Miracle-dz/UniFAR-FTUs huggingface dataset:
Using network pharmacology and molecular docking verification to explore the mechanism of ursolic acid in the treatment of osteoporosis

Whether ursolic acid is an effective drug in treatment of osteoporosis (OP) and how it exhibit activity effect on OP is unclear. To investigated the potential molecular mechanism of ursolic acid in the treatment of OP and figured out its possible mechanism is necessary. The target genes of ursolic acid were screened by using the database of traditional chinese medicine systems pharmacology, PubMed database and UniProt database. OP-related target genes were searched by GeneCards database, and utilized online mapping tool to obtain common target genes of component-disease. String database was used to construct a protein-protein interaction (PPI) network of component-disease common target genes and perform topological analysis to screen core target genes. DAVID database was performed gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for component-disease shared target genes. Using the core target protein as the receptor and ursolic acid as the ligand, the molecular docking was performed using AutoDockVina 1.1. 2 software. A total of 52 ursolic acid-related target genes and 4657 OP-related target genes were excavated, with a total of collective 43 target genes. The above-mentioned PPI network with shared target genes contains 43 nodes and 510 edges, with an average node degree value of 23.32. A total of 24 core target genes were obtained, mainly including tumor protein p53 (TP53), vascular endothelial growth factor A (VEGFA), interleukin-6 (IL6), tumor necrosis factor (TNF), caspase3 (CASP3), matrix metallo protein (MMP9), transcription factor AP-1 (JUN), activator of transcription 3 (STAT3), mitogen-activated protein kinase 8 (MAPK8), and prostaglandin endoperoxidase 2 (PTGS2), respectively. According to KEGG enrichment analysis, there are 126 treatment of OP signaling pathway were enriched. GO enrichment analysis revealed that 313 biological processes were identified. The molecular docking result showed that the binding energies were all lower than −5 kcal/mol, indicating strong binding activity to the protein by the 6 core target gene. The therapeutic effect of ursolic acid on OP may be achieved by regulating TP53, JUN, IL6, VEGFA, CASP3, and MAPK8 genes, respectively. It exhibits possible biological function in the treatment of OP mainly involve positive regulation of apoptotic process, response to drug, incytoplasm, cytosol, protein binding, identical protein binding. Its mechanism may related to multiple therapeutic targets and signaling pathways such as cancer pathway, hepatitis B, and TNF signaling pathway.
Structural modal identification using data sets with missing observations

System identification algorithms currently require a full data set, i.e., no missing observations, to estimate the natural vibration properties of a structural system. These algorithms are often based on parameters estimated from a state-space model. There are circumstances in which a Missing Data Problem can arise during data collection; therefore, it is important to adjust these algorithms to facilitate Structural Modal Identification. Despite having missing observations, state-space parameters can be estimated for a time series; subsequently, structural modal properties can be identified. This paper will use the EM algorithm to identify structural modal properties from a data set with missing observations. The end of the paper will focus on the search for a missingness threshold which can be used to assess the probability of extracting useful structural modal properties from a given data set with missing observations. This assessment will be based on the accuracy of modal estimates for data sets with varying magnitudes and patterns of missingness. It is clear that missingness can only reduce the accuracy of modal estimates; however, it is important to establish the associated scale and behavior of the reduction. An example is presented to illustrate the main concepts of this approach.
Inferred Impacts of Extreme Environments on Hawksbill Turtle (Eretmochelys imbricata) Body Size and Reproductive Output

