Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Least-Squares Finite Element Method Enriched with Residual-Free Bubbles for Solving Convection-Dominated Problems

In this paper we devise a novel least-squares finite element method (LSFEM) for solving scalar convection-dominated convection-diffusion problems. First, we convert a second-order convection-diffusion problem into a first-order system formulation by introducing the gradient $\mathbf{p}:=-\kappa\nabla u$ as an additional variable. The LSFEM using continuous piecewise linear elements enriched with residual-free bubbles for both variables $u$ and $\mathbf{p}$ is applied to solve the first-order mixed problem. The residual-free bubble functions are assumed to strongly satisfy the associated homogeneous second-order convection-diffusion equations in the interior of each element, up to the contribution of the linear part, and vanish on the element boundary. To implement this two-level least-squares approach, a stabilized method of Galerkin/least-squares type is used to approximate the residual-free bubble functions. This enriched LSFEM not only inherits the advantages of the primitive LSFEM, such as the resulting linear system being symmetric and positive definite, but also exhibits the characteristics of the residual-free bubble method without involving stability parameters. Several numerical experiments are given to demonstrate the effectiveness of the proposed enriched LSFEM. The accuracy and computational cost of this enriched LSFEM are also compared with those of the primitive LSFEM. We find that for a small diffusivity $\kappa$, the enriched LSFEM is much better able to capture the nature of layer structure in the solution than the primitive LSFEM, even if the primitive LSFEM uses a very fine mesh or higher-order elements. In other words, the enriched LSFEM provides a significant improvement, with a lower computational cost, over the primitive LSFEM for solving convection-dominated problems.
The modified quadratic residue number system (MQRNS) for complex high-speed signal processing

Recently, the Quadratic Residue Number System ,(QRNS) has been introduced [5], [6], which allows the multiplication of complex integers with two real multiplications. The restriction is that this special residue number system has all moduli with prime factors of the form 4 k + 1 . If an increase in real multiplications from two to three can be tolerated, the restriction can be lifted to allow moduli of any form.
Spanning balanced trees in Boolean cubes

A Spanning Balancedn-tree (SBnT) in a Boolean n-cube is a spanning tree in which the root has fanout n, and all the subtrees of the root have $O({{2^n } / n})$ nodes. The number of tree edges in each dimension of the n-cube is of order $O({{2^n } / n})$. The spanning balanced n-tree allows for scheduling disciplines that realize lower bound (within a factor of two) one-to-all personalized communication, all-to-all broadcasting, and all-to-all personalized communication on a Boolean n-cube [C. -T. Ho and S. L. Johnsson, Proc. 1986 International Conference on Parallel Processing, pp. 640–648, IEEE Computer Society, 1986; Tech. Report YALEU/DCS/RR–483, May 1986], [S. L. Johnsson and C. -T. Ho, Tech. Report YALEU/DCS/RR–610, Dept. of Computer Science, Yale Univ., New Haven, CT, November 1987]. The improvement in data transfer time over the familiar binomial tree routing is a factor of ${n / 2}$ for concurrent communication on all ports and one-to-all personalized communication and all-to-all broadcasting. For all-to-all personalized communication on all ports concurrently, the improvement is of order $O(\sqrt n )$. Distributed routing algorithms defining the spanning balanced n-tree are given. The balanced n-tree is not unique, and a few definitions of n-trees that are effectively edge-disjoint are provided. Some implementation issues are also discussed.Binary numbers obtained from each other through rotation form necklaces that are full if the period is equal to the length of the number; otherwise, they are degenerate. As an intermediary result, it is shown that the ratio between the number of degenerate necklaces and the total number of necklaces with l bits equal to one is at most ${4 / {(4 + n)}}$ for $1 \leqq l < n$.
Running head: Orchid mycorrhizal fungi 1 2 Root-associated Fungi in Orchidaceae: Diversity, Phylogeny, Ecology, and 3 Outstanding Questions

