Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport

While single-cell technologies have allowed scientists to characterize cell states that emerge during cancer progression through temporal sampling, connecting these samples over time and inferring gene-gene relationships that promote cancer plasticity remains a challenge. To address these challenges, we developed TrajectoryNet, a neural ordinary differential equation network that learns continuous dynamics via interpolation of population flows between sampled timepoints. By running causality analysis on the output of TrajectoryNet, we compute rich and complex gene-gene networks that drive pathogenic trajectories forward. Applying this pipeline to scRNAseq data generated from in vitro models of breast cancer, we identify and validate a refined CD44hiEPCAM+CAV1 + marker profile that improves the identification and isolation of cancer stem cells (CSCs) from bulk cell populations. Studying the cell plasticity trajectories emerging from this population, we identify comprehensive temporal regulatory networks that drive cell fate decisions between an epithelial-to-mesenchymal (EMT) trajectory, and a mesenchymal-to-epithelial (MET) trajectory. Through these studies, we identify and validate estrogen related receptor alpha as a critical mediator of CSC plasticity. We further apply TrajectoryNet to an in vivo xenograft model and demonstrate it’s ability to elucidate trajectories governing primary tumor metastasis to the lung, identifying a dominant EMT trajectory that includes elements of our newly-defined temporal EMT regulatory network. Demonstrated here in cancer, the TrajectoryNet pipeline is a transformative approach to uncovering temporal molecular programs operating in dynamic cell systems from static single-cell data.
Mycobacterium ulcerans not detected by PCR on human skin in Buruli ulcer endemic areas of south eastern Australia

Introduction Mycobacterium ulcerans (MU) causes Buruli ulcer (BU), a geographically restricted infection that can result in skin loss, contracture, and permanent scarring. Lesion-location maps compiled from more than 640 cases in south eastern Australia suggest biting insects are likely involved in transmission, but it is unclear whether MU is brought by insects to their target or if MU is already on the skin and inoculation is an opportunistic event that need not be insect dependent. Methods We validated a PCR swab detection assay and defined its dynamic range using laboratory cultured M. ulcerans and fresh pigskin. We invited volunteers in Buruli-endemic and non-endemic areas to sample their skin surfaces with self-collected skin swabs tested by IS2404 quantitative PCR. Results Pigskin validation experiments established a limit-of-detection of 0.06 CFU/cm2 at a qPCR cycle threshold (Ct) of 35. Fifty-seven volunteers returned their self-collected kits of 4 swabs (bilateral ankles, calves, wrists, forearms), 10 from control areas and 47 from endemic areas. Collection was timed to coincide with the known peak-transmission period of Buruli. All swabs from human volunteers tested negative (Ct ≥35). Conclusions M. ulcerans was not detected on the skin of humans from highly BU endemic areas. Author Summary Buruli ulcer (BU) incidence is increasing in temperate south eastern Australia. We have yet to develop public health programs to assist people avoid BU partly because the precise mode of transmission is contentious. Recent research has shown that environmental contamination with M. ulcerans (the cause of BU) is widespread in endemic areas as a result of faecal shedding from infected possums that live close to humans, although direct human-possum contact is rare. We investigated the possibility that the skin of humans in endemic areas could become transiently contaminated with M. ulcerans while outdoors. If this were the case then BU prevention programs could be developed around skin protection and regular washing/showering. To study this possibility, we developed a sensitive skin swab PCR-assay that we tested using a pigskin laboratory model so we could be confident in our results. We asked volunteers to collect their own skin swabs after spending at least 4 hours outside during the known period of peak Buruli transmission. Fifty seven volunteers returned swab sets for testing. Our results were negative. We did not find evidence that humans in our endemic zone have M. ulcerans contamination on their skin.
Targeted memory reactivation during post-learning sleep does not enhance motor memory consolidation in older adults

