Miracle-dz/UniFAR-FTUs huggingface dataset:
Design of a Dynamical Core Based on the Nonhydrostatic “Unified System” of Equations*

AbstractThis paper presents the design of a dry dynamical core based on the nonhydrostatic “unified system” of equations. The unified system filters vertically propagating acoustic waves. The dynamical core predicts the potential temperature and horizontal momentum. It uses the predicted potential temperature to determine the quasi-hydrostatic components of the Exner pressure and density. The continuity equation is diagnostic (and used to determine the vertical mass flux) because the time derivative of the quasi-hydrostatic density is obtained from the predicted potential temperature. The nonhydrostatic component of the Exner pressure is obtained from an elliptic equation. The main focus of this paper is on the integration procedure used with this unique dynamical core. In the implementation described in this paper, height is used as the vertical coordinate, and the equations are vertically discretized on a Lorenz-type grid. Cartesian horizontal coordinates are used along with an Arakawa C grid. A detaile.
Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes

Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina22 (Aus, heat tolerant) in the short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat stress. The proteins upregulated in long-term heat stress in Nagina22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina22 anthers were enriched in proteins associated with vitamin E biosynthesis and GTPase activator activity. In contrast, downregulated proteins were related to ribosomal proteins. The expression of different Hsp20 and DnaJ was genotype specific. Overall, the heat response in Nagina22 was associated with its capacity for adequate metabolic control and cellular homeostasis, which may be critical for its higher reproductive thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis and lays a foundation for breeding thermotolerant varieties via molecular breeding.
An operational improvement of A-4DEnVar and its application to the estimation of the spatially varying bottom friction coefficients of the M2 constituent in the Bohai and Yellow seas

The analytical four-dimensional ensemble variational (A-4DEnVar) data assimilation scheme inherits the advantages of the conventional four-dimensional variational (4D-Var) data assimilation scheme and removes the adjoint model. However, compatible operational improvements such as the reduction of the computational costs and the localization method should be considered when it is used in realistic systems. In this paper, the computational complexity of calculating the inverse of background error covariance (the B matrix) is decreased by a precondition transform method, i.e., introducing a new state variable whose product with the B matrix is the original state variable to be optimized in the cost function. Furthermore, an independent point (IP) scheme is combined to construct an implicit localization method and further decreases the computational cost. Based on the Princeton Ocean Model with the generalized coordinate system (POMgcs), the operational improved A-4DEnVar is applied to optimize the spatially varying bottom friction coefficients (BFCs) of the M2 constituent in the Bohai and Yellow seas. A twin experiment with idealized observations is designed to validate the effectiveness of the proposed method. In practical experiments, with no more than 10 IPs, the algorithm can assimilate observations from the National Astronomical Observatory (NAO) dataset and obtain a good simulation. The experimental performances increase with the increase of either the IPs or observations, which indicates the efficacy of the proposed algorithm.
Impact of air quality on enterprise productivity: Evidence from Chinese listed companies

We provide insights and innovative ideas for China to achieve green development and promote high-quality economic development by studying the impact of air quality on enterprise productivity. This paper uses data from 2008 to 2016 for A-share companies listed on the Shanghai and Shenzhen stock markets, as well as the levels of particulate matter under 2.5 μm in diameter for 214 major Chinese cities. At the same time, this paper innovatively applies regression discontinuity and the Spatial Durbin Model for empirical testing. Considering the endogeneity, we choose the air flow index as an instrumental variable and the generalized space two-stage least squares method for the endogenous test. Additionally, we use dynamic regression and different spatial weight matrix to conduct robustness tests and reselect data from 2008 to 2012 and 2013 to 2016 as samples. Moreover, we test corporate heterogeneity from three perspectives: pollutant type, firm equity, and an industry’s technological level. The results show that the deterioration of local air quality significantly inhibits firm productivity, while the spatial spillover effects of pollution from surrounding cities also have a significant dampening effect on firm productivity. This negative effect is transmitted through research and development innovation capacity, human capital, and government subsidies. This empirical evidence from listed companies can be used for evaluating air quality management to enhance enterprise productivity, as well as to provide policy recommendations for boosting firm productivity through improved air quality.
A new species of Decimoconularia (Cnidaria, Medusozoa) from the Lower Cambrian of South China

