Miracle-dz/UniFAR-FTUs huggingface dataset:
Social intelligence model with multiple internal models

To exhibit social intelligence, animals have to recognize who they are communicating with. One way to make this inference is to select among multiple internal generative models of each conspecific. This induces an interesting problem: when receiving sensory input generated by a particular conspecific, how does an animal know which internal model to update? We consider a theoretical and neurobiologically plausible solution that enables inference and learning under multiple generative models by integrating active inference and (online) Bayesian model selection. This scheme fits sensory inputs under each generative model. Model parameters are then updated in proportion to the probability it could have generated the current input (i.e., model evidence). We show that a synthetic bird who employs the proposed scheme successfully learns and distinguishes (real zebra finch) birdsongs generated by several different birds. These results highlight the utility of having multiple internal models to make inferences in complicated social environments.
Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown under Two Watering Regimes: Implications for Management of Genetic Resources

Management of forest genetic resources requires experimental data related to the genetic variation of the species and populations under different climatic conditions. Foresters also demand to know how the main selective drivers will influence the adaptability of the genetic resources. To assess the inter- and intraspecific variation and plasticity in seedling drought tolerance at a relevant genetic resource management scale, we tested the changes in growth and biomass allocation of seedlings of Pinus oocarpa, P. patula and P. pseudostrobus under two contrasting watering regimes. We found general significant intraspecific variation and intraspecific differences in plasticity, since both population and watering by population interaction were significant for all three species. All the species and populations share a common general avoidance mechanism (allometric adjustment of shoot/root biomass). However, the intraspecific variation and differences in phenotypic plasticity among populations modify the adaptation strategies of the species to drought. Some of the differences are related to the climatic conditions of the location of origin. We confirmed that even at reduced geographical scales, Mexican pines present differences in the response to water stress. The differences among species and populations are relevant in afforestation programs as well as in genetic conservation activities.
Australian Canola Oil - the influence of varietal traits, processing and storage on phytosterols, tocopherols and carotenoids

XI CHAPTER ONE Literature review. 1 1. Vegetable oils . 2 2. Canola origin and history . 5 3. Seed varieties and seed breeding . 6 4. Canola production and processing . 9 4.1 From paddock to seed . 9 4.2 From seed harvest to oil processing . 10 4.3 From oil processing to the supermarket shelf . 11 5. Canola oil composition . 5.1 Major components . 15 5.2 Minor components . 19 5.2. 1 Sterols. 20 5.2. 2 Tocopherols . 21 5.2. 3 Carotenoids . 5.2. 4 Other minor components . 6. Canola quality control and associated methods of analysis . 6.1 Seed quality testing . 6.2 Oil quality testing. 7. Analyses of bioactive compounds . 5 7.1 Phytosterols . 7. Tocopherols. 7. Carotenoids . 8. Considerations for the preservation of bioactive compounds. 8.1 General considerations . 8.2 Seed variety and growing location effects . 40 8.3 Processing techniques . 42 8.4 Seed and oil storage . 43 9. Concluding remarks . 45 10. Research Question and Objectives. 4 References . CHAPTER TWO Rapid method for the determination of phytosterols, tocopherols, and carotenoids in canola oil . 6 Paper 1: HPLC-DAD-MS/MS method for rapid analysis of bioactives in canola oil . 6 CHAPTER THREE Effects of genotype and environment . 7 Paper 2: A multiphase experiment for the analysis of bioactive compounds in canola oil: Sources of error from field and laboratory . 7 Paper 3: Genotype x environment interaction for several classes of bioactive compounds in canola oil . 8 CHAPTER FOUR Effects of seed and oil processing . Paper 4: Effects of processing on bioactive compounds in Australian grown and processed canola (Brassica napus) seed and oil . CHAPTER FIVE Effects of storage temperature and duration phytosterol, tocopherol, and carotenoid . 1 Paper 5: Effects of storage on bioactive concentrations in the seed and oil CHAPTER SIX Discussion and concluding remarks . 1 CERTIFICATE OF AUTHORSHIP I, Clare Flakelar, hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma at Charles Sturt University, or any other educational institution, except where due acknowledgment is made in the thesis. Any contribution made to the research, by colleagues with whom I have worked at Charles Sturt University or elsewhere during my candidature, is fully acknowledged. I agree that the thesis be accessible for the purpose of study and research in accordance with the normal conditions established by the Executive Director of Library Services at Charles Sturt University, for the care, loan and reproduction of the thesis, subject to confidentiality provisions as approved by the University. Name: Clare L. Flakelar
Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of cerebellar CHIPopathy

