Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct disease-modifying therapies are associated with different blood immune cell profiles in people with relapsing-remitting multiple sclerosis

Disease modifying therapies (DMTs) used for treating people with relapsing-remitting multiple sclerosis (pwRRMS) target the immune system by different mechanisms of action. However, there is a lack of a comprehensive comparison of their effects on the immune system. Herein, we evaluated the numbers of circulating B cells, CD4+ and CD8+ T cells, regulatory T cells (Tregs), natural killer (NK) cells and NKT cells, and their subsets, in pwRRMS who were treatment-naïve or treated with different DMTs. Compared to treatment-naïve pwRRMS, common and divergent effects on immune system cells were observed on pwRRMS treated with different DMTs, with no consistent pattern across all therapies in any of the cell populations analysed. PwRRMS treated with fingolimod, dimethyl fumarate (DMF), or alemtuzumab have reduced numbers of CD4+ and CD8+ T cells, as well as Treg subsets, with fingolimod causing the most pronounced decrease in T cell subsets. In contrast, teriflunomide and interferon (IFN) β have minimal impact on T cells, and natalizumab marginally increases the number of memory T cells in the blood. The effect of DMTs on the B cell, NKT and NK cell subsets is highly variable with alemtuzumab inducing a strong increase in the number of the most immature NK cells and its subsets. This study highlights the absence of a consistent pattern of the impact of various DMTs on immune system cells, with variations in both direction and magnitude of effect thus reenforcing the notion that distinct immune cell subsets are potential players in MS pathophysiology and/or DMT efficacy.
Diagnostic histone modification analysis of individual preimplantation embryos

Background We previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). Results WOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. Conclusions These results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.
Molecular responses of agroinfiltrated Nicotiana benthamiana leaves expressing suppressor of silencing P19 and influenza virus-like particles

The production of influenza vaccines in plants is achieved through transient Agrobacterium-mediated expression of viral hemagglutinins (HAs). These proteins are produced and matured through the secretory pathway of plant cells, before being trafficked to the plasma membrane where they induce formation of virus-like particles (VLPs). Production of VLPs unavoidably impacts plant cells, as do viral suppressors of RNA silencing (VSRs) that are often co-expressed to increase protein yields. However, little information is available on host molecular responses to these foreign proteins. The present work provides a comprehensive overview of transcriptomic, metabolic, and signaling changes occurring in Nicotiana benthamiana leaf cells transiently expressing the VSR P19, or co-expressing P19 and an influenza HA. Our data identifies generic responses to Agrobacterium-mediated expression of foreign proteins, including shutdown of chloroplast gene expression, activation of oxidative stress responses, and reinforcement of the plant cell wall through lignification. Our results also indicate that P19 expression promotes salicylic acid (SA) signaling, a process apparently antagonized by co-expression of HA. As the latter induces specific signatures, with effects on lipid metabolism, lipid distribution, and oxylipin signaling, dampening of P19 responses suggests crosstalk between SA and oxylipin pathways. Consistent with the upregulation of oxidative stress-related genes and proteins, we finally show that reduction of oxidative stress damage through exogenous application of ascorbic acid improves plant biomass quality during production of VLPs. One-sentence summary Agrobacterium-mediated expression of influenza virus-like particles induces a unique molecular signature in Nicotiana benthamiana leaf cells.
Charting cellular differentiation trajectories with Ricci flow

Complex biological processes, such as cellular differentiation, require an intricate rewiring of intra-cellular signalling networks. Previous characterisations of these networks revealed that promiscuity in signalling, quantified by a raised network entropy, underlies a less differentiated and malignant cell state. A theoretical connection between entropy and Ricci curvature has led to applications of discrete curvatures to characterise biological signalling networks at distinct time points during differentiation and malignancy. However, understanding and predicting the dynamics of biological network rewiring remains an open problem. Here we construct a framework to apply discrete Ricci curvature and Ricci flow to the problem of biological network rewiring. By investigating the relationship between network entropy and Forman-Ricci curvature, both theoretically and empirically on single-cell RNA-sequencing data, we demonstrate that the two measures do not always positively correlate, as has been previously suggested, and provide complementary rather than interchangeable information. We next employ discrete normalised Ricci flow, to derive network rewiring trajectories from transcriptomes of stem cells to differentiated cells, which accurately predict true intermediate time points of gene expression time courses. In summary, we present a differential geometry toolkit for investigation of dynamic network rewiring during cellular differentiation and cancer.
Experimental test of the crossover between the inertial and the dissipative range in a turbulent swirling flow