Hexangulaconulariids, a family of biradially symmetrical medusozoan cnidarians, have been widely reported from the Lower Cambrian of South China. The four currently recognized genera of hexangulaconulariids differ from each other mainly in the number of faces in the abapical region of the periderm. However, previously published illustrations of the monospecific type genus, Hexangulaconularia, clearly show two distinct morphotypes, one with six faces and the other with 10. Specimens with 10 faces are herein reassigned to the genus Decimoconularia. In addition, the new species D. anisfacialis is described from the Kuanchuanpu Formation (Cambrian Fortunian Stage) in the Kuanchuanpu and Shizhonggou sections in Ningqiang County, southern Shaanxi Province, China. Also described are additional specimens of H. formosa from the same formation in the Zhangjiagou section in Xixiang County, southern Shaanxi Province, and from Member 2 of the Yanjiahe Formation (Cambrian Fortunian Stage) in western Hubei Province. The discovery of D. anisfacialis extends the known stratigraphical range of Decimoconularia, now composed of two species, downward from Cambrian Stage 2 into the Fortunian Stage. Additionally, certain specimens previously assigned to H. formosa are reassigned to D. anisfacialis. The diagnoses of Hexangulaconularia, Decimoconularia, and Hexangulaconulariidae are emended accordingly. In accordance with the rule of time priority, the previously designated type genus and species, Hexaconularia He and Yang, 1986 and Hexaconularia sichuanensis He and Yang, 1986, are replaced herein by Hexangulaconularia He, in Xing et al., 1983.
Tiller estimation method using deep neural networks

This paper describes a method based on a deep neural network (DNN) for estimating the number of tillers on a plant. A tiller is a branch on a grass plant, and the number of tillers is one of the most important determinants of yield. Traditionally, the tiller number is usually counted by hand, and so an automated approach is necessary for high-throughput phenotyping. Conventional methods use heuristic features to estimate the tiller number. Based on the successful application of DNNs in the field of computer vision, the use of DNN-based features instead of heuristic features is expected to improve the estimation accuracy. However, as DNNs generally require large volumes of data for training, it is difficult to apply them to estimation problems for which large training datasets are unavailable. In this paper, we use two strategies to overcome the problem of insufficient training data: the use of a pretrained DNN model and the use of pretext tasks for learning the feature representation. We extract features using the resulting DNNs and estimate the tiller numbers through a regression technique. We conducted experiments using side-view whole plant images taken with plan backgroud. The experimental results show that the proposed methods using a pretrained model and specific pretext tasks achieve better performance than the conventional method.
The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI regulates primary root growth and lateral root elongation

Roots are the main organs through which plants absorb water and nutrients. As the key phytohormone involved in root growth, auxin functions in plant environmental responses by modulating auxin synthesis, distribution and polar transport. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI can improve root architecture, and tppi1 mutants have significantly shortened primary roots. However, the mechanism underlying the short roots of the tppi1 mutant and the upstream signaling pathway and downstream genes regulated by AtTPPI are unclear. Here, we demonstrated that the AtTPPI gene could promote auxin accumulation in AtTPPI-overexpressing plants. By comparing the transcriptomic data of tppi1 and wild-type roots, we found several upregulations of auxin-related genes, including GH3.3, GH3.9 and GH3.12, may play an important role in the AtTPPI gene-mediated auxin transport signaling pathway, ultimately leading to changes in auxin content and primary root length. Moreover, increased AtTPPI expression can regulate primary root growth and lateral root elongation under different concentration of nitrate conditions. Overall, constitutive expression of AtTPPI increased auxin contents and improved lateral root elongation, constituting a new method for improving the nitrogen utilization efficiency of plants.
Occurrence of respiratory viruses among outpatients with diarrhea in Beijing, China, 2019–2020

Objectives To investigate respiratory virus infections in diarrhea cases and identify the risk of respiratory virus transmission through feces. Methods Fecal specimens were collected from diarrhea cases in enteric disease clinics in Beijing, China, from 2019 to 2020. Cases that tested negative for norovirus, rotavirus, sapovirus, astrovirus, and enteric adenovirus were included in the study. Real-time RT-PCR was used to detect 16 groups of respiratory viruses, and the major viruses were genotyped. Viruses isolation and digestion of clinical specimens and nucleic acid by artificial gastric acid or artificial bile/pancreatic juice were used to evaluate the risk of respiratory virus transmission through feces. Results A total of 558 specimens were collected and 47 (8.42%) specimens were detected positive, 40 (13.33%, 40/300) in 2019, and 7 (2.71%, 7/258) in 2020, including 20 (3.58%) for human rhinovirus (HRV), 13 (2.32%) for Bocavirus (BoV), 6 (1.08%) for parainfluenza virus I (PIV), 4 (0.72%) for coronavirus (CoV) OC43, 3 (0.54%) for respiratory syncytial virus (RSV) A, and 1 (0.18%) for both BoV and CoV OC43. Syndrome coronavirus 2 (SARS-CoV-2) and other viruses were not detected in this study. Eight genotypes were identified in the 13 HRV specimens. BoVs 1 and 2 were identified in nine BoV specimens. HRV infectious virions were successfully isolated from 2 clinical specimens and clinical specimens of HRV, RSV, PIV, and CoV could not be detected after 4 h of digestion and their nucleic acid could not be detected after 2 h of digestion by artificial gastric acid or artificial bile/pancreatic juice. Conclusion There may be a risk of respiratory virus transmission from diarrhea cases, and interventions against SARS-COV-2 epidemics are also effective for other respiratory viruses.
Racial disparities in diabetes prevalence among cancer patients

