Miracle-dz/UniFAR-FTUs huggingface dataset:
A Metabolism-Related Gene Landscape Predicts Prostate Cancer Recurrence and Treatment Response

Background Prostate cancer (PCa) is the most common malignant tumor in men. Although clinical treatments of PCa have made great progress in recent decades, once tolerance to treatments occurs, the disease progresses rapidly after recurrence. PCa exhibits a unique metabolic rewriting that changes from initial neoplasia to advanced neoplasia. However, systematic and comprehensive studies on the relationship of changes in the metabolic landscape of PCa with tumor recurrence and treatment response are lacking. We aimed to construct a metabolism-related gene landscape that predicts PCa recurrence and treatment response. Methods In the present study, we used differentially expressed gene analysis, protein–protein interaction (PPI) networks, univariate and multivariate Cox regression, and least absolute shrinkage and selection operator (LASSO) regression to construct and verify a metabolism-related risk model (MRM) to predict the disease-free survival (DFS) and response to treatment for PCa patients. Results The MRM predicted patient survival more accurately than the current clinical prognostic indicators. By using two independent PCa datasets (International Cancer Genome Consortium (ICGC) PCa and Taylor) and actual patients to test the model, we also confirmed that the metabolism-related risk score (MRS) was strongly related to PCa progression. Notably, patients in different MRS subgroups had significant differences in metabolic activity, mutant landscape, immune microenvironment, and drug sensitivity. Patients in the high-MRS group were more sensitive to immunotherapy and endocrine therapy, while patients in the low-MRS group were more sensitive to chemotherapy. Conclusions We developed an MRM, which might act as a clinical feature to more accurately assess prognosis and guide the selection of appropriate treatment for PCa patients. It is promising for further application in clinical practice.
Influences of Tidal Flat and Thermal Discharge on Heat Dynamics in Xiangshan Bay

Water temperature in estuaries is sensitive to thermal discharges and expansive tidal flats; as such, this parameter is essential in maintaining estuarine ecosystem. Semi-enclosed water bodies with poor water exchange easily accumulate heat. This is especially true for Xiangshan Bay, which contains two power plants and a large area of tidal flats. This bay was used as an example to study water temperature and heat dynamics, considering the thermal discharge and tidal flats. This study developed and validated a three-dimensional hydro-heat flux numerical model using field data on tidal elevation, currents, water temperature, and tidal flat temperature. The Finite Volume Community Ocean Model combines an accurate thermal discharge model with the air-water-tidal flat heat flux model. The findings showed that thermal discharge provides heat to the bay in summer and winter, and increases the water temperature of the entire bay by 0.7°C in summer, while maintaining water temperature at 0.52°C in winter. The atmosphere and open seas had greater impacts on heat in the bay in winter and summer. The atmosphere and tidal flats provided heat to the bay in summer and absorbed heat from the bay during winter; the opposite was true for the open sea. The effect of tidal flats in summer is less than that in winter, and provides 1.31 × 1013 J of heat to the bay in summer, while taking 8.63 × 1013 J of heat from the bay in winter. This study provides a comprehensive understanding of the effects of tidal flats and thermal discharge on water temperature and heat in macro-tidal bays and estuaries; its results are applicable to similar bays around the world.
Modification Patterns of DNA Methylation-Related lncRNAs Regulating Genomic Instability for Improving the Clinical Outcomes and Tumour Microenvironment Characterisation of Lower-Grade Gliomas