Targeted memory reactivation (TMR) during sleep enhances memory consolidation in young adults by modulating electrophysiological markers of neuroplasticity. Interestingly, older adults exhibit deficits in motor memory consolidation, an impairment that has been linked to age-related degradations in the same sleep features sensitive to TMR. We hypothesized that TMR would enhance consolidation in older adults via the modulation of these markers. Seventeen older participants were trained on a motor task involving two auditory-cued sequences. During a post-learning nap, two auditory cues were played: one associated to a learned (i.e., reactivated) sequence and one control. Performance during two delayed retests did not differ between reactivated and non-reactivated sequences. Moreover, both associated and control sounds modulated brain responses, yet there were no consistent differences between the auditory cue types. Our results collectively demonstrate that older adults do not benefit from specific reactivation of a motor memory trace by an associated auditory cue during post-learning sleep. It is possible, however, that auditory stimulation during post-learning sleep boosts motor memory consolidation in a non-specific manner.
DIRECTED POLYMERS, CRITICAL TEMPERATURE AND UNIFORM INTEGRABILITY

In this paper, we consider directed polymers in random environ- ment. More accurately, we consider the critical temperaturec be- tween weak and strong disorder. We find a necessary condition that ensures that this critical temperature is generally different from its lower bound obtained with the second moment method introduced by E. Bolthausen. To do this, we study a condition of uniform integra- bility originally due to B. Derrida and M.R. Evans. We also illustrate our result by examples of environments that satisfy this condition.
On Discrete Subgroups of Lie Groups (II)

1. This is a continuation of my paper [7] with the same title, which will be referred to as D', and which has to be supplemented in the manner described below in Appendix I. Indeed, the present paper is nothing else than a combination of the ideas of D' with the method of variation of structure, as applied to special types of semisimple groups by Calabi and by Calabi-Vesentini in their recent work'. We shall mainly be concerned with semisimple groups without compact components, i.e., with connected semisimple Lie groups having no connected compact normal subgroup. However, we begin by considering any connected Lie group G having at least one discrete subgroup with compact quotient; this implies that G is unimodular (it would even be enough for this to assume that G has a discrete subgroup H such that G/H has a finite measure, for the measure determined on G/Hby a right-invariant measure on G). Let n be the dimension of G; choose a basis X1, * , Xn for the space of right-invariant vector-fields on G; we have
Bulk and Grain Boundary Ionic Conductivity in Polycrystalline β″‐ Alumina

Measurements of conductance and capacitance are made on polycrystalline β″-alumina over a range of frequencies from 10 to 107 Hz and temperatures from −130 to 400 °C. The results are analyzed using complex impedance plots which exhibited a bulk and grain boundary component. Above 220 °C the resistance of the grains exceeded that of the grain boundaries. The activation energy for bulk conductivity is found to be 0.18 eV. The low-temperature results indicated that the grain boundary impedance is being short-circuited either by easy paths through the grain boundaries and/or by some very low impedance boundaries leading to conduction, through preferred grains and grain boundaries.
Anisotropic equations: Uniqueness and existence results

in a bounded domain Ω ⊂ R with Lipschitz continuous boundary Γ = ∂Ω. We consider in particular mixed boundary conditions -i.e., Dirichlet condition on one part of the boundary and Neumann condition on the other part. We study also uniqueness of weak solutions for the parabolic equations  ∂tu = ∂xi ( ai(x, t, u) |∂xiu| pi−2 ∂xiu ) + f in Ω× (0, T ), u = 0 on Γ× (0, T ) = ∂Ω× (0, T ), u(x, 0) = u0 x ∈ Ω. It is assumed that the constant exponents pi satisfy 1 < pi < ∞ and the coefficients ai are such that 0 < λ ≤ λi ≤ ai(x, u) < ∞, ∀i, a.e. x ∈ Ω, (a.e. t ∈ (0, T )), ∀u ∈ R. We indicate also conditions which guarantee existence of solutions.
New contributions to hyperbolic polyhedra, reflection groups, and their commensurability

