Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating transmission dynamics of African swine fever virus from experimental studies

Abstract African swine fever virus (ASFV) continues to spread across the world, and currently, there are no treatments or vaccines available to combat this virus. Reliable estimates of transmission parameters for ASFV are therefore needed to establish effective contingency plans. This study used data from controlled ASFV inoculations of pigs to assess the transmission parameters. Three models were developed with (binary, piecewise‐linear and exponential) time‐dependent levels of infectiousness based on latency periods of 3–5 days derived from the analysis of 294 ethylenediamine tetraacetic acid–stabilized blood samples originating from 16 pigs with direct and 10 pigs with indirect contact to 8 inoculated pigs. The models were evaluated for three different discrete latency periods of infection. The likelihood ratio test showed that a binary model had an equally good fit for a latency period of 4 or 5 days as the piecewise‐linear and exponential model. However, for a latency period of 3 days, the piecewise‐linear and exponential models had the best fit. The modelling was done in discrete time as testing was conducted on specific days. The main contribution of this study is the estimation of ASFV genotype II transmission through the air in a confined space. The estimated transmission parameters via air are not much lower than for direct contact between pigs. The estimated parameters should be useful for future simulations of control measures against ASFV.
Relationship of self-reported and performance-based visual function with performance-based measures of physical function: the Health ABC study.

BACKGROUND To assess the relationship between self-reported and performance-based visual impairment (VI) and lower extremity physical function. METHODS Cross-sectional analysis of 2219 Health ABC participants who completed vision testing and the Short Physical Performance Battery (SPPB). Linear regression models used either self-reported (weighted visual function question (VFQ) score)) or performance-based (visual acuity (VA), log contrast sensitivity (LCS), Frisby stereoacuity (SA)) to predict SPPB or its components-gait speed, chair stands, or standing balance-with and without covariate adjustment. RESULTS Mean age was 73.5 years (range 69-80); 52.4% were female and 37.4% African American. All VI measures were strongly associated with SPPB in unadjusted and adjusted models (p<0.001). A self-reported VFQ score 1 standard deviation lower than the mean (mean 87.8 out of 100) demonstrated a -0.241(95% CI:-0.325, -0.156) adjusted difference in SPPB. After controlling for covariates, VA of <20/40 (41%) demonstrated a -0.496(-0.660, -0.331) lower SPPB score while SA score>85 arcsec (30%) had a -0.449(-0.627, -0.271) adjusted SPPB score versus those with better visual function. LCS<1.55 (28.6%) was associated with a -0.759(-0.938, -0.579) lower and LCS≤1.30 (8%) with a -1.216(-1.515, -0.918) lower adjusted SPPB score relative to better LCS. In a final multivariable model containing multiple vision measures, LCS remained independently associated with SPPB and all components, while SA remained associated with balance (all p<0.05). CONCLUSIONS Both self-reported and performance-based VI are strongly associated with poor lower extremity physical function. These findings may identify a subgroup of older adults with co-existing visual and physical dysfunction who may benefit from targeted screening and intervention to prevent disability.
CAN SOLID BODY DESTRUCTION EXPLAIN ABUNDANCE DISCREPANCIES IN PLANETARY NEBULAE?

In planetary nebulae (PNe), abundances of oxygen and other heavy elements derived from optical recombination lines are systematically higher than those derived from collisionally excited lines. We investigate the hypothesis that the destruction of solid bodies may produce pockets of cool, high-metallicity gas that could explain these abundance discrepancies. Under the assumption of maximally efficient radiative ablation, we derive two fundamental constraints that the solid bodies must satisfy in order that their evaporation during the PN phase should generate a high enough gas-phase metallicity. A local constraint implies that the bodies must be larger than tens of meters, while a global constraint implies that the total mass of the solid body reservoir must exceed a few hundredths of a solar mass. This mass greatly exceeds the mass of any population of comets or large debris particles expected to be found orbiting evolved low- to intermediate-mass stars. We therefore conclude that contemporaneous solid body destruction cannot explain the observed abundance discrepancies in PNe. However, similar arguments applied to the sublimation of solid bodies during the preceding asymptotic giant branch phase do not lead to such a clear-cut conclusion. In this case, the required reservoir of volatile solids is only one ten-thousandth of a solar mass, which is comparable to the most massive debris disks observed around solar-type stars, implying that this mechanism may contribute to abundance discrepancies in at least some PNe, so long as mixing of the high-metallicity gas is inefficient.
Complete Genome Sequence of Rhodococcus qingshengii N9T-4