Background: DNA methylation is an important epigenetic modification that affects genomic instability and regulates gene expression. Long non-coding RNAs (lncRNAs) modulate gene expression by interacting with chromosomal modifications or remodelling factors. It is urgently needed to evaluate the effects of DNA methylation-related lncRNAs (DMlncRNAs) on genome instability and further investigate the mechanism of action of DMlncRNAs in mediating the progression of lower-grade gliomas (LGGs) and their impact on the immune microenvironment. Methods: LGG transcriptome data, somatic mutation profiles and clinical features analysed in the present study were obtained from the CGGA, GEO and TCGA databases. Univariate, multivariate Cox and Lasso regression analyses were performed to establish a DMlncRNA signature. The KEGG and GO analyses were performed to screen for pathways and biological functions associated with key genes. The ESTIMATE and CIBERSORT algorithms were used to determine the level of immune cells in LGGs and the immune microenvironment fraction. In addition, DMlncRNAs were assessed using survival analysis, ROC curves, correlation analysis, external validation, independent prognostic analysis, clinical stratification analysis and qRT-PCR. Results: We identified five DMlncRNAs with prognostic value for LGGs and established a prognostic signature using them. The Kaplan–Meier analysis revealed 10-years survival rate of 10.10% [95% confidence interval (CI): 3.27–31.40%] in high-risk patients and 57.28% (95% CI: 43.17–76.00%) in low-risk patients. The hazard ratio (HR) and 95% CI of risk scores were 1.013 and 1.009–1.017 (p < 0.001), respectively, based on the univariate Cox regression analysis and 1.009 and 1.004–1.013 (p < 0.001), respectively, based on the multivariate Cox regression analysis. Therefore, the five-lncRNAs were identified as independent prognostic markers for patients with LGGs. Furthermore, GO and KEGG analyses revealed that these lncRNAs are involved in the prognosis and tumorigenesis of LGGs by regulating cancer pathways and DNA methylation. Conclusion: The findings of the study provide key information regarding the functions of lncRNAs in DNA methylation and reveal that DNA methylation can regulate tumour progression through modulation of the immune microenvironment and genomic instability. The identified prognostic lncRNAs have high potential for clinical grouping of patients with LGGs to ensure effective treatment and management.
Overexpression of the Hsa21 Transcription Factor RUNX1 Modulates the Extracellular Matrix in Trisomy 21 Cells

Down syndrome is a neurodevelopmental disorder frequently characterized by other developmental defects, such as congenital heart disease. Analysis of gene expression profiles of hearts from trisomic fetuses have shown upregulation of extracellular matrix (ECM) genes. The aim of this work was to identify genes on chromosome 21 potentially responsible for the upregulation of ECM genes and to pinpoint any functional consequences of this upregulation. By gene set enrichment analysis of public data sets, we identified the transcription factor RUNX1, which maps to chromosome 21, as a possible candidate for regulation of ECM genes. We assessed that approximately 80% of ECM genes overexpressed in trisomic hearts have consensus sequences for RUNX1 in their promoters. We found that in human fetal fibroblasts with chromosome 21 trisomy there is increased expression of both RUNX1 and several ECM genes, whether located on chromosome 21 or not. SiRNA silencing of RUNX1 reduced the expression of 11 of the 14 ECM genes analyzed. In addition, collagen IV, an ECM protein secreted in high concentrations in the culture media of trisomic fibroblasts, was modulated by RUNX1 silencing. Attenuated expression of RUNX1 increased the migratory capacity of trisomic fibroblasts, which are characterized by a reduced migratory capacity compared to euploid controls.
Exploring Orthographic Representation in Chinese Handwriting: A Mega-Study Based on a Pedagogical Corpus of CFL Learners

Writing and reading are closely related and are thus likely to have a common orthographic representation. A fundamental question in the literature on the production of written Chinese characters concerns the structure of orthographic representations. We report on a Chinese character handwriting pedagogical corpus involving a class of 22 persons, 232 composite character types, 1,913 tokens, and 13,057 stroke records, together with the inter-stroke interval (ISI), which reflects the parallel processing of multilevel orthographic representation during the writing execution, and 50 orthographic variables from the whole character, logographeme, and stroke. The results of regression analyses show that orthographic representation has a hierarchy and that different representational levels are active simultaneously. In the multilevel structure of orthographic representation, the representation of the logographeme is absolutely dominant. Writing and reading have both commonalities and individual differences in their orthographic representations. The online processing of the logographeme unit probably occurs at the ISI before the initial stroke of the current logographeme, which may also cascade to the first subsequent logographeme. In addition, we propose a new effective character structure unit for describing orthographic complexity.
Editorial: Metabolism and Epigenetics

Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Barcelona, Spain, Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China, Oncology Discovery, AbbVie Inc., San Francisco, IL, United States, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, , United States, Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
PaP1, a Broad-Spectrum Lysin-Derived Cationic Peptide to Treat Polymicrobial Skin Infections

