Miracle-dz/UniFAR-FTUs huggingface dataset:
Editing Fluid Animation Using Flow Interpolation

The computational cost for creating realistic fluid animations by numerical simulation is generally expensive. In digital production environments, existing precomputed fluid animations are often reused for different scenes in order to reduce the cost of creating scenes containing fluids. However, applying the same animation to different scenes often produces unacceptable results, so the animation needs to be edited. In order to help animators with the editing process, we develop a novel method for synthesizing the desired fluid animations by combining existing flow data. Our system allows the user to place flows at desired positions and combine them. We do this by interpolating velocities at the boundaries between the flows. The interpolation is formulated as a minimization problem of an energy function, which is designed to take into account the inviscid, incompressible Navier-Stokes equations. Our method focuses on smoke simulations defined on a uniform grid. We demonstrate the potential of our method by showing a set of examples, including a large-scale sandstorm created from a few flow data simulated in a small-scale space.
New Insights on Emotional Contributions to Human Postural Control

It has been just over 20 years since the effects of height-induced threat on human postural control were first investigated. Raising the height of the support surface on which individuals stood increased the perceived consequences of instability and generated postural control changes. Since this initial work, converging evidence has accumulated supporting the efficacy of using height-induced threat to study the effects of emotions on postural control and confirming a direct influence of threat-related changes in arousal, anxiety, and fear of falling on all aspects of postural control, including standing, anticipatory, and reactive balance. In general, threat-related postural changes promote a greater physical safety margin while maintaining upright stance. We use the static balance literature to critically examine the current state of knowledge regarding: (1) the extent to which threat-related changes in postural control are sensitive to threat-related changes in emotions; (2) the underlying neurophysiological and cognitive mechanisms that may contribute to explaining the relationship between emotions and postural control; and (3) the generalizability of threat-related changes across different populations and types of threat. These findings have important implications for understanding the neuromechanisms that control healthy balance, and highlight the need to recognize the potential contributions of psychological and physiological factors to balance deficits associated with age or pathology. We conclude with a discussion of the practical significance of this research, its impact on improving diagnosis and treatment of postural control deficits, and potential directions for future research.
Brainstem astroblastoma with MN1 translocation

Astroblastoma is a rare glial neoplasm that occurs mostly in the cerebral hemisphere of children, adolescents and young adults. Although astroblastic perivascular pseudorosettes are unique histopathology of this neoplasm, diagnosis is usually challenging. Recently, it was discovered that the meningioma 1 gene (MN1)‐altered pediatric central nervous system high‐grade neuroepithelial tumors are actually astroblastomas. This case report presents a rare brainstem astroblastoma, with an unusual immunoprofile: negative for glial fibrillary acidic protein and oligodendrocyte transcription factor 2, but with a robust expression of pancytokeratin and epithelial membrane antigen. The diagnosis was confirmed based on the detection of MN1 rearrangement in a fluorescence in situ hybridization study, in addition to typical histopathology. Here we discuss the diagnostic pitfalls and unclear grading system along with a literature review.
Dystrophin Cardiomyopathies: Clinical Management, Molecular Pathogenesis and Evolution towards Precision Medicine

Duchenne’s muscular dystrophy is an X-linked neuromuscular disease that manifests as muscle atrophy and cardiomyopathy in young boys. However, a considerable percentage of carrier females are often diagnosed with cardiomyopathy at an advanced stage. Existing therapy is not disease-specific and has limited effect, thus many patients and symptomatic carrier females prematurely die due to heart failure. Early detection is one of the major challenges that muscular dystrophy patients, carrier females, family members and, research and medical teams face in the complex course of dystrophic cardiomyopathy management. Despite the widespread adoption of advanced imaging modalities such as cardiac magnetic resonance, there is much scope for refining the diagnosis and treatment of dystrophic cardiomyopathy. This comprehensive review will focus on the pertinent clinical aspects of cardiac disease in muscular dystrophy while also providing a detailed consideration of the known and developing concepts in the pathophysiology of muscular dystrophy and forthcoming therapeutic options.
Biochemical characterization of the PHARC-associated serine hydrolase ABHD12 reveals its preference for very-long-chain lipids

Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract (PHARC) is a rare genetic human neurological disorder caused by null mutations to the Abhd12 gene, which encodes the integral membrane serine hydrolase enzyme ABHD12. Although the role that ABHD12 plays in PHARC is understood, the thorough biochemical characterization of ABHD12 is lacking. Here, we report the facile synthesis of mono-1-(fatty)acyl-glycerol lipids of varying chain lengths and unsaturation and use this lipid substrate library to biochemically characterize recombinant mammalian ABHD12. The substrate profiling study for ABHD12 suggested that this enzyme requires glycosylation for optimal activity and that it has a strong preference for very-long-chain lipid substrates. We further validated this substrate profile against brain membrane lysates generated from WT and ABHD12 knockout mice. Finally, using cellular organelle fractionation and immunofluorescence assays, we show that mammalian ABHD12 is enriched on the endoplasmic reticulum membrane, where most of the very-long-chain fatty acids are biosynthesized in cells. Taken together, our findings provide a biochemical explanation for why very-long-chain lipids (such as lysophosphatidylserine lipids) accumulate in the brains of ABHD12 knockout mice, which is a murine model of PHARC.
Moderating Factors Associated With Interrupting the Transmission of Domestic Violence Among Adolescents

Exposure to child maltreatment in the family-of-origin has consistently been linked to intimate partner violence (IPV) perpetration in adulthood. Although the concept of a cycle of violence presumes that the transmission of violence is expressed directly across generations, some protective factors such as social support, self-esteem, and relationship quality with parents may ultimately be influential in nonviolent behavior in adult relationships. Using the National Longitudinal Study of Adolescent Health data set, we tested protective factors to see if and to what extent they disrupted the association from early childhood maltreatment to experiencing violence later on in adult relationships. We found that there was a positive association between adolescence exposure to maltreatment and adult perpetration and victimization of IPV. Also, social support in adolescence was identified as a predictor of lower levels of violence in adult relationship. Clinical implications were discussed to help therapists intervene with adolescents in the hopes of reducing their propensity toward violent relationships in adulthood.
ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data

ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at https://github.com/arosenfeld/immunedb, on PyPi at https://pypi.org/project/ImmuneDB, and a Docker container is provided at https://hub.docker. com/r/arosenfeld/immunedb. Full documentation is available at http://immunedb.com.
Identification of an eight-gene prognostic signature for lung adenocarcinoma

Background Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide. The main obstacle to early diagnosis or monitoring of patients at high risk of poor survival has been the lack of essential predictive biomarkers. Methods RNA-sequencing was performed on LUAD affected tissue and paired adjacent to noncancerous tissue samples and Gene Expression Omnibus dataset GSE19188 and GSE33532 were used to obtain an intersection of differential expressed genes and construct a protein–protein interaction network to get hub genes. Then corresponding overall survival information of two cohorts of LUAD patients from our hospital and The Cancer Genome Atlas project-LUAD were included in the present study. An analysis of the Kyoto Encyclopedia of Genes and Genomes database and Gene Ontology were carried out to study the signature mechanism. Results In our study, we identified eight candidate genes (DLGAP5, KIF11, RAD51AP1, CCNB1, AURKA, CDC6, OIP5 and NCAPG) closely related to survival in LUAD. A linear prognostic model of the eight genes was constructed and weighted by the regression coefficient (β) from the multivariate Cox regression analysis of The Cancer Genome Atlas-LUAD cohort to divide patients into low- and high-risk groups. The prognostic ability of the signature was validated in LUAD patients at our hospital. Patients assigned to the high-risk group exhibited poor overall survival compared to patients in the low-risk group. Finally, functional enrichment analysis showed that cell division played a vital role in the development of LUAD. Conclusion The study identified an mRNA signature including eight genes, which may serve as a potential prognostic marker of LUAD.
Race Detection in Two Dimensions

