Miracle-dz/UniFAR-FTUs huggingface dataset:
Theoretical Insight Into the Ultralong Room-Temperature Phosphorescence of Nonplanar Aromatic Hydrocarbon

Purely aromatic hydrocarbon materials with ultralong room-temperature phosphorescence (RTP) were reported recently, but which is universally recognized as unobservable. To reveal the inherent luminescent mechanism, two compounds, i.e., PT with a faint RTP and HD with strong RTP featured by nonplanar geometry, were chosen as a prototype to study their excited-state electronic structures by using quantum mechanics/molecular mechanics (QM/MM) model. It is demonstrated that the nonplanar ethylene brides can offer σ-electron to strengthen spin-orbit coupling (SOC) between singlet and triplet excited states, which can not only promote intersystem crossing (ISC) of S1→Tn to increase the population of triplet excitons, but also accelerate the radiative decay rate of T1→S0, and thus improving RTP. Impressively, the nonradiative decay rate only has a small increase, owing to the synergistic effect between the increase of SOC and the reduction of reorganization energy of T1→S0 caused by the restricted torsional motions of aromatic rings. Therefore, a bright and long-lived RTP was obtained in aromatic hydrocarbon materials with twisted structure. This work provided a new insight into the ultralong RTP in pure organic materials.
Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis

Iron (Fe) is an essential micronutrient that plays pivotal roles as electron donor and catalyst across organisms. In plants, variable, often insufficient Fe supply necessitates mechanisms that constantly attune Fe uptake rates and recalibrate cellular Fe homeostasis. Here, we show that short-term (0.5, 6, and 12 h) exposure of Arabidopsis thaliana plants to Fe deficiency triggered massive changes in gene activity governed by transcription and alternative splicing (AS), regulatory layers that were to a large extent mutually exclusive. Such preclusion was not observed for genes that are directly involved in the acquisition of Fe, which appears to be concordantly regulated by both expression and AS. Generally, genes with lower splice site strengths and higher intron numbers were more likely to be regulated by AS, no dependence was on gene architecture was observed for transcriptionally controlled genes. Conspicuously, specific processes were associated with particular genomic features and biased towards either regulatory mode, suggesting that genomic hardwiring is functionally biased. Early changes in splicing patterns were, in many cases, congruent with later changes in transcript or protein abundance, thus contributing to the pronounced transcriptome-proteome discordance observed in plants.
Species composition and distribution of Alcyonacea (Octocorallia) in the northern Persian Gulf

Abstract Studies concerning octocoral species from the Persian Gulf coral reefs are few. This study documents the diversity and abundance of octocoral communities from three islands in the north Persian Gulf, namely, Larak Island, Hengam Island and Qeshm Island. Belt transects were used to survey the octocoral communities at these islands. We used a rapid ecological assessment technique (REA) to assess the status and abundance of octocorals. Also, K Independent sample analysis was conducted on abundance and Shannon Diversity index data to determine if octocoral abundance and species diversity varied between islands. A total of 22 morphospecies, belonging to seven alcyonacean families, including Plexauridae, Ellisellidae, Alcyoniidae, Nephtheidae, Briareidae, Acanthogorgiidae and Subergorgiidae, were identified in this study. Statistical analysis indicated octocoral abundance and diversity at Larak Island reefs were higher than those around Hengam and Qeshm islands. The primary data presented in this study could serve as the baseline data for long-term biomonitoring programmes to estimate the status of octocorals in the Persian Gulf.
Identification of a Novel Prognostic Gene Signature From the Immune Cell Infiltration Landscape of Osteosarcoma

Background: The tumor microenvironment (TME) mainly comprises tumor cells and tumor-infiltrating immune cells mixed with stromal components. Latestresearch hasdisplayed that tumor immune cell infiltration (ICI) is associated with the clinical outcome of patients with osteosarcoma (OS). This work aimed to build a gene signature according to ICI in OS for predicting patient outcomes. Methods: The TARGET-OS dataset was used for model training, while the GSE21257 dataset was taken forvalidation. Unsupervised clustering was performed on the training cohort based on the ICI profiles. The Kaplan–Meier estimator and univariate Cox proportional hazards models were used to identify the differentially expressed genes between clusters to preliminarily screen for potential prognostic genes. We incorporated these potential prognostic genes into a LASSO regression analysis and produced a gene signature, which was next assessed with the Kaplan–Meier estimator, Cox proportional hazards models, ROC curves, IAUC, and IBS in the training and validation cohorts. In addition, we compared our signature to previous models. GSEAswere deployed to further study the functional mechanism of the signature. We conducted an analysis of 22 TICsfor identifying the role of TICs in the gene signature’s prognosis ability. Results: Data from the training cohort were used to generate a nine-gene signature. The Kaplan–Meier estimator, Cox proportional hazards models, ROC curves, IAUC, and IBS validated the signature’s capacity and independence in predicting the outcomes of OS patients in the validation cohort. A comparison with previous studies confirmed the superiority of our signature regarding its prognostic ability. Annotation analysis revealed the mechanism related to the gene signature specifically. The immune-infiltration analysis uncoveredkey roles for activated mast cells in the prognosis of OS. Conclusion: We identified a robust nine-gene signature (ZFP90, UHRF2, SELPLG, PLD3, PLCB4, IFNGR1, DLEU2, ATP6V1E1, and ANXA5) that can predict OS outcome precisely and is strongly linked to activated mast cells.
Testing the Interspecific Function of Female Common Cuckoo “Bubbling” Call

