Miracle-dz/UniFAR-FTUs huggingface dataset:
An energy-conserving dynamical model of GRB afterglows from magnetized forward and reverse shocks

In the dynamical models of gamma-ray burst (GRB) afterglows, the uniform assumption of the shocked region is known as provoking total energy conservation problem. In this work we consider shocks originating from magnetized ejecta, extend the energy-conserving hydrodynamical model of Yan et al. (2007) to the MHD limit by applying the magnetized jump conditions from Zhang & Kobayashi (2005). Compared with the non-conservative models, our Lorentz factor of the whole shocked region is larger by a factor . √ 2. The total pressure of the forward shocked region is higher than the reversed shocked region, in the relativistic regime with a factor of about 3 in our interstellar medium (ISM) cases while ejecta magnetization degree σ < 1, and a factor of about 2.4 in the wind cases. For σ ≤ 1, the non-conservative model loses 32 − 42% of its total energy for ISM cases, and for wind cases 25 − 38%, which happens specifically in the forward shocked region, making the shock synchrotron emission from the forward shock less luminous than expected. Once the energy conservation problem is fixed, the late time light curves from the forward shock become nearly independent of the ejecta magnetization. The reverse shocked region doesn’t suffer from the energy conservation problem since the changes of the Lorentz factor are recompensed by the changes of the shocked particle number density. The early light curves from the reverse shock are sensitive to the magnetization of the ejecta, thus are an important probe of the magnetization degree.
Quadratic and Cubic Regularisation Methods with Inexact function and Random Derivatives for Finite-Sum Minimisation

This paper focuses on regularisation methods using models up to the third order to search for up to second-order critical points of a finite-sum minimisation problem. The variant presented belongs to the framework of [1]: it employs random models with accuracy guaranteed with a sufficiently large prefixed probability and deterministic inexact function evaluations within a prescribed level of accuracy. Without assuming unbiased estimators, the expected number of iterations is ${\mathcal{O}}\left( { \in _1^{ - 2}} \right){\text{ or }}{\mathcal{O}}\left( { \in _1^{ - 3/2}} \right)$ when searching for a first-order critical point using a second or third order model, respectively, and of ${\mathcal{O}}\left( {\max \left[ { \in _1^{ - 3/2}, \in _2^{ - 3}} \right]} \right)$ when seeking for second-order critical points with a third order model, in which ${ \in _j},j \in \{ 1,2\}$, is the j th-order tolerance. These results match the worst-case optimal complexity for the deterministic counterpart of the method. Preliminary numerical tests for first-order optimality in the context of nonconvex binary classification in imaging, with and without Artifical Neural Networks (ANNs), are presented and discussed.
Force-and-moment-based Model Predictive Control for Achieving Highly Dynamic Locomotion on Bipedal Robots

In this paper, we propose a novel framework on force-and-moment-based Model Predictive Control (MPC) for dynamic legged robots. Specifically, we present a formulation of MPC designed for 10 degree-of-freedom (DoF) bipedal robots using simplified rigid body dynamics with input forces and moments. This MPC controller will calculate the optimal inputs applied to the robot, including 3-D forces and 2-D moments at each foot. These desired inputs will then be generated by mapping these forces and moments to motor torques of 5 actuators on each leg. We evaluate our proposed control design on physical simulation of a 10 degree-of-freedom (DoF) bipedal robot. The robot can achieve fast walking speed up to 1.6m/s on rough terrain, with accurate velocity tracking. With the same control framework, our proposed approach can achieve a wide range of dynamic motions including walking, hopping, and running using the same set of control parameters.
Identifying brain hierarchical structures associated with Alzheimer's disease using a regularized regression method with tree predictors

