Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Semantic Web technologies in Informatics Education (short paper)

The Semantic Web is an extension of the World Wide Web in which information is represented in a machine-understandable way. In addition, hyperlinks of the Semantic Web connect semantically re-lated information based on ontologies. Thanks to these properties, it becomes possible to automate reasoning over a set of hyerlinked information on the Semantic Web using computational agents. In this paper, we propose to use a Semantic Web reasoner in order to help students understand concepts in informatics. More speciﬁcally, our approach consists of three parts. First, learning materials are collected from DBpedia (https://wiki.dbpedia.org) that is an online knowledge base whose contents are provided in several formats including RDF, Notation3, etc. Second, a teacher deﬁnes inference rules according to which new facts can be derived from the set of learning materials taken from DBpedia. Third, a learner executes a system called EBRS that is a simple-to-use interface for a well-known Semantic Web reasoner, EYE (http://eulersharp.sourceforge.net/). EBRS shows the result of reasoning on a screen so that learners can understand the relationship of learning materials easily. The theme of this research is to exploit Semantic Web technologies such as RDF, ontologies, reasoning programs, etc in order to support informatics education.
First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes

Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of non-marine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96%, and thus exceed the quality of several other published crustacean genomes obtained with similar techniques. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
Acid-catalyzed intramolecular Diels-Alder reactions. The cycloaddition of allyl cations to 1,3-dienes

Cyclisation d'undecatetraenes-1,3,8,10 disubstitues en derives de tetrahydro-3a,6,7,7a indane, catalysee par l'hexachloroantimoniate de tris-(bromo-4 phenyl) aminium
Lipid Droplets Promote Phase Separation of Ago2 to Accelerate Dicer1 Loss and Decelerate miRNA Activity in Lipid Exposed Hepatic Cells

miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostasis in mammalian liver cells. Interestingly, miR-122 on exposure to lipotoxic stress is reduced in liver cells. To fight stress, miRNA processor Dicer1 is depleted to cause reduced miR-122 production and the lowering of miRNA level ensures a better stress response in hepatocytes under lipotoxic stress. Interestingly, lipid droplets, formed in the liver cells on exposure to high fat, ensure cytoplasmic phase separation of Ago2 and prevent interaction of Ago2 with Dicer1. Lipid droplets bind miRNA and enhance miRNA-Ago2 uncoupling and Ago2 phase separation. Loss of interaction between Ago2 and Dicer1 eventually facilitates export and lowering of cellular Dicer1, a process also dependent on the endosomal maturation controller protein Alix, thereby ceasing pre-miRNA processing by Dicer1 in lipid exposed cells. Depletion of lipid droplets by downregulation of Perilipins with siRNAs resulted in a rescue of cellular Dicer1 level and Ago2-Dicer1 interaction. This is a novel mechanism that liver cells adopt to restrict cellular miRNA levels under stress condition. Thus, lipid droplets prevent cell death upon exposure to high fat by reducing intra and extracellular pool of miR-122 in hepatic tissue.
Applications of CCTO supercapacitor in energy storage and electronics

Since the discovery of colossal dielectric constant in CCTO supercapacitor in 2000, development of its practical application to energy storage has been of great interest. In spite of intensive efforts, there has been thus far, no report of proven application. The object of this research is to understand the reason for this lack of success and to find ways to overcome this limitation. Reported herein is the synthesis of our research in ceramic processing of this material and its characterization, particularly with the objective of identifying potential applications. Experimental results have shown that CCTO's permittivity and loss tangent, the two most essential dielectric parameters of fundamental importance for the efficiency of a capacitor device, are intrinsically coupled. They increase or decrease in tandem. Therefore, efforts to simultaneously retain the high permittivity while minimizing the loss tangent of CCTO might not succeed unless an entirely non-typical approach is taken for processing this m.
Modeling the circadian regulation of the immune system: Sexually dimorphic effects of shift work