CHIP (carboxyl terminus of heat shock 70-interacting protein) has long been recognized as an active member of the cellular protein quality control system given the ability of CHIP to function as both a co-chaperone and ubiquitin ligase. Mutations in CHIP are the driver of spinocerebellar autosomal recessive 16 (SCAR16), or cerebellar CHIPopathy, as we initially discovered this disease was caused by a loss of CHIP ubiquitin ligase function. The initial mutation describing SCAR16 was a missense mutation in the ubiquitin ligase domain of CHIP (p.T246M). Using multiple biophysical and cellular approaches, we demonstrate that T246M mutation results in structural disorganization and misfolding of the CHIP U-box domain, promoting oligomerization, and increased proteasome-dependent turnover. CHIP-T246M has no ligase activity, but maintains interactions with chaperones and alters the co-chaperone function of CHIP. To establish preclinical models of SCAR16, we engineered T246M at the endogenous locus in both mice and rats. Animals homozygous for T246M had both cognitive and motor cerebellar dysfunction distinct from those observed in the CHIP null animal model, as well as deficits in learning and memory, reflective of the cognitive deficits reported in SCAR16 patients. We conclude that the T246M mutation is not equivalent to the total loss of CHIP, supporting the concept that disease-causing CHIP mutations have different biophysical and functional repercussions on CHIP function that may directly correlate to the spectrum of clinical phenotypes observed in SCAR16 patients. Our findings both further expand our basic understanding of CHIP biology and provide meaningful mechanistic insight underlying the molecular drivers of SCAR16 disease pathology, which may be used to inform the development of novel therapeutics for this devastating disease.
Réponse d’Arabidopsis thaliana au Turnip mosaic virus (TuMV) en conditions extérieures et en conditions contrôlées : phénotypage fin de traits de maladie et métaboliques et architecture génétique associée

Les plantes sont des organismes immobiles qui doivent repondre et s’adapter a des contraintes abiotiques et biotiques. Parmi les stress biotiques, les maladies virales, etablies ou emergentes, peuvent etre responsables de pertes de rendement majeures aux consequences economiques importantes. Face aux phytovirus la lutte genetique constitue le moyen de lutte le plus efficace, le plus respectueux de l’environnement et du consommateur. Comprendre l’interaction entre les plantes et les virus reste indispensable pour rechercher de nouvelles sources de resistances. Ce travail de these s’interesse a l’etude du pathosysteme naturel Arabidopis thaliana/Turnip mosaic virus (TuMV). Les essais ont ete menes majoritairement en conditions exterieures permettant une analyse de l’interaction dans un environnement multistress. La reponse d’A. thaliana a ete exploree par l’etude de traits lies a la maladie et par la variation en metabolites primaires et secondaires. Ce travail a permis i) de caracteriser de facon fine la reponse d’A. thaliana au TuMV en conditionsmultistress en exploitant la diversite naturelle d’une population mondiale et francaise ii) de determiner l’architecture genetique de cette interaction par des approches de genetique d’association et de QTL mapping. Plusieurs nouveaux loci potentiellement impliques dans la reponse ont ete identifies iii) de montrer l’interet du phenotypage metabolique pour discriminer les accessions en fonction de leur sensibilite au TuMV. La multidisciplinarite des approches constitue la richesse de ce travail de these qui contribue a une meilleure caracterisation et comprehension de la reponse des plantes lors d’une infection virale.
Corrections of fish school area and mean volume backscattering strength by simulation of an omnidirectional multi-beam sonar