The kinetic energy spectrum of high-Reynolds turbulent swirling flows is experimentally studied. This spectrum, obtained from direct measurements in space, exhibits nearly two decades of Kol-mogorov k −5/3 decay in the inertial range of scales. Beyond this regime, in the dissipative range of scales, a crossover to a stretched exponential decay on scale k 2/3 is observed, in full agreement with a recent theoretical prediction based on Non-Perturbative Renormalization Group theory.
Polarimetric and spectrographic instrumentation to enable next generation x-ray observatories

Ultraluminous X-ray (ULX) sources are non-nuclear extragalactic accreting compact objects whose X-ray luminosities exceed the Eddington limit for stellar mass black hole binaries (BHB). Their high luminosities suggest they are either intermediate mass black holes, that their emission is beamed, or that they are emitting at superEddington rates. We observed the ULX IC 342 X-1 simultaneously in X-ray and radio with Chandra and the VLA to investigate previously reported unresolved radio emission coincident with the ULX. The Chandra spectrum appears to be consistent with an accretion disc-dominated thermal state and suggests a mass of the black hole using the modeled inner disc temperature to be 157 M ≤ M √ cos i ≤ 200 M . No significant radio emission was observed, consistent with the source being in a thermal disc-dominated state. Reanalysis of previous X-ray observations of the source shows that high energy curvature often interpreted as evidence for supercritical accretion cannot confidently be identified using the 2-10 keV energy band. Black hole systems such as BHBs, ULXs, and AGN represent the greatest test labs in the universe for the study of extreme gravity. Emission from the accretion disk and scattering from the surrounding corona allow study of the ultra-strong gravity and magnetic fields very near the central BH engine. However, many of these effects are imprinted as polarization of the emission and are invisible to spectral and timing studies alone. The outflows from AGN are also thought to play a key role in galaxy shaping and cluster formation. High efficiency and spectral resolution are required to measure ionization-velocities and density parameters from these sources to constrain the outflow structure. Beamline studies and theoretical modeling were carried out to characterize the throughput and spectral resolving power of off-plane gratings for use in future x-ray observatories which will make these measurements. Additionally, synchrotron measurements were carried out to test theoretical predictions of strong polarization response for off-plane diffraction gratings. The empirical results of this
Pump as Turbine - Symmetry Prediction Method for Pump as Turbine Characteristics

As a cheap and available source of renewable energy, regular centrifugal pumps may be run in reverse to act as hydro turbines. Pumps as turbines (PAT) are especially relevant for isolated rural areas, or in developing countries, where efficiency is not necessarily the highest priority. The main challenge, however, is to be able to pick a suitable pump for a given site, which coincides with the available head and discharge. In order to make this decision, one has to be able to predict how a certain pump will perform as a turbine. A lot of work has been done in the past to establish such prediction methods, based on tests and empirical correlations. Many of these methods only predict one optimal point of operation, but as pumps do not have any guide vanes, it will be difficult to constantly operate a PAT at this specific point. Therefore, this may be insufficient. With this in mind, and because of the inaccuracies of these methods, a new approach has been suggested an approach in which full head-flow characteristics are predicted based solely on the pump’s impeller geometry. By assuming symmetry in the velocity diagrams of pump and turbine operation, a method for establishing the PAT characteristic was made. For validation purposes, this method was applied to one specific pump. Experimental results revealed a slight asymmetry, and shortcomings in the initial assumptions. Therefore, the model was modified thereafter, with the introduction of an empirical constant. The predicted characteristic lacks some accuracy in comparison to the real PAT characteristic found through testing, but its optimal point of operation is in line with previous established prediction methods. Still, the modifications, and the empirical constant, may be enhanced further through comprehensive testing of numerous pumps, of various type.
Management of Bite Wounds in the Head and Neck

An estimated 50% of people in the United States will incur an animal or human bite wound at least once in their lifetimes. Although the majority of these individuals do not seek medical attention, bite wounds to the head and neck are a common reason for emergency department visits. Facial bites are complex injuries due to the functional and cosmetic nature of the area, as well as the unique polymicrobial infection potential that exists. We present a review of the epidemiology and microbiology of bite injuries to the head and neck and provide evidence-based recommendations regarding surgical wound closure and antibiotic therapy.
Axisymmetric buoyant–thermocapillary flow in sessile and hanging droplets

The steady axisymmetric incompressible flow in a droplet sitting on or hanging from a flat plate is calculated numerically. In the limit of large mean surface tension the liquid–gas interface is spherical which allows the use of boundary-fitted toroidal coordinates. The flow is driven by thermocapillary and buoyant forces induced by a linear variation of the ambient temperature normal to the perfectly conducting wall. We present benchmark-quality results for the streamfunction and temperature fields, varying the contact angle, the thermocapillary Reynolds number, the Prandtl number, the Grashof number and the interfacial heat-transfer coefficient including the latent heat of evaporation. Scaling laws for the strength of the flow are provided for asymptotically large Marangoni numbers.
Microdermabrasion: A Review

