Miracle-dz/UniFAR-FTUs huggingface dataset:
Forward Modeling of Simulated Transverse Oscillations in Coronal Loops and the Influence of Background Emission

We simulate transverse oscillations in radiatively cooling coronal loops and forward-model their spectroscopic and imaging signatures, paying attention to the influence of background emission. The transverse oscillations are driven at one footpoint by a periodic velocity driver. A standing kink wave is subsequently formed and the loop cross section is deformed due to the Kelvin–Helmholtz instability, resulting in energy dissipation and heating at small scales. Besides the transverse motions, a long-period longitudinal flow is also generated due to the ponderomotive force induced slow wave. We then transform the simulated straight loop to a semi-torus loop and forward-model their spectrometer and imaging emissions, mimicking observations of Hinode/EIS and SDO/AIA. We find that the oscillation amplitudes of the intensity are different at different slit positions, but are roughly the same in different spectral lines or channels. X-t diagrams of both the Doppler velocity and the Doppler width show periodic signals. We also find that the background emission dramatically decreases the Doppler velocity, making the estimated kinetic energy two orders of magnitude smaller than the real value. Our results show that background subtraction can help recover the real oscillation velocity. These results are helpful for further understanding transverse oscillations in coronal loops and their observational signatures. However, they cast doubt on the spectroscopically estimated energy content of transverse waves using the Doppler velocity.
Unified Equation of State for Neutron Stars Based on the Gogny Interaction

The effective Gogny interactions of the D1 family were established by D. Gogny more than forty years ago with the aim to describe simultaneously the mean field and the pairing field corresponding to the nuclear interaction. The most popular Gogny parametrizations, namely D1S, D1N and D1M, describe accurately the ground-state properties of spherical and deformed finite nuclei all across the mass table obtained with Hartree–Fock–Bogoliubov (HFB) calculations. However, these forces produce a rather soft equation of state (EoS) in neutron matter, which leads to predict maximum masses of neutron stars well below the observed value of two solar masses. To remove this limitation, we built new Gogny parametrizations by modifying the density dependence of the symmetry energy predicted by the force in such a way that they can be applied to the neutron star domain and can also reproduce the properties of finite nuclei as good as their predecessors. These new parametrizations allow us to obtain stiffer EoS’s based on the Gogny interactions, which predict maximum masses of neutron stars around two solar masses. Moreover, other global properties of the star, such as the moment of inertia and the tidal deformability, are in harmony with those obtained with other well tested EoSs based on the SLy4 Skyrme force or the Barcelona–Catania–Paris–Madrid (BCPM) energy density functional. Properties of the core-crust transition predicted by these Gogny EoSs are also analyzed. Using these new Gogny forces, the EoS in the inner crust is obtained with the Wigner–Seitz approximation in the Variational Wigner–Kirkwood approach along with the Strutinsky integral method, which allows one to estimate in a perturbative way the proton shell and pairing corrections. For the outer crust, the EoS is determined basically by the nuclear masses, which are taken from the experiments, wherever they are available, or by HFB calculations performed with these new forces if the experimental masses are not known.
Serre functors and dimensions of residual categories

We describe in terms of spherical twists the Serre functors of many interesting semiorthogonal components, called residual categories, of the derived categories of projective varieties. In particular, we show the residual categories of Fano complete intersections are fractional Calabi–Yau up to a power of an explicit spherical twist. As applications, we compute the Serre dimensions of residual categories of Fano complete intersections, thereby proving a corrected version of a conjecture of Katzarkov and Kontsevich, and deduce the nonexistence of Serre invariant stability conditions when the degrees of the complete intersection do not all coincide.
Annular Khovanov homology and augmented links

Given an annular link $L$, there is a corresponding augmented link $\widetilde{L}$ in $S^3$ obtained by adding a meridian unknot component to $L$. In this paper, we construct a spectral sequence with the second page isomorphic to the annular Khovanov homology of $L$ and it converges to the reduced Khovanov homology of $\widetilde{L}$. As an application, we classify all the links with the minimal rank of annular Khovanov homology. We also give a proof that annular Khovanov homology detects unlinks.
STATISTICAL FRAMEWORKS FOR TIME-TO-EVENT DOSE-FINDING DESIGNS: A REVIEW