Dynamic race detection is a program analysis technique for detecting errors caused by undesired interleavings of concurrent tasks. A primary challenge when designing efficient race detection algorithms is to achieve manageable space requirements. State-of-the-art algorithms for unstructured parallelism require Θ (n) space per monitored memory location, where n is the total number of tasks. This is a serious drawback when analyzing programs with many tasks. In contrast, algorithms for programs with a series-parallel (SP) structure require only Θ (1) space. Unfortunately, it is currently not well understood if there are classes of parallelism beyond SP that can also benefit from and be analyzed with Θ (1) space complexity. In this work, we show that structures richer than SP graphs, namely, that of two-dimensional (2D) lattices, can also be analyzed in Θ (1) space. Toward that (a) we extend Tarjan’s algorithm for finding lowest common ancestors to handle 2D lattices; (b) from that extension we derive a serial algorithm for race detection that can analyze arbitrary task graphs with a 2D lattice structure; (c) we present a restriction to fork-join that admits precisely the 2D lattices as task graphs (e.g., it can express pipeline parallelism). Our work generalizes prior work on structured race detection and aims to provide a deeper understanding of the interplay between structured parallelism and program analysis efficiency.
Contextual support for children’s recall within working memory

Measures of working memory capacity (WMC) are extremely popular, yet we know relatively little about the specific processes that support recall. We focused on children’s and adults’ ability to use contextual support to access working memory representations that might otherwise not be reported. Children (N = 186, 5-10 years) and adults (N = 64) completed a listening span task and a delayed recall task with semantic probes or cues. Clear age-related increases in listening span were evident. All age groups benefitted from contextual support to retrieve degraded target memoranda, particularly on listening span tasks when the cues provided semantic support for processing events, in comparison to cues associated specifically with memoranda. Response latencies suggested a developing efficiency in children’s use of contextual support for delayed recall correlated with listening span performance. These probe tasks support accounts of working memory that recognise reconstructive and cued search processes.
Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution

Abstract Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41–15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 10−7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
Optimally designing virtualized CDN

: Using virtualized CDN such as Amazon CloudFront in which cache servers are provided on virtual machines, content providers can ﬂ exibly select the regions of using cache servers according to the geographical demand pattern of their users, so they can expect to reduce the cost of using CDN. However, to maximize the pro ﬁ t of content providers, they need to carefully select the locations of cache servers which a ﬀ ect the quality perceived by users as well as the total cost. We propose a method of optimally selecting the geographical regions to use cache servers maximizing the pro ﬁ t of content providers.
Echo chambers and viral misinformation: Modeling fake news as complex contagion

The viral spread of digital misinformation has become so severe that the World Economic Forum considers it among the main threats to human society. This spread have been suggested to be related to the similarly problematized phenomenon of “echo chambers”, but the causal nature of this relationship has proven difficult to disentangle due to the connected nature of social media, whose causality is characterized by complexity, non-linearity and emergence. This paper uses a network simulation model to study a possible relationship between echo chambers and the viral spread of misinformation. It finds an “echo chamber effect”: the presence of an opinion and network polarized cluster of nodes in a network contributes to the diffusion of complex contagions, and there is a synergetic effect between opinion and network polarization on the virality of misinformation. The echo chambers effect likely comes from that they form the initial bandwagon for diffusion. These findings have implication for the study of the media logic of new social media.
Exploiting Soil Moisture, Precipitation, and Streamflow Observations to Evaluate Soil Moisture/Runoff Coupling in Land Surface Models

Accurate partitioning of precipitation into infiltration and runoff is a fundamental objective of land surface models tasked with characterizing the surface water and energy balance. Temporal variability in this partitioning is due, in part, to changes in prestorm soil moisture, which determine soil infiltration capacity and unsaturated storage. Utilizing the National Aeronautics and Space Administration Soil Moisture Active Passive Level‐4 soil moisture product in combination with streamflow and precipitation observations, we demonstrate that land surface models (LSMs) generally underestimate the strength of the positive rank correlation between prestorm soil moisture and event runoff coefficients (i.e., the fraction of rainfall accumulation volume converted into stormflow runoff during a storm event). Underestimation is largest for LSMs employing an infiltration‐excess approach for stormflow runoff generation. More accurate coupling strength is found in LSMs that explicitly represent subsurface stormflow or saturation‐excess runoff generation processes.
Membrane curvature allosterically regulates the phosphatidylinositol cycle, controlling its rate and acyl-chain composition of its lipid intermediates