Abstract. This study presents the first published data on the morphometrics of nesting hawksbill turtles (Eretmochelys imbricata) and their eggs and counts of yolked and yolkless eggs per clutch from Iranian Islands in the northern Persian Gulf. We found significant variation in some variables among 4 main nesting islands (e.g., weight of yolked eggs, p = 0.000; number of yolkless eggs per clutch, p = 0.017), but effect size was moderate or less (r < 0.5 or d < 0.8). The diameter (p = 0.039), weight (p = 0.028), and number of yolked eggs (p = 0.000) per clutch increased significantly with curved carapace length (CCL), but the effect size was only large for the number of yolked eggs (f2 = 0.152). The number of yolkless eggs did not vary with CCL (p = 0.453) or with the number of yolked eggs (p = 0.523). A meta-analysis of global hawksbill turtle morphometrics and reproductive output revealed significant variation in CCL (p = 0.000) and number of yolked eggs (p < 0.001), with nesting region having a very large effect size on both variables (g2 = 0.880 and 0.616, respectively). Hawksbill turtles from the Gulf were smaller than populations from the Gulf of Oman (p < 0.001), Arabian Sea (p = 0.000), Caribbean (p = 0.000), West Atlantic (p = 0.000), and Southwest Pacific (p = 0.000) but not the Red Sea (p = 0.104), and laid fewer yolked eggs than populations in the Caribbean (p < 0.001) and West Atlantic (p = 0.001) but not the Red Sea (p = 0.636). This may be due to hawksbill turtles nesting in the Gulf remaining within its waters postnesting so adult body size is restricted by the relatively poor foraging habitat and/or success and/or the extreme environments, subsequently limiting clutch size. More information on home range and foraging habitat is required to draw similar conclusions about hawksbill turtles nesting in the Red Sea. Hawksbill turtles nesting in the Gulf, Red Sea, and Arabian Sea also appear to lay larger number of yolkless eggs per clutch than other populations worldwide (mean = 17.6 ± 10.8 SD [range = 0–59]). The functional role of yolkless eggs, potentially in the maintenance of thermal and hydric conditions within tolerable conditions in shallow nests laid in extreme environments, requires further investigation. Similarly, the potential for yolkless eggs to be an adaptation to extreme nest environments in other sea turtle species also nesting in the northern Indian Ocean also warrants examination.
Special Collection: World-Scale Ecology and Management of Fall Armyworm (Spodoptera frugiperda) The Spodoptera frugiperda Host Strains: What They Are and Why They Matter for Understanding and Controlling This Global Agricultural Pest

Fall armyworm (Spodoptera frugiperda [J.E. Smith]) is a moth native to the Western Hemisphere where it is a major pest of corn (maize) and multiple other crops. It is now a global threat with its recent discovery and dissemination in the Eastern Hemisphere. Its broad host range is in part due to two subpopulations denoted as ‘host strains’ that differ in host plant specificity. Therefore, identifying the strains present in a location is critical to assessing what crops are at risk of infestation. However, much remains uncertain about how the strains differ and even on the fundamental issue of how they are identified. Complicating factors include the host strains are morphologically indistinguishable, the defining behavior of the strains (host plant specificity) is variable, and the existence of significant differences between geographical populations and laboratory colonies that are independent of strain identity. These factors contribute to substantial disagreements in the literature on presumptive strain differences. This paper presents a summary of strain characteristics and suggests the criteria that should be met before concluding a trait is ‘strain-specific’. The intent is to facilitate a common understanding of what the strains represent and to develop a more consistent experimental framework for studies on strain phenotypes. Evidence is summarized that supports a primary role for Z-linked genes in strain identity, which has potential implications for genetic approaches to define the strains, and we discuss the possibility that the strains arose from allopatric (rather than sympatric) speciation processes.
Diversity of the GRB‐Supernova Connection: X‐Ray Flashes and Dark Hypernovae

We review the following types of the GRB‐Supernova (SN) connection, which has revealed interesting diversity. (1) GRB‐SNe: The three SNe all explode with energies much larger than those of typical SNe, thus being called Hypernovae (HNe). They are massive enough for forming black holes. (2) Non‐GRB HNe/SNe: Some HNe are not associated with GRBs. (3) XRF‐SN: SN 2006aj associated with X‐Ray Flash 060218 is dimmer than GRB‐SNe and has very weak oxygen lines. Its progenitor mass is estimated to be small enough to form a neutron star rather than a black hole. (4) Non‐SN GRB: Two nearby long GRBs were not associated SNe. Such “dark HNe” have been predicted in order to explain the origin of C‐rich (hyper) metal‐poor stars. This would be an important confirmation of the Hypernova‐First Star connection. We will show our attempt to explain the diversity in a unified manner with the jet‐induced explosion model.
Predicted electron transport coefficients at high E/N values. II. Nitrogen