Most skin infections, including those complicating burns, are polymicrobial involving multiple causative bacteria. Add to this the fact that many of these organisms may be antibiotic-resistant, and a simple skin lesion or burn could soon become life-threatening. Membrane-acting cationic peptides from Gram-negative bacteriophage lysins can potentially aid in addressing the urgent need for alternative therapeutics. Such peptides natively constitute an amphipathic region within the structural composition of these lysins and function to permit outer membrane permeabilization in Gram-negative bacteria when added externally. This consequently allows the lysin to access and degrade the peptidoglycan substrate, resulting in rapid hypotonic lysis and bacterial death. When separated from the lysin, some of these cationic peptides kill sensitive bacteria more effectively than the native molecule via both outer and cytoplasmic membrane disruption. In this study, we evaluated the antibacterial properties of a modified cationic peptide from the broad-acting lysin PlyPa01. The peptide, termed PaP1, exhibited potent in vitro bactericidal activity toward numerous high priority Gram-positive and Gram-negative pathogens, including all the antibiotic-resistant ESKAPE pathogens. Both planktonic and biofilm-state bacteria were sensitive to the peptide, and results from time-kill assays revealed PaP1 kills bacteria on contact. The peptide was bactericidal over a wide temperature and pH range and could withstand autoclaving without loss of activity. However, high salt concentrations and complex matrices were found to be largely inhibitory, limiting its use to topical applications. Importantly, unlike other membrane-acting antimicrobials, PaP1 lacked cytotoxicity toward human cells. Results from a murine burn wound infection model using methicillin-resistant Staphylococcus aureus or multidrug-resistant Pseudomonas aeruginosa validated the in vivo antibacterial efficacy of PaP1. In these studies, the peptide enhanced the potency of topical antibiotics used clinically for treating chronic wound infections. Despite the necessity for additional preclinical drug development, the collective data from our study support PaP1 as a potential broad-spectrum monotherapy or adjunctive therapy for the topical treatment of polymicrobial infections and provide a foundation for engineering future lysin-derived peptides with improved antibacterial properties.
Sulfur Stable Isotope Discrimination in Rice: A Sulfur Isotope Mass Balance Study

The use of sulfur (S) stable isotopes to study S metabolism in plants is still limited by the relatively small number of studies. It is generally accepted that less S stable isotope discrimination occurs during sulfate (SO42–) uptake. However, S metabolism and allocation are expected to produce separations of S stable isotopes among the different plant S pools and organs. In this study, we measured the S isotope composition of the main S pools of rice plants grown under different SO42– availabilities in appropriate closed and open hydroponic-plant systems. The main results indicate that fractionation against 34S occurred during SO42– uptake. Fractionation was dependent on the amount of residual SO42– in the solution, showing a biphasic behavior related to the relative expression of two SO42– transporter genes (OsSULTR1;1 and OsSULTR1;2) in the roots. S isotope separations among S pools and organs were also observed as the result of substantial S isotope fractionations and mixing effects occurring during SO42– assimilation and plant S partitioning. Since the S stable isotope separations conserve the memory of the physiological and metabolic activities that determined them, we here underline the potential of the 32S/34S analysis for the detailed characterization of the metabolic and molecular processes involved in plant S nutrition and homeostasis.
Deep Learning-Based Classification of Inflammatory Arthritis by Identification of Joint Shape Patterns—How Neural Networks Can Tell Us Where to “Deep Dive” Clinically