In dose-finding trials, due to staggered enrollment, it might be desirable to make dose assignment decisions in real-time in the presence of pending toxicity outcomes, for example, when patient accrual is fast or the dose-limiting toxicity is late-onset. Patients’ time-to-event information may be utilized to facilitate such decisions. We review statistical frameworks for time-to-event modeling in dose-finding trials and summarize existing designs into two classes: TITE deigns and POD designs. TITE designs are based on inference on toxicity probabilities, while POD designs are based on inference on dose-finding decisions. These two classes of designs contain existing individual designs as special cases and also give rise to new designs. We discuss and study theoretical properties of these designs, including large-sample convergence properties, coherence principles, and the underlying decision rules. To facilitate the use of time-to-event designs in practice, we introduce efficient computational algorithms and review common practical considerations, such as safety rules and suspension rules. Finally, the operating characteristics of several designs are evaluated and compared through computer simulations.
Characterization of Contextuality with Semi-Module \v{C}ech Cohomology and its Relation with Cohomology of Effect Algebras

I present a generalized notion of obstruction in Čech cohomology on semi-modules, which allows one to characterize non-disturbing contextual behaviors with any semi-field. This framework generalizes the usual Čech cohomology used in the sheaf approach to contextuality, avoiding false positives. I revise a similar work done in the framework of effect algebras with cyclic and order cohomologies and explore the relationship with the one presented here.
Cross-Task Generalization via Natural Language Crowdsourcing Instructions

Humans (e.g., crowdworkers) have a remarkable ability in solving different tasks, by simply reading textual instructions that define them and looking at a few examples. Despite the success of the conventional supervised learning on individual datasets, such models often struggle with generalization across tasks (e.g., a question-answering system cannot solve classification tasks). A long-standing challenge in AI is to build a model that learns a new task by understanding the human-readable instructions that define it. To study this, we introduce NATURAL INSTRUCTIONS, a dataset of 61 distinct tasks, their human-authored instructions, and 193k task instances (input-output pairs). The instructions are obtained from crowdsourcing instructions used to create existing NLP datasets and mapped to a unified schema. Using this meta-dataset, we measure cross-task generalization by training models on seen tasks and measuring generalization to the remaining unseen ones. We adopt generative pre-trained language models to encode task-specific instructions along with input and generate task output. Our results indicate that models benefit from instructions when evaluated in terms of generalization to unseen tasks (19% better for models utilizing instructions). These models, however, are far behind an estimated performance upperbound indicating significant room for more progress in this direction.
Koopman Operator Framework for Spectral Analysis and Identification of Infinite-Dimensional Systems

We consider the Koopman operator theory in the context of nonlinear infinite-dimensional systems, where the operator is defined over a space of bounded continuous functionals. The properties of the Koopman semigroup are described and a finite-dimensional projection of the semigroup is proposed, which provides a linear finite-dimensional approximation of the underlying infinite-dimensional dynamics. This approximation is used to obtain spectral properties from the data, a method which can be seen as a generalization of the Extended Dynamic Mode Decomposition for infinite-dimensional systems. Finally, we exploit the proposed framework to identify (a finite-dimensional approximation of) the Lie generator associated with the Koopman semigroup. This approach yields a linear method for nonlinear PDE identification, which is complemented with theoretical convergence results.
Theory of planned behavior as a conceptual framework for the willingness to self-isolate during the COVID-19 pandemic: A regional cross-sectional study.

BACKGROUND Due to an unavailability of a vaccine, one of the efficient methods to prevent the spread of the novel coronavirus (COVID-19) is by applying self-isolation (SI). Hence there is an urgent need to investigate the factors leading to an individuals' willingness to choose to self-isolate. OBJECTIVES The current study utilized the Theory of Planned Behavior (TPB) as a conceptual model and aimed to investigate the extent to which subjective norms, personal attitudes and perceived control influences an individual's willingness to self-isolate during COVID-19 risk. METHOD A cross-sectional study was performed on 800 Saudi respondents aged≥18 years by using a validated self-administered questionnaire about factors related to willingness to self-isolate during COVID-19 pandemic risk based on the TPB. The effects of different variables on SI were analyzed by using ordinal logistic regression model. RESULTS A total of 756 (94.5% ) were completed and analyzed. Subjective norms and perceived control over the behavior significantly (p < 0.05) influenced the intention of willingness to self-isolate, while attitude was found to be insignificant. The odds of letting others to know about self COVID status were 2.40 times higher than not telling the neighbors or colleagues. A statistically significant difference (p≤0.001) existed between males and females regarding the willingness to self-isolate. Similarly the odds of willingness to self-isolate with a presence of disabled person in family were 2.88 times higher than the absence of a disability in the family. Few recommendations for the policymakers that are needed to curb the spread of COVID-19 infection are also proposed. CONCLUSION The outcomes of study might be considered as an initial understanding of the factors that significantly influences an individual's willingness to SI when facing an unprecedented pandemic risk. Additionally, these factors provide a plan for policymakers to encourage citizens for self-isolation during pandemic infections.
Scalp‐recorded N40 visual evoked potential: Sensory and attentional properties