Transport coefficients of electrons in nitrogen are calculated over the range 10−16⩽E/N⩽7.3×10−15 V cm2 by solving the Boltzmann equation using the classical two‐term expansion in spherical harmonics. However, as in the case of H2 treated in a previous paper, the sources of new electrons produced by ionization has been accounted for in the Boltzmann equation. It is shown that the release of these new electrons has an effect on the distribution function starting from E/N≃2×10−15 V cm2, which increases rapidly as E/N increases. The recently available cross sections for the excitation of the electronic states of N2 have been used along with the total‐momentum‐transfer cross section derived by Cartwright. The predicted values of the ionization coefficient are in very good agreement with the experimentally measured values except at low E/N values, for which our predicted ionization coefficients are slightly less than the experimental ones. The agreement is also good for the drift velocities over the entire E/N.
Evaluation of Urine Nitrogen Excretion as the Measure of the Environmental Load and the Efficiency of Nitrogen Utilization

Abstract The aim of this study was to evaluate the relationship between nutrition, the concentration of milk urea nitrogen (MUN) and the urinary nitrogen excretion in farm conditions and to use the MUN concentration as a tool to control protein nutrition and environmental load in dairy farming. Urinary N excretion was evaluated by an empirical model according to the intake and metabolic transformation of N to milk protein in selected farms was on average 208.8 ± 34.8 g with a range of values from 127.7 to 277.8 g N.day−1. The evaluated proportion of excreted N in relation to crude protein (CP) intake in the total mix ration (TMR) was statistically significant (R2 = 0.504; P < 0.0001). Urinary N excretion, evaluated according to the analysis of the MUN content, using selected regression equations, was on average 211.8 ± 24.3 g.day−1 with an individual variation of 157.2‒274.7 g.day−1 with a significantly higher positive correlation to the received CP in the TMR (R2 = 0.693; P < 0.0001). The evaluated effect of CP concentration in the TMR on urine N excretion confirmed the higher nitrogen excretion in the urine by 25.6 g per day with an increased CP in the TMR by 1 %. The proportion of urea nitrogen in the total N excreted in the urine was on average 80.5 %. The validation of the models for the prediction of nitrogen excretion, according to the MUN for the practical application on farms, was determined the best equation by Kaufmann a St-Pierre, which used available data from routine analysis of milk composition by the Breeding service of Slovakia. The MUN analysis offered a simple and non-invasive approach to the evaluation of the urinary N excretion, as well as, the efficiency of N utilization from feed to milk.
Editorial: Therapies and influences in urothelial carcinoma

COPYRIGHT © 2022 Ozgun, Isharwal and Eigl. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 29 December 2022 DOI 10.3389/fonc.2022. 1126494
Ring finger protein 128 promotes, rather than inhibits, colorectal cancer progression by regulating the Hippo signaling pathway