Objective: We investigated whether a neural network based on the shape of joints can differentiate between rheumatoid arthritis (RA), psoriatic arthritis (PsA), and healthy controls (HC), which class patients with undifferentiated arthritis (UA) are assigned to, and whether this neural network is able to identify disease-specific regions in joints. Methods We trained a novel neural network on 3D articular bone shapes of hand joints of RA and PsA patients as well as HC. Bone shapes were created from high-resolution peripheral-computed-tomography (HR-pQCT) data of the second metacarpal bone head. Heat maps of critical spots were generated using GradCAM. After training, we fed shape patterns of UA into the neural network to classify them into RA, PsA, or HC. Results Hand bone shapes from 932 HR-pQCT scans of 617 patients were available. The network could differentiate the classes with an area-under-receiver-operator-curve of 82% for HC, 75% for RA, and 68% for PsA. Heat maps identified anatomical regions such as bare area or ligament attachments prone to erosions and bony spurs. When feeding UA data into the neural network, 86% were classified as “RA,” 11% as “PsA,” and 3% as “HC” based on the joint shape. Conclusion We investigated neural networks to differentiate the shape of joints of RA, PsA, and HC and extracted disease-specific characteristics as heat maps on 3D joint shapes that can be utilized in clinical routine examination using ultrasound. Finally, unspecific diseases such as UA could be grouped using the trained network based on joint shape.
Effects of internal components on designing MIMO terminal antennas using characteristic modes

The Theory of Characteristic Modes has been shown capable of facilitating the development of many high-quality antennas through providing the characteristic modes (CMs) inherent to a structure. The CMs will change if the structure is altered; this property has been used to adapt terminal antennas, enabling good MIMO performance in compact structures. Previously these designs focused on altering the terminal structure without consideration into the effects of essential internal components on the desired CMs. Components such as touch screens, cameras, microphones, and batteries will change the CMs of the structure, which can in turn lead to the CM-based MIMO antennas to become non-orthogonal or non-resonant. Until now, relatively little work has been done to analyze the impact of these internal components on CM-based antennas. This article studies the effects internal components on the CMs of a MIMO terminal chassis, and how these effects can be mitigated. (Less)
Evaluation of the anesthetic depth and bispectral index during propofol sequential target-controlled infusion in dogs

Background and Aim: The use of anesthetic infusions based on pharmacokinetic values associated with anesthetic plan and bispectral index in dogs have not been well-documented in the literature. This study aimed to evaluate the bispectral index (BIS) change based on pre-propofol and establish clinical anesthetic depth changes during propofol sequential target-controlled infusion (STCI) in dogs with a plasma target of 5 μg/mL. Materials and Methods: Twenty healthy male dogs aged 1-3 years and weighing 9.8-44 kg were recruited. These dogs were pre-medicated intramuscularly with methadone (0.2 mg/kg) and acepromazine (0.03 mg/kg). After 30 min, propofol anesthetic induction and maintenance were initiated using STCI according to dog pharmacokinetic (PK) parameters. Subsequently, the target plasma concentration of propofol was set at 5 μg/mL for both anesthetic induction and the 120 min maintenance. Then, TivaTrainer v.9. 1 software was used to calculate anesthetic infusion rates in a TCI plasmatic concentration mode using the PKs model optimized by covariates for propofol TCI in dogs. The BIS value was recorded every 5 min from the beginning of induction until the end of anesthesia. Finally, analysis of variance was performed on numerical data using the Friedman test, followed by the Bonferroni adjustment (p<0.05). Results: A statistical difference was observed between the baseline BIS value (T0), with a median value of 84.5 (81-97), and BIS after every 15 min (T15) of inducing anesthesia. Surgical anesthetic depth was also reached in 18 of 20 dogs after 10 min of infusion and in all dogs after 20 min, with a median BIS value of 72 (53-89) at the time of surgical anesthesia depth. Results also showed no BIS variation (p<0.05) between anesthetic moments after anesthetic induction with a substantial amplitude of BIS in the surgical anesthetic depth. Moreover, the maximum depth of anesthesia in all dogs by clinical evaluation was reached after 20 min of anesthesia and then remained stable throughout the anesthetic period. Conclusion: This study suggested that most dogs (90%) attained a surgical depth of anesthesia within 15 min of STCI onset, with a plasma target of 5 μg/mL and no change in anesthetic depth throughout the period anesthesia lasted. Furthermore, median BIS values remained high even after dogs reached the surgical depth of anesthesia, indicating that the comparison of BIS values of dogs and humans should not be considered for classifying anesthetic and hypnotic depths in dogs.
Polymorphism of the heat shock protein 70 gene in indigenous chickens from different agro-climatic zones in Kenya