The circadian clock exerts significance influence on the immune system and disruption of circadian rhythms has been linked to inflammatory pathologies. shift workers often experience circadian misalignment as their irregular work schedules disrupt the natural sleep-wake cycle, which in turn can cause serious health problems associated with alterations in genetic expressions of clock genes. In particular, shift work is associated with impairment in immune function, and those alterations are sex-specific. The goal of this study is to better understand the mechanisms that explain the weakened immune system in shift workers. To achieve that goal, we have constructed a mathematical model of the mammalian pulmonary circadian clock coupled to an acute inflammation model. shift work was simulated by an 8h-phase advance of the circadian system with sex-specific modulation of clock genes. The model reproduces the clock gene expression in the lung and the immune response to various doses of lipopolysaccharide (LPS). Under normal conditions, our model predicts that a host is more sensitive to LPS at CT12 versus CT0 due to a change in the dynamics of IL-10. We identify REV-ERB as a key modulator of IL-10 activity throughout the circadian day. The model also predicts a reversal of the times of lowest and highest sensitivity to LPS, with males and females exhibiting an exaggerated response to LPS at circadian time (CT) 0, which is countered by a blunted immune response at CT12. Overall, females produce fewer pro-inflammatory cytokines than males, but the extent of sequelae experienced by males and females varies across the circadian day. This model can serve as an essential component in an integrative model that will yield mechanistic understanding of how shift work-mediated circadian disruptions affect the inflammatory and other physiological responses. Author summary Shift work has a negative impact on health and can lead to chronic diseases and illnesses. Under regular work schedules, rest is a night time activity and work a daytime activity. Shift work relies on irregular work schedules which disrupt the natural sleep-wake cycle. This can in turn disrupt our biological clock, called the circadian clock, a network of molecular interactions generating biochemical oscillations with a near 24-hour period. Clock genes regulate cytokines before and during infection and immune agents can also impact the clock function. We provide a mathematical model of the circadian clock in the lung coupled to an acute inflammation model to study how the disruptive effect of shift work manifests itself in males and females during inflammation. Our results show that the extent of sequelae experienced by male and female mice depends on the time of infection. The goal of this study is to provide a mechanistic insight of the dynamics involved in the interplay between these two systems.
Monoseptic growth of fungal lipase producers under minimized sterile conditions: Cultivation of Phialemonium curvatum in 350 L scale

A disadvantage of most microbial production processes is the need for sterile techniques. The objective of this study was the development of a robust fungal system allowing monoseptic growth with a minimum of sterile technique in plastic barrels. Selective growth conditions were achieved by mineral salts medium, known for the cultivation of Botrytis cinerea, but containing rapeseed oil instead of glucose as the sole source of carbon and energy. Furthermore, pH 3 was adjusted. A screening of fungi suitable for that system revealed Phialemonium curvatum AW02 isolated from compost. P. curvatum AW02 was superior in comparison with four further fungal isolates because high titers of hydrophilic spores were found in submerged production. Second, a biofilm formation on plastic segments or moving beds made harvesting of the biomass comfortable. Cultivations with volumes of 100 or 350 L showed no contaminations by bacteria when all conditions were controlled. Two independent approaches showed the dependance of growth on lipases in the cultivation system. A B. cinerea strain knocked out in lip1 showed reduced growth in comparison to the wild type because the first catabolic step is the triglyceride hydrolysis. P. curvatum AW02 lipase activity was detected. More than 90% was found to be cell wall associated. Solid shear stress liberated two active proteins showing IEPs of 4.7 or 5.6.
The association of child maltreatment and systemic inflammation in adulthood: A systematic review

Introduction Child maltreatment (CM) is associated with mental and physical health disorders in adulthood. Some studies have identified elevated markers of systemic inflammation in adult survivors of CM, and inflammation may mediate the association between CM with later health problems. However, there are methodological inconsistencies in studies of the association between CM and systemic inflammation and findings are conflicting. We performed a systemic review to examine the association of CM with systemic inflammation in adults. Methods A systematic review was performed following PRISMA . Medline, Embase, Scopus and PsychInfo were searched for studies of the association of CM with blood markers of inflammation in adults. Quality was assessed using the Crowe Critical Appraisal Tool. We had intended to perform a meta-analysis but this was not possible due to variation in study design and reporting. Results Forty-six articles met criteria for inclusion in the review. The most widely reported biomarkers were C-Reactive Protein (CRP) (n=29), interleukin-6 (n=25) and Tumour Necrosis Factor-alpha (TNF-a). Four studies were prospective (all relating to CRP) and the remainder were retrospective. 85% of studies were based in Western settings. In the prospective studies, CM was associated with elevated CRP in adulthood. Results of retrospective studies were conflicting. Methodological issues relating to the construct of CM, methods of analysis, and accounting for confounding or mediating variables (particularly Body Mass Index) may contribute to the uncertainty in the field. Conclusions There is some robust evidence from prospective studies that CM is associated with elevated CRP in adulthood. We have identified significant methodological issues in the literature and have proposed measures that future researchers could employ to improve consistency across studies. Further prospective, longitudinal, research using robust and comparable measures of CM with careful consideration of confounding and mediating variables are required to bring clarity to this field.
Cumulative impacts across Australia’s Great Barrier Reef: A mechanistic evaluation