Introduction Cancer inequity is one of the most critical public health issues faced by ethnic minorities and people of lower socioeconomic status. The disparate burden of cancer is caused by poor access to care and inadequate delivery of cancer treatment, as well as comorbid and co-occurring conditions. Diabetes is a common and serious comorbid condition of cancer. Methods To better understand diabetes prevalence among diverse cancer patients, this study analyzed and described characteristics of cancer patients with diabetes from local-level Service Planning Area (SPA) data using City of Hope Comprehensive Cancer Center data, and United States national-level data from The National Health Interview Survey. Results Findings from national level data showed that patients in racial/ethnic minority groups had a higher occurrence of being diagnosed with diabetes, especially for non-Hispanic Blacks (OR=1.76, 95% CI=1.51, 2.03) and Hispanic/Latino individuals (OR=1.34, 95% CI=1.18, 1.52). Cancer patients who are older, ethnic minority, overweight/obese and with lower educational levels were more likely to have co-occurring diabetes. SPA-level patient data found similar results. Discussion In response to our findings and other reports, clinicians and health system including health coverage organizations should routinely assess cancer patients for cooccurring chronic illnesses, in particular diabetes. Interventions improving coordinated care that integrates oncology, endocrinology and primary care, targeting cancer patients --especially racial/ethnic minorities, overweight/obese, and older patients who are at increased risk for diabetes -- ought to be considered as best practice Whole Person care. With coordinated care management, ethnic disparities in cancer may be better addressed and reduced. Additionally, policymakers can contribute by enacting policies improving access to and coverage of integrated oncology, chronic disease prevention, and associated specialty care i.e., endocrinology to equalize quality care for ethnic minority, lower educated, overweight/obese and older cancer patients who are more likely to suffer greater comorbidity, and inadequate oncology and coordinated care to reduce disparities.
Platelet–lymphocyte ratio is a prognostic marker in small cell lung cancer—A systemic review and meta-analysis

Aim The aim of this study was to evaluate the relationship between platelet–lymphocyte ratio (PLR) and prognosis in small cell lung cancer (SCLC) patients. Method A comprehensive search was carried out to collect related studies. Two independent investigators extracted the data of hazard ratio (HR) and 95% confidence interval (CI) for overall survival (OS) or progression-free survival (PFS). A random-effect model was applied to analyze the effect of different PLR levels on OS and PFS in SCLC patients. Moreover, subgroup analysis was conducted to seek out the source of heterogeneity. Results A total of 26 articles containing 5,592 SCLC patients were included for this meta-analysis. SCLC patients with a high PLR level had a shorter OS compared with patients with a low PLR level, in both univariate (HR = 1.56, 95% CI 1.28–1.90, p < 0.0001) and multivariate (HR = 1.31, 95% CI 1.08–1.59, p = 0.007) models. SCLC patients with a high PLR level had a shorter PFS compared with patients with a low PLR level, in the univariate model (HR = 1.71, 95% CI 1.35–2.16, p < 0.0001), but not in the multivariate model (HR = 1.17, 95% CI 0.95–1.45, p = 0.14). Subgroup analysis showed that a high level of PLR shortened OS in some subgroups, including the Asian subgroup, the younger subgroup, the mixed-stage subgroup, the chemotherapy-dominant subgroup, the high-cutoff-point subgroup, and the retrospective subgroup. PLR level did not affect OS in other subgroups. Conclusion PLR was a good predictor for prognosis of SCLC patients, especially in patients received chemotherapy dominant treatments and predicting OS. Systematic review registration https://www.crd. york.ac. uk/PROSPERO/, identifier CRD42022383069.
CRISPR-mediated rapid arming of poxvirus vectors enables facile generation of the novel immunotherapeutic STINGPOX

Poxvirus vectors represent versatile modalities for engineering novel vaccines and cancer immunotherapies. In addition to their oncolytic capacity and immunogenic influence, they can be readily engineered to express multiple large transgenes. However, the integration of multiple payloads into poxvirus genomes by traditional recombination-based approaches can be highly inefficient, time-consuming and cumbersome. Herein, we describe a simple, cost-effective approach to rapidly generate and purify a poxvirus vector with multiple transgenes. By utilizing a simple, modular CRISPR/Cas9 assisted-recombinant vaccinia virus engineering (CARVE) system, we demonstrate generation of a recombinant vaccinia virus expressing three distinct transgenes at three different loci in less than 1 week. We apply CARVE to rapidly generate a novel immunogenic vaccinia virus vector, which expresses a bacterial diadenylate cyclase. This novel vector, STINGPOX, produces cyclic di-AMP, a STING agonist, which drives IFN signaling critical to the anti-tumor immune response. We demonstrate that STINGPOX can drive IFN signaling in primary human cancer tissue explants. Using an immunocompetent murine colon cancer model, we demonstrate that intratumoral administration of STINGPOX in combination with checkpoint inhibitor, anti-PD1, promotes survival post-tumour challenge. These data demonstrate the utility of CRISPR/Cas9 in the rapid arming of poxvirus vectors with therapeutic payloads to create novel immunotherapies.
Protective effects of conditioned media of immortalized stem cells from human exfoliated deciduous teeth on pressure ulcer formation