N40 is a well‐known component of evoked potentials with respect to the auditory and somatosensory modality but not much recognized with regard to the visual modality. To be detected with event‐related potentials (ERPs), it requires an optimal signal‐to‐noise ratio. To investigate the nature of visual N40, we recorded EEG/ERP signals from 20 participants. Each of them was presented with 1800 spatial frequency gratings of 0.75, 1.5, 3 and 6 c/deg. Data were collected from 128 sites while participants were engaged in both passive viewing and attention conditions. N40 (30–55 ms) was modulated by alertness and selective attention; in fact, it was larger to targets than irrelevant and passively viewed spatial frequency gratings. Its strongest intracranial sources were the bilateral thalamic nuclei of pulvinar, according to swLORETA. The active network included precuneus, insula and inferior parietal lobule. An N80 component (60–90 ms) was also identified, which was larger to targets than irrelevant/passive stimuli and more negative to high than low spatial frequencies. In contrast, N40 was not sensitive to spatial frequency per se, nor did it show a polarity inversion as a function of spatial frequency. Attention, alertness and spatial frequency effects were also found for the later components P1, N2 and P300. The attentional effects increased in magnitude over time. The data showed that ERPs can pick up the earliest synchronized activity, deriving in part from thalamic nuclei, before the visual information has actually reached the occipital cortex.
Quantitative Susceptibility Mapping versus R2*-based Histogram Analysis for Evaluating Liver Fibrosis: Preliminary Results

Purpose: The staging of liver fibrosis is clinically important, and a less invasive method is preferred. Quantitative susceptibility mapping (QSM) has shown a great potential in estimating liver fibrosis in addition to R2* relaxometry. However, few studies have compared QSM analysis and liver fibrosis. We aimed to evaluate the feasibility of estimating liver fibrosis by using QSM and R2*-based histogram analyses by comparing it with ultrasound-based transient elastography and the stage of histologic fibrosis. Methods: Fourteen patients with liver disease were enrolled. Data sets of multi-echo gradient echo sequence with breath-holding were acquired on a 3-Tesla scanner. QSM and R2* were reconstructed by water–fat separation method, and ROIs were analyzed for these images. Quantitative parameters with histogram features (mean, variance, skewness, kurtosis, and 1st, 10th, 50th, 90th, and 99th percentiles) were extracted. These data were compared with the elasticity measured by ultrasound transient elastography and histological stage of liver fibrosis (F0 to F4, based on the new Inuyama classification) determined by biopsy or hepatectomy. The correlation of histogram parameters with intrahepatic elasticity and histologically confirmed fibrosis stage was examined. Texture parameters were compared between subgroups divided according to fibrosis stage. Receiver operating characteristic (ROC) analysis was also performed. P < 0.05 indicated statistical significance. Results: The six histogram parameters of both QSM and R2*were significantly correlated with intrahepatic elasticity. In particular, three parameters (variance, percentiles [90th and 99th]) of QSM showed high correlation (r = 0.818–0.844), whereas R2* parameters showed a moderate correlation with elasticity. Four parameters of QSM were significantly correlated with fibrosis stage (ρ = 0.637–0.723) and differentiated F2–4 from F0–1 fibrosis and F3–4 from F0–2 fibrosis with areas under the ROC curve of > 0.8, but those of R2* did not. Conclusion: QSM may serve as a promising surrogate indicator in detecting liver fibrosis.
Inactivation of RNase P in Escherichia coli significantly changes post‐transcriptional RNA metabolism

Ribonuclease P (RNase P), which is required for the 5'‐end maturation of tRNAs in every organism, has been shown to play a limited role in other aspects of RNA metabolism in Escherichia coli. Using RNA‐sequencing (RNA‐seq), we demonstrate that RNase P inactivation affects the abundances of ~46% of the expressed transcripts in E. coli and provide evidence that its essential function is its ability to generate pre‐tRNAs from polycistronic tRNA transcripts. The RNA‐seq results agreed with the published data and northern blot analyses of 75/83 transcripts (mRNAs, sRNAs, and tRNAs). Changes in transcript abundances in the RNase P mutant also correlated with changes in their half‐lives. Inactivating the stringent response did not alter the rnpA49 phenotype. Most notably, increases in the transcript abundances were observed for all genes in the cysteine regulons, multiple toxin‐antitoxin modules, and sigma S‐controlled genes. Surprisingly, poly(A) polymerase (PAP I) modulated the abundances of ~10% of the transcripts affected by RNase P. A comparison of the transcriptomes of RNase P, RNase E, and RNase III mutants suggests that they affect distinct substrates. Together, our work strongly indicates that RNase P is a major player in all aspects of post‐transcriptional RNA metabolism in E. coli.
CELL STRUCTURE AND FUNCTION Advance Publication by J-STAGE In vivo roles of Rab27 and its effectors in exocytosis