Brain segmentation at different levels is generally represented as hierarchical trees. Brain regional atrophy at specific levels was found to be marginally associated with Alzheimer's disease outcomes. In this study, we propose an ℓ1‐type regularization for predictors that follow a hierarchical tree structure. Considering a tree as a directed acyclic graph, we interpret the model parameters from a path analysis perspective. Under this concept, the proposed penalty regulates the total effect of each predictor on the outcome. With regularity conditions, it is shown that under the proposed regularization, the estimator of the model coefficient is consistent in ℓ2‐norm and the model selection is also consistent. When applied to a brain sMRI dataset acquired from the Alzheimer's Disease Neuroimaging Initiative (ADNI), the proposed approach identifies brain regions where atrophy in these regions demonstrates the declination in memory. With regularization on the total effects, the findings suggest that the impact of atrophy on memory deficits is localized from small brain regions, but at various levels of brain segmentation. Data used in preparation of this paper were obtained from the ADNI database.
Characteristics of Imperial College London's COVID‐19 research outputs

We identified 651 research outputs on the topic of COVID‐19 in the form of preprint, report, journal article, dataset, and software/code published by Imperial College London authors between January to September 2020. We sought to understand the distribution of outputs over time by output type, peer review status, publisher, and open access status. Search of Scopus, the institutional repositories, Github, and other databases identified relevant research outputs, which were then combined with Unpaywall open access data and manually‐verified associations between preprints and journal articles. Reports were the earliest output to emerge [median: 103 days, interquartile range (IQR): 57.5–129], but journal articles were the most commonly occurring output type over the entire period (60.8%, 396/651). Thirty preprints were identified as connected to a journal article within the set (15.8%, 30/189). A total of 52 publishers were identified, of which 4 publishers account for 59.6% of outputs (388/651). The majority of outputs were available open access through gold, hybrid, or green route (66.1%, 430/651). The presence of exclusively non‐peer reviewed material from January to March suggests that demand could not be met by journals in this period, and the sector supported this with enhanced preprint services for authors. Connections between preprints and published articles suggests that some authors chose to use both dissemination methods and that, as some publishers also serve across both models, traditional distinctions of output types might be changing. The bronze open access cohort brings widespread ‘free’ access but does not ensure true open access.
The complete mitochondrial genome of the hybrid species Pungtungia herzi (♀) × Pseudopungtungia nigra (♂) from Korea

Abstract This study reports the complete mitochondrial genome of a Pungtungia herzi (♀) × Pseudopungtungia nigra (♂) hybrid. The P. herzi (♀) × P. nigra (♂) mitochondrial genome consists of 16,601 bp with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete mitochondrial genome is 29.99% A, 26.97% T, 17.11% G, and 25.92% C. In the phylogenetic tree, P. herzi (♀) × P. nigra (♂) is closer to P. herzi than to P. nigra. Obtaining the complete mitogenome of P. herzi (♀) × P. nigra (♂) will provide useful data regarding P. herzi and P. nigra conservation and evolution.
Application of time-series regularity metrics to ion flux data from a population of pollen tubes

ABSTRACT Detecting the presence of an irregularity/regularity or chaos in the ion flows of an evolving plant cell is an important task that can be unraveled by performing the analyses by different metrics. Here I show that the results of the advanced fluctuation estimation methods that are obtained from the time series that is generated by the extracellular ion fluxes of tobacco pollen tubes (Nicotiana tabacum L.) have long-range correlations at critical temperatures. Further experimental evidence has been found to support the claim that the autonomous growth organization of extreme plant cell expansion is accomplished by self-organizing criticality (SOC), which is an orchestrated instability that occurs in an optimally evolving cell. The temperature-induced synchronous action of the ionic fluxes that are manifested, inter alia, by minimal dynamic entropy enabled the molecularly encoded information about germination and optimal growth temperatures of tobacco pollen tubes to be determined.
The impact of COVID‐19 pandemic on hospitality stock returns in China