Background Colorectal cancer is a common malignancy of the gastrointestinal tract, and its incidence and mortality rates have increased in recent years. RNF128 is an E3 ubiquitin ligase that plays an important role as a suppressor gene or oncogene in various cancers, but its mechanism in colorectal cancer is not yet clear. The aim of this study was to investigate the role and mechanism of RNF128 in colorectal cancer. Methods The expression of RNF128 in colorectal cancer tissues was assessed by immunohistochemistry and western blotting. The proliferation ability of colorectal cancer cells was measured by colony formation assay and CCK-8 assay, the migration and invasion ability of colorectal cancer cells was measured by wound healing assay and transwell assay, and the protein expression levels of the Hippo signaling pathway and its target gene were examined by western blotting. Immunoprecipitation was used to assess the interaction of RNF128 with MST. In vivo, a xenograft tumor model was used to detect the effect of RNF128 on tumor growth. Results At the tissue level, the expression level of RNF128 was significantly higher in colorectal cancer tissues than in adjacent normal tissues. In LoVo cells and HCT116 cells, the proliferation, migration and invasion abilities were significantly reduced with RNF128 knockdown. At the protein level, knockdown of RNF128 resulted in significant activation of the Hippo signaling pathway. In vivo experiments, the volume and weight of xenograft tumors in nude mice were significantly decreased compared with those in the normal control group with RNF128 knockdown. Conclusion RNF128 promotes the malignant behaviors of colorectal cancer cells by inhibiting the Hippo signaling pathway, which may provide a new target for colorectal cancer prevention and treatment.
Editorial: Multimodal management of advanced gastric cancer

COPYRIGHT © 2022 Garg, Brandl and Marano. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 29 December 2022 DOI 10.3389/fonc.2022. 1113856
Explaining Why Fake Photos are Fake

Today's disinformation campaigns may use deceptively altered photographs to promote a false narrative. In some cases, viewers may be unaware of the alteration and thus may more readily accept the promoted narrative. In this work, we consider whether this effect can be lessened by explaining to the viewer how an image has been manipulated. To explore this idea, we conduct a two-part study. We started with a survey (n=113) to examine whether users are indeed bad at identifying manipulated images. Our result validated this conjecture as participants performed barely better than random guessing (60% accuracy). Then we explored our main hypothesis in a second survey (n=543). We selected manipulated images circulated on the Internet that pictured political figures and opinion influencers. Participants were divided into three groups to view the original (unaltered) images, the manipulated images, and the manipulated images with explanations, respectively. Each image represents a single case study and is evaluated independently of the others. We find that simply highlighting and explaining the manipulation to users was not always effective. When it was effective, it did help to make users less agreeing with the intended messages behind the manipulation. However, surprisingly, the explanation also had an opposite (e.g.,negative) effect on users' feeling/sentiment toward the subjects in the images. Based on these results, we discuss open-ended questions which could serve as the basis for future research in this area.
Demo: Bi-static Scatter Underwater Acoustic Communications

Scatter radio achieves communication by reflection and requires low-cost and low-power radio frequency (RF) front-ends, however RF does not propagate more than a few centimeters through water. In this demo, we show the feasibility of near-zero power underwater communications using passive sensor/tags in a bistatic topology to communicate sensor data by means of acoustic reflections. We present a non-classic bi-static scatter communications architecture, where the carrier emitter is an acoustic wave generator detached from an acoustic receiver. We built a tag prototype that consumes less than 4 mW for communications and less than 0.5 mW in sleep mode. In the demo, we will demonstrate low communication rates of 100 bps at small distances inside a small 10 gallon fish tank.
Numerical Analysis of Laminar Forced Convection in the Entrance Region of Tubes With Longitudinal Internal Fins

Steady, laminar, forced convection heat transfer in the thermal entrance region of internally finned tubes is investigated numerically for the case of fully developed hydrodynamics using the uniform heat input axially with uniform wall (tube fins) temperature cross-sectionally and uniform wall temperature axially and cross-sectionally thermal boundary conditions. Results are presented for 16 geometries including the local Nusselt number and developing length corresponding to each boundary condition. These results indicate that internal finning influences the thermal development in a complicated way, which makes it inappropriate to extend the smooth tube results to internally finned tubes on a hydraulic diameter basis.
Performance Analysis of Sweep-Spread Carrier (S2C) Modulation for Underwater Communications

