Miracle-dz/UniFAR-FTUs huggingface dataset:
Epoxyeicosatrienoic acids and sEH inhibition prevent cardiac dysfunction in CVB3-induced myocarditis by positively regulating type I interferon signaling

Myocarditis is a challenging inflammatory disease of the heart and better understanding of its etiology is needed to develop specific drug therapies. Epoxyeicosatrienoic acids (EETs), active molecules synthesized by cytochrome P450 enzymes from arachidonic acids and hydrolyzed to less active dihydroxyeicosatrienoic acids by soluble epoxide hydrolase (sEH), have been attributed anti-inflammatory activity. Here, we investigated whether EETs have immunomodulatory activity and exert protective effects on coxsackie B3 virus (CVB3)-induced myocarditis. Viral infection altered eicosanoid epoxide and diol levels in both patients with myocarditis and, in the murine heart, and correlated with the increased expression and activity of the sEH after CVB3 infection. Administration of a sEH inhibitor prevented CVB3-induced cardiac dysfunction and inflammatory infiltration. Importantly, EET/sEH inhibitor treatment attenuated vial infection/ improved viral resistance by activating type I interferon (IFN) signaling. At the molecular level, EETs enhanced the interaction between glycogen synthase kinase 3β (GSK3β) and TANK-binding kinase 1 (TBK1) to promote IFN-β production. Our findings revealed that EETs and sEH inhibitors prevent the progress of CVB3-induced myocarditis, particularly by promoting viral resistance by increasing IFN production.
A New Model for Progenitor Systems of Type Ia Supernovae

We propose a new model for progenitor systems of Type Ia supernovae. The model consists of an accreting white dwarf and a lobe-filling, low-mass red giant. When the mass accretion rate exceeds a certain critical rate, there is no static envelope solution on the white dwarf. For this case, we find a new strong wind solution, which replaces the static envelope solution. Even if the mass-losing star has a deep convective envelope, the strong wind stabilizes the mass transfer until the mass ratio, q, between the mass-losing star and the mass-accreting white dwarf reaches 1.15, i.e., q < 1.15. A part of the transferred matter can be accumulated on the white dwarf at a rate that is limited to Ṁcr = 9.0 × 10-7 (MWD/M☉ - 0.50) M☉ yr-1, and the rest is blown off in the wind. The photospheric temperature is kept around T ~ 1 × 105-2 × 105 K during the wind phase. After the wind stops, the temperature quickly increases up to ~1 × 106 K. The white dwarf steadily burns hydrogen and accretes helium, thereby being able to increase its mass up to 1.38 M☉ and explode as a Type Ia supernova. The expected birth rate of this type of supernovae is consistent with the observed rate of Type Ia supernovae. The hot white dwarf may not be observed during the strong wind phase due to self-absorption by the wind itself. The Strong wind stops when the mass transfer rate decreases below Ṁcr. Then it can be observed as a supersoft X-ray source.
HOPS-dependent lysosomal fusion controls Rab19 availability for ciliogenesis in polarized epithelial cells

Primary cilia are sensory cellular organelles crucial for organ development and homeostasis. Ciliogenesis in polarized epithelial cells requires Rab19-mediated clearing of apical cortical actin to allow the cilium to grow from the apically-docked basal body into the extracellular space. Loss of the lysosomal membrane-tethering HOPS complex disrupts this actin-clearing and ciliogenesis, but it remains unclear how ciliary function of HOPS relates to its canonical function in regulating late endosome-lysosome fusion. Here, we show that disruption of HOPS-dependent lysosomal fusion indirectly impairs actin-clearing and ciliogenesis by disrupting the targeting of Rab19 to the basal body. We also find that Rab19 functions in endolysosomal cargo trafficking apart from its previously-identified role in ciliogenesis. In summary, we show that inhibition of lysosomal fusion abnormally accumulates Rab19 on late endosomes, thus depleting Rab19 from the basal body and thereby disrupting Rab19-mediated actin-clearing and ciliogenesis. Summary statement Loss of HOPS-mediated lysosomal fusion indirectly blocks apical actin clearing and ciliogenesis in polarized epithelia by trapping Rab19 on late endosomes and depleting Rab19 from the basal body.
A new inverse probability of selection weighted Cox model to deal with outcome-dependent sampling in survival analysis