Female common cuckoo (Cuculus canorous) predator-like “bubbling” calls distract host parental attention and reduce the egg rejection rate. Such “bubbling” calls are also frequently used to attract males and deter territorial rivals in intraspecies contact, and these calls are an ancestral character in many cuckoo species. Although hosts have had sufficient time to become familiar with this call and evolve anti-parasitic strategies, why are the hosts fooled by this “bubbling” call? We propose two hypotheses. The first hypothesis proposes that call variation reduces the opportunity for host species to correctly assess cuckoo tricks. In contrast, the second hypothesis proposes that the cost of behavior may prevent the antiparasitic strategy from evolving. In the study, we tested the prerequisites of these hypotheses, by investigating whether cuckoo calls vary during the day and testing whether the predator-like calls suppress bird activities. Based on field recordings from three different areas, we found high overlap in the calls generated during different periods. Oriental great reed warblers (Acrocephalus orientalis), a host species, did not show different responses toward the playback of female common cuckoo calls generated before noon or afternoon. Based on bird count data, we found that predator-like call playback is insufficient for suppressing bird activities. Therefore, none of the prerequisites were supported by our field data. We discuss the potential reasons for our findings and hope to inspire more research examining female cuckoo vocalizations.
DNA Methylation Regulator-Meditated Modification Patterns Define the Distinct Tumor Microenvironment in Lung Adenocarcinoma

Background Epigenetic changes of lung adenocarcinoma (LUAD) have been reported to be a relevant factor in tumorigenesis and cancer progression. However, the molecular mechanisms responsible for DNA methylation patterns in the tumor immune-infiltrating microenvironment and in cancer immunotherapy remain unclear. Methods We conducted a global analysis of the DNA methylation modification pattern (DMP) and immune cell-infiltrating characteristics of LUAD patients based on 21 DNA methylation regulators. A DNA methylation score (DMS) system was constructed to quantify the DMP model in each patient and estimate their potential benefit from immunotherapy. Results Two DNA methylation modification patterns able to distinctly characterize the immune microenvironment characterization were identified among 513 LUAD samples. A lower DMS, characterized by increased CTLA-4/PD-1/L1 gene expression, greater methylation modifications, and tumor mutation burden, characterized a noninflamed phenotype with worse survival. A higher DMS, characterized by decreased methylation modification, a greater stromal-relevant response, and immune hyperactivation, characterized an inflamed phenotype with better prognosis. Moreover, a lower DMS indicated an increased mutation load and exhibited a poor immunotherapeutic response in the anti-CTLA-4/PD-1/PD-L1 cohort. Conclusion Evaluating the DNA methylation modification pattern of LUAD patients could enhance our understanding of the features of tumor microenvironment characterization and may promote more favorable immunotherapy strategies.
Natural Language Processing as an Emerging Tool to Detect Late-Life Depression

Late-life depression (LLD) is a major public health concern. Despite the availability of effective treatments for depression, barriers to screening and diagnosis still exist. The use of current standardized depression assessments can lead to underdiagnosis or misdiagnosis due to subjective symptom reporting and the distinct cognitive, psychomotor, and somatic features of LLD. To overcome these limitations, there has been a growing interest in the development of objective measures of depression using artificial intelligence (AI) technologies such as natural language processing (NLP). NLP approaches focus on the analysis of acoustic and linguistic aspects of human language derived from text and speech and can be integrated with machine learning approaches to classify depression and its severity. In this review, we will provide rationale for the use of NLP methods to study depression using speech, summarize previous research using NLP in LLD, compare findings to younger adults with depression and older adults with other clinical conditions, and discuss future directions including the use of complementary AI strategies to fully capture the spectrum of LLD.
Natural Compounds With Antimicrobial and Antiviral Effect and Nanocarriers Used for Their Transportation