Rhodococcus qingshengii N9T-4 can grow on media without added carbon sources. Here, we report the complete nucleotide sequence of the N9T-4 genome, consisting of a chromosome (6,439,972 bp), a linear plasmid (pN9T4-1 [565,206 bp]), and two circular plasmids (pN9T-4-2 [99,662 bp] and pN9T-4-3 [30,419 bp]). ABSTRACT Rhodococcus qingshengii N9T-4 can grow on media without added carbon sources. Here, we report the complete nucleotide sequence of the N9T-4 genome, consisting of a chromosome (6,439,972 bp), a linear plasmid (pN9T4-1 [565,206 bp]), and two circular plasmids (pN9T-4-2 [99,662 bp] and pN9T-4-3 [30,419 bp]).
High Resolution Melting (HRM) based marker development for wheat leaf rust resistance gene Lr34.

Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat breeding programs. The gene Lr34 is an effective and widely deployed broad spectrum APR gene in wheat against leaf rust fungus Puccinia triticina. Various molecular markers have been developed for Lr34 but, either they require post-PCR handling processes or are not economical. Herein, we developed a high resolution melting (HRM) based diagnostic assay for Lr34 based on a three bp 'TTC' deletion in exon 11 of the resistant allele. The susceptible cv. Thatcher (Tc) and the near-isogenic Thatcher line (RL6058) with Lr34, yielded distinct melting profiles and were differentiated with high reproducibility. For further validation, all three copies of Lr34 were cloned in plasmid vectors and HRM analysis using individual and combination (equimolar mixture of three copies) of homoeologs yielded distinguishing melting profiles. An additional layer of genotyping was provided by a LunaProbe assay. The allele-specific probes successfully distinguished the homoeologs but not Tc and RL6058. Further, the practical deployment of the HRM assay was tested by running the marker on a set of breeding lines. When compared with a kompetitive allele-specific PCR (KASP) Lr34 assay, the HRM assay had similar genotyping results and was able to accurately differentiate the resistant and susceptible breeding lines. However, our HRM assay was unable to detect the heterozygote. To our knowledge, this is the first report of an HRM assay for genotyping a wheat rust resistance gene.
Quasiparticle band-edge energy and band offsets of monolayer of molybdenum and tungsten chalcogenides

We report the quasiparticle band-edge energy of monolayer of molybdenum and tungsten dichalcogenides, MX2 (M = Mo, W; X = S, Se, Te). Beyond calculating bandgaps, we have achieved converged absolute band-edge energies relative to the vacuum level. Compared with the results from other approaches, the GW calculation reveals substantially larger bandgaps and different absolute quasiparticle energies because of enhanced many-electron effects. Interestingly, our GW calculations ratify the band-gap-center approximation, making it a convenient way to estimate band-edge energy. The absolute band-edge energies and band offsets obtained in this work are important for designing heterojunction devices and chemical catalysts based on monolayer dichalcogenides.
Walk Smarter, Not Harder: Effects of Cadence Manipulation on Gait Biomechanics in Patients with Patellofemoral Osteoarthritis