Motivated by the study of genetic effect modifiers of cancer, we examined weighting approaches to correct for ascertainment bias in survival analysis. Family-based outcome-dependent sampling is common in genetic epidemiology leading to study samples with too many events in comparison to the population and an overrepresentation of young, affected subjects. A usual approach to correct for ascertainment bias in this setting is to use an inverse probability-weighted Cox model, using weights based on external available population-based age-specific incidence rates of the type of cancer under investigation. However, the current approach is not general enough leading to invalid weights in relevant practical settings if oversampling of cases is not observed in all age groups. Based on the same principle of weighting observations by their inverse probability of selection, we propose a new, more general approach. We show the advantage of our new method using simulations and two real datasets. In both applications the goal is to assess the association between common susceptibility loci identified in Genome Wide Association Studies (GWAS) and cancer (colorectal and breast) using data collected through genetic testing in clinical genetics centers.
Segmentation des tissus et structures sur les IRM cérébrales : agents markoviens locaux et coopératifs et formulation bayésienne

La segmentation des IRM cerebrales est une etape cruciale pour de nombreuses applications, tant dans le domaine clinique que pour les neurosciences. Elle est rendu difficile par les artefacts inherents a ce type d'image, leur faible contraste et les importantes variations individuelles qui limitent l'introduction de connaissances a priori. Dans cette these nous proposons une nouvelle approche de segmentation des IRM cerebrales dont l'originalite reside (1) dans le couplage de la segmentation des tissus, de la segmentation des structures et de l'integration de connaissances anatomiques et (2) la volonte de prendre en compte la localite de l'information. La localite est modelisee via un cadre multi-agents : des agents sont distribues dans le volume et realisent une segmentation markovienne locale. Dans une premiere approche (LOCUS, Local Cooperative Unified Segmentation) nous proposons des mecanismes intuitifs de cooperation et de couplage pour assurer la coherence des modeles locaux. Les structures sont segmentees via l'integration de contraintes de localisation floue decrites par des relations spatiales entre structures. Dans une seconde approche (LOCUS-B, LOCUS in a Bayesian framework) nous considerons l'introduction d'un atlas statistique des structures. Nous reformulons le probleme dans un cadre bayesien nous permettant une formalisation statistique du couplage et de la cooperation. Segmentation des tissus, regularisation des modeles locaux, segmentation des structures et recalage local affine de l'atlas sont alors realises de maniere couplee dans un cadre EM, chacune des etapes s'ameliorant mutuellement. L'evaluation sur des images simulees et reelles montrent les performances de l'approche et en particulier sa robustesse aux artefacts pour de faibles temps de calculs. Les modeles markoviens locaux distribues et cooperatifs apparaissent alors comme une approche prometteuse pour la segmentation d'images medicales.
Speeding up interval estimation for R2-based mediation effect of high-dimensional mediators via cross-fitting

Mediation analysis is a useful tool in biomedical research to investigate how molecular phenotypes, such as gene expression, mediate the effect of an exposure on health outcomes. However, commonly used mean-based total mediation effect measures may suffer from cancellation of component-wise mediation effects of opposite directions in the presence of high-dimensional omics mediators. To overcome this limitation, a variance-based R-squared total mediation effect measure has been recently proposed, which, nevertheless, relies on the computationally intensive nonparametric bootstrap for confidence interval estimation. In this work, we formulate a more efficient two-stage cross-fitted estimation procedure for the R-squared measure. To avoid potential bias, we perform iterative Sure Independence Screening (iSIS) in two subsamples to exclude the non-mediators, followed by ordinary least squares (OLS) regressions for the variance estimation. We then construct confidence intervals based on the newly-derived closed-form asymptotic distribution of the R-squared measure. Extensive simulation studies demonstrate that the proposed procedure is hundreds of times more computationally efficient than the resampling-based method with comparable coverage probability. Furthermore, when applied to the Framingham Heart Study, the proposed method replicated the established finding of gene expression mediating age-related variation in systolic blood pressure and discovered the role of gene expression profiles in the relationship between sex and high-density lipoprotein cholesterol. The proposed cross-fitted interval estimation procedure is implemented in R package RsqMed.
THE AGE OF THE LOCAL INTERSTELLAR BUBBLE

The Local Interstellar Bubble is an irregular region from 50 to 150 pc from the Sun in which the interstellar gas density is 10−2–10−3 of that outside the bubble and the interstellar temperature is 106 K. Evidently most of the gas was swept out by one or more supernovae. I explored the stellar contents and ages of the region from visual double stars, spectroscopic doubles, single stars, open clusters, emission regions, X-ray stars, planetary nebulae, and pulsars. The bubble has three sub-regions. The region toward the galactic center has stars as early as O9.5 V and with ages of 2–4 M yr. It also has a pulsar (PSRJ1856−3754) with a spin-down age of 3.76 Myr. That pulsar is likely to be the remnant of the supernova that drove away most of the gas. The central lobe has stars as early as B7 V and therefore an age of about 160 Myr or less. The Pleiades lobe has stars as early as B3 and therefore an age of about 50 Myr. There are no obvious pulsars that resulted from the supernovae that cleared out those areas. As found previously by Welsh & Lallement, the bubble has five B stars along its perimeter that show high-temperature ions of O vi and C ii along their lines of sight, confirming its high interstellar temperature.
RNA G-quadruplex folding is a multi-pathway process with a variety of short-lived intermediates

