Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological conditions experienced by bat reservoir hosts predict the intensity of Hendra virus excretion over space and time

The ecological conditions experienced by wildlife reservoir hosts affect the amount of pathogen they excrete into the environment. This then shapes pathogen pressure, the amount of pathogen available to recipient hosts over space and time, which affects spillover risk. Few systems have data on both long-term ecological conditions and pathogen pressure, yet such data are critical for advancing our mechanistic understanding of ecological drivers of spillover risk. To identify these ecological drivers, we here reanalyze shedding data from a spatially replicated, multi-year study of Hendra virus excretion from Australian flying foxes in light of 25 years of long-term data on changing ecology of the bat reservoir hosts. Using generalized additive mixed models, we show that winter virus shedding pulses, previously considered idiosyncratic, are most pronounced after recent food shortages and in bat populations that have been displaced to novel habitats. We next derive the area under each annual shedding curve (representing cumulative virus excretion) and show that pathogen pressure is also affected by the ecological conditions experienced by bat populations. Finally, we illustrate that pathogen pressure positively predicts observed spillover frequency. Our study suggests that recent ecological conditions of flying fox hosts are shifting the timing, magnitude, and cumulative intensity of Hendra virus shedding in ways that shape the landscape of spillover risk. This work provides a mechanistic approach to understanding and estimating risk of spillover from reservoir hosts in complex ecological systems and emphasizes the importance of host ecological context in identifying the determinants of pathogen shedding.
Selection for seed size has indirectly shaped specialized metabolite abundance in oat (Avena sativa L.)

Plant breeding strategies to optimize metabolite profiles are necessary to develop health-promoting food crops. In oats (Avena sativa L.), seed metabolites are of interest for their antioxidant properties and their agronomic role in mitigating disease severity, yet have not been a direct target of selection in breeding. In a diverse oat germplasm panel spanning a century of breeding, we investigated the degree of variation of these specialized metabolites and how it has been molded by selection for other traits, like yield components. We also ask if these patterns of variation persist in modern breeding pools. Integrating genomic, transcriptomic, metabolomic and phenotypic analyses for three types of seed specialized metabolites – avenanthramides, avenacins, and avenacosides – we found reduced genetic variation in modern germplasm compared to diverse germplasm, in part due to increased seed size associated with more intensive breeding. Specifically, we found that abundance of avenanthramides increases with seed size, but additional variation is attributable to expression of biosynthetic enzymes, but avenacoside abundance decreases with seed size and plant breeding intensity. Overall, we show that increased seed size associated with plant breeding has uneven effects on the seed metabolome, and broadly contributes to understanding how selection shapes plant specialized metabolism.
Heterozygous loss of ZBTB38 leads to early embryonic lethality in mice via suppressing Nanog and Sox2

Mammalian DNA methylation is an epigenetic modification which is involved in various biological processes, including gene expression regulation. In mice, methyltransferases are responsible for DNA methylation, which are critical for early embryogenesis. However, the significance of methyl-CpG binding proteins (MBPs) that bind methylated CpG remains largely unknown. We previously demonstrated that ZBTB38/CIBZ-a zinc finger type of MBP-is required for ES cell proliferation by positively regulating Nanog expression. However, the physiological function of ZBTB38 remains unclear. In this study, we generated conditional ZBTB38 knockout mice using Cre-loxP technology. Unexpectedly, our results showed that germline loss of the ZBTB38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. We found that heterozygous loss of ZBTB38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Despite this lethal phenotype, ZBTB38 is dispensable for ES cell establishment and identity. Together, these findings indicate that ZBTB38 is essential for early embryonic development, providing new insights into the roles of MBP in implantation.
Geometric Deep Learning of the Human Connectome Project Multimodal Cortical Parcellation

Understanding the topographic heterogeneity of cortical organisation is an essential step towards precision modelling of neuropsychiatric disorders. While many cortical parcellation schemes have been proposed, few attempt to model inter-subject variability. For those that do, most have been proposed for high-resolution research quality data, without exploration of how well they generalise to clinical quality scans. In this paper, we benchmark and ensemble four different geometric deep learning models on the task of learning the Human Connectome Project (HCP) multimodal cortical parcellation. We employ Monte Carlo dropout to investigate model uncertainty with a view to propagate these labels to new datasets. Models achieved an overall Dice overlap ratio of >0.85 ± 0.02. Regions with the highest mean and lowest variance included V1 and areas within the parietal lobe, and regions with the lowest mean and highest variance included areas within the medial frontal lobe, lateral occipital pole and insula. Qualitatively, our results suggest that more work is needed before geometric deep learning methods are capable of fully capturing atypical cortical topographies such as those seen in area 55b. However, information about topographic variability between participants was encoded in vertex-wise uncertainty maps, suggesting a potential avenue for projection of this multimodal parcellation to new datasets with limited functional MRI, such as the UK Biobank.
Alterations of Ultra Long-Chain Fatty Acids in Hereditary Skin Diseases—Review Article