Hyperbolic Coxeter groups form an important class of discrete subgroups of Isom(Hn) : they have a simple presentation, they enjoy nice combinatorial and algebraic properties, and they provide examples of hyperbolic n-orbifolds of small volume. However, they are far from being classified, and a number of their properties remain cryptic. Hence, the study of hyperbolic Coxeter groups and of the related Coxeter polyhedra is a rich and diversified domain, harbouring numerous open problems. In this work, we solve the three following problems : (P1) Find an upper dimensional bound for the existence of hyperbolic Coxeter hypercubes, and classify the ideal Coxeter hypercubes. (P2) Find the inradius of a hyperbolic truncated simplex. (P3) Classify up to commensurability the hyperbolic Coxeter pyramid groups. Our results are inspired by previous works respectively of Felikson-Tumarkin [21], Milnor [47], Vinberg [65], Maclachlan [39] and Johnson-KellerhalsRatcliffe-Tschantz [31]. Our solution to Problem (P2) has partially been published in [29]. Moreover, the solution to Problem (P3) results from a joint work with Rafael Guglielmetti and Ruth Kellerhals [24].
The spreading and stability of a surfactant-laden drop on a prewetted substrate

We consider a viscous drop, loaded with an insoluble surfactant, spreading over a flat plane that is covered initially with a thin liquid film. Lubrication theory allows the flow to be modelled using coupled nonlinear evolution equations for the film thickness and surfactant concentration. Exploiting high-resolution numerical simulations, we describe the multi-region asymptotic structure of the spatially one-dimensional spreading flow and derive a simplified ODE model that captures its dominant features at large times. The model includes a version of Tanner's law accounting for a Marangoni flux through the drop's effective contact line, the magnitude of which is influenced by a rarefaction wave in the film ahead of the contact line. Focusing on the neighbourhood of the contact line, we then examine the stability of small-amplitude disturbances with spanwise variation, using long-wavelength asymptotics and numerical simulations to describe the growth-rate/wavenumber relationship. In addition to revealing physical mechanisms and new scaling properties, our analysis shows how initial conditions and transient dynamics have a long-lived influence on late-time flow structures, spreading rates and contact-line stability.
Computational analysis of the effects of matrix-degrading enzymes on cancer-cell invasion

Cancer cells secrete matrix degrading enzymes (MDEs) and invade the extracellular matrix (ECM) that is degraded by MDEs. This paper presents a dynamic model that incorporates multiple components and mechanisms to investigate the invasion process of cancer cells. The degradation of ECM by MDEs secreted by cancer cells and the consequent influence on cancer-cell invasion are systematically investigated. The morphology and velocity of cancer cells are analytically characterized by critical factors with the developed model, which are the secreting rate of MDEs, the natural degrading rate of MDEs, and the degrading rate of ECM. The simulation results are consistent with the experimental observations and suggest a substantial potential of the presented model for computational cancer research.
Noninvasive Blood Pressure Prediction Based on Dual Encoder U-Net

Cardiovascular disease is one of the most serious causes of death, causing serious loss of life in the world every year. In this paper, we present a deep learning approach to estimate the continuous arterial blood pressure(ABP) waveform using the photoplethysmogram(PPG) signals. We propose a U-Net model structure of dual channel encoder, which extracts the semantic information roughly and finely through two encodings. In view of the strong periodicity and continuity of PPG signal, information distillation model with improved attention mechanism block is added to the U-Net network encoder, which can not only improve the ability of U-Net network to mine deep-seated semantic information, but also suppress unimportant channels and effectively reduce information redundancy. In addition, a multi-scale information fusion module is designed to fuse semantic information at different scales and improve the prediction accuracy of the model. Independent test on MIMIC-II dataset provides an MAE of 3.80mmHg and 1.81mmHg for SBP and DBP. The results met British Hypertension Society(BHS) Grade A and surpassed the studies from the current literature.
NEW ASPECTS OF A LID-REMOVAL MECHANISM IN THE ONSET OF AN ERUPTION SEQUENCE THAT PRODUCED A LARGE SOLAR ENERGETIC PARTICLE (SEP) EVENT