Climate change leads to heat stress, which is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance in poultry is crucial because it may identify genetic lines that can withstand heat stress. This study aimed to investigate polymorphisms in the heat shock protein 70 (HSP70) gene in indigenous chicken. In Kenya, we collected 277 blood samples from selected chicken ecotypes from Turkana, Western Highlands, Lake Victoria, and Lamu and extracted their genomic DNA. The first 360 bp region of HSP70 was amplified using conventional PCR and then sequenced using the Sanger ABI 3730 method. The detailed analysis of the HSP70 gene fragment revealed three HSP70 haplotypes (GC, AC, and AG). Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC, which dominated in Turkana ecotype. High HSP70 nucleotide diversity indices were recorded in the Turkana ecotype, while low values were recorded in the Lamu ecotype. In addition, most of the HSP70 gene variations occurred within populations. Our study provides the first account of the HSP70 polymorphisms in indigenous chickens in Kenya. The results obtained should pave the way for further in-depth studies on genes involved in heat stress regulation.
Utilization of Biochar and Mycorrhiza to Increase the Absorption of Elemental Nutrients of Cayenne Chili (Capsicum frutescens L.)

This study aimed to study the relationship between biochar as a soil enhancer and mycorrhizal dose on the nutrient uptake of cayenne plants. The experiment was done in a split-plot design with a randomized block design. The main plot was a vesicular-arbuscular mycorrhiza or VAM (m) with three levels: 10 g plant mycorrhiza (m 1 ), 15 g plant mycorrhiza (m 2 ), and 20 g plant mycorrhiza (m 3 ). The subplot was a biochar composition as soil enhancer (b) with three levels: 50% rice husk biochar + 25% soil + 25% sand (b 1 ), 25% wood biochar + 25% soil + 50% sand (b 2 ), and 50% wood biochar + 25% soil + 25% rice husk biochar (b 3 ). Each level of the VAM dose factor was combined with each level of the biochar composition; each combination was repeated three times, accounting for 27 experimental units. The phosphorus uptake, potassium uptake, and fresh root weight positively correlated to the percentage of mycorrhizal infections. The combination treatment of 20 g plant mycorrhiza and 50% rice husk biochar + 25% soil + 25% sand; 15 g plant mycorrhiza with 50% wood biochar + 25% soil + 25% rice husk biochar; and 20 g plant mycorrhiza are the best planting medium.
Do thiazolidine compounds act on intracellular amastigotes of Trypanosoma cruzi? A systematic review

Benznidazole (Bdz) are the drug of choice to treat Chagas Disease. However, the drug causes several side effects, and Trypanosoma cruzi, the etiological agent of Chagas disease, can be less susceptible to the action of drugs in the chronic phase, due to its reduced metabolism and dormancy in tissues. Thus, using compounds that are lethal to amastigote forms, which are prevalent in the Chagas disease chronic phase, is essential for the success of therapy. We propose to evaluate, though a systematic review, the efficacy of thiazolidine and its imidazolidine derivatives against T. cruzi intracellular amastigotes, and to compare the results with those for Bdz, A systematic search was made on eight English Language Systematic Databases - Science Direct, Scopus, Pubmed, Google Scholar, LILACS, Scielo, Trip Database and Cochrane, to collect studies, without a time scale. IC50 values, cytotoxic effects (CC50), a selective index (SI), the mechanism of action of each compound and the length of treatment was included in this review to evaluate the effectiveness of each compound. The compound 2-Iminothiazolidin-4-one 18 was more effective than Bdz, as it affected intracellular amastigotes by making a structural modification in the parasite, and by inhibiting cruzain, being promising for the antichagasic therapy.
Demonstration of a Fully Integrated 85-Gbit/s ETDM Receiver in a Transmission Experiment over 500 km of Standard Fiber

We performed optical transmission experiments proving the feasibility of a fully integrated 85-Gbit/s electrical time division multiplex (ETDM) receiver, which incorporates a 1:2-demultiplexer and a clock & data recovery (CDR) unit, including the voltage-controlled oscillator (VCO), on a single chip. Error free transmission was demonstrated. Index Terms – ETDM, high-speed integrated circuits, optical transmission, 100-Gbit/s Ethernet