ABSTRACT Purpose This study aimed to investigate the effect of walking cadence on knee flexion angular impulse and peak external flexion moment in patients with patellofemoral osteoarthritis (OA). Methods Forty-eight patients with patellofemoral OA underwent repeated quantitative gait analyses on an instrumented treadmill using a randomized crossover design. Walking trials were conducted at a fixed gait speed, under three cadence conditions: (i) preferred cadence, (ii) +10% increased cadence, and (iii) −10% decreased cadence, completed in random order. Using a linear mixed model, we tested the association of cadence conditions with surrogate measures of patellofemoral load (primary outcome measure: knee flexion angular impulse) while controlling for body mass. We then repeated the analyses while sequentially replacing the dependent variable with secondary outcome measures. Results Walking with increased cadence decreased (adjusted mean difference [95% confidence interval]) the knee flexion angular impulse (−0.85 N·m·s−1 [−1.52 to −0.18], d = 0.20) and peak knee flexion moment (−4.11 N·m [−7.35 to −0.86], d = 0.24), whereas walking with decreased cadence increased the knee flexion angular impulse (1.83 N·m·s−1 [1.15 to 2.49], d = 0.42) and peak knee flexion moment (3.55 N·m [0.30 to 6.78], d = 0.21). Similar decreases and increases were observed for secondary outcome measures. Conclusions Walking with increased cadence, while maintaining a fixed gait speed, reduces knee flexion angular impulse as well as other surrogate measures of knee loading in patients with patellofemoral OA.
A DISK-WIND MODEL FOR THE NEAR-INFRARED EXCESS EMISSION IN PROTOSTARS

Protostellar systems, ranging from low-luminosity classical T Tauri and Herbig Ae stars to high-luminosity Herbig Be stars, exhibit a near-infrared (NIR) excess in their spectra that is dominated by a bump in the monochromatic luminosity with a peak near 3 μm. The bump can be approximated by a thermal emission component of temperature ∼1500 K that is of the order of the sublimation temperature of interstellar dust grains. In the currently popular “puffed-up rim” scenario, the bump represents stellar radiation that propagates through the optically thin inner region of the surrounding accretion disk and is absorbed and reemitted by the dust that resides just beyond the dust sublimation radius rsub. However, this model cannot account for the strongest bumps measured in these sources, and it predicts a pronounced secondary bounce in the interferometric visibility curve that is not observed. In this paper we present an alternative interpretation, which attributes the bump to reemission of stellar radiation by dust that is uplifted from the disk by a centrifugally driven wind. Winds of this type are a leading candidate for the origin of the strong outflows associated with protostars, and there is observational evidence for disk winds originating on scales ∼rsub. Using a newly constructed Monte Carlo radiative transfer code and focusing on low-luminosity sources, we show that this model can account for the NIR excess emission even in bright Herbig Ae stars such as AB Auriga and MWC 275, and that it successfully reproduces the basic features of the visibilities measured in these protostars. We argue that a robust dusty outflow in these sources could be self-limiting—through shielding of the stellar FUV photons—to a relatively narrow launching region between rsub and ∼2 rsub. We also suggest that the NIR and scattered-light variability exhibited by a source like MWC 275 can be attributed in this picture to the uplifting of dust clouds from the disk.
Accuracy Preserving ENO and WENO Schemes using Novel Smoothness Measurement

A novel procedure is given for choosing smoothest stencil to construct less oscillatory ENO schemes. The procedure is further used to define smoothness parameter in the non-linear weights of new WENO schemes. The main significant features of these new ENO and WENO schemes is that they are less oscillatory and achieve their relevant order of accuracy in the presence of critical points in the exact solution. It is shown theoretically as well as computationally in $L^1$ and $L^\infty$ norm. Moreover, computational results are given to show less oscillatory behavior of the new WENO scheme compared to WENO5-JS and WENO5-Z schemes.
Effects of chronic and binge ethanol administration on mouse cerebellar and hippocampal neuroinflammation

ABSTRACT Background: Hippocampal and cerebellar neuropathology occurs in individuals with alcohol use disorders (AUD), resulting in impaired cognitive and motor function. Objectives: Evaluate the effects of ethanol on the expression of pro- and anti-inflammatory molecules, as well as the effects of the anti-inflammatory PPAR-γ agonist pioglitazone in suppressing ethanol-induced neuroinflammation. Methods: Adult male and female mice were treated chronically with ethanol for just under a month followed by a single acute binge dose of ethanol. Animals were provided liquid diet in the absence of ethanol (Control; n = 18, 9 M/9F), liquid diet containing ethanol (ethanol; n = 22, 11 M/11F), or liquid diet containing ethanol plus gavage administration of 30.0 mg/kg pioglitazone (ethanol + pioglitazone; n = 20, 10 M/10F). The hippocampus and cerebellum were isolated 24 h following the binge dose of ethanol, mRNA was isolated, and pro- and anti-inflammatory molecules were quantified by qRT-PCR. Results: Ethanol significantly (p < .05) increased the expression of pro-inflammatory molecules IL-1β, TNF-α, CCL2, and COX2; increased the expression of inflammasome-related molecules NLRP3 and Casp1 but decreased IL-18; and altered the expression of anti-inflammatory molecules including TGFβR1 in the hippocampus and cerebellum, though some differences were observed between males and females and the two brain regions. The anti-inflammatory pioglitazone inhibited ethanol-induced alterations in the expression of most, but not all, inflammation-related molecules. Conclusion: Chronic plus binge administration of ethanol induced the expression of inflammatory molecules in adult mice and pioglitazone suppressed ethanol-induced neuroinflammation.
Summary of WG6: Spin Physics