Cumulative impacts assessments on marine ecosystems have been hindered by the difficulty of collecting environmental data and identifying drivers of community dynamics beyond local scales. On coral reefs, an additional challenge is to disentangle the relative influence of multiple drivers that operate at different stages of coral ontogeny. We integrated coral life history, population dynamics and spatially-explicit environmental drivers to assess the relative and cumulative impacts of multiple stressors across 2,300 km of the world’s largest coral reef ecosystem, Australia’s Great Barrier Reef (GBR). Using literature data, we characterized relationships between coral life history processes (reproduction, larval dispersal, recruitment, growth and mortality) and environmental variables. We then simulated coral demographics and stressor impacts at the organism (coral colony) level on >3,800 individual reefs linked by larval connectivity, and exposed to temporally- and spatially-realistic regimes of acute (crown-of-thorns starfish outbreaks, cyclones and mass coral bleaching) and chronic (water quality) stressors. Model simulations produced a credible reconstruction of recent (2008–2020) coral trajectories consistent with monitoring observations, while estimating the impacts of each stressor at reef and regional scales. Overall, corals declined by one third across the GBR, from an average ∼29% to ∼19% hard coral cover. By 2020, less than 20% of the GBR had coral cover higher than 30%. Global annual rates of coral mortality were driven by bleaching (48%) ahead of cyclones (41%) and starfish predation (11%). Beyond the reconstructed status and trends, the model enabled the emergence of complex interactions that compound the effects of multiple stressors while promoting a mechanistic understanding of coral cover dynamics. Drivers of coral cover growth were identified; notably, water quality (suspended sediments) was estimated to delay recovery for at least 25% of inshore reefs. Standardized rates of coral loss and recovery allowed the integration of all cumulative impacts to determine the equilibrium cover for each reef. This metric, combined with maps of impacts, recovery potential, water quality thresholds and reef state metrics, facilitates strategic spatial planning and resilience-based management across the GBR.
Coolant passage heat transfer with rotation

In current and advanced gas turbine engines, increased speeds, pressures and temperatures are used to reduce specific fuel consumption and increase thrust/weight ratios. Hence, the turbine airfoils are subjected to increased heat loads escalating the cooling requirements to satisfy life goals. The efficient use of cooling air requires that the details of local geometry and flow conditions be adequately modeled to predict local heat loads and the corresponding heat transfer coefficients. The objective of this program is to develop a heat transfer and pressure drop data base, computational fluid dynamic techniques and correlations for multi-pass rotating coolant passages with and without flow turbulators. The experimental effort is focused on the simulation of configurations and conditions expected in the blades of advanced aircraft high pressure turbines. With the use of this data base, the effects of Coriolis and buoyancy forces on the coolant side flow can be included in the design of turbine blades.
A Kernel-Based Change Detection Method to Map Shifts in Phytoplankton Communities Measured by Flow Cytometry

Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world’s oceans. They therefore pave the way for understanding how environmental conditions shape community structure. Identification of community changes along a cruise transect commonly segments the data into distinct regions. However, existing segmentation methods are generally not applicable to flow cytometry data, as this data is recorded as “point cloud” data, with hundreds or thousands of particles measured during each time interval. Moreover, nonparametric segmentation methods that do not rely on prior knowledge of the number of species, are desirable to map community shifts. We present CytoSegmenter, a kernel-based change-point estimation method for segmenting point cloud data that does not rely on parametric assumptions on the data distributions. Our method relies on a Hilbertian embedding of point clouds that allows us to work with point cloud data similarly to vectorial data. The change-point locations can be found using an efficient dynamic programming algorithm. The method can be used to automatically segment long series of underway flow cytometry data. Through an analysis of 12 cruises, we demonstrate that CytoSegmenter allows us to locate abrupt changes in phytoplankton community structure. We show that the changes in community structure generally coincide with changes in the temperature and salinity of the ocean. We also illustrate how the main parameter of CytoSegmenter can be easily calibrated using limited auxiliary annotated data. CytoSegmenter is publicly available and implemented in the programming language Python. The method is generally applicable for segmenting series of point cloud data from any domain. Moreover, it readily scales to thousands of point clouds, each containing thousands of points. In the context of underway flow cytometry data, it does not require prior clustering of particles to define taxa labels, eliminating a potential source of error. This represents an important advance in automating the analysis of large datasets now emerging in biological oceanography and other fields. It also allows for the approach to potentially be applied during research cruises.
Oct1 recruits the histone lysine demethylase Utx to canalize lineage specification