Corrections of fish school area and mean volume backscattering strength by simulation of an omnidirectional multi-beam sonar Vasilis Trygonis* and Zacharias Kapelonis University of the Aegean, Department of Marine Sciences, University Hill, Mytilene 81100, Greece Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Agios Kosmas, Athens 16777, Greece *Corresponding author: tel: þ 3
Lipid utilization in skeletal muscle cells is modulated in vitro and in vivo by specific miRNAs

Skeletal muscle is composed by different myofiber types that can preferentially use glycolysis or lipids for ATP production. How fuel preference is specified in these post-mitotic cells is unknown. Here we show that miRNAs are important players in defining the myofiber metabolic profile. mRNA and miRNA signatures of all myofiber types obtained at single cell level unveiled fiber-specific regulatory networks and identified two master miRNAs that coordinately control myofiber fuel preference and mitochondrial morphology. Our work provides a complete and integrated myofiber type-specific catalogue of genes and miRNAs expressed and establishes miR-27a-3p and miR-142-3p as key regulators of lipid utilization in skeletal muscle. HIGHLIGHTS Transcriptional networking in single cells distinguished myofibers based on glycolytic or oxidative metabolism, regulated by specific miRNAs miR-27a-3p and −142-3p influence mitochondrial morphology miR-27a-3p improves lipid utilization and increases glycogen storage both in vitro and in vivo miR-142-3p reduces lipid utilization both in vitro and in vivo
BioFeatureFinder: Flexible, unbiased analysis of biological characteristics associated with genomic regions

BioFeatureFinder is a novel algorithm which allows analyses of many biological genomic landmarks (including alternatively spliced exons, DNA/RNA-binding protein binding sites, and gene/transcript functional elements, nucleotide content, conservation, k-mers, secondary structure) to identify distinguishing features. BFF uses a flexible underlying model that combines classical statistical tests with Big Data machine-learning strategies. The model is created using thousands of biological characteristics (features) that are used to build a feature map and interpret category labels in genomic ranges. Our results show that BFF is a reliable platform for analyzing large-scale datasets. We evaluated the RNA binding feature map of 110 eCLIP-seq datasets and were able to recover several well-known features from the literature for RNA-binding proteins; we were also able to uncover novel associations. BioFeatureFinder is available at https://github.com/kbmlab/BioFeatureFinder/.
Effect of silvicultural gap size on 51 year species recruitment, growth and volume yields in Quercus dominated stands of the Northern Cumberland Plateau, USA

This manuscript seeks to further the understanding of how silvicultural gap size affects stand development and growth patterns among species. The authors studied an experiment established more than 50 years ago in oak ( Quercus spp.) dominated stands that tested three gap sizes, 0.02 ha, 0.16 ha and 0.46 ha. Statistical analysis addressed stand-level trends associated with tree size, density, and sawtimber volume as well as species recruitment and individual tree growth and volume. Distinct patterns among gap sizes were present in overall structural characteristics including a signi ﬁ cant increase in year 51 sawtimber volume with increasing gap size. Data also indicated that conditions present in the different gap sizes had an in ﬂ uence on individual tree size and that the nature of this effect varied among species group. Tree recruitment among the primary species groups, maple ( Acer spp.), oak and yellow-poplar ( Liriodendron tulipifera L. ), was strongly related to gap size and a notable trend with species shade tolerance was present. Results highlighted how shifting species proportions and changes in tree size associated with different gap sizes can alter important stand characteristics that affect management and forest utility within gap-based silvicultural approaches for upland mixed oak forests in the study region.
Celtis sinensis Pers. (Ulmaceae) naturalised in northern South Africa and keys to distinguish between Celtis species commonly cultivated in urban environments