Abstract Coronavirus disease (COVID‐19) has already devastated the world, and the economy becomes the most critical challenge for any country worldwide. The increasing uncertainty of the COVID‐19 outbreak has made stock markets in China more turbulent and less predictable. Under the current exceptional circumstances, the hospitality industry suffered the most due to the travel restrictions. This research thus assesses the dynamic relationship among the COVID‐19 outbreak, macroeconomic fluctuations and hospitality stock returns based on a structural VAR framework from 13 January to 11 May 2020, in China. Evidence reveals that macroeconomic fluctuations and hospitality stock returns are significantly affected by shocks from the COVID‐19 outbreak. An unanticipated positive change of the COVID‐19 explosion triggers an addition in exchange rates and causes a reduction in the stock market and hospitality industry returns. For the impacts of the exchange rate, findings reveal that a surprise increase in exchange rates (currency depreciation) exerts a significant negative influence on stock market returns. Additionally, a positive change of stock market returns is linked to a decline in exchange rates and a rise in hospitality industry returns. Therefore, knowledge of these relationships can enable policymakers to evaluate and implement effective policies to stabilize the stock markets and help investors to make appropriate investment strategies.
The complete chloroplast genome of Hippeastrum rutilum (Ker-Gawl.) Herb.

Abstract Hippeastrum rutilum (Ker-Gawl.) Herb. is a high-end ornamental flower in the family Amaryllidaceae. In this study, the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. was determined from Illumina pair-end sequencing data. The sequencing results indicated the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. 162,696 base pairs (bp) in length, including one large single-copy region (LSC, 86,933 bp), one small single-copy region (SSC, 5418 bp), and a pair of inverted repeat regions (IRs) of 34,932 bp. Besides, the complete chloroplast genome contained 128 genes, including 82 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic analysis suggested that H. rutilum (Ker-Gawl.) Herb. is closely related to H. rutilum. The complete chloroplast genome sequencing results will provide a reference for the further investigation and research of H. rutilum (Ker-Gawl.) Herb.
The complete chloroplast genome sequence of Prunus discadenia (Rosaceae), a species with great ornamental value

Abstract Prunus discadenia is a Cerasus species with great ornamental value and endemic to China. Here, the complete chloroplast (cp) genome of P. discadenia was assembled based on the Illumina reads. The cp genome is 157,915 bp in length, which contains two inverted repeat regions (26,415 bp) separated by the small single copy (19,119 bp) and the large single copy (85,966 bp) regions. The plastome contains 131 genes, and the overall GC content is 36.7%. Complete chloroplast genome of P. discadenia is of great significance to rebuilt the phylogeny of Cerasus.
Purchase experience during the COVID‐19 pandemic and social cognitive theory: The relevance of consumer vulnerability, resilience, and adaptability for purchase satisfaction and repurchase

Abstract This study explores consumer behavior during the pandemic through the lens of social cognitive theory (SCT). Using the SCT framework and assessing the pandemic as an environmental set, this study strives to fill the gaps in the underexplored impacts of the personal processes of consumer vulnerability, resilience, and adaptability on the behavioral processes of purchase satisfaction and repurchase. The research results show that consumers are self‐efficacious to a degree when it comes to purchase decision making in the context of pandemics. Vulnerability and resilience directly influence the purchase satisfaction and indirectly influence the repurchase intention via satisfaction. Furthermore, purchase satisfaction positively affects the repurchase intention. In addition, research results show that consumer adaptability to online shopping moderates the relationship between consumer resilience and purchase satisfaction. These findings have practical implications in terms of marketers’ communication strategy development.
The first complete mitochondrial DNA of the Chinese short-limbed skink (Ateuchosaurus chinensis Gray, 1845) determined by next-generation sequencing

Abstract The complete mitochondrial DNA (mtDNA) for the Chinese short-limbed skink (Ateuchosaurus chinensis Gray, 1845) was described by using next-generation sequencing. The total length of mtDNA was 16,840 bp, which contained 13 PCGs (COI-III, ND1-6, ND4L, ATP6, ATP8, and CYTB), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). The Bayesian inference tree showed that A. chinensis was a sister taxon to other scincid lizards in genera of Scincella, Isopachys, Sphenomorphus and Tropidophorus. The complete mtDNA of A. chinensis will be an important genetic resource to the studies of conservation and restoration of A. chinensis.
Complete plastome sequence of Macaranga tanarius (L.) Muell. Arg. (Euphorbiaceae): a fast-growing timber species

