Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Data-driven Microscopic Trafic Simulation using Jointly Trained Physics-guided Long Short-term Memory

Symbiotic simulation systems that incorporate data-driven methods (such as machine/deep learning) are efective and eicient tools for just-in-time (JIT) operational decision making. With the growing interest on Digital Twin City, such systems are ideal for real-time microscopic traic simulation. However, learning-based models are heavily biased towards the training data and could produce physically inconsistent outputs. In terms of microscopic traic simulation, this could lead to unsafe driving behaviours causing vehicle collisions in the simulation. As for symbiotic simulation, this could severely afect the performance of real-time base simulation model resulting in inaccurate or unrealistic forecasts, which could, in turn, mislead JIT what-if analysis. To overcome this issue, a physics-guided data-driven modelling paradigm should be adopted so that the resulting model could capture both accurate and safe driving behaviours. However, very few works exist in the development of such a car-following model that can balance between simulation accuracy and physical consistency. Therefore, in this paper, a new łjointly-trained physics-guided Long Short-term Memory (JTPG-LSTM)ž neural network, is proposed and integrated to a dynamic data-driven simulation system to capture dynamic car-following behaviours. An extensive set of experiments was conducted to demonstrate the advantages of the proposed model from both modelling and simulation perspectives.
A deep learning method to predict ankle joint moment during walking at different speeds with ultrasound imaging: A framework for assistive devices control

Abstract Robotic assistive or rehabilitative devices are promising aids for people with neurological disorders as they help regain normative functions for both upper and lower limbs. However, it remains challenging to accurately estimate human intent or residual efforts non-invasively when using these robotic devices. In this article, we propose a deep learning approach that uses a brightness mode, that is, B-mode, of ultrasound (US) imaging from skeletal muscles to predict the ankle joint net plantarflexion moment while walking. The designed structure of customized deep convolutional neural networks (CNNs) guarantees the convergence and robustness of the deep learning approach. We investigated the influence of the US imaging’s region of interest (ROI) on the net plantarflexion moment prediction performance. We also compared the CNN-based moment prediction performance utilizing B-mode US and sEMG spectrum imaging with the same ROI size. Experimental results from eight young participants walking on a treadmill at multiple speeds verified an improved accuracy by using the proposed US imaging + deep learning approach for net joint moment prediction. With the same CNN structure, compared to the prediction performance by using sEMG spectrum imaging, US imaging significantly reduced the normalized prediction root mean square error by 37.55% ($ p $ < .001) and increased the prediction coefficient of determination by 20.13% ($ p $ < .001). The findings show that the US imaging + deep learning approach personalizes the assessment of human joint voluntary effort, which can be incorporated with assistive or rehabilitative devices to improve clinical performance based on the assist-as-needed control strategy.
Reply to the Comment by M. Biskup, L. Chayes and R. Kotecky

In their comment to the paper ``Theory of the evaporation/condensation transition of equilibrium droplets in finite volumes'' [Physica A, 319, 99 (2003)], Biskup et al. claim that in finite systems at fixed density ``the physical significance of the conjugate thermodynamic variable is of dubious value''. This claim is critically discussed.
Virasoro constraints for stable pairs on toric threefolds

Abstract Using new explicit formulas for the stationary Gromov–Witten/Pandharipande–Thomas ( $\mathrm {GW}/{\mathrm {PT}}$ ) descendent correspondence for nonsingular projective toric threefolds, we show that the correspondence intertwines the Virasoro constraints in Gromov–Witten theory for stable maps with the Virasoro constraints for stable pairs proposed in [18]. Since the Virasoro constraints in Gromov–Witten theory are known to hold in the toric case, we establish the stationary Virasoro constraints for the theory of stable pairs on toric threefolds. As a consequence, new Virasoro constraints for tautological integrals over Hilbert schemes of points on surfaces are also obtained.
Robust visualization of trajectory data

Abstract The analysis of movement trajectories plays a central role in many application areas, such as traffic management, sports analysis, and collective behavior research, where large and complex trajectory data sets are routinely collected these days. While automated analysis methods are available to extract characteristics of trajectories such as statistics on the geometry, movement patterns, and locations that might be associated with important events, human inspection is still required to interpret the results, derive parameters for the analysis, compare trajectories and patterns, and to further interpret the impact factors that influence trajectory shapes and their underlying movement processes. Every step in the acquisition and analysis pipeline might introduce artifacts or alterate trajectory features, which might bias the human interpretation or confound the automated analysis. Thus, visualization methods as well as the visualizations themselves need to take into account the corresponding factors in order to allow sound interpretation without adding or removing important trajectory features or putting a large strain on the analyst. In this paper, we provide an overview of the challenges arising in robust trajectory visualization tasks. We then discuss several methods that contribute to improved visualizations. In particular, we present practical algorithms for simplifying trajectory sets that take semantic and uncertainty information directly into account. Furthermore, we describe a complementary approach that allows to visualize the uncertainty along with the trajectories.
The invention of the “weird” Southern child: Mapping coloniality in the political problematization of disadvantaged children’s lives in the global South