The skin is a flexible organ that forms a barrier between the environment and the body's interior; it is involved in the immune response, in protection and regulation, and is a dynamic environment in which skin lipids play an important role in maintaining homeostasis. The different layers of the skin differ in both the composition and amount of lipids. The epidermis displays the best characteristics in this respect. The main lipids in this layer are cholesterol, fatty acids (FAs) and ceramides. FAs can occur in free form and as components of complex molecules. The most poorly characterized FAs are very long-chain fatty acids (VLCFAs) and ultra long-chain fatty acids (ULCFAs). VLCFAs and ULCFAs are among the main components of ceramides and are part of the free fatty acid (FFA) fraction. They are most abundant in the brain, liver, kidneys, and skin. VLCFAs and ULCFAs are responsible for the rigidity and impermeability of membranes, forming the mechanically and chemically strong outer layer of cell membranes. Any changes in the composition and length of the carbon chains of FAs result in a change in their melting point and therefore a change in membrane permeability. One of the factors causing a decrease in the amount of VLCFAs and ULCFAs is an improper diet. Another much more important factor is mutations in the genes which code proteins involved in the metabolism of VLCFAs and ULCFAs—regarding their elongation, their attachment to ceramides and their transformation. These mutations have their clinical consequences in the form of inborn errors in metabolism and neurodegenerative disorders, among others. Some of them are accompanied by skin symptoms such as ichthyosis and ichthyosiform erythroderma. In the following review, the structure of the skin is briefly characterized and the most important lipid components of the skin are presented. The focus is also on providing an overview of selected proteins involved in the metabolism of VLCFAs and ULCFAs in the skin.
Oscillatory Microrheology, Creep Compliance and Stress Relaxation of Biological Cells Reveal Strong Correlations as Probed by Atomic Force Microscopy

The mechanical properties of cells are important for many biological processes, including wound healing, cancers, and embryogenesis. Currently, our understanding of cell mechanical properties remains incomplete. Different techniques have been used to probe different aspects of the mechanical properties of cells, among them microplate rheology, optical tweezers, micropipette aspiration, and magnetic twisting cytometry. These techniques have given rise to different theoretical descriptions, reaching from simple Kelvin-Voigt or Maxwell models to fractional such as power law models, and their combinations. Atomic force microscopy (AFM) is a flexible technique that enables global and local probing of adherent cells. Here, using an AFM, we indented single retinal pigmented epithelium cells adhering to the bottom of a culture dish. The indentation was performed at two locations: above the nucleus, and towards the periphery of the cell. We applied creep compliance, stress relaxation, and oscillatory rheological tests to wild type and drug modified cells. Considering known fractional and semi-fractional descriptions, we found the extracted parameters to correlate. Moreover, the Young’s modulus as obtained from the initial indentation strongly correlated with all of the parameters from the applied power-law descriptions. Our study shows that the results from different rheological tests are directly comparable. This can be used in the future, for example, to reduce the number of measurements in planned experiments. Apparently, under these experimental conditions, the cells possess a limited number of degrees of freedom as their rheological properties change.
Potential Analysis of the Attention-Based LSTM Model in Ultra-Short-Term Forecasting of Building HVAC Energy Consumption

Predicting system energy consumption accurately and adjusting dynamic operating parameters of the HVAC system in advance is the basis of realizing the model predictive control (MPC). In recent years, the LSTM network had made remarkable achievements in the field of load forecasting. This paper aimed to evaluate the potential of using an attentional-based LSTM network (A-LSTM) to predict HVAC energy consumption in practical applications. To evaluate the application potential of the A-LSTM model in real cases, the training set and test set used in experiments are the real energy consumption data collected by Kitakyushu Science Research Park in Japan. Pearce analysis was first carried out on the source data set and built the target database. Then five baseline models (A-LSTM, LSTM, RNN, DNN, and SVR) were built. Besides, to optimize the super parameters of the model, the Tree-structured of Parzen Estimators (TPE) algorithm was introduced. Finally, the applications are performed on the target database, and the results are analyzed from multiple perspectives, including model comparisons on different sizes of the training set, model comparisons on different system operation modes, graphical examination, etc. The results showed that the performance of the A-LSTM model was better than other baseline models, it could provide accurate and reliable hourly forecasting for HVAC energy consumption.
Reducing Urban Flood Risk Through Building- and Lot-Scale Flood Mitigation Approaches: Challenges and Opportunities