Pressure ulcers (PUs) are increasing with aging worldwide, but there is no effective causal therapy. Although mesenchymal stem cells (MSCs) promote cutaneous wound healing, the effects of the conditioned medium (CM) of MSCs on cutaneous PU formation induced by ischemia-reperfusion injury have been poorly investigated. To address this issue, herein, we first established an immortalized stem cell line from human exfoliated deciduous teeth (SHED). This cell line was revealed to have superior characteristics in that it grows infinitely and vigorously, and stably and consistently secretes a variety of cytokines. Using the CM obtained from the immortalized SHED cell line, we investigated the therapeutic potential on a cutaneous ischemia-reperfusion mouse model for PU formation using two magnetic plates. This is the first study to show that CM from immortalized SHEDs exerts therapeutic effects on PU formation by promoting angiogenesis and oxidative stress resistance through vascular endothelial growth factor and hepatocyte growth factor. Thus, the CM of MSCs has potent therapeutic effects, whereas these therapies have not been implemented in human medicine. To try to meet the regulatory requirements for manufacturing and quality control as much as possible, it is necessary to produce CM that is consistently safe and effective. The immortalization of stem cells could be one of the breakthroughs to meet the regulatory requirements and consequently open up a novel avenue to create a novel type of cell-free regenerative medicine, although further investigation into the quality control is warranted.
Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia

Introduction The pandemic coronavirus disease 19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is marked by thromboembolic events and an inflammatory response throughout the body, including the brain Methods Employing the machine learning approach BrainDead we systematically screened for SARS-CoV-2 genome-derived single-stranded (ss) RNA fragments with high potential to activate the viral RNA-sensing innate immune receptors Toll-like receptor (TLR)7 and/or TLR8. Analyzing HEK TLR7/8 reporter cells we tested such RNA fragments with respect to their potential to induce activation of human TLR7 and TLR8 and to activate human macrophages, as well as iPSC-derived human microglia, the resident immune cells in the brain. Results We experimentally validated several sequence-specific RNA fragment candidates out of the SARS-CoV-2 RNA fragments predicted in silico as activators of human TLR7 and TLR8. Moreover, these SARS-CoV-2 ssRNAs induced cytokine release from human macrophages and iPSC-derived human microglia in a sequence- and species-specific fashion. Discussion Our findings determine TLR7 and TLR8 as key sensors of SARS-CoV-2-derived ssRNAs and may deepen our understanding of the mechanisms how this virus triggers, but also modulates an inflammatory response through innate immune signaling.
Transmission line model for mutual coupling between microstrip antennas

Although more rigorous treatments have been developed for mutual coupling between microstrip antennas, the purpose of this transmission line model is to provide a numerically efficient substitute for them. Therefore, two approximations have been introduced: first, the surface waves have been neglected and second, each rectangular resonator is replaced by two equivalent radiating slots. In most practical cases the approximations are acceptable; this has been proved while comparing the transmission line model with other published results. It is obvious that the efficieney of the transmission model and can be used to include mutual coupling in practical analysis or synthesis routines for arrays of rectangular microstrip antennas.
Analysis of heat transfer mechanism in supercritical fluids from the aspect of pool heating

For the special phenomena of heat transfer deterioration or enhancement in supercritical fluid heat transfer, existing research still presents inconsistent opinions. In this study, we perform an analysis of the property changes, and present new understandings for pseudo-boiling theory. More importantly, essential differences between subcritical boiling and supercritical pseudo-boiling are highlighted; the critical factors being thermodynamic instability and stability. For isothermal heating cases, pseudo film boiling can be regarded as an extension of near-critical boiling. Moreover, pseudo nucleate boiling only appears in non-isothermal heating cases and is strongly dependent on the heater geometry, materials, etc. A coupled level-set and volume-of-fluid method is used to simulate the near-critical film boiling of carbon dioxide at pressures of 7.0 and 7.37 MPa. In comparison, supercritical cases at a pressure of 7.5 MPa are the natural convections of single-phase fluid with variable physical properties. The numerical results indicate the similar motions of low-density fluids in subcritical and supercritical cases. All results are consistent with prior experiments, providing a better understanding of the special features of supercritical fluid heat transfer.