Abstract Macaranga tanarius (L.) Muell. Arg. is a tree species within Euphorbiaceae, which can be used for building timber and its extract can be used to treat diabetes. In this report, we describe the complete plastome sequence of Macaranga tanarius. The complete plastome of Macaranga tanarius (L.) Muell. Arg. is of 165,362 bp in length, and it is with typical plastome structure and gene content of angiosperm plastome, including two reverse repeat regions (IRs) of 27,503 bp, large single copy region (LSC) of 91,443 bp, and small single copy (SSC) region of 18,913 bp. The plastome contains 131 genes, including 85 protein coding genes, 38 tRNA genes, eight rRNA genes (i.e., 5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). The total G/C content of Macaranga tanarius (L.) Muell. Arg.plastome is 35.6%. The complete plastome sequence is conducive to the development and utilization of Euphorbiaceae resources and the phylogenetic study.
Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity

ABSTRACT Immunotherapy via interleukin-2 (IL-2) mediated activation of anti-tumor immune response is a promising approach for cancer treatment. The multi-potent cytokine, IL-2 has a central role in immune cell activation and homeostasis. Since IL-2 preferentially activates immunosuppressive T regulatory cells by IL-2Rα dependent manner, blocking IL-2:IL-2Rα interaction is a key to amplify the IL-2 activity in effector T cells toward anti-tumor response. Anti-IL-2 monoclonal antibodies are good candidates to control the IL-2:IL-2Rα interaction. In a previous study, we developed a new IL-2Rα mimetic antibody, TCB2, and showed that the human IL-2(hIL-2):TCB2 complex can stimulate T effector cells specifically and elicit potent anti-cancer immunotherapeutic effect, especially when administered in combination with immune checkpoint inhibitors. To understand the molecular mechanism, we determined the crystal structure of TCB2-Fab in a complex with hIL-2 at 2.5 Å resolution. Our structural analysis reveals that TCB2 binds to the central area of the hIL-2Rα binding region on hIL-2, and binding angle and epitope are different from previously known hIL-2Rα mimicking antibody NARA1 which recognizes the top part of hIL-2. TCB2 binding to hIL-2 also induces an allosteric effect that increases the affinity for the hetero-dimeric hIL-2 receptor, IL-2R(β + γ), on effector T cells.
Atg27p co-fractionates with clathrin-coated vesicles in budding yeast

Atg27p, a single-pass transmembrane protein that functions in autophagy, localizes to a variety of cellular compartments including the pre-autophagosomal structure, late Golgi, vacuolar membrane, as well as early and late endosomes. Its cytoplasmic C-terminus contains a tyrosine sorting motif that allows for its transport to the vacuolar membrane and an additional sequence that allows for its retrieval from the vacuolar membrane to the endosome. Since clathrin is well known to mediate vesicular transport in the endomembrane system, the trafficking of Atg27p and its tyrosine sorting motif suggested that it might be trafficked inside clathrin-coated vesicles (CCVs). In our previous studies, Atg27p was identified by mass spectrometry as a potential component in CCVs, as it was present in CCVs isolated from both WT and auxilin-depleted cells. We now confirm that Atg27p is a component of CCVs using immunoblotting and additional mass spectrometry data.
Early responders within seven days of dupilumab treatment for severe asthma evaluated by patient-reported outcome: a pilot study