Microdermabrasion is used by clinicians and aestheticians worldwide to rejuvenate facial skin. The microdermabrator contains aluminum oxide or sodium chloride crystals that strike the skin and produce superficial trauma. It is theorized that the repetitive intraepidermal injury causes gradual improvement in damaged skin by stimulating fibroblast proliferation and collagen production, leading to new collagen deposition in the dermis. In this review of microdermabrasion, we discuss studies performed to elucidate the mechanism of action by which microdermabrasion promotes facial resurfacing. We also discuss other existing techniques for facial rejuvenation and resurfacing.
Segregation-induced finger formation in granular free-surface flows

Geophysical granular flows, such as landslides, pyroclastic flows and snow avalanches, consist of particles with varying surface roughnesses or shapes that have a tendency to segregate during flow due to size differences. Such segregation leads to the formation of regions with different frictional properties, which in turn can feed back on the bulk flow. This paper introduces a well-posed depth-averaged model for these segregation-mobility feedback effects. The full segregation equation for dense granular flows is integrated through the avalanche thickness by assuming inversely graded layers with large particles above fines, and a Bagnold shear profile. The resulting large particle transport equation is then coupled to depth-averaged equations for conservation of mass and momentum, with the feedback arising through a basal friction law that is composition dependent, implying greater friction where there are more large particles. The new system of equations includes viscous terms in the momentum balance, which are derived from the $\unicode[STIX]{x1D707}(I)$ -rheology for dense granular flows and represent a singular perturbation to previous models. Linear stability calculations of the steady uniform base state demonstrate the significance of these higher-order terms, which ensure that, unlike the inviscid equations, the growth rates remain bounded everywhere. The new system is therefore mathematically well posed. Two-dimensional simulations of bidisperse material propagating down an inclined plane show the development of an unstable large-rich flow front, which subsequently breaks into a series of finger-like structures, each bounded by coarse-grained lateral levees. The key properties of the fingers are independent of the grid resolution and are controlled by the physical viscosity. This process of segregation-induced finger formation is observed in laboratory experiments, and numerical computations are in qualitative agreement.
A Comprehensive Observational Study of Graupel and Hail Terminal Velocity, Mass Flux, and Kinetic Energy

This study uses novel approaches to estimate the fall characteristics of hail, covering a size range from about 0.5 to 7 cm, and the drag coefficients of lump and conical graupel. Three-dimensional (3D) volume scans of 60 hailstones of sizes from 2.5 to 6.7 cm were printed in three dimensions using acrylonitrile butadiene styrene (ABS) plastic, and their terminal velocities were measured in the Mainz, Germany, vertical wind tunnel. To simulate lump graupel, 40 of the hailstones were printed with maximum dimensions of about 0.2, 0.3, and 0.5 cm, and their terminal velocities were measured. Conical graupel, whose three dimensions (maximum dimension 0.1–1 cm) were estimated from an analytical representation and printed, and the terminal velocities of seven groups of particles were measured in the tunnel. From these experiments, with printed particle densities from 0.2 to 0.9 g cm−3, together with earlier observations, relationships between the drag coefficient and the Reynolds number and between the Reynolds number and the Best number were derived for a wide range of particle sizes and heights (pressures) in the atmosphere. This information, together with the combined total of more than 2800 hailstones for which the mass and the cross-sectional area were measured, has been used to develop size-dependent relationships for the terminal velocity, the mass flux, and the kinetic energy of realistic hailstones.
Volumetric Cine Imaging for On-board Target Localization in Radiation Therapy

Volumetric Cine Imaging for On-board Target Localization in Radiation Therapy by Wendy Beth Harris Graduate Program in Medical Physics Duke University Date:_______________________ Approved: ___________________________ Lei Ren, Supervisor ___________________________ Fang-Fang Yin, Supervisor ___________________________ Bastiaan Driehuys, Chair ___________________________ Jing Cai ___________________________ Zheng (Jim) Chang ___________________________ Brian Czito An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Medical Physics Graduate Program in the Graduate School of Duke University
A Study of the Surface Air Temperature Variations in Nigeria

Received: December 13, 2016 Revised: February 16, 2017 Accepted: March 10, 2017 Abstract: Background: Simultaneous measurements of air temperature were carried out using automatic weather stations at 14 tropical locations in Nigeria. Diurnal variations were derived from the 5-minute update cycle initial data for the years ranging between 2007 and 2013. The temperature trends in Nigeria revealed a continuous variability that is seasonally dependent within any particular year considered.
H1 versus C1 local minimizers