In this article, the pervasiveness of coloniality in Southern childhoods’ policyscapes is mapped. By analyzing Chilean child nutrition policies, this article illustrates how coloniality fabricates children’s ontological “weirdness” to naturalize racial optimization through compulsory abledment. The “weird” Southern child is theorized as the preferred policy subject of an ableist assemblage that racializes disadvantaged children as biologically unfit for civilized life. Finally, this article argues that Childhood Studies must be decolonized by decentering models of childhood where coloniality remains deeply entrenched.
Complexity of Brain Dynamics Inferred from the Sample Entropy Analysis of Electroencephalogram

Nonlinear time series analysis is a potential method for gaining information regarding the dynamics of complex physiological systems. The human brain is by far one of the most complex systems in nature and the electrical signal from the brain, the electroencephalogram (EEG) has been a subject of nonlinear techniques to delve the dynamics of the brain. This paper deals with the computation of a measure of complexity for dense array EEG signals and the subsequent analysis of various brain conditions. The complexity measure used in the study is the Sample Entropy (SampEn), which quantifies the regularity and ‘randomness’ in a time varying signal arising from a system The present work computes the SampEn of the EEG signal recorded for the three cases of passive, eyes closed condition; mental arithmetic task and for epileptic spike data. The analysis helps in gaining an insight into the nature of complexity variations with brain state. It is observed that while during the mental task only specific brain regions exhibit lowered complexity, the dynamical complexity is very much lowered for the pathological spike condition. KeywordsBrain, EEG, Nonlinear time series analysis, Sample Entropy (SampEn).
Explicit dynamics of shells with a flat‐facet triangular finite element

The use of a flat‐facet finite element with three nodes and six degrees of freedom per node for modeling of linear wave‐propagation events is discussed. The triangular shell finite element was presented in a preceding publication. The main novelty of the current approach is the treatment of the drilling rotations that decouples the drilling degree of freedoms on the global level, and hence makes it possible to eliminate negative effects of these degrees of freedom on the explicit time‐stepping algorithms employed to compute the dynamic response, such as deterioration in accuracy or artificially reduced time step. The element is shown to be robust for wave propagation simulations, and its performance is illustrated with examples including guided‐wave scenarios.
Early social experience, rather than kinship affecting aggression in an egg parasitoid wasp, Anastatus disparis (Hymenoptera: Eupelmidae), that exhibits extreme male–male combat behaviour

Fighting behaviour is important for acquiring crucial resources and is widely observed in the animal kingdom. Based on the conflict consequence, fighting behaviour is usually classified into non‐extreme and extreme fighting patterns. Numerous factors that influence aggression, such as resource value, resource‐holding potential, kinship, and prior experience, have been extensively studied, resulting in the emergence of many important theories. To secure mating opportunities, males of the quasi‐gregarious parasitoid, Anastatus disparis (Hymenoptera: Eupelmidae), exhibit extreme fighting behaviour. Inconsistent with the general kin selection theory prediction, there is no evidence that male A. disparis competitors alter their fighting behaviour in response to relatedness with resource presence or interacted with altering resource value. The results of our current study do not clearly indicate whether unchanged kin‐based aggression is caused by a lack of kin recognition ability or overriding by competition for resources, which A. disparis males rarely exhibit fighting behaviour under condition of resource female absence in the environment. However, significant decreases in the fighting frequency and intensity in A. disparis were shown in males with early social experience, which was also not influenced by the kinship between the contestants. Our result suggests that in A. disparis, male aggression was likely mediated by early social experience rather than kinship.
Determination of the functional response in the orb‐weaving spider Araneus diadematus (Araneae: Araneidae) according to insecticide type