Urban flooding events are a significant driver of disaster loss, resulting in insured and uninsured losses, property damage, and negative impacts on residents and communities in Canada and internationally. The risk of flooding in urban environments is affected by watershed characteristics, environmental conditions, and the presence and condition of flood management and mitigation technologies. Several building- and lot-scale (or private-side) flood mitigation options are available to better protect properties from the risk of flooding, including backwater valves and foundation drainage systems to reduce the risks of sewer surcharge and infiltration flooding into basements, respectively. The overall success of private-side approaches to reduce the risk of flooding into buildings is reliant upon consistent installation procedures, building code interpretation and enforcement, public engagement, and maintenance. Current research into private-side approaches is presenting many opportunities and solutions for improved flood protection against water-related disasters at home. A greater understanding of the performance of private-side technologies under complex site-specific conditions can help to appoint flood prevention strategies better suited to individual home characteristics. This review paper explores the inter-related factors that affect the risk of basement flooding and explores the challenges and opportunities associated with the adoption and success of private-side flood mitigation approaches. Developing a greater understanding of basement flood vulnerability at the lot-scale will assist in identifying and prioritizing private-side strategies for homeowners to adopt and reduce the risk of flooding based on site-specific conditions affecting flood vulnerability. Continued efforts to evaluate and identify flood risk factors and the performance of private-side strategies are needed to better manage urban flooding events.
Prebiotic, Antioxidant, and Immunomodulatory Properties of Acidic Exopolysaccharide From Marine Rhodotorula RY1801

In this study, an extracellular acidic polysaccharide (EAPS) from marine Rhodotorula sp. RY1801 was extracted, and its biological properties were investigated. EAPS is mainly composed of monosaccharides, including mannose, rhamnose, glucose, galactose, and fucose, had an average molecular weight of 5.902 × 107 Da. The results indicated that EAPS can promote the growth of Lactobacillus acidophilus and L. acidophilus plantarum. EAPS is capable of scavenging both superoxide anion and hydroxyl radicals in vitro. The highest scavenging rate of superoxide anion and hydroxyl radicals is 29 and 84%, respectively. Using in vivo model, we found that the EAPS can expand the lifespan and increase the disease resistance of Caenorhabditis elegans against Klebsiella pneumoniae infection via the DAF-2/DAF-16 pathway. These results suggested that EAPS from marine Rhodotorula sp. RY1801 could promote the growth of beneficial bacteria and can be used as an antioxidant and immunomodulator, which had considerable potential in the food and health industry.
T1 Bladder Cancer: Comparison of the Prognostic Impact of Two Substaging Systems on Disease Recurrence and Progression and Suggestion of a Novel Nomogram

Background: The T1 substaging of bladder cancer (BCa) potentially impacts disease progression. The objective of the study was to compare the prognostic accuracy of two substaging systems on the recurrence and progression of primary pathologic T1 (pT1) BCa and to test a nomogram based on pT1 substaging for predicting recurrence-free survival (RFS) and progression-free survival (PFS). Methods: The medical records of 204 patients affected by pT1 BCa were retrospectively reviewed. Substaging was defined according to the depth of lamina propria invasion in T1a−c and the extension of the lamina propria invasion to T1-microinvasive (T1m) or T1-extensive (T1e). Uni- and multivariable Cox regression models evaluated the independent variables correlated with recurrence and progression. The predictive accuracies of the two substaging systems were compared by Harrell's C index. Multivariate Cox regression models for the RFS and PFS were also depicted by a nomogram. Results: The 5-year RFS was 47.5% with a significant difference between T1c and T1a (p = 0.02) and between T1e and T1m (p < 0.001). The 5-year PFS was 75.9% with a significant difference between T1c and T1a (p = 0.011) and between T1e and T1m (p < 0.001). Model T1m−e showed a higher predictive power than T1a−c for predicting RFS and PFS. In the univariate and multivariate model subcategory T1e, the diameter, location, and number of tumors were confirmed as factors influencing recurrence and progression after adjusting for the other variables. The nomogram incorporating the T1m−e model showed a satisfactory agreement between model predictions at 5 years and actual observations. Conclusions: Substaging is significantly associated with RFS and PFS for patients affected by T1 BCa and should be included in innovative prognostic nomograms.
Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified, four were highly significantly rhythmically expressed (per1a.1, per1a.2, per1b, per2b) and one was marginally significantly rhythmically expressed (per2a). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 1,642 rhythmically expressed genes (p < 0.001), of which 12 were clock genes. The majority of rhythmically expressed genes peaked two hours before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.
Fluorogenic EXO-Probe Aptamers for Imaging and Tracking Exosomal RNAs

