Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytotoxic and pro-apoptotic effects of botanical drugs derived from the indigenous cultivated medicinal plant Paris polyphylla var. yunnanensis

Background: Cancer is one of the top two leading causes of death worldwide. Ethnobotanical research, it is one of methods, which is able to discover effective anticancer drugs based on “prototype” of indigenous people’s historical experiences and practices. The rhizomes of Paris polyphylla var. yunnanensis (Franch.) Hand. -Mazz. have been used as botanical drugs to treat cancer by Yi, Bai, Dai, and Naxi ethnic groups in Yunnan, China, where this species is widely cultivated in a large scale in Yunnan. Materials and methods: To identify the substances of anticancer activities based on indigenous medicine knowledge, chromatography was performed to separate saponins from the rhizomes of P. polyphylla var. yunnanensis, followed by spectroscopy to determine the structure of six isolated saponins. The cytotoxicity of five extracts and six pure compounds were evaluated by MTS method. Quantitative determination of total saponins of P. polyphylla var. yunnanensis was analyzed by HPLC. Cell cycle assay, apoptosis assay, and mitochondrial membrane potential were used to evaluate the pro-apoptotic activity in vitro. Results: Five extracts and six pure saponins showed significant inhibitory cytotoxic activities of three human liver cancer cell lines (SMMC-7721, HepG2, and SK-HEP-1) and one non-small-cell lung cancer cell line (A549). The contents of Paris saponins I, II, and VII were 6.96% in the rhizomes of P. polyphylla var. yunnanensis, much higher than Chinese Pharmacopoeia standards (0.6%). Six saponins induced significant apoptosis and cell cycle arrest in three human cancer cell lines (A549, SMMC-7721, and HepG2), which was associated with the loss of mitochondrial membrane potential. Conclusion: The result of this study support that cultivated P. polyphylla var. yunnanensis could be a substitute for wild resource as an anticancer medicine based on indigenous medicine knowledge.
The differences of orthostatic hypotension in patients with Parkinson's disease and multiple system atrophy

Background Multiple system atrophy (MSA) and Parkinson's disease (PD) have similar clinical presentations in their early stages. Orthostatic hypotension (OH) is a common autonomic dysfunction associated with MSA and PD. Heart rate (HR) and systolic blood pressure (SBP) changes are measured in response to the active standing test, which is widely used to screen for cardiovascular autonomic function. Objectives and methods Overall, 255 patients (67 MSA, 188 PD) underwent continuous beat-to-beat non-invasive BP monitoring and active standing test. The total standing time was 10 min, and the BP differences between both groups were compared to determine whether the ΔHR/ΔSBP can differentiate both conditions. Results Classical orthostatic hypotension (COH) (52%) and initial OH (19%) were most common in MSA and PD, respectively. MSA had a higher HR (75.0 ± 9.7 vs. 71.0 ± 10.7, P = 0.008) than PD in the supine position. SBP (135.70 ± 15.68 mmHg vs. 127.31 ± 15.14 mmHg, P = 0.106), diastolic BP (78.45 ± 12.36 mmHg vs. 67.15 ± 13.39 mmHg, P = 0.009) and HR (73.94 ± 8.39 bpm vs. 71.08 ± 13.52 bpm, P = 0.389) at baseline were higher in MSA-COH than in PD-COH. After adjusting for age and disease duration, the ΔHR/ΔSBP-10 min significantly discriminated MSA-COH from PD-COH (P = 0.031). An ΔHR/ΔSBP-10 min of 0.517 showed a sensitivity of 67% and specificity of 84% (AUC = 0.77, 95% CI: 0.63–0.91). Conclusion The SBP, diastolic BP, and HR were higher in the supine position; however, ΔHR and ΔSBP were lower after standing in MSA patients than in PD patients. The ΔHR/ΔSBP-10 min discriminated between MSA-COH and PD-COH with quiet acceptable accuracy.
The effect of using fresh farmyard manure (animal manure) on the severity of Fusarium verticilioides in soil, root, stem, and kernels as well as lodging and borer incidence of maize plants