Background The management of severe asthma-associated symptoms is essential since they are distressing to the affected patients, and also greatly impair their quality of life. Dupilumab, a monoclonal antibody, blocks interleukin (IL)-4 and IL-13 signaling, both of which are crucial in acquired and innate immunity pathways through fast signal transduction, leading to an early response to treatment. Although rapid improvement within 1–3 days after dupilumab treatment was observed in moderate-to-severe atopic dermatitis, an early response within 7 days of dupilumab treatment in severe asthma has not been reported. Methods Twelve consecutive patients with severe asthma who were newly treated with dupilumab between July 2019 and April 2020 were retrospectively investigated. We evaluated the early response (within 7 days) of patients with severe asthma receiving dupilumab therapy. Asthma control test (ACT) and the daily ACT, which was modified from the ACT to evaluate daily symptoms associated with asthma, were adopted as patient-reported outcomes (PROs) at week 8 and within 7 days, respectively. Patients were stratified into early responders (7 days), late responders (week 8), and non-responders without significant improvement in PROs. Descriptive statistics were adopted due to the limited number of patients. Results Four of these 12 patients were early responders, with the following baseline characteristics: body mass index, <25 kg/m2; without depression; baseline forced expiratory volume in 1 second, <1.50 L; and more than one exacerbation in 1 year. On the other hand, five were late responders, and 44.4% of the nine responders were early responders. The higher the eosinophilic count and/or FeNO did not show any relationship between the early responder and nonresponder. Conclusions The effect of dupilumab on severe asthma in patients with atopic features could be started earlier than 2 weeks, similar to atopic dermatitis. Daily ACT may be useful in monitoring the early efficacy of dupilumab in treating severe asthma.
Characterization of the complete mitochondrial genome of Ficus variegata (Littorinimorpha: Ficidae) and molecular phylogeny of Caenogastropoda

Abstract Ficidae is a family of chiefly tropical marine gastropod mollusks with approximately 20 described species. Hitherto, there are no complete mitochondrial genome (mitogenome) of Ficidae available for the Ficoidea. Here, we determined the complete mitogenome of Ficus variegata Röding, 1798 representing the first species from the family Ficidae. The newly sequenced mitogenome consists of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. All of 13 PCGs use ATG as initiation codons and end with conventional stop codons TAA and TAG, and the genome organization is similar to those of other documented caenogastropod mitogenomes. Tonnoidea and Ficoidea were recovered as sister group in the Caenogastropoda tree.
Unequal but essential: How subsistence consumer–entrepreneurs negotiate unprecedented shock with extraordinary resilience during COVID‐19

Abstract We use qualitative interviews to study subsistence consumers confronting the global, pervasive and extended challenges of COVID‐19, encompassing literally all realms of daily life. For subsistence consumers whose circumstances are filled with day‐to‐day uncertainty and a small margin of error to begin with, the pandemic has led to manifold uncertainties and a disappearing margin of error, with potentially lethal consequences. Their constraints to thinking and lack of self‐confidence arising from both low income and low literacy are magnified in the face of the complex, invisible pandemic and the fear and panic it has caused. Characteristic relational strengths are weakened with social distancing and fear of infection. Yet, subsistence consumers display humanity in catastrophe, and confront the uncontrollable by reiterating a higher power. Consumption is reduced to the very bare essentials and income generation involves staying the course versus finding any viable alternative. We derive implications for consumer affairs.
Atg27p localization is clathrin- and Ent3p/5p-dependent

The autophagy-related protein Atg27p has been previously shown to localize to the autophagy-specific pre-autophagosomal structure (PAS) as well as to several organelles, including the late Golgi, the vacuolar membrane, and the endosome. Given that Atg27p localization to the vacuolar membrane in particular has been shown to be dependent on both its C-terminal tyrosine sorting motif and the AP-3 adaptor, and that Atg27p can be found in clathrin-coated vesicles, we set out to determine whether Atg27p localization inside cells is dependent on clathrin or on any of its cargo adaptors. We report that Atg27p localization is clathrin- and Ent3p/5p-dependent.
The complete mitochondrial genome of Chelidonichthys spinosus (Scorpaeniformes: Triglidae) from Jiangsu Province, China

Abstract In this study, we present the complete mitogenome and a phylogenetic analysis of Chelidonichthys spinosus characterized using Illumina next-generation and Pacific Biosciences (PacBio, Menlo Park, CA) sequencing technologies. The complete mitochondrial genome is a circular molecule 16,511 bp in length and contains the same set of 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. The base composition of the entire mitogenome showed a slight AT bias. Phylogenetic analysis of the mitogenome of C. spinosus fully resolved it in a clade with other species classified to the Triglidae. The mitogenome data produced in this study provide the genomic resources available for future evolutionary studies.