28 Mycorrhizal fungi form ubiquitous symbiotic associations with almost all land plants and are of key 29 interest to evolutionary biologists and ecologists because this ancient symbiosis was essential for the 30 colonization of land by plants – a major turning point in the evolutionary history of the earth – and the 31 subsequent development and functioning of the terrestrial ecosystems. Within the orchid family 32 (Orchidaceae), plants establish unique interactions with specific orchid mycorrhizal fungi. These fungal 33 symbionts are essential for the development of orchids as they provide carbon and soil nutrients to 34 germinating orchid seeds and the nutritional supply continues for adult orchids to different degrees. 35 Fueled by the development of DNA sequencing techniques, the diversity of mycorrhizal and other root- 36 associated fungi in orchid roots has been extensively reported in evolutionary and ecophysiological 37 studies. However, the full taxonomic range of orchid-associated fungi remains to be investigated in a 38 broad phylogenetic framework, hampering a further understanding of the evolution and ecological 39 adaptation of orchid mycorrhizal interactions. In this study, we used the most complete DNA dataset to 40 date to map the phylogenetic distribution and ecological lifestyles of root-associated fungi in 41 Orchidaceae by phylogenetic reconstructions at the fungal order level. We found that a broad 42 taxonomic range of fungi (clustered into 1898 operational taxonomic units) resided in orchid roots, 43 belonging to at least 150 families in 28 orders in Basidiomycota and Ascomycota . These fungi were 44 assigned to diverse ecological lifestyles including typical orchid mycorrhizal fungi (‘rhizoctonia’), 45 ectomycorrhizal fungi, wood-or litter-decaying saprotrophic fungi, and other 46 endophytes/pathogens/saprotrophs. This overview reveals that among the four different mycorrhizal 47 types, the orchid mycorrhizal symbiosis probably involves the highest diversity of fungal taxa. We 48 hope that our newly reconstructed phylogenetic framework of orchid-associated fungi and the 49 assessment of their potential mycorrhizal status will benefit future ecological and evolutionary studies 50 on orchid-fungal interactions.
Cooling functions for low-density astrophysical plasmas

The cooling functions for a plasma slab are investigated under equilibrium and nonequilibrium conditions, over a range of 10 4 -10 8.5 K and for a range of abundances. Radiative transfer and diffuse field are calculated in the isobaric nonequilibrium models using a one-dimensional cooling flow model, and the plasma is not assumed to be optically thin to all radiation. Limiting cases of the plasma diffuse field coupling are calculated, and the resulting cooling functions are presented. Some functions are terminated before reaching 10 4 K when the internal photoionization halts the cooling. The functions represent a self-consistent set of curves covering a wide grid of temperature and metallicities using recently published atomic data and processes
Chimeric antigen receptor T-cell therapy for multiple myeloma

Multiple myeloma (MM) is a malignant plasma cell disorder that remains incurable for most patients, as persistent clonal evolution drives new mutations which confer MM high-risk signatures and resistance to standard care. The past two decades have significantly refashioned the therapeutic options for MM, especially adoptive T cell therapy contributing to impressive response rate and clinical efficacy. Despite great promises achieved from chimeric antigen receptor T-cell (CAR-T) therapy, the poor durability and severe toxicity (cytokine release syndrome and neurotoxicity) are still huge challenges. Therefore, relapsed/refractory multiple myeloma (RRMM), characterized by the nature of clinicopathologic and molecular heterogeneity, is frequently associated with poor prognosis. B Cell Maturation Antigen (BCMA) is the most successful target for CAR-T therapy, and other potential targets either for single-target or dual-target CAR-T are actively being studied in numerous clinical trials. Moreover, mechanisms driving resistance or relapse after CAR-T therapy remain uncharacterized, which might refer to T-cell clearance, antigen escape, and immunosuppressive tumor microenvironment. Engineering CAR T-cell to improve both efficacy and safety continues to be a promising area for investigation. In this review, we aim to describe novel tumor-associated neoantigens for MM, summarize the data from current MM CAR-T clinical trials, introduce the mechanism of disease resistance/relapse after CAR-T infusion, highlight innovations capable of enhanced efficacy and reduced toxicity, and provide potential directions to optimize manufacturing processes.
Modeling of anisotropic grating structures with active dipole layers

In our previous paper [T. Fördös, et al., J. Opt. 16 (2014) 065008] we have proposed a new approach for modeling of polarized light emission from anisotropic multilayers with active dipole layers. The method is suitable to model spin-polarized light emitting diodes (spin-LED) and spin-lasers. This paper deals with generalization of the approach to scattering matrix (S-matrix) formalism and to laterally periodic structures in the frame of rigorous coupled wave algorithm (RCWA). We use expansion of the permittivity tensor in a grating layer into Fourier series and the periodic electromagnetic field in the structure is expressed using a matrix method including appropriate boundary conditions. The new approach based on S-matrix formalism is also suitable for modeling of monomode emission from MQW laser structures with multiple source layers.
Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice

The plant hormone gibberellic acid (GA) is important for plant growth and productivity. Actin-related proteins (ARPs) also play central roles in plant growth, including cell elongation and development. However, the relationships between ARPs and GA signaling and biosynthesis are not fully understood. Here, we isolated OsGASD, encoding an ARP subunit from rice (Oryza sativa), using the Ac/Ds knockout system. The osgasd knockout (Ko) mutation reduced GA3 content in shoots as well as plant growth and height. However, GA application restored the plant height of the osgasd Ko mutant to a height similar to that of the wild type (WT). Rice plants overexpressing OsGASD (Ox) showed increased plant height and grain yield compared to the WT. Transcriptome analysis of flag leaves of OsGASD Ox and osgasd Ko plants revealed that OsGASD regulates cell development and the expression of elongation-related genes. These observations suggest that OsGASD is involved in maintaining GA homeostasis to regulate plant development, thereby affecting rice growth and productivity.
FGF10 ameliorates lipopolysaccharide-induced acute lung injury in mice via the BMP4-autophagy pathway

Introduction: Damage to alveolar epithelial cells caused by uncontrolled inflammation is considered to be the main pathophysiological change in acute lung injury. FGF10 plays an important role as a fibroblast growth factor in lung development and lung diseases, but its protective effect against acute lung injury is unclear. Therefore, this study aimed to investigate protective effect and mechanism of FGF10 on acute lung injury in mice. Methods: ALI was induced by intratracheal injection of LPS into 57BL/6J mice. Six hours later, lung bronchoalveolar lavage fluid (BALF) was acquired to analyse cells, protein and the determination of pro-inflammatory factor levels, and lung issues were collected for histologic examination and wet/dry (W/D) weight ratio analysis and blot analysis of protein expression. Results: We found that FGF10 can prevent the release of IL-6, TNF-α, and IL-1β, increase the expression of BMP4 and autophagy pathway, promote the regeneration of alveolar epithelial type Ⅱ cells, and improve acute lung injury. BMP4 gene knockdown decreased the protective effect of FGF10 on the lung tissue of mice. However, the activation of autophagy was reduced after BMP4 inhibition by Noggin. Additionally, the inhibition of autophagy by 3-MA also lowered the protective effect of FGF10 on alveolar epithelial cells induced by LPS. Conclusions: These data suggest that the protective effect of FGF10 is related to the activation of autophagy and regeneration of alveolar epithelial cells in an LPS-induced ALI model, and that the activation of autophagy may depend on the increase in BMP4 expression.
NR4A2 may be a potential diagnostic biomarker for myocardial infarction: A comprehensive bioinformatics analysis and experimental validation

Background Myocardial infarction is a well-established severe consequence of coronary artery disease. However, the lack of effective early biomarkers accounts for the lag time before clinical diagnosis of myocardial infarction. The present study aimed to predict critical genes for the diagnosis of MI by immune infiltration analysis and establish a nomogram. Methods Gene microarray data were downloaded from Gene Expression Omnibus (GEO). Differential expression analysis, single-cell sequencing, and disease ontology (DO) enrichment analysis were performed to determine the distribution of Differentially Expressed Genes (DEGs) in cell subpopulations and their correlation with MI. Next, the level of infiltration of 16 immune cells and immune functions and their hub genes were analyzed using a Single-sample Gene Set Enrichment Analysis (ssGSEA). In addition, the accuracy of critical markers for the diagnosis of MI was subsequently assessed using receiver operating characteristic curves (ROC). One datasets were used to test the accuracy of the model. Finally, the genes with the most diagnostic value for MI were screened and experimentally validated. Results 335 DEGs were identified in GSE66360, including 280 upregulated and 55 downregulated genes. Single-cell sequencing results demonstrated that DEGs were mainly distributed in endothelial cells. DO enrichment analysis suggested that DEGs were highly correlated with MI. In the MI population, macrophages, neutrophils, CCR, and Parainflammation were significantly upregulated compared to the average population. NR4A2 was identified as the gene with the most significant diagnostic value in the immune scoring and diagnostic model. 191 possible drugs for the treatment of myocardial infarction were identified by drug prediction analysis. Finally, our results were validated by Real-time Quantitativepolymerase chain reaction and Western Blot of animal samples. Conclusion Our comprehensive in silico analysis revealed that NR4A2 has huge prospects for application in diagnosing patients with MI.
Efficacy of topical and systemic treatments for atopic dermatitis on pruritus: A systematic literature review and meta-analysis