The monomeric GTPase Rab27 regulates exocytosis of a broad range of vesicles in multicellular organisms. Several effectors bind GTP-bound Rab27a and/or Rab27b on secretory vesicles to execute a series of exocytic steps, such as vesicle maturation, movement along microtubules, anchoring within the peripheral F-actin network, and tethering to the plasma membrane, via interactions with specific proteins and membrane lipids in a local milieu. Although Rab27 effectors generally promote exocytosis, they can also temporarily restrict it when they are involved in the rate-limiting step. Genetic alterations in Rab27-related molecules cause discrete diseases manifesting pigment dilution and immunodeficiency, and can also affect common diseases such as diabetes and cancer in complex ways. Although the function and mechanism of action of these
Population dynamics of caribou shaped by glacial cycles before the last glacial maximum

Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.
Estimation of phosphorus requirements of sows based on 24-h urinary phosphorus excretion during gestation and lactation

Abstract Phosphorus requirements of reproducing sows were estimated using 24-h urinary P excretion. Thirty-six multiparous sows were fed one of six maize–soybean meal-based diets with total P ranging from 0·40 to 0·80 % in 0·08 % increments with a constant Ca:total P ratio (1·25:1). Diets were fed from day 7·5 ± 1 after breeding until the end of lactation (day 26 ± 1). Urine samples were collected in mid and late gestation (days 77·1 ± 2 and 112·4 ± 1) and early and late lactation (days 4·5 ± 1 and 18·2 ± 1). Phosphorus requirements were estimated using linear and nonlinear regression models. Based on a single 24-h urinary P excretion, estimated daily dietary total P requirements in mid and late gestation were 10·3 g (6·0 g standardised total tract digestible P, STTD P), and estimates for early and late lactation were 31·1 g (16·6 g STTD P) and 40·3 g (22·1 g STTD P), respectively. Plasma P and Ca concentrations were maintained within normal ranges at the estimated levels of P requirements. No differences among treatments were observed for plasma parathyroid hormone (P ≥ 0·06) and bone formation marker (P ≥ 0·16). In lactation, bone resorption marker decreased (P ≤ 0·001) as sows consumed more P. Among the analysed variables, urinary P was the most sensitive response to changes in dietary P intake. Urinary P excretion offers a practical method to estimate P requirements in sows. Our recommended daily total P requirements are 10·3 g for gestation and 35·7 g for lactation.
Impact of maternal late gestation undernutrition on surfactant maturation, pulmonary blood flow and oxygen delivery measured by magnetic resonance imaging in the sheep fetus

Restriction of fetal substrate supply has an adverse effect on surfactant maturation in the lung and thus affects the transition from in utero placental oxygenation to pulmonary ventilation ex utero. The effects on surfactant maturation are mediated by alteration in mechanisms regulating surfactant protein and phospholipid synthesis. This study aimed to determine the effects of late gestation maternal undernutrition (LGUN) and LGUN plus fetal glucose infusion (LGUN+G) compared to Control on surfactant maturation and lung development, and the relationship with pulmonary blood flow and oxygen delivery ( DO2 ) measured by magnetic resonance imaging (MRI) with molecules that regulate lung development. LGUN from 115 to 140 days’ gestation significantly decreased fetal body weight, which was normalized by glucose infusion. LGUN and LGUN+G resulted in decreased fetal plasma glucose concentration, with no change in fetal arterial PO2 compared to control. There was no effect of LGUN and LGUN+G on the mRNA expression of surfactant proteins (SFTP) and genes regulating surfactant maturation in the fetal lung. However, blood flow in the main pulmonary artery was significantly increased in LGUN, despite no change in blood flow in the left or right pulmonary artery and DO2 to the fetal lung. There was a negative relationship between left pulmonary artery flow and DO2 to the left lung with SFTP‐B and GLUT1 mRNA expression, while their relationship with VEGFR2 was positive. These results suggest that increased pulmonary blood flow measured by MRI may have an adverse effect on surfactant maturation during fetal lung development.