Fusarium verticillioides, an important maize pathogen, produce fumonisins, causes stalk rot and consequentially reduce crop growth and yield. Therefore, herein we aimed to evaluate the potential use of two farmyard soil organic manures, i.e., fresh (5-6 days old) and stored (5-6 months old) organic manure, to manage F. verticillioides infections as well as borer incidence and lodging in maize plants. After 30, 60, and 90 days of sowing, samples of soil, roots, and stems were collected to isolate F. verticillioides. Moreover, we estimated ear and kernel rot induced by F. verticillioides at the final harvest. Fresh organic manure treatment increased infection rates of F. verticillioides in soil, roots, stem and kernels compared to the control treatment. In contrast, stored organic manure plots treatments decrease F. verticillioides frequency. At 90 days after sowing, stored organic manure suppressed the survival of F. verticillioides, which reduced the F. verticillioides incidence percent. These results were similar to the effect of herbicides-and insecticide-treated plots demonstrated, which show a significant decrease in F. verticillioides incidence rates. Mycological analysis on symptomless kernels revealed a higher % of pathogen infection in opened husks variety (Balady) than closed husks variety (SC10). Compared with stored organic manure, the stem borer incidence and lodging percentage were the highest in fresh organic manure plots. Finally, these results demonstrated that storing organic manure within five to six months as farmyard manure led to high-temperature centigrade within organic manure, thereby destroying spores of F. verticillioides, whereas fresh organic manure did not.
Nanobodies in cell-mediated immunotherapy: On the road to fight cancer

The immune system is essential in recognizing and eliminating tumor cells. The unique characteristics of the tumor microenvironment (TME), such as heterogeneity, reduced blood flow, hypoxia, and acidity, can reduce the efficacy of cell-mediated immunity. The primary goal of cancer immunotherapy is to modify the immune cells or the TME to enable the immune system to eliminate malignancies successfully. Nanobodies, known as single-domain antibodies, are light chain-free antibody fragments produced from Camelidae antibodies. The unique properties of nanobodies, including high stability, reduced immunogenicity, enhanced infiltration into the TME of solid tumors and facile genetic engineering have led to their promising application in cell-mediated immunotherapy. They can promote the cancer therapy either directly by bridging between tumor cells and immune cells and by targeting cancer cells using immune cell-bound nanobodies or indirectly by blocking the inhibitory ligands/receptors. The T-cell activation can be engaged through anti-CD3 and anti-4-1BB nanobodies in the bispecific (bispecific T-cell engagers (BiTEs)) and trispecific (trispecific T-cell engager (TriTEs)) manners. Also, nanobodies can be used as natural killer (NK) cell engagers (BiKEs, TriKEs, and TetraKEs) to create an immune synapse between the tumor and NK cells. Nanobodies can redirect immune cells to attack tumor cells through a chimeric antigen receptor (CAR) incorporating a nanobody against the target antigen. Various cancer antigens have been targeted by nanobody-based CAR-T and CAR-NK cells for treating both hematological and solid malignancies. They can also cause the continuation of immune surveillance against tumor cells by stopping inappropriate inhibition of immune checkpoints. Other roles of nanobodies in cell-mediated cancer immunotherapy include reprogramming macrophages to reduce metastasis and angiogenesis, as well as preventing the severe side effects occurring in cell-mediated immunotherapy. Here, we highlight the critical functions of various immune cells, including T cells, NK cells, and macrophages in the TME, and discuss newly developed immunotherapy methods based on the targeted manipulation of immune cells and TME with nanobodies.
Microbial characterization based on multifractal analysis of metagenomes

Introduction The species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research. Method and Results Firstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences. Conclusion and Discussion There is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants’ gut microbiomes are related to the development of the infants.
Free energy minimisation algorithm for decoding and cryptanalysis

An algorithm is derived for inferring a binary vector s given noisy observations of As modulo 2, where A is a binary matrix. The binary vector is replaced by a vector of probabilities, optimised by free energy minimisation. Experiments on the inference of the state of a linear feedback shift register indicate that this algorithm supersedes the Meier and Staffelbach polynomial algorithm.
Regulation of autophagy and lipid accumulation under phosphate limitation in Rhodotorula toruloides

Background It is known that autophagy is essential for cell survival under stress conditions. Inorganic phosphate (Pi) is an essential nutrient for cell growth and Pi-limitation can trigger autophagy and lipid accumulation in oleaginous yeasts, yet protein (de)-phosphorylation and related signaling events in response to Pi limitation and the molecular basis linking Pi-limitation to autophagy and lipid accumulation remain elusive. Results Here, we compared the proteome and phosphoproteome of Rhodotorula toruloides CGMCC 2.1389 under Pi-limitation and Pi-repletion. In total, proteome analysis identified 3,556 proteins and the phosphoproteome analysis identified 1,649 phosphoproteins contained 5,659 phosphosites including 4,499 pSer, 978 pThr, and 182 pTyr. We found Pi-starvation-induced autophagy was regulated by autophagy-related proteins, but not the PHO pathway. When ATG9 was knocked down, the engineered strains produced significantly less lipids under Pi-limitation, suggesting that autophagy required Atg9 in R. toruloides and that was conducive to lipid accumulation. Conclusion Our results provide new insights into autophagy regulation under Pi-limitation and lipid accumulation in oleaginous yeast, which should be valuable to guide further mechanistic study of oleaginicity and genetic engineering for advanced lipid producing cell factory.
Materials informatics for developing new restorative dental materials: A narrative review