Introduction Pruritus is a major and burdensome symptom in atopic dermatitis (AD). The number of systemic treatments available for AD has increased recently, enabling improved patient relief. Objective To evaluate the effect of AD treatments on pruritus. Methods A systematic literature review and a meta-analysis were conducted to evaluate and compare the effects of treatment used in AD on pruritus. PubMed and Embase databases were searched to find articles published between January 1990 and December 2021. Topical and systemic treatments were studied in patients aged ≥10 years. Results Among the 448 articles identified, 56 studies were retained in the systematic review. A total of 15 studies evaluated topical treatments: topical corticosteroids (TCS; 2), calcineurin inhibitors (6), PDE4 inhibitors (3), and Jak inhibitors (4). A total of five studies were included in the meta- analysis. All treatments had a positive effect on pruritus, with a mean overall reduction of 3.32/10, 95% IC [2.32–4.33]. The greatest reduction was observed with halometasone (mean: 4.75), followed by tofacitinib 2% (mean: 4.38). A total of 41 studies evaluated systemic therapies: cyclosporine (6), phototherapy (5), azathioprine (2), dupilumab (9), anti-IL 13 (5), nemolizumab (3), Jak inhibitors (9), mepolizumab (1), and apremilast (1). A total of 17 studies were included in 2 meta-analyses according to the concomitant use or not of TCS. In the meta-analysis without TCS, the overall decrease was 3.07/10, 95% IC [2.58–3.56]. The molecules with the highest efficacy on pruritus were upadacitinib 30 mg (mean: 4.90) and nemolizumab (mean: 4.81). Discussion The therapeutic arsenal for AD has increased rapidly, and many molecules are under development. The primary endpoint of clinical trials is most often a score that assesses the severity of AD; however, the assessment of pruritus is also essential. The majority of molecules have a positive effect on pruritus, but the improvement varies between them. Efficacy on pruritus is not always correlated with efficacy on AD lesions; therefore, these two criteria are crucial to evaluate. The limitations of this study were the heterogeneity in the assessment of pruritus, the moment of the assessment, and the concomitant application of TCS or not for studies evaluating systemics. In the future, it would be useful to use standardized criteria for assessing pruritus.
Physician antibiotic hydration preferences for biologic antibacterial envelopes during cardiac implantable device procedures

Background Cardiac implantable electronic device (CIED) infection is a potentially serious complication of CIED procedures. Infection risk mitigation includes using guideline-recommended pre-operative intravenous antibacterial prophylaxis (IV ABX). The use of antibiotic-eluting CIED envelopes has also been shown to reduce infection risk. The relationship between and potential benefits associated with guideline-recommended IV ABX in combination with antibacterial envelopes have not been characterized. Methods Biologic envelopes made from non-crosslinked extracellular matrix (ECM) were implanted into 1,102 patients receiving CIEDs. The implanting physician decided patient selection for using a biologic envelope and envelope hydration solution. Observational data was analyzed on IV ABX utilization rates, antibacterial envelope usage, and infection outcomes. Results Overall compliance with IV ABX was 96.6%, and most patients received a biologic envelope hydrated in antibiotics (77.1%). After a mean follow-up of 223 days, infection rates were higher for sites using IV ABX <80% of the time vs. sites using ≥80% (5.6% vs. 0.8%, p = 0.008). Physicians demonstrated preference for hydration solutions containing gentamicin in higher-risk patients, which was found by multivariate analysis to be associated with a threefold reduction in infection risk (OR 3.0, 95% CI, 1.0–10.0). Conclusion These findings suggest that use of antibiotics, particularly gentamicin, in biologic envelope hydration solution may reduce infection risk, and use of antibacterial envelopes without adjunct IV ABX may not be sufficient to reduce CIED infections. Clinical trial registration [https://clinicaltrials.gov/], identifier [NCT02530970].
Serum cytokine profiling reveals different immune response patterns during general and severe Mycoplasma pneumoniae pneumonia