Background: Alien Celtis species are commonly cultivated in South Africa. They are easily confused with indigenous C. africana Burm.f. and are often erroneously traded as such. Celtis australis L. is a declared alien invasive tree. Celtis sinensis Pers. is not, but has become conspicuous in urban open spaces. Objectives: This study investigates the extent to which C. sinensis has become naturalised, constructs keys to distinguish between indigenous and cultivated Celtis species, and provides a descriptive treatment of C. sinensis . Methods: Land-cover types colonised by C. sinensis were randomly sampled with 16 belt transects. Woody species were identified, counted and height measured to determine the population structure. C. africana and the three alien Celtis species were cultivated for 2 years and compared morphologically. Results: Celtis sinensis, Ligustrum lucidum and Melia azedarach were found to be alien species, most abundant in urban areas. The population structure of C. sinensis corresponds to that of the declared invasive alien, M. azedarach . Although C. africana occurs naturally, it is not regularly cultivated. This is ascribed to erroneous plantings because of its resemblance to juvenile plants of C. sinensis . Keys are provided to identify Celtis species based on leaf shape and margin, and drupe characters. Conclusion: Celtis sinensis is naturalised in central South Africa, especially in urban open spaces and beginning to colonise natural areas. It is flagged as a species with invasive potential. Characteristics of the leaves and fruits allow for accurate identification of indigenous and alien Celtis species, both as juvenile or adult trees.
The role of ripk1 in tnf-induced cell death in intestinal epithelial cells

Inflammatory bowel diseases (IBD) are chronic inflammatory processes that affect the gastrointestinal tract. IBD is characterized by an intestinal inflammation and epithelial cell injury leading to a poor psychosocial wellbeing and increased the risk for cancer. IBD pathogenesis is multifactorial, involving genetic predisposition, epithelial barrier defects, dysregulated immune responses, and environmental factors. The current gold standard therapy is TNF blockade, a key proinflammatory cytokine. TNF activates the NF-κB pathway inducing an anti-apoptotic cell response and it plays an important role in the regulation of the intestinal homeostasis. However, in certain situations, TNF can also trigger cell death through different signaling cascades, a typical feature seen in IBD. This work shows how apoptotic IEC areas in IBD human samples co-localize with NF-κB activation and A20 upregulation. Furthermore, using animal models as well as in vitro studies, we show how NF-κB activation and A20 upregulation are required events to trigger TNFdependent cell death in intestinal epithelial cells. We also show how other cytokines that are usually upregulated in IBD interact with TNF to induce cell death. Specifically, lymphotoxin β receptor activation synergizes with TNF to trigger apoptosis. We have proven that intestinal epithelial cells undergo apoptotsis downstream of TNFR in a RIPK1 dependent manner, and that kinase inhibition of RIPK1 prevents cell death. Chronic NF-κB induces apoptosis downstream of TNF in a ROS dependent manner and A20 requires its linear ubiquitin binding domain, zinc finger seven, to enhance the formation of complex IIb or ripoptosome after TNF stimulation. Overall these results help to further understand the pathogenesis of IBD and suggests RIPK1 as a possible target for new drugs to treat IBD.
Modelling Large, Dynamic, and Heterogeneous Populations Using DNA Libraries

The study of any population of large size and high diversity is limited by the lack of data and associated insights. For a pool of individuals, each associated with a unique characteristic feature, as the pool size grows, the possible interactions increase exponentially, quickly beyond the scope of computation, not to mention experimental manipulation and analysis. Herein, we report a facile RT-PCR-based method, to correlate the amplification curves with various DNA libraries of defined diversity, and perform operations with groups of quaternary numbers as input and diversity as output. An attractive feature of this approach is the possibility of realizing parallel computation with an eventually unlimited number of variables. We demonstrate that DNA libraries can be used to model heterogeneous populations, exhibiting functions such as self-protection, subjected to biased expansion, and to evolve into complex structures. Moreover, the method can be applied to drug discovery using DNA-encoded chemical library (DECL) technology, to optimize selection conditions for identifying potent and specific bio-molecular interactions.
Overexpression of S-Adenosylmethionine Synthetase Gene from Pyropia tenera Enhances Tolerance to Abiotic Stress