Materials informatics involves the application of computational methodologies to process and interpret scientific and engineering data concerning materials. Although this concept has been well established in the fields of biology, drug discovery, and classic materials research, its application in the field of dental materials is still in its infancy. This narrative review comprehensively summarizes the advantages, limitations, and future perspectives of materials informatics from 2003 to 2022 for exploring the optimum compositions in developing new materials using artificial intelligence. The findings indicate that materials informatics, which is a recognized and established concept in the materials science field, will accelerate the process of restorative materials development and contribute to produce new insights into dental materials research.
The incorporation of Mg2+ ions into aragonite during biomineralization: Implications for the dolomitization of aragonite

Bacteria can facilitate the increase of Mg2+ content in biotic aragonite, but the molecular mechanisms of the incorporation of Mg2+ ion into aragonite facilitated by bacteria are still unclear and the dolomitization of aragonite grains is rarely reported. In our laboratory experiments, the content of Mg2+ ions in biotic aragonite is higher than that in inorganically-precipitated aragonite and we hypothesize that the higher Mg content may enhance the subsequent dolomitization of aragonite. In this study, biotic aragonite was induced by Bacillus licheniformis Y1 at different Mg/Ca molar ratios. XRD data show that only aragonite was precipitated in the media with Mg/Ca molar ratios at 6, 9, and 12 after culturing for 25 days. The EDS and atomic absorption results show that the content of Mg2+ ions in biotic aragonite increased with rising Mg/Ca molar ratios. In addition, our analyses show that the EPS from the bacteria and the organics extracted from the interior of the biotic aragonite contain the same biomolecules, including Ala, Gly, Glu and hexadecanoic acid. The content of Mg2+ ions in the aragonite precipitates mediated by biomolecules is significantly higher than that in inorganically-precipitated aragonite. Additionally, compared with Ala and Gly, the increase of the Mg2+ ions content in aragonite promoted by Glu and hexadecanoic acid is more significant. The DFT (density functional theory) calculations reveal that the energy needed for Mg2+ ion incorporation into aragonite mediated by Glu, hexadecanoic acid, Gly and Ala increased gradually, but was lower than that without acidic biomolecules. The experiments also show that the Mg2+ ion content in the aragonite significantly increased with the increasing concentration of biomolecules. In a medium with high Mg2+ concentration and with bacteria, after 2 months, micron-sized dolomite rhombs were precipitated on the surfaces of the aragonite particles. This study may provide new insights into the important role played by biomolecules in the incorporation of the Mg2+ ions into aragonite. Moreover, these experiments may contribute towards our understanding of the dolomitization of aragonite in the presence of bacteria.
The Consistency of Holt's Conjectures on Cohomological Dimension of Locally Finite Groups

Let G be a locally finite group of cardinality ℵn where n is a natural number. Let π(G) be the set of primes p for which G has an element of order p. In [5], Holt conjectures that if k is a finite field with char k ∉ π(G) then
Simplified interaction tests for non‐normal data in psychological research

This study examined three simple transformations which increase the power of F tests of main effects and interaction in 2 × 2 factorial designs under violation of normality. The study obtained Monte Carlo results from various heavy-tailed densities, including mixed-normal, exponential, Cauchy and Laplace densities, which are associated with grossly distorted probabilities of Type I and Type II errors. Transformation of scores to ranks made the F test for interaction robust and comparable in power to the Mann—Whitney-Wilcoxon test for the same distributions. Transformation to ‘modular ranks’, having one-fourth the number of values of conventional ranks, was equally effective. Detection and downweighting of outliers before performing the F test was more effective than rank methods for several distributions. Implications of these findings for the role of scales of measurement and nonparametric methods in psychological research are discussed.
Structural optimization based on preconditioned conjugate gradient analysis methods

An efficient method for structural optimization is presented. Instead of classical direct decomposition methods, Preconditioned Conjugate Gradient (PCG) methods, in conjunction with two proposed starting-vector generation schemes, are used to solve the systems of linear equations associated with the finite element analysis and behaviour sensitivity analysis problems. These inherently iterative analysis procedures are then used to carry out the analyses needed at the beginning of each stage in an approximation concepts approach to structural optimization. This technique has been implemented in a research program and used to solve a collection of minimum weight truss sizing design problems subject to static deflection and stress constraints. The effectiveness of the PCG methods of analysis in structural optimization is demonstrated. Comparison among different preconditioners is made. The effect of the proposed starting-vector generation schemes is shown. The comparative merits of analytical sensitivity analysis and finite difference sensitivity analysis, when using PCG methods of analysis, are assessed. The parallel computation potential of PCG methods is discussed. Because of the iterative nature of PCG analysis methods and the prospects they offer for parallel computation, it is found that PCG analysis methods show promise in the context of structural optimization.
Darboux integrability for 3D Lotka-Volterra systems