Mycoplasma pneumoniae (MP) is an important human pathogen that mainly affects children causing general and severe Mycoplasma pneumoniae pneumonia (G/SMPP). In the present study, a comprehensive immune response data (33 cytokines) was obtained in school-age children (3–9 years old) during MPP, aiming to analyze the immune response patterns during MPP. At acute phase, changes of cytokines were both detected in GMPP (24/33) and SMPP (23/33) groups compared to the healthy group (p < 0.05), with 20 identical cytokines. Between MPP groups, the levels of 13 cytokines (IL-2, IL-10, IL-11, IL-12, IL-20, IL-28A, IL-32, IL-35, IFN-α2, IFN-γ, IFN-β, BAFF, and TSLP) were higher and three cytokines (LIGHT, OPN and CHI3L1) were lower in the SMPP group than in the GMPP group (p < 0.05). Function analysis reveals that macrophage function (sCD163, CHI3L1) are not activated in both MPP groups; difference in regulatory patterns of T cells (IL26, IL27, OPN, LIGHT) and defective activation of B cells (BAFF) were detected in the SMPP group compared to the GMPP group. Besides, the level of osteocalcin; sIL-6Rβ and MMP-2 are both decreased in MPP groups at acute and convalescent phases compared to the healthy group, among which the levels of sIL-6Rβ and MMP-2 showed negative correlations (p < 0.1) to the application of bronchial lavage in SMPP group, indicating their roles in the development of MPP. At the convalescent phase, more cytokines recovered in GMPP (18) than SMPP (11), revealing better controlled immune response during GMPP. These results reveal different immune response patterns during GMPP and SMPP. In addition, the differentiated cytokines may serve as potential indicators of SMPP; early intervention on immune response regulations may be helpful in reducing the severity of SMPP.
MODAL PROPORTIES OF BEAMS AND PLATES ON RESILIENT SUPPORTS WITH ROTATIONAL AND TRANSLATIONAL COMPLEX STIFFNESS

Abstract For beam and plate vibrations, energy dissipation may be mostly attributed to internal damping inside the structure and external damping at the supports. Surface damping treatment is one of the most effective tools to control vibrations of beam and plate in general. Sometimes it is not always desirable, however, to apply this damping treatment, for practical reasons. In such cases, one must rely on the damping treatment at the supports. In this presentation, the effects of damped compliant boundary conditions on modal parameters are investigated for two types of continuous systems; an elastic beam and a circular plate. The impedances at the boundaries to translational and rotational motions are given by springs with complex stiffness. The governing equations are solved numerically to obtain the natural frequencies and modal loss factors. Numerical results are represented in dimensionless terms, based on which a procedure of selecting the support parameters is illustrated to obtain desirable modal properties.
Methylome-wide association study of different responses to risperidone in schizophrenia

Background: Accumulating evidence shows that DNA methylation plays a role in antipsychotic response. However, the mechanisms by which DNA methylation changes are associated with antipsychotic responses remain largely unknown. Methods: We performed a methylome-wide association study (MWAS) to evaluate the association between DNA methylation and the response to risperidone in schizophrenia. Genomic DNA methylation patterns were assessed using the Agilent Human DNA Methylation Microarray. Results: We identified numerous differentially methylated positions (DMPs) and regions (DMRs) associated with antipsychotic response. CYP46A1, SPATS2, and ATP6V1E1 had the most significant DMPs, with p values of 2.50 × 10–6, 3.53 × 10–6, and 5.71 × 10–6, respectively. The top-ranked DMR was located on chromosome 7, corresponding to the PTPRN2 gene with a Šidák-corrected p-value of 9.04 × 10–13. Additionally, a significant enrichment of synaptic function and neurotransmitters was found in the differentially methylated genes after gene ontology and pathway analysis. Conclusion: The identified DMP- and DMR-overlapping genes associated with antipsychotic response are related to synaptic function and neurotransmitters. These findings may improve understanding of the mechanisms underlying antipsychotic response and guide the choice of antipsychotic in schizophrenia.