The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes. Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates
Deletion of MEC1 suppresses the replicative senescence of the cdc13-2 mutant in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, telomerase recruitment to telomeres depends on a direct interaction between Cdc13, a protein that binds single-stranded telomeric DNA, and the Est1 subunit of telomerase. The cdc13-2 allele disrupts telomerase association with telomeres, resulting in progressive telomere shortening and replicative senescence. The Mec1/ATR kinase is both a positive and negative regulator of telomerase activity, and is required for the cell cycle arrest in telomerase-deficient senescent cells. In this study, we find that deletion of MEC1 suppresses the replicative senescence of cdc13-2. This suppression is dependent on telomerase, indicating that Mec1 antagonizes telomerase-mediated telomere extension in cdc13-2 cells to promote senescence.
The relationship between residential burglaries and urban environments in Taipei City: a data mining approach

ABSTRACT Although the overall crime rate in Taiwan has shown a declining trend in recent years, the proportion of burglaries remains high. Most studies regarding the prevention of burglaries proceed from the perspectives of population composition or criminal psychology, and place focus on the internal spatial planning of buildings without mentioning the association between case locations and urban environments. In order to effectively prevent crime and improve the quality of life, this study utilized cases provided by the Taipei City Government Open Platform (Data. Taipei) to confirm the surrounding environmental factors and building data of burglary cases for data mining application. The proposed method consists of two phases: clustering and association rule mining. In the clustering phase, the key substructures of environmental information are collected; then characteristics in each cluster are analyzed based on the association rule. The results of analysis showed that the first group (Group 1) in the classification should give priority to improving the visibility of idle space and streets, while the second group (Group 2) should improve the efficiency of personnel surveillance and solve the problem of crowds caused by business activities. The third group (Group 3), which featured narrow lanes and insufficient street lamps on chaotic streets, should engage in overall planning and design. Some studies have found that the environmental characteristics of burglary cases in Taipei City are different from the characteristics of crime-saddled urban areas defined by international scholars. Such differences deserve further study. The findings of this study can serve as an environmental design model for future urban development.
BiGPICC: a graph-based approach to identifying carcinogenic gene combinations from mutation data

Genome data from cancer patients encapsulates explicit and implicit relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations. Identifying these combinations through traditional exhaustive search requires the amount of computation that scales exponentially with the combination size and in most cases is intractable even for even cutting-edge supercomputers. We propose a parameter-free heuristic approach that leverages the intrinsic topology of gene-patient mutations to identify carcinogenic combinations. The biological relevance of the identified combinations is measured by using them to predict the presence of tumor in previously unseen samples. The resulting classifiers for 16 cancer types perform on par with exhaustive search results, and score the average of 80.1% sensitivity and 91.6% specificity for the best choice of hit range per cancer type. Our approach is able to find higher-hit carcinogenic combinations targeting which would take years of computations using exhaustive search.
Correlations between human mating partners: a comprehensive meta-analysis of 22 traits and raw data analysis of 133 traits in the UK Biobank

Positive correlations between human mating partners are consistently observed across traits. Such correlations can increase phenotypic variation and, to the extent that they reflect genetic similarity in co-parents, can also increase prevalence for rare phenotypes and bias estimates in genetic designs. We conducted the largest set of meta-analyses on human partner correlations to date, incorporating 480 partner correlations across 22 traits. We also calculated 133 trait correlations between up to 79,074 male-female couples in the UK Biobank (UKB). Estimates of the mean meta-analyzed correlations ranged from rmeta=. 08 for extraversion to rmeta=. 58 for political values. UKB correlations ranged from rUKB=-. 18 for chronotype to rUKB=. 87 for birth year. Overall, attitudes, education, and substance use traits mostly showed the highest correlations, while psychological and biological traits generally yielded lower but still positive correlations. We observed high between-study heterogeneity for most meta-analyzed traits, likely because of both systematic differences between samples and true differences in partner correlations across populations.
Quantum cascade lasers tuned by amorphous As2S3 claddings

Quantum cascade lasers (QCLs) have become a key component in the development of optical approaches to sensing applications. Recent experiments have shown the ability to achieve second harmonic generation from these structures suggesting the possibility of achieving short wave-infrared output. However, in these cases the power of the non-linear mode is limited by its phase mismatch with the fundamental cavity mode. By modifying the effective index of the laser system through cladding, one may ameliorate the mismatch to increase power output. In this study, we develop a simple method for drop-coating arsenic sulfide (As2S3) glass on QCLs. The glass is processed by above band-gap illumination, which induces a change in the refractive index resulting in a shift of the output mode of the laser. We observe the effective index to change by a factor 1.3 x 10-4 after 20 minutes of illumination at 312 nm for the fundamental wavelength of the QCL. Below band-gap irradiation, such as that occurring during device operation, is confirmed to have no effect on the material. Studies of the output of QCLs reveal for the first time mode shifting of the spectra as a result of optical modification to a cladding layer.
Modeling and analysis of a multi-cantilever beam frequency up-converted energy harvester for powering animal wearable devices