In the last decades, underwater acoustic communications have seen a growing development with a variety of research as well as commercial applications, dealing with channel distortions, multipath and Doppler effects typical of underwater channels. A very robust modulation able to guarantee connectivity in harsh environments (where spectral efficient solutions such as OFDM can be prevented) is the so called sweep-spread carrier (S2C) modulation, which is based on the usage of a linearly time-varying carrier. Underwater modems based on S2C modulations have been patented and successfully adopted in real-world deployments. In this paper, we analyze the performance of S2C both in simulation and infield experiments, based on our own S2C implementation. We undertake extensive simulation experiments, quantitatively measuring the impact of a variety of modulation parameters (such as the sweep duration and the number of coded symbols per sweep), and under different channel characteristics (depth, range, Doppler speed, etc.). Moreover, we test the performances of the S2C modulation at sea, obtaining good results also in shallow waters.
Tunable Electronic and Magnetic Properties of T-CrTe2 Monolayer by Li Adsorption

Abstract Using first-principle calculations, we investigate the electronic and magnetic properties of Li-adsorbed T-CrTe2 monolayer. We demonstrate that Li adsorption turns the electronic properties mainly through electron doping and lattice expansion. As the adsorption concentration increases from 3.7% to 33.3%, the magnetic moment of Cr increases from 2.25 to 2. 98μB linearly. More interesting, the T-CrTe2 monolayer becomes ferromagnetic semiconductors with indirect band gaps under the tensile strain. While a tensile strain is applied, a transformation from metal to half-metal has been found. Our work provides an efficient strategy to seek magnetism and produce two-dimensional magnetic semiconductors and half-metals from metals.
Frequency Spectra of Acoustic Fluctuations Caused by Oceanic Internal Waves and Other Finestructure

The frequency spectrum of log‐amplitude fluctuations is substantially modified (flattened) by a previously neglected effect: the vertical advection of short internal waves by the more energetic internal waves with large vertical wavelength. The log‐amplitude spectrum is sensitive to this vertical advection and to curvature of the equilibrium sound ray, whereas the phase spectrum is not. Noninternal‐wave ’’frozen’’ finestructure contributes to the log‐amplitude frequency spectrum through vertical advection, but not to the phase spectrum. The Cobb Seamount experiment is treated as an example; the spectrum of the modified theory agrees well with observations except at high frequency ( near the buoyancy frequency ).
Coding nucleic acid sequences with graph convolutional network

Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets.However, the highly variable lengths of nucleic acid sequences severely impair the presentation of sequences as input to the neural network. Genetic variations further complicate tasks that involve sequence comparison or alignment. Here, we propose a graph representation of nucleic acid sequences called gapped pattern graphs. These graphs can be transformed through a Graph Convolutional Network to form lower-dimensional embeddings for downstream tasks. On the basis of the gapped pattern graphs, we implemented a neural network model and demonstrated its performance in studying phage sequences. We compared our model with equivalent models based on other forms of input in performing four tasks related to nucleic acid sequences—phage and ICE discrimination, phage integration site prediction, lifestyle prediction, and host prediction. Other state-of-the-art tools were also compared, where available. Our method consistently outperformed all the other methods in various metrics on all four tasks. In addition, our model was able to identify distinct gapped pattern signatures from the sequences.
Link Prediction Method in Graph Objects by Auto Encoding in Graph Neural Networks

Link prediction problem is significant for a better understanding of the hidden or lost connections between objects in hierarchical structures like networks, for example, in social, business, biological, medical, and other domains. Recently, Graph Autoencoders (GAE) and Variational Graph Autoencoders (VGAE) deep neural networks (DNNs) emerged as effective tools for resolving various problems. In this paper, their variations were used to solve the link prediction problem for graph objects in the legal document context. For this purpose, the customized dataset in the shape of the hierarchical set of Ukrainian legal acts adopted by the Ukrainian parliament (Verkhovna Rada of Ukraine) and Ukrainian government (the Cabinet of Ministers of Ukraine) was constructed, and its exploratory data analysis (EDA) was performed. Several GAE and VGAE models were proposed and applied for the dataset, the comparison analysis was performed for all of the models considered, and a conclusion was made as to possible further improvements of the method proposed for other real-world graph data in various domains.