The working group on Spin Physics at the XXIV International Workshop on Deep-Inelastic Scattering and Related Subjects (DIS2016) witnessed a significant progress in the theoretical and experimental investigations aiming at unveiling the innermost structure of the proton. Results ranged from proton's one-dimensional representation to its multi-dimensional imaging. In this contribution, we summarize a selection of the topics discussed and of the results presented. For details, we refer to the individual contributions collected in the proceedings of this workshop.
A Multimodal, Reconfigurable Workspace Soft Gripper for Advanced Grasping Tasks

A new generation of soft functional materials and actuator designs has ushered the development of highly advanced soft grippers as adaptive alternatives to traditional rigid end-effectors for grasping and manipulation applications. While being advantageous over their rigid counterparts, soft gripper capabilities such as contact effort are mostly a consequence of the gripper workspace, which in turn is largely constrained by the gripper design. Moreover, soft grippers designed for highly specific grasping tasks such as scooping grains or wide payloads are usually limited in grasping other payload types or in their manipulation versatility. This article describes a reconfigurable workspace soft (RWS) gripper that exploits compliant structures and pneumatic actuators to reconfigure its workspace to suit a wide range of grasping tasks. To achieve desired kinematics, finite element analysis (FEA) studies are conducted to dictate actuator design and materials used. Various grasping modes and their reconfiguration of the gripper workspace are presented and characterized, including the gripper's capability to reliably scoop granular items with radii as small as 1.5 mm, precisely pick items as thin as 300 μm from flat surfaces, as well as grasp large convex, nonconvex, and deformable items as heavy as 1.4 kg. The RWS gripper can modify and increase its grasping workspace volume by 397%, enabling the widest range of grasping capabilities to date achieved by a single soft gripper.
SPATIALLY RESOLVED SPECTROSCOPIC OBSERVATIONS OF A POSSIBLE E+A PROGENITOR: SDSS J160241.00+521426.9

In order to investigate the evolution of E+A galaxies, we observed a galaxy, SDSS J160241.00+521426.9, a possible E+A progenitor which shows both emission and strong Balmer absorptions, and its neighbor galaxy. We used the integral field spectroscopic mode of the Kyoto Tridimensional Spectrograph (Kyoto3DII), mounted on the University of Hawaii 88 inch telescope located on Mauna Kea, and the slit-spectroscopic mode of the Faint Object Camera and Spectrograph on the Subaru Telescope. We found a strong Balmer absorption region at the center of the galaxy and an emission-line region located 2 kpc from the center, in the direction of its neighbor galaxy. The recession velocities of the galaxy and its neighbor galaxy differ only by 100 km s−1, which suggests that they are a physical pair and would have been interacting. Comparing observed Lick indices of Balmer lines and color indices with those predicted from stellar population synthesis models, we find that a suddenly quenched star formation scenario is plausible for the star formation history of the central region. We consider that star formation started in the galaxy due to galaxy interactions and was quenched in the central region, whereas star formation in a region offset from the center still continues or has begun recently. This work is the first study of a possible E+A progenitor using spatially resolved spectroscopy.
Mixed-method assessment of caregiver feeding practices in early care and education centres during COVID-19