We examine a sequence of two ejective eruptions from a single active region on 2012 January 23, using magnetograms and EUV images from the Solar Dynamics Observatory's (SDO) Helioseismic and Magnetic Imager (HMI) and Atmospheric and Imaging Assembly (AIA), and EUV images from STEREO/EUVI. This sequence produced two coronal mass ejections (CMEs) and a strong solar energetic particle event (SEP); here we focus on the magnetic onset of this important space weather episode. Cheng et al. showed that the first eruption's (“Eruption 1”) flux rope was apparent only in “hotter” AIA channels, and that it removed overlying field that allowed the second eruption (“Eruption 2”) to begin via ideal MHD instability; here we say that Eruption 2 began via a “lid removal” mechanism. We show that during Eruption 1's onset, its flux rope underwent a “tether weakening” (TW) reconnection with field that arched from the eruption-source active region to an adjacent active region. Standard flare loops from Eruption 1 developed over Eruption 2's flux rope and enclosed filament, but these overarching new loops were unable to confine that flux rope/filament. Eruption 1's flare loops, from both TW reconnection and standard-flare-model internal reconnection, were much cooler than Eruption 2's flare loops (GOES thermal temperatures of ∼7.5 MK and 9 MK, compared to ∼14 MK). The corresponding three sequential GOES flares were, respectively, due to TW reconnection plus earlier phase Eruption 1 tether-cutting reconnection, Eruption 1 later-phase tether-cutting reconnection, and Eruption 2 tether-cutting reconnection.
Large eddy simulation of turbulent channel flow using an algebraic model

In this paper an algebraic model from the constitutive equations of the subgrid stresses has been developed. This model has an additional term in comparison with the mixed model, which represents the backscatter of energy explicitly. The proposed model thus provides independent modelling of the different energy transfer mechanisms, thereby capturing the effect of subgrid scales more accurately. The model is also found to depict the flow anisotropy better than the linear and mixed models. The energy transfer capability of the model is analysed for the isotropic decay and the forced isotropic turbulence. The turbulent plane channel flow simulation is performed over three Reynolds numbers, Reτ=180, 395 and 590, and the results are compared with that of the dynamic model, Smagorinsky model, and the DNS data. Both the algebraic and dynamic models are in good agreement with the DNS data for the mean flow quantities. However, the algebraic model is found to be more accurate for the turbulence intensities and the higher‐order statistics. The capability of the algebraic model to represent backscatter is also demonstrated. Copyright © 2005 John Wiley & Sons, Ltd.
Detection of five C-13 isotopic species of HC5N in TMC-1

Les raies rotationnelles J = 14-13 des 5 especes isotopiques 13 C du cyanodiacetylene HC 5 N ont ete detectees dans le nuage moleculaire TMC-1. Les rapports isotopiques du carbone sont calcules a partir des abondances des especes normales et isotopiques de HC 5 N, et les rapports sont trouves proches de ceux du voisinage solaire. Le degre de fractionnement chimique de l'isotope du carbone pour les 5 especes isotopiques de HC 5 N est etudie.
Airborne Retrievals of Snow Microwave Emissivity at AMSU Frequencies Using ARTS/SCEM-UA

Abstract The remote sounding, by satellite, of atmospheric temperature and humidity is an important source of data for assimilation into operational weather forecasting routines. For retrievals of these variables near the surface, wavebands with low optical depths are monitored to allow penetration through the overlying atmosphere. Brightness temperatures in these relatively transparent bands are also sensitive to the land surface emissivity and effective temperature. Inadequate understanding of these land surface emissivities is a major issue when assimilating Advanced Microwave Sounding Unit data for the land-covered portion of the globe. One approach for estimating the emissivity of snow-covered surfaces is an empirical model derived from satellite-based and land-based retrievals of emissivity for a variety of snow types. The Met Office’s Hercules C-130 aircraft flew over snow-covered Arctic terrain of northern Finland during the Polar Experiment (POLEX) of March 2001. On these flights, microwave radio.
Evidence against an antarctic stratospheric vortex split during the periods of Pre-IGY temperature measurements

Historic upper-air observations from Antarctica are inspected to investigate the uniqueness of the vortex split in the Antarctic spring of 2002. No comprehensive meteorological observations are available prior to the International Geophysical Year (IGY) 1957/58, but stratospheric temperature observations from single stations provide evidence of varying strengths against the possibility of a split vortex in 1940 and in the early and middle 1950s.
Experimental, computational, and observational analysis of primordial nucleosynthesis