On considere de fonctionelles de la forme Φ (u)=(1/2)∫ Ω |⊇u| 2 -∫ Ω F(x, u). Sous des hypotheses convenables on prouve qu'un minimum local de Φ au sens de la norme C 1 est necessairement un minimum local au sens de la norme H 1 . Ce resultat est particulierement utile dons le cas ou l'equation correspondante admet une sous-solution et une sur-solution
X-ray diffraction and imaging with a coherent beam : application to X-Ray optical elements and crystal exhibiting phase inhomogeneities

The exceptional properties of synchrotron light sources have been and increasingly are exploited in very different disciplines, from archaeology to chemistry, from material science to biology, from medicine to physics. Among these properties it is important to mention the high brilliance, continuum spectrum, high degree of polarization, time structure, small source size and divergence of the beam, the last resulting in a high transversal coherence of the produced radiation. This high transversal coherence of the synchrotron sources has permitted the development of new techniques, e.g. phase contrast imaging, X-ray photon correlation spectroscopy and coherent X-ray diffraction imaging (CXDI). The thesis work will consist essentially of three parts. In the first part it will be presented the work done as a member of the X-ray Optics Group of ESRF in the characterization of high quality diamond crystals foreseen as X-ray optical elements. The characterization has been done using different complementary X-ray techniques, such as high resolution diffraction, topography, grazing incidence diffraction, reflectivity and measurements of the coherence preservation using the Talbot effect. In the second part, I will show the result obtained in the study of the temperature behaviours of the domain in periodically poled ferroelectrics crystals. This type of measurements, based on Bragg-Fresnel diffraction, are possible only thanks to the high degree of coherence of the beam In the third part, I will present the results obtained in the characterization of diamonds foreseen for applications other than X-ray optical elements.
Identifying Changes in Source Regions Impacting Speciated Atmospheric Mercury at a Rural Site in the Eastern United States

AbstractTo investigate the effectiveness of emission reductions on the concentrations of gaseous elemental mercury (GEM), gaseous oxidized mercury (GOM), and particulate-bound mercury (PBM) at a rural site in Maryland (MD08), long-term (2005–14) measurements of speciated atmospheric mercury were analyzed using concentration-weighted trajectory (CWT) analysis. CWT results suggested that the number of major source regions contributing to GEM, GOM, and reactive mercury (RM = GOM + PBM) over the eastern United States and southeastern Canada declined over time. Across much of these regions, source contributions in 2011–14 decreased by up to 20% for GEM, by greater than 60% for GOM, and by 20%–60% for PBM compared to 2006–08, largely because of the decreases in power-plant mercury emissions since 2009. Changes in the spatial distribution of the source regions were also observed over time. Increases in source contributions of GEM after 2011 over the northeastern United States and southeastern Canada were predomi.
On Geodesics in Asymptotic Universal Teichmüller Space

Abstract Let AT(Δ) be the asymptotic universal Teichmüller space, viewed as the space of all asymptotic Teichmüller equivalence classes [[μ]]. We show that if μ is asymptotically extremal in AT(Δ) and h p ([[μ]]) < h([[μ]]) for some boundary point p of Δ, then there are infinitely many geodesics joining [[0]] and [[μ]] in AT(Δ). As a corollary, a necessary condition for a complex dilatation to be uniquely extremal in AT(Δ) is given.
Impact of the Diurnal Radiation Contrast on the Contraction of Radius of Maximum Wind during Intensification of Hurricane Edouard (2014)

This work examines the impacts of the diurnal radiation contrast on the contraction rate of the radius of maximum wind (RMW) during intensification of Hurricane Edouard (2014) through convection-permitting simulations. Rapid contraction of RMW occurs both in the low and midlevels for the control run and the sensitivity run without solar insolation, while the tropical cyclone contracts more slowly in the low levels and later in the midlevels and thereafter fails to intensify continuously in the absence of the night phase, under weak vertical wind shear (~4 m s−1). The clouds at the top of the boundary layer absorb solar shortwave heating during the daytime, which enhanced the temperature inversion there and increased the convective inhibition, while nighttime destabilization and moistening in low levels through radiative cooling decrease convective inhibition and favor more convection inside the RMW than in the daytime phase. The budget analysis of the tangential wind tendency reveals that the greater positive radial vorticity flux inside of the RMW is the key RMW contraction mechanism in the boundary layer at night because of the enhanced convection. However, the greater positive vertical advection of tangential wind inside of the RMW dominates the RMW contraction in the midlevels.