Pyropia tenera is an intertidal red alga of commercial significance owing to its popularity as a health-promoting seafood product. This alga grows in marine environments and is frequently exposed to high salinity and osmotic stress, which impact its growth. Therefore, the enhancement of stress tolerance in P. tenera is critical. In the present work, we aimed to elucidate the mechanisms underlying abiotic stress tolerance in this species; specifically, we identified the P. tenera S-adenosylmethionine synthetase-encoding gene ( PtSAMS ) and characterized its biological function. This gene, which is known to play a role in stress tolerance in other plants, was cloned and overexpressed in Escherichia coli under high-salinity conditions. The PtSAMS gene was found to encode a 385-amino-acid protein with a molecular weight of 41.8 kDa. In silico sequence alignment and phylogenetic analysis of the PtSAMS amino acid sequence showed that the encoded protein comprises three conserved domains and two motifs that are highly conserved in other plants. Growth assay results indicated that PtSAMS -overexpressing E. coli cells exhibit enhanced tolerance to salt stress. The results suggest that PtSAMS expression is induced by a combination of ion toxicity and osmotic stress resulting from exposure to high salinity in marine environments, and that this gene is expressed at housekeeping levels owing to growth in such conditions. The findings suggest that PtSAMS could be used as a potentially valuable bioresource with utility in the genetic engineering of salt stress-tolerant crop plants.
Prevalence and Characterization of Staphylococcus aureus and Methicillin‐Resistant Staphylococcus aureus on Public Recreational Beaches in Northeast Ohio

Staphylococcus aureus can cause severe life‐threatening illnesses such as sepsis and endocarditis. Although S. aureus has been isolated from marine water and intertidal beach sand, only a few studies have been conducted to assess prevalence of S. aureus at freshwater recreational beaches. As such, we aimed to determine prevalence and molecular characteristics of S. aureus in water and sand at 10 freshwater recreational beaches in Northeast Ohio, USA. Samples were analyzed using standard microbiology methods, and resulting isolates were typed by spa typing and multilocus sequence typing. The overall prevalence of S. aureus in sand and water samples was 22.8% (64/280). The prevalence of methicillin‐resistant S. aureus (MRSA) was 8.2% (23/280). The highest prevalence was observed in summer (45.8%; 55/120) compared to fall (4.2%; 5/120) and spring (10.0%; 4/40). The overall prevalence of Panton‐Valentine leukocidin genes among S. aureus isolates was 21.4% (15/70), and 27 different spa types were identified. The results of this study indicate that beach sand and freshwater of Northeast Ohio were contaminated with S. aureus, including MRSA. The high prevalence of S. aureus in summer months and presence of human‐associated strains may indicate the possibility of role of human activity in S. aureus contamination of beach water and sand. While there are several possible routes for S. aureus contamination, S. aureus prevalence was higher in sites with wastewater treatment plants proximal to the beaches.
The complete mitochondrial genome of Graphomya rufitibia (Diptera: Muscidae)

Abstract Graphomya rufitibia (Diptera: Muscidae) was distributed worldwide. In this study, the complete mitogenome of G. rufitibia was sequenced and annotated, and the full-length was a 15,374 bp fragment, consisting of A (40.64%), G (8.96%), T (36.80%), and C (13.59%). The mitogenome is composed of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region. Most PCGs used the canonical putative codon to start and stop, 21 tRNAs are folded into the classic clover-leaf structure, with the one exception of tRNA-Ser (AGN). A total length of 11,182 bp encoding 3727 amino acids, and account for 72.7% of the whole mitogenome. Phylogenetic analyses showed that G. rufitibia belongs to family Mydaeinae.