Orb‐weaving spiders are abundant predators in agroecosystems and serve as key natural enemies for pest control. However, studies have demonstrated that many insecticides can negatively affect the predatory behaviours of spiders when exposed to sublethal concentrations, thus disrupting their biocontrol potential and subsequent ecosystem dynamics. Understanding how insecticides impact spiders is, therefore, of great importance. This study investigated the effects of two conventional insecticides (thiamethoxam and deltamethrin), and a common biopesticide (neem oil) compared to a tap water control on the functional response of a common orb‐weaver Araneus diadematus. Spiders were collected from the wild and maintained under laboratory conditions in containers (20 × 20 × 5 cm) to allow for web production. Spiders were then exposed to one of the four treatments and Drosophila melanogaster were added to the webs as prey at densities of 1, 3, 5, 10, 20, and 40, with the number of consumed prey quantified after 16‐h to determine the functional response. Overall, A. diadematus exhibited a type II functional response when exposed to the control, thiamethoxam and neem oil treatments, with comparable consumption rates, search coefficients and handling times. This contrasted with deltamethrin‐treated spiders which exhibited a type III functional response and a lower consumption rate of prey compared to the control. This study demonstrates that deltamethrin, unlike thiamethoxam and neem oil, is capable of negatively affecting the biocontrol potential of A. diadematus. However, further research is required to fully understand the impact insecticides have on the predatory behaviours of orb‐weaving spiders.
Spatially coordinated cell cycle activity and motility govern mammary ductal growth and tip bifurcation

Branching morphogenesis is the common evolutionary solution of multiple organs to combine maximal epithelial function with compact organ size. It involves successive rounds of branch elongation and branch point generation to generate a branched epithelial network. Branch points form most commonly at the tips of branches as they split into two. However, it is unclear how epithelial cells in tips drive both elongation and branching. In this study, we used ex vivo live imaging to identify these fundamental cellular mechanisms in the embryonic mammary gland. Our 4D analyses show that tips of branches are driven forward by directional cell migration, while elongation of the subtending duct is supported by cell proliferation that feeds a retrograde flow of lagging cells into the duct, established upon differential cell motility. Tip bifurcation involved localized repression of both cell cycle and cell motility at the branch point. Cells in the nascent daughter tips remained proliferative, but changed the direction of their movement to elongate new branches. Our study also reports the fundamental importance of the contractile actin cytoskeleton in regulating branch point generation in the mammary epithelium.
Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression

Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Highlights By curating metadata from uniformly processed human RNA-seq studies, we created a database of 3162 differential expression analyses. These analyses include TCGA, GTEx, and 142 unique studies in SRA, involving 985 distinct experimental conditions. The Differential Expression Enrichment Tool (DEET) allows users to systematically compare their gene lists to this database.
Chitosan diet alters the microbiome of adult house flies

House flies are disease vectors, carrying human pathogens which include Escherichia coli and Vibrio cholera. To explore the use of chitosan as a bioinsecticide, we evaluated the effects of a chitosan-amended diet on Musca domestica (house fly). We first conducted longevity experiments to understand the impact of chitosan on house fly longevity. We confirmed that chitosan diet amendment is associated with reduced longevity and that this is not due to starvation. We then extracted fly microbiome DNA and used 16S ribosomal RNA gene amplicon sequencing and quantitative PCR to assess the composition and load of the microbiome for flies fed chitosan-amended diets compared to controls. Diversity of the chitosan-fed fly microbiomes was lower than the control, with significant dissimilarities in community composition. Chitosan-fed flies showed lower Ralstonia relative abundance but increased relative abundance of Serratia. Both control and chitosan-fed flies had highly uneven communities, but the control flies were dominated by genera Ralstonia and Providencia, while the chitosan-fed flies were dominated by genera Serratia, Kosakonia, and Providencia. Contrary to our expected results, chitosan-fed flies also contained 56% more bacteria compared to controls. Gut microbiome changes appear to result from chitinolytic bacteria becoming more relatively abundant, and our results suggest that chitosan-amended diet alters the house fly microbiome resulting in higher fly mortality.
Gli2 and Gli3 Regulate Horizontal Basal Cell-Mediated Regeneration of the Olfactory Epithelium

The olfactory epithelium (OE) is a specialized neuroepithelium that is replenished by two stem cell populations: globose basal cells (GBCs) and horizontal basal cells (HBCs). Previous work indicated that HBCs contain primary cilia, organelles that mediate Hedgehog (HH) pathway activity. However, a role for HH signaling in HBCs has not been investigated. We find that GLI2 and GLI3, transcriptional effectors of the HH pathway, are expressed in HBCs in the adult OE and that their expression expands following injury. Further, Gli2-expressing descendants contribute to all major OE cell types during OE regeneration. HBC-specific expression of constitutively active GLI2 drives inappropriate HBC proliferation, alters HBC identity, and culminates in a failure of HBCs to differentiate into olfactory sensory neurons (OSNs) following injury. HBC- specific deletion of endogenous Gli2 and Gli3 results in decreased HBCs and OSNs following OE injury. These data identify GLI2 and GLI3 as key regulators of HBC-mediated OE regeneration.
Dexamethasone Enhances CAR T Cell Persistence and Function by Upregulating Interleukin 7 Receptor

