeddings explain nearly identical regions of variance across the inferior-parietal lobule. However, when the encoding model is trained to encode only socially surprising events, hidden states explain far more distributed ventral and dorsal activations over pre-projected CLIP embeddings.

neuroscience↗

Impaired LAIR-1-mediated immune control due to collagen degradation in fibrosis

Tissue repair is disturbed in fibrotic diseases like systemic sclerosis (SSc), where the deposition of large amounts of extracellular matrix components such as collagen interferes with organ function. LAIR-1 is an inhibitory collagen receptor highly expressed on tissue immune cells. We questioned whether in SSc, impaired LAIR-1-collagen interaction is contributing to the ongoing inflammation and fibrosis. We found that SSc patients do not have an intrinsic defect in LAIR-1 expression or function. Instead, fibroblasts from SSc patients deposit disorganized collagen products in vitro, which are dysfunctional LAIR-1 ligands. This can be mimicked in healthy fibroblasts stimulated by soluble factors that drive inflammation and fibrosis in SSc and is dependent of matrix metalloproteinases and platelet-derived growth factor receptor signaling. In support of a non-redundant role of LAIR-1 in the control of fibrosis, we found that LAIR-1-deficient mice have increased skin fibrosis in response to repeated injury and in the bleomycin mouse model for SSc. Thus, LAIR-1 represents an essential control mechanism for tissue repair. In fibrotic disease, excessive collagen degradation may lead to a disturbed feedback loop. The presence of functional LAIR-1 in patients provides a therapeutic opportunity to reactivate this intrinsic negative feedback mechanism in fibrotic diseases.

immunology↗

Tolerance of combined drought and heat stress is associated with transpiration maintenance and water soluble carbohydrates in wheat grains

Wheat (Triticum aestivum L.) production is increasingly challenged by simultaneous drought and heatwaves. We assessed the effect of both stresses combined on whole plant water use and carbohydrate partitioning in eight bread wheat genotypes that showed contrasting tolerance. Plant water use was monitored throughout growth, and water-soluble carbohydrates (WSC) and starch were measured following a three-day heat treatment during drought. WSC were predominantly allocated to the spike in modern Australian varieties, whereas the stem contained most WSC in older genotypes. Combined drought and heat stress increased WSC partitioning to the spike in older genotypes but not in the modern varieties. Glucose and fructose concentrations in grains measured 12 days after anthesis were associated with final grain weight in the main spike. At the whole plant level, combined drought and heat stress differentially altered daily water use and transpiration response to vapour pressure deficit during grain filling, compared to drought only. Final grain yield was increasingly associated with aboveground biomass and total water use with increasing stress intensity. Ability to maintain transpiration, especially following combined drought and heat stress, appears essential for maintaining wheat productivity. One sentence summaryHigher yield following drought and heat stress in wheats that maintain transpiration and have higher water-soluble carbohydrates content in grains.

plant biology↗

The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates

Wheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits with high temperature and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We completed the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene - seven in absentia, TaSINA. This was associated with the QTLs effects on early vigour, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.\n\nSignificance statementWheat is the worlds most widely grown crop and a staple of human diet. Even brief episodes of high temperature in the growing season cause severe yield reductions. Finding and deploying genes for heat stress tolerance in new varieties is a priority for food security with climate change. We narrowed a genetic locus to a small genomic region where genetic variation was present only in one gene that showed clear differences of expression and improved yield and physiology under stress in the populations. Using diagnostic markers to track the positive haplotype in nearly 750 accessions, we found many regions where the allele could be used in breeding programmes to increase wheats heat tolerance.

genetics↗

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗

A MODULAR PHOTOSYNTHETIC MICROBIAL FUEL CELL WITH INTERCHANGEABLE ALGAESOLAR COMPARTMENTS

This project trial provides a novel small-scale solar harnessing technology which increases environmental effectiveness while maintaining optimal energy efficiency. Although modern solar panels are purposed in producing clean energy, the materials and byproducts of solar cell manufacturing are not eco-friendly. Thus, considering an organic, renewable and energy efficient solar cell model is necessary. Investigations explored multiple highly-photosynthetic algal species which were later integrated into a controlled microbial fuel cell system (MFC). The MFC1 contained algae culture species, including Chlorella Vulgaris, Nannochloropsis, and Spirulina. Parameters, such as periodic lipid yields, algal biomass, and light absorption were assessed throughout the cultivation process while maintaining a controlled environment. After 30 days of cultivation, the culture was transferred to an anode chamber in a closed loop small-scale MFC. Following the first day of algae transfer, microwatt output was analyzed from independent test trials. Statistical comparisons were drawn between electrical energy and light absorption, finding a generally positive correlation. Thus, it is concluded that mid-high algae concentrations significantly increased electrical micro-wattage in highly absorptive algal cultures. The optimal electric levels occurred at 286 A (absorbance) and 35 mW-Nannochloropsis, 123 A-Chlorella (30.2 mW), and 142 A (31 mW)-Spirulina culture. Due to higher absorption rates in the Nannochloropsis culture, this corresponds with the record high voltage levels. The analysis of data indicates that Algae-based MFCs are proven hopeful for alternative high-yield energy production.

ecology↗