Abstract Objective: The COVID-19 pandemic changed early care and education (ECE) mealtimes. Feeding practices that support children’s emerging autonomy may support children’s healthy eating, but it is unknown whether and how COVID-19 changed feeding practices. This paper describes caregiver feeding practices in ECE centres in Florida during COVID-19. Design: A mixed-methods design was used to understand mealtime feeding practices. Survey and interview questions were developed based on the Trust Model. More than 7000 surveys were sent to ECE centres. Analysis included descriptive statistics for survey data and thematic analysis for interview data. Setting: This statewide study included teachers in all licensed and license-exempt ECE centres. Participants: Four hundred and thirty-one teachers completed a survey, and twenty-nine participated in follow-up interviews. Results: Surveys showed most teachers engaged in autonomy-supportive behaviours, such as letting children eat until they were finished (90 %). The most common controlling behaviour was praising children for cleaning their plates (70 %). The most common responses about changes to mealtimes were keeping physical distance and serving healthy food. Interview themes were Autonomy Support, Controlling Feeding Practices, Interactions are the Same, Interactions are Different, Physical Distancing and Healthy Eating. Conclusions: Mealtimes are a central part of the day for young children and teachers in ECE environments. COVID-19 continues to influence ECE routines as behaviour change remains the primary method of reducing the risk of COVID-19 in the absence of a vaccine for young children. Understanding teachers’ practices and perspectives is important for reducing the risk of COVID-19 and supporting children’s autonomy and healthy eating.
TIME-DEPENDENT ELECTRON ACCELERATION IN BLAZAR TRANSIENTS: X-RAY TIME LAGS AND SPECTRAL FORMATION

Electromagnetic radiation from blazar jets often displays strong variability, extending from radio to γ-ray frequencies. In a few cases, this variability has been characterized using Fourier time lags, such as those detected in the X-rays from Mrk 421 using BeppoSAX. The lack of a theoretical framework to interpret the data has motivated us to develop a new model for the formation of the X-ray spectrum and the time lags in blazar jets based on a transport equation including terms describing stochastic Fermi acceleration, synchrotron losses, shock acceleration, adiabatic expansion, and spatial diffusion. We derive the exact solution for the Fourier transform of the electron distribution and use it to compute the Fourier transform of the synchrotron radiation spectrum and the associated X-ray time lags. The same theoretical framework is also used to compute the peak flare X-ray spectrum, assuming that a steady-state electron distribution is achieved during the peak of the flare. The model parameters are constrained by comparing the theoretical predictions with the observational data for Mrk 421. The resulting integrated model yields, for the first time, a complete first-principles physical explanation for both the formation of the observed time lags and the shape of the peak flare X-ray spectrum. It also yields direct estimates of the strength of the shock and the stochastic magnetohydrodynamical wave acceleration components in the Mrk 421 jet.
Fault-Tolerant Quantum Walks

Quantum walks are expected to serve important modelling and algorithmic applications in many areas of science and mathematics. Although quantum walks have been successfully implemented physically in recent times, no major efforts have been made to combat the error associated with these physical implementations in a fault-tolerant manner. In this paper, we propose a systematic method to implement fault-tolerant quantum walks in discrete time on arbitrarily complex graphs, using quantum states encoded with the Steane code and a set of universal fault tolerant matrix operations.
Speed of Markovian relaxation toward the ground state

For sufficiently low reservoir temperatures, it is known that open quantum systems subject to decoherent interactions with the reservoir relax toward their ground state in the weak coupling limit. Within the framework of quantum master equations, this is formalized by the Born-Markov-secular (BMS) approximation, where one obtains the system Gibbs state with the reservoir temperature as a stationary state. When the solution to some problem is encoded in the (isolated) ground state of a system Hamiltonian, decoherence can therefore be exploited for computation. The computational complexity is then given by the scaling of the relaxation time with the system size $n$. We study the relaxation behavior for local and nonlocal Hamiltonians that are coupled dissipatively with local and nonlocal operators to a bosonic bath in thermal equilibrium. We find that relaxation is generally more efficient when coherences of the density matrix in the system energy eigenbasis are taken into account. In addition, the relaxation speed strongly depends on the matrix elements of the coupling operators between initial state and ground state. We show that Dicke superradiance is a special case of our relaxation models and can thus be understood as a coherence-assisted relaxation speedup.