Small extracellular vesicles (sEVs), or exosomes, play important roles in physiological and pathological cellular communication. sEVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. Studying the intricacies of sEV function and RNA-based communication requires tools capable of labeling sEV RNA. Here we developed a novel genetically encodable reporter system for tracking sEV RNAs comprising an sEV-loading RNA sequence, termed the EXO-Code, fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of RNA puncta and colocalization with markers of multivesicular bodies; imaging RNA puncta within sEVs; and quantification of sEVs. This technology represents a useful and versatile tool to interrogate the role of sEVs in cellular communication via RNA trafficking to sEVs, cellular sorting decisions, and sEV RNA cargo transfer to recipient cells.
Dynamics of Visual Adaptation With Simultaneous Stimulation of Two Visual Pathways

Primates’ retinal ganglion cells in different visual pathways have been shown to adapt independently (Current Biology 22 (2012) 220–224). However, the manner in which adaptation occurs under simultaneous stimulation of two visual pathways has not yet been explored. In this study, the dynamics of color afterimages were measured while stimulating one or two visual pathway using a time-varying afterimage paradigm. The dynamics of adaptation was approximately equivalent among the three primary visual pathways, but adaptation was slower for simultaneous stimulation of two visual pathways compared to the stimulation of one visual pathway. In addition, we found that the speed of adaptation also depends upon which two pathways are combined. We developed a two-stage adaptation model, both with the same dynamics, to account for the results with simultaneous stimulation of two pathways.
The Alkali Tolerance of Broomcorn Millet (Panicum miliaceum L.) at the Germination and Seedling Stage: The Case of 296 Broomcorn Millet Genotypes

Broomcorn millet (BM), one of the earliest domesticated cereal crops originating in northern China, can tolerate extreme conditions, such as drought and high temperatures, which are prevalent in saline-alkali, arid, and barren landscapes. However, its adaptive mechanism to alkali stress is yet to be comprehensively understood. In this study, 80 and 40 mM standard alkali stress concentrations were used to, respectively, evaluate the alkali tolerance at the germination and seedling stages of 296 BM genotypes. Principal component analysis (PCA), Pearson's correlation analysis, and F-value comprehensive analysis were performed on the germination parameters (germination potential, germination index, germination rate, vigor index, root length/weight, sprout length/weight, and alkali damage rate). Based on their respective F-values, the BM genotypes were divided into five categories ranging from highly alkali resistant to alkali sensitive. To study the response of seedlings to alkaline stress, we investigated the phenotypic parameters (plant height, green leaf area, biomass, and root structure) of 111 genotypes from the above five categories. Combining the parameters of alkali tolerance at the germination and seedling stages, these 111 genotypes were further subdivided into three groups with different alkali tolerances. Variations in physiological responses of the different alkali-tolerant genotypes were further investigated for antioxidant enzyme activity, soluble substances, malondialdehyde (MDA) content, electrolyte leakage rate, and leaf structure. Compared with alkali-sensitive genotypes, alkali-tolerant genotypes had high antioxidant enzyme activity and soluble osmolyte content, low MDA content and electrolyte leakage rate, and a more complete stomata structure. Taken together, this study provides a comprehensive and reliable method for evaluating alkali tolerance and will contribute to the improvement and restoration of saline-alkaline soils by BM.
Advanced Imaging of the Vestibular Endolymphatic Space in Ménière's Disease

The diagnosis of “definite” Méniére's disease (MD) relies upon its clinical manifestations. MD has been related with Endolymphatic Hydrops (EH), an enlargement of the endolymphatic spaces (ES) (cochlear duct, posterior labyrinth, or both). Recent advances in Magnetic Resonance (MR) imaging justify its increasing role in the diagnostic workup: EH can be consistently recognized in living human subjects by means of 3-dimensional Fluid-Attenuated Inversion-Recovery sequences (3D-FLAIR) acquired 4 h post-injection of intra-venous (i.v.) Gadolinium-based contrast medium, or 24 h after an intratympanic (i.t.) injection. Different criteria to assess EH include: the comparison of the area of the vestibular ES with the whole vestibule on an axial section; the saccule-to-utricle ratio (“SURI”); and the bulging of the vestibular organs toward the inferior 1/3 of the vestibule, in contact with the stapedial platina (“VESCO”). An absolute link between MD and EH has been questioned, since not all patients with hydrops manifest MD symptoms. In this literature review, we report the technical refinements of the imaging methods proposed with either i.t. or i.v. delivery routes, and we browse the outcomes of MR imaging of the ES in both MD and non-MD patients. Finally, we summarize the following imaging findings observed by different researchers: blood-labyrinthine-barrier (BLB) breakdown, the extent and grading of EH, its correlation with clinical symptoms, otoneurological tests, and stage and progression of the disease.