Signaling events at membranes are often mediated by membrane lipid composition or membrane physical properties. These membrane properties could act either by favoring the membrane binding of downstream effectors or by modulating their activity. Several proteins can sense/generate membrane physical curvature (i.e. shape). However, the modulation of the activity of enzymes by a membrane's shape has not yet been reported. Here, using a cell-free assay with purified diacylglycerol kinase ϵ (DGKϵ) and liposomes, we studied the activity and acyl-chain specificity of an enzyme of the phosphatidylinositol (PI) cycle, DGKϵ. By systematically varying the model membrane lipid composition and physical properties, we found that DGKϵ has low activity and lacks acyl-chain specificity in locally flat membranes, regardless of the lipid composition. On the other hand, these enzyme properties were greatly enhanced in membrane structures with a negative Gaussian curvature. We also found that this is not a consequence of preferential binding of the enzyme to those structures, but rather is due to a curvature-mediated allosteric regulation of DGKϵ activity and acyl-chain specificity. Moreover, in a fine-tuned interplay between the enzyme and the membrane, DGKϵ favored the formation of structures with greater Gaussian curvature. DGKϵ does not bear a regulatory domain, and these findings reveal the importance of membrane curvature in regulating DGKϵ activity and acyl-chain specificity. Hence, this study highlights that a hierarchic coupling of membrane physical property and lipid composition synergistically regulates membrane signaling events. We propose that this regulatory mechanism of membrane-associated enzyme activity is likely more common than is currently appreciated.
Evolutionary history predicts the response of tree species to forest loss: A case study in peninsular Spain

Evolutionary history can explain species resemblance to a large extent. Thus, if closely related species share combinations of traits that modulate their response to environmental changes, then phylogeny could predict species sensitivity to novel stressors such as increased levels of deforestation. To test this hypothesis, we used 66,949 plots (25-m-radius) of the Spanish National Forest Inventory and modelled the relationships between local (plot-level) stem density of 61 Holarctic tree species and forest canopy cover measured at local and landscape scales (concentric circles centred on the plots with radiuses of 1.6, 3.2 and 6.4 km, respectively). Then, we used the output model equations to estimate the probability of occurrence of the species as a function of forest canopy cover (i.e. response to forest loss), and quantified the phylogenetic signal in their responses using a molecular phylogeny. Most species showed a lower probability of occurrence when forest canopy cover in the plots (local scale) was low. However, the probability of occurrence of many species increased when forest canopy cover decreased across landscape scales. We detected a strong phylogenetic signal in species response to forest loss at local and small landscape (1.6 km) scales. However, phylogenetic signal was weak and non-significant at intermediate (3.2 km) and large (6.4 km) landscape scales. Our results suggest that phylogenetic information could be used to prioritize forested areas for conservation, since evolutionary history may largely determine species response to forest loss. As such, phylogenetically diverse forests might ensure contrasted responses to deforestation, and thus less abrupt reductions in the abundances of the constituent species.
Neuropilins guide preganglionic sympathetic axons and chromaffin cell precursors to establish the adrenal medulla

ABSTRACT The adrenal medulla is composed of neuroendocrine chromaffin cells that secrete adrenaline into the systemic circulation to maintain physiological homeostasis and enable the autonomic stress response. How chromaffin cell precursors colonise the adrenal medulla and how they become connected to central nervous system-derived preganglionic sympathetic neurons remain largely unknown. By combining lineage tracing, gene expression studies, genetic ablation and the analysis of mouse mutants, we demonstrate that preganglionic axons direct chromaffin cell precursors into the adrenal primordia. We further show that preganglionic axons and chromaffin cell precursors require class 3 semaphorin (SEMA3) signalling through neuropilins (NRP) to target the adrenal medulla. Thus, SEMA3 proteins serve as guidance cues to control formation of the adrenal neuroendocrine system by establishing appropriate connections between preganglionic neurons and adrenal chromaffin cells that regulate the autonomic stress response. Summary: A new role is revealed for semaphorin/neuropilin signalling in guiding preganglionic sympathetic axons and chromaffin cell precursors into the adrenal primordia, ensuring correct regulation of the autonomic stress response.