The pathways used by cells to transition between undifferentiated, pluripotent state and tissue-specific states are incompletely understood. Here we show that the transcription factor Oct1/Pou2f1 activates silent, developmental lineage-appropriate genes to “canalize” developmental progression. Using inducible knockout embryonic stem cells and single-cell gene expression profiling, we show that Oct1 deficiency impairs mesodermal differentiation. Oct1-deficient cells show inappropriate developmental lineage branching and display a poorly differentiated state with hallmarks of pluripotency. Like Oct4, Oct1 directly binds genes critical for mesoderm induction and chromatin modification. Oct1 recruits the Utx/Kdm3a histone lysine demethylase to remove inhibitory H3K27me3 marks and activate their expression. The specificity of the ubiquitous Oct1 protein for mesodermal genes is explained by cooperative interactions with the Smad3 transcription factor. We also show that ectopic Oct1 expression improves the ability of cells to differentiate accurately under mesoderm lineage-inducing conditions. Overall, these results identify Oct1 as a key regulator of mesoderm differentiation.Oct1 “canalizes” gene expression to promote developmentally accurate gene expression and differentiationOct1 is necessary for proper bivalency resolutionOct1 recruits Utx to demethylate H3K27me3 at mesoderm lineage-appropriate targets
Visual perceptual learning of a primitive feature in human V1/V2 as a result of unconscious processing, revealed by Decoded fMRI Neurofeedback (DecNef)

While numerous studies have shown that visual perceptual learning (VPL) occurs as a result of exposure to a visual feature in a task-irrelevant manner, the underlying neural mechanism is poorly understood. In a previous psychophysical study, subjects were repeatedly exposed to a task-irrelevant global motion display that induced the perception of not only the local motions but also a global motion moving in the direction of the spatiotemporal average of the local motion vectors. As a result, subjects enhanced their sensitivity only to the local moving directions, suggesting that early visual areas (V1/V2) that process local motions are involved in task-irrelevant VPL. However, this hypothesis has never been examined by directly examining the involvement of early visual areas (V1/V2). Here, we employed a decoded neurofeedback technique (DecNef) using functional magnetic resonance imaging. During the DecNef training, subjects were trained to induce the activity patterns in V1/V2 that were similar to those evoked by the actual presentation of the global motion display. The DecNef training was conducted with neither the actual presentation of the display nor the subjects’ awareness of the purpose of the experiment. As a result, subjects increased the sensitivity to the local motion directions but not specifically to the global motion direction. The training effect was strictly confined to V1/V2. Moreover, subjects reported that they neither perceived nor imagined any motion during the DecNef training. These results together suggest that that V1/V2 are sufficient for exposure-based task-irrelevant VPL to occur unconsciously. Significance Statement While numerous studies have shown that visual perceptual learning (VPL) occurs as a result of exposure to a visual feature in a task-irrelevant manner, the underlying neural mechanism is poorly understood. Previous psychophysical experiments suggest that early visual areas (V1/V2) are involved in task-irrelevant VPL. However, this hypothesis has never been examined by directly examining the involvement of early visual areas (V1/V2). Here, using decoded fMRI neurofeedback, the activity patterns similar to those evoked by the presentation of a complex motion display were repeatedly induced only in early visual areas. The training sensitized only the local motion directions and not the global motion direction, suggesting that V1/V2 are involved in task-irrelevant VPL.
Improving continuity of care of patients with respiratory disease at hospital discharge

Continuity of care refers to the delivery of coherent, logical and timely care to an individual. It is threatened during the transition of care at hospital discharge, which can contribute to worse patient outcomes. In a traditional acute care model, the roles of hospital and community healthcare providers do not overlap and this can be a barrier to continuity of care at hospital discharge. Furthermore, the transition from inpatient to outpatient care is associated with a transition from acute to chronic disease management and, in a busy hospital, attention to this can be crowded out by the pressures of providing acute care. This model is suboptimal for the large proportion of patients admitted to hospital with acute-on-chronic respiratory disease. In a chronic care model, the healthcare system is designed to give adequate priority to care of chronic disease. Integrated care for the patient with respiratory disease fits the chronic care model and responds to the fragmentation of care in a traditional acute care model: providers integrate their respiratory services to provide continuous, holistic care tailored to individuals. This promotes greater continuity of care for individuals, and can improve patient outcomes both at hospital discharge and more widely. Educational aims To understand the concept of continuity of care and its effect at the transition between inpatient and outpatient care. To understand the difference between the acute and chronic models of healthcare. To understand the effect of integration of care on continuity of care for patients with respiratory disease and their health outcomes. The transition of care at hospital discharge is a time when continuity of care is threatened and this can contribute to adverse events. Increased integration of care by health providers at this time permits greater continuity of care and better outcomes. https://bit.ly/3iEIq0I