Dexamethasone (dex) is a glucocorticoid that is a mainstay for treatment of inflammatory pathologies, including immunotherapy-associated toxicities. Dex suppresses the endogenous immune response and is also believed to suppress the function of chimeric antigen receptor (CAR) T cells. However, recent reports observed higher CAR T cell numbers in patients treated with dex, highlighting the rationale for interrogating the specific effects of dex on CAR T cells. Here, we found that dex did not inhibit CAR T cell expansion or function. A single dose of dex during the manufacturing process upregulated the pro-persistence interleukin 7 receptor α (IL7Rα) on CAR T cells and induced expression of genes involved in activation, migration, and persistence. The ex vivo upregulation of IL7Rα induced by dex significantly enhanced CAR T cell persistence and anti-tumor efficacy in vivo when combined with exogenous IL-7. Moreover, the combination of dex and IL-7 resulted in increased persistence of CAR T cells and led to complete remission of mice. Overall, our studies in both in vitro and in vivo treatment support a positive role of dex on CAR T cell potency and provide insight into the application of glucocorticoids in cellular anti-cancer therapy.
Protein composition of axonal dopamine release sites in the striatum

Mechanisms of neuromodulatory transmission in the brain remain ambiguous. Dopamine is a prototypical neuromodulator, and it was recently found that its secretion relies on active zone-like release site assemblies. Here, we use in vivo biotin-identification (iBioID) proximity proteomics in mouse striatum to isolate dopamine release site proteins enriched over the general dopamine axonal protein content. Using three bait proteins, we identified 527 proteins that fall into several synaptic protein classes, including active zone, Ca2+ regulatory and synaptic vesicle proteins. We also detected many proteins not previously associated with synaptic exocytosis. Knockout of the presynaptic organizer protein RIM profoundly disrupted dopamine release site composition assessed by iBioID, while Synaptotagmin-1 knockout did not. α-Synuclein, a protein linked to Parkinson’s disease, was enriched at release sites, and this enrichment was lost in both tested mutants. We conclude that RIM organizes scaffolded dopamine release sites and we define the protein composition of these sites.
Plasmodium falciparum CRK4 links early mitotic events to the onset of S-phase during schizogony

ABSTRACT Plasmodium falciparum proliferates through schizogony in the clinically relevant blood stage of infection. During schizogony, consecutive rounds of DNA replication and nuclear division give rise to multinucleated stages before cellularization occurs. Although these nuclei reside in a shared cytoplasm, DNA replication and nuclear division occur asynchronously. Here, by mapping the proteomic context of the S-phase-promoting kinase PfCRK4, we show that it has a dual role for nuclear-cycle progression: PfCRK4 orchestrates not only DNA replication, but in parallel also the rearrangement of intranuclear microtubules from hemispindles into early mitotic spindles. Live-cell imaging of a reporter parasite showed that these microtubule rearrangements coincide with the onset of DNA replication. Together, our data render PfCRK4 a key factor for nuclear-cycle progression, linking entry into S-phase with the initiation of mitotic events. In part, such links may compensate for the absence of canonical cell cycle checkpoints in P. falciparum. IMPORTANCE The human malaria parasite Plasmodium falciparum proliferates in erythrocytes through schizogony, forming multinucleated stages before cellularization occurs. In marked contrast to the pattern of proliferation seen in most model organisms, P. falciparum nuclei multiply asynchronously despite residing in a shared cytoplasm. This divergent mode of replication is, thus, a good target for therapeutic interventions. To exploit this potential, we investigated a key regulator of the parasite’s unusual cell cycle, the kinase PfCRK4 and found that this kinase regulated not only DNA replication but also in parallel the rearrangement of nuclear microtubules into early mitotic spindles. Since canonical cell cycle checkpoints have not been described in P. falciparum parasites, linking entry into S-phase and the initiation of mitotic events via a kinase, may be an alternative means to exert control, which is typically achieved by checkpoints. The human malaria parasite Plasmodium falciparum proliferates in erythrocytes through schizogony, forming multinucleated stages before cellularization occurs. In marked contrast to the pattern of proliferation seen in most model organisms, P. falciparum nuclei multiply asynchronously despite residing in a shared cytoplasm. This divergent mode of replication is, thus, a good target for therapeutic interventions. To exploit this potential, we investigated a key regulator of the parasite’s unusual cell cycle, the kinase PfCRK4 and found that this kinase regulated not only DNA replication but also in parallel the rearrangement of nuclear microtubules into early mitotic spindles. Since canonical cell cycle checkpoints have not been described in P. falciparum parasites, linking entry into S-phase and the initiation of mitotic events via a kinase, may be an alternative means to exert control, which is typically achieved by checkpoints.