We present a comprehensive evaluation of the current status of the standard theory of primordial nucleosynthesis. We determine the 12 nuclear reactions most important for the production of the light elements and conduct a detailed study of their rates and uncertainties, incorporating these into a Monte Carlo analysis to properly evaluate uncertainties in the computed elemental abundances. We then compare these predicted abundances with primordial abundances deduced from astronomical observations of the light elements D, 3 He, 4 He, and 7 Li and find a consistent agreement over a narrow range of the baryon-to-photon ratio η, thereby supporting the standard theory of big bang nucleosynthesis. This η range corresponds to a constraint on the baryon density parameter of 0.01≤Ω b ≤0.09, where the primordial D+ 3 He abundance sets the lower bound and the 4 He abundance sets the upper bound
The motion of long bubbles in tubes

A long bubble of a fluid of negligible viscosity is moving steadily in a tube filled with liquid of viscosity μ at small Reynolds number, the interfacial tension being σ. The angle of contact at the wall is zero. Two related problems are treated here. In the first the tube radius r is so small that gravitational effects are negligible, and theory shows that the speed U of the bubble exceeds the average speed of the fluid in the tube by an amount UW, where $W \simeq 1\cdot 29(3 \mu U|\sigma)^{\frac {2}{3}}\;\;\; as\;\;\; \mu U|\sigma$ (This result is in error by no more than 10% provided $\mu U |\sigma \; \textless \;5 \times 10^{-3}\rightarrow 0$). The pressure drop, P, across such a bubble is given by $P \simeq 3\cdot 58(3\mu U|\sigma)^{\frac {2}{3}}\sigma|r \; \; \;as\; \; \; \mu U|\sigma \rightarrow 0$ and W is uniquely determined by conditions near the leading meniscus. The interface near the rear meniscus has a wave-like appearance. This provides a partial theory of the indicator bubble commonly used to measure liquid flowrates in capillaries. A similar theory is applicable to the two-dimensional motion round a meniscus between two parallel plates. Experimental results given here for the value of W agree well neither with theory nor with previous experiments by other workers. No explanation is given for the discrepancies. In the second problem the tube is wider, vertical, and sealed at one end. The bubble now moves under the effect of gravity, but it is shown that it will not rise at all if $\rho gr^2| \sigma \; \textless \; 0 \cdot 842,$ where ρ is the difference in density between the fluids inside and outside the bubble. If $0 \cdot 842 \; \textless \; 1 \cdot 04,$ then $\rho gr^2| \sigma - 0 \cdot842 \simeq 1 \cdot 25 (\mu U|\sigma)^{\frac {2}{9}} + 2 \cdot 24(\mu U|\sigma)^{\frac {1}{3}},$ accurate to within 10%. Experiments are adduced in support of these results, though there is disagreement with previous work.
Composite indices based on partial least squares

In this paper, we compare Principal Component Analysis (PCA) and Partial Least Squares (PLS) methods to generate weights for composite indices. In this context we also consider various treatments of non-metric variables when constructing such composite indices. Using simulation studies we find that dummy coding for non-metric variables yields satisfactory performance compared to more sophisticated statistical procedures. In our applications we illustrate how PLS can generate weights that differ substantially from those obtained with PCA, increasing the composite indices' predictive performance for the outcome variable considered.
Photometric study of the eclipsing binary V1034 Sco

We present multi-colour Stromgren photometry of the eclipsing binary V1034 Sco in the galactic open cluster NGC 6231, providing for the first time a full coverage of the orbital period (P = 2.44 days) and a complete analysis of the orbit. This extensive new photometry was analyzed together with multiband spectroscopy and results in an improved ephemeris, photometric elements and absolute parameters of the components. The system is close, but clearly detached. The masses of the components M1 = 16.8 ± 0.5 Mand M2 = 9.4 ± 0.3 Mdo not correspond to the published spectral classification (O9III + B1III). The parameters of the components are consistent with the main-sequence luminosity class. We independently derive a distance modulus V0 − MV = 10.73 ± 0.02.