Abstract This paper presents development of a frequency up conversion piezoelectric energy harvesting system that takes cattle movement vibrations and convert it into electrical energy. The harvested power can be used to power some devices relating to cattle precision farming operations. The design should get excitation from cattle motion frequency in the range of 5-8 Hz and upconverts it to a much high resonant frequency of 47.2-76.05 Hz. A Finite Element Analysis (FEA) is modeled and studied using COMSOL Multiphysics. The model is expected to generate power sufficient enough to operate devices like pedometers which consume on average 1.8 V.
Bäcklund transformations and Painlevé analysis: Exact soliton solutions for the unstable nonlinear Schrödinger equation modeling electron beam plasma

In this paper the Backlund transformations technique and Painleve analysis are used to generate classes of exact soliton solutions for some nonlinear evolution equations. For the (1+1)-dimensional problem, the unstable system of plasma equations where an electron beam is injected under a high-frequency electric field is reduced to the unstable nonlinear Schrodinger (UNLS) equation. Using the Darboux–Bargmann technique, we obtain the Backlund transformations for UNLS equation solvable by the inverse scattering method of Zakharov–Shabat/Ablowitz–Kaup–Newell–Segur (ZS/AKNS) and the ZS/AKNS wave functions corresponding to the soliton solutions of this equation.
Body size, not species identity, drives body heating in alpine Erebia butterflies

Efficient thermoregulation is crucial for animals living under fluctuating climatic and weather conditions. We studied the body heating of six butterfly species of the genus Erebia (Lepidoptera: Nymphalidae) that co-occur in the European Alps. We tested whether butterfly physical characteristics (body size, wing loading) are responsible for the inter-specific differences in body temperatures recorded previously under natural conditions. We used a thermal camera to measure body heating of wild butterfly individuals in a laboratory experiment with artificial light and heating sources. We revealed that physical characteristics had a small effect on explaining inter-specific differences in mean body temperatures recorded in the field. Our results show that larger butterflies, with higher weight and wing loading, heated up more slowly but reached the same asymptotic body temperature as smaller butterflies. Altogether, our results suggest that differences in body temperatures among Erebia species observed in the field might be caused mainly by species-specific microhabitat use and point towards an important role of active behavioural thermoregulation in adult butterflies. We speculate that microclimate heterogeneity in mountain habitats facilitates behavioural thermoregulation of adults. Similarly, microclimate structuring might also increase survival of less mobile butterfly life stages, i.e., eggs, larvae and pupae. Thus, landscape heterogeneity in management practices may facilitate long term survival of montane invertebrates under increased anthropogenic pressures.
Frequency optimization of laminated composite annular sector plates

This paper deals with frequency optimization of symmetrically laminated angle-ply annular sector plates. The design objective is the maximization of the fundamental frequency and the design variable is the fiber orientation in the layers. The first order shear deformation theory is used for the finite element solution of laminates. Nine-node Lagrangian rectangular plate element which have five degrees of freedom per node is used for the finite element solution of the laminated annular sector plates. The modified feasible direction method is used for the optimization routine. For this purpose, a program based on FORTRAN is used. The numerical analysis is carried out to investigate the effects of annularity, boundary conditions and sector angle on the optimal designs and the results are shown in tabular and graphical forms. Finally, the obtained results are compared. It can be shown that the parameters have a key role on the optimum design of laminated annular sector plates.
Topology evolutions of silhouettes

We give the topology changing of the silhouette in 3D space while others study the projections in an image. Silhouettes play a crucial role in visualization, graphics and vision. This work focuses on the global behaviors of silhouettes, especially their topological evolutions, such as splitting, merging, appearing and disappearing. The dynamics of silhouettes are governed by the topology, the curvature of the surface, and the view point. In this paper, we work on a more theoretical level to give enumerative properties of the silhouette including: the integration of signed geodesic curvature along a silhouette is equal to the view cone angle; in elliptic regions, no silhouette can be contained in another one; in hyperbolic regions, if a silhouette is homotopic to a point, then it has at least 4 cusps; finally, critical events can only happen when the view point is on the aspect surfaces (ruled surface of the asymptotic lines of parabolic points with surface itself). We also introduce a method to visualize the evolution of silhouettes, especially all the critical events where the topologies of the silhouettes change. The results have broad applications in computer vision for recognition, graphics for rendering and visualization.