We describe the improved Darboux theory of integrability for polynomial ordinary differential equations in three dimensions. Using this theory and computer algebra, we study the existence of first integrals for the three-dimensional Lotka-Volterra systems. Only working up to degree two with the invariant algebraic surfaces and the exponential factors, we find the major part of the known first integrals for such systems, and in addition we find three new classes of integrability. The method used is of general interest and can be applied to any polynomial ordinary differential equations in arbitrary dimension.
An Improved Method for Obtaining the Water Content Values of Ice Hydrometeors from Aircraft and Radar Data

Abstract Uncertainty analyses and operational experience at the Air Force Geophysics Laboratory (AFGL) have shown that for single samples of ice hydrometeors, the factor κ = M/(? ), where M (spectral liquid water content) and Z (spectral radar reflectivity factor) are computed from aircraft particle size information, is less subject to the uncertainties of converting the physical size of the particles into equivalent melted diameter than are M and Z themselves. Consequently, in correlating multiple-sample aircraft data with simultaneously acquired, independent radar measurements of ZR, there is an appreciable accuracy enhancement that can be attained in the derivation of M vs Z equations by regression means, if κ is used as the correlation parameter, versus ZR, rather than if spectral M is used as the correlation parameter.
Exploiting unsupervised and supervised classification for segmentation of the pathological lung in CT

Delineation of lung fields in presence of diffuse lung diseases (DLPDs), such as interstitial pneumonias (IP), challenges segmentation algorithms. To deal with IP patterns affecting the lung border an automated image texture classification scheme is proposed. The proposed segmentation scheme is based on supervised texture classification between lung tissue (normal and abnormal) and surrounding tissue (pleura and thoracic wall) in the lung border region. This region is coarsely defined around an initial estimate of lung border, provided by means of Markov Radom Field modeling and morphological operations. Subsequently, a support vector machine classifier was trained to distinguish between the above two classes of tissue, using textural feature of gray scale and wavelet domains. 17 patients diagnosed with IP, secondary to connective tissue diseases were examined. Segmentation performance in terms of overlap was 0.924±0.021, and for shape differentiation mean, rms and maximum distance were 1.663±0.816, 2.334±1.574 and 8.0515±6.549 mm, respectively. An accurate, automated scheme is proposed for segmenting abnormal lung fields in HRC affected by IP
A Relationship Between Stratification, Cloud Depth, and Permitted Cloud Radii

Abstract A one-dimensional cumulus model is used to interrelate cloud radius, stratification and cloud height. It is suggested that if only certain ranges of cloud height and radius are permitted, then from the stratification, one can predict, using a model, allowed cloud radii and a corresponding depth to the convective layer.
Finite Reynolds number properties of a turbulent channel flow similarity solution

Finite Reynolds number behaviors of the asymptotically logarithmic mean velocity profile in fully developed turbulent channel flow are investigated. The scaling patch method of Fife et al. [“Multiscaling in the presence of indeterminacy: Wall-induced turbulence,” Multiscale Model. Simul. 4, 936 (2005)] is used to reveal invariance properties admitted by the appropriately simplified form of the mean momentum equation. These properties underlie the existence of a similarity solution to this equation over an interior inertial domain. The classical logarithmic mean velocity profile equation emerges from this similarity solution as the Reynolds number becomes large. Originally demonstrated via numerical integration, it is now shown that the solution to the governing nonlinear equation can be found by straight-forward analytical integration. The resulting solution contains both linear and logarithmic terms, but with the coefficient on the linear term decaying to zero as the Reynolds number tends to infinity. In this way, the universality of the classical logarithmic law comports with the existence of an invariant form of the mean momentum equation and is accordingly described by the present similarity solution. Existing numerical simulation data are used to elucidate Reynolds number dependent properties of the finite Reynolds number form of the similarity solution. Correspondences between these properties and those indicated by finite Reynolds number corrections to the classical overlap layer formulation for the mean velocity profile are described and discussed.
Comments on Minimum Volume Simple and Compensated Superconducting Coils

The increasing use of superconducting magnets in many fields of research and technology raises more and more often the question: Which is the cheapest magnet for a given field, subject to constraints such as field homogeneity or radial access? In this paper minimum volume coils of three types are analyzed: simple (Fabry), sixth order compensated (outside notch corrected), split (Helmholtz) of internal radii from 1 to 10 cm, and axial apertures (of the Helmholtz coils) from 0.5 to 10 cm. To obtain a given field with a given effective current density Jλ, about the same amount of wire is necessary for a Fabry coil of internal radius 2a1, a sixth order or split coil of internal radii a1, or a split coil with window aperture a1.