Due to the increasing prevalence of life-threatening bacterial, fungal and viral infections and the ability of these human pathogens to develop resistance to current treatment strategies, there is a great need to find and develop new compunds to combat them. These molecules must have low toxicity, specific activity and high bioavailability. The most suitable compounds for this task are usually derived from natural sources (animal, plant or even microbial). In this review article, the latest and most promising natural compounds used to combat bacteria, filamentous fungi and viruses are presented and evaluated. These include plant extracts, essential oils, small antimicrobial peptides of animal origin, bacteriocins and various groups of plant compounds (triterpenoids; alkaloids; phenols; flavonoids) with antimicrobial and antiviral activity. Data are presented on the inhibitory activity of each natural antimicrobial substance and on the putative mechanism of action against bacterial and fungal strains. The results show that among the bioactive compounds studied, triterpenoids have significant inhibitory activity against coronaviruses, but flavonoids have also been shown to inhibit SARS-COV-2. The last chapter is devoted to nanocarriers used to improve stability, bioavailability, cellular uptake/internalization, pharmacokinetic profile and reduce toxicity of natural compunds. There are a number of nanocarriers such as liposomes, drug delivery microemulsion systems, nanocapsules, solid lipid nanoparticles, polymeric micelles, dendrimers, etc. However, some of the recent studies have focused on the incorporation of natural substances with antimicrobial/antiviral activity into polymeric nanoparticles, niosomes and silver nanoparticles (which have been shown to have intrinsic antimicrobial activity). The natural antimicrobials isolated from animals and microorganisms have been shown to have good inhibitory effect on a range of pathogens, however the plants remain the most prolific source. Even if the majority of the studies for the biological activity evaluation are in silico or in vitro, their internalization in the optimum nanocarriers represents the future of “green therapeutics” as shown by some of the recent work in the field.
Tissue-Resident-Memory CD8+ T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes

Tissue-resident-memory T cells (TRM) populate the body’s barrier surfaces, functioning as frontline responders against reencountered pathogens. Understanding of the mechanisms by which CD8TRM achieve effective immune protection remains incomplete in a naturally recurring human disease. Using laser capture microdissection and transcriptional profiling, we investigate the impact of CD8TRM on the tissue microenvironment in skin biopsies sequentially obtained from a clinical cohort of diverse disease expression during herpes simplex virus 2 (HSV-2) reactivation. Epithelial cells neighboring CD8TRM display elevated and widespread innate and cell-intrinsic antiviral signature expression, largely related to IFNG expression. Detailed evaluation via T-cell receptor reconstruction confirms that CD8TRM recognize viral-infected cells at the specific HSV-2 peptide/HLA level. The hierarchical pattern of core IFN-γ signature expression is well-conserved in normal human skin across various anatomic sites, while elevation of IFI16, TRIM 22, IFITM2, IFITM3, MX1, MX2, STAT1, IRF7, ISG15, IFI44, CXCL10 and CCL5 expression is associated with HSV-2-affected asymptomatic tissue. In primary human cells, IFN-γ pretreatment reduces gene transcription at the immediate-early stage of virus lifecycle, enhances IFI16 restriction of wild-type HSV-2 replication and renders favorable kinetics for host protection. Thus, the adaptive immune response through antigen-specific recognition instructs innate and cell-intrinsic antiviral machinery to control herpes reactivation, a reversal of the canonical thinking of innate activating adaptive immunity in primary infection. Communication from CD8TRM to surrounding epithelial cells to activate broad innate resistance might be critical in restraining various viral diseases.
In vitro antimicrobial and cytotoxic activity of Lippia origanoides essential oil against bacteria of potential health concern

Due to the growing resistance they develop of bacteria to drugs, the search for alternatives in natural products is considered important such as Lippia origanoides essential oil. Here, the antibacterial activity of the oil and two of its major chemical components were tested against bacteria of potential health concern. The cytotoxicity of these compounds was evaluated in human erythrocytes and Vero cells. 51 compounds were identified in the LOEO, being terpinen-4-ol, γ-Terpinene, citronellal and thymol the main. LOEO and thymol showed antibacterial activity from 904 μg/mL and 200 μg/mL, respectively. γ-Terpinene did not show activity any concentration tested. LOEO showed hemolysis at concentration of 3000 μg/mL and thymol at 100 μg/mL. LOEO and thymol showed cytotoxicity in the evaluated cell lines at 250 μg/mL and 100 μg/mL, respectively. These compounds have a moderate cytotoxicity so it’s considered necessary to study alternatives to reduce the in vitro cytotoxicity of these compounds.
Parasitoid Causes Cascading Effects on Plant-Induced Defenses Mediated Through the Gut Bacteria of Host Caterpillars

Koinobiont endoparasitoid wasps whose larvae develop inside a host insect alter several important facets of host physiology, potentially causing cascading effects across multiple trophic levels. For instance, the hijacking of the host immune responses may have effects on how insects interact with host plants and microbial associates. However, the parasitoid regulation of insect–plant–microbiome interactions is still understudied. In this study, we used the fall armyworm (FAW), Spodoptera frugiperda, and the braconid parasitoid Cotesia marginiventris to evaluate impacts of parasitism on the gut microbiome of FAW larvae, and respective maize plant defense responses. The level of reactive oxygen species and the microbial community in larval gut underwent significant changes in response to parasitism, leading to a significant reduction of Enterococcus, while elevating the relative abundance of Pseudomonas. FAW with parasitism had lower glucose oxidase (GOX) activity in salivary glands and triggered lower defense responses in maize plants. These changes corresponded to effects on plants, as Pseudomonas inoculated larvae had lower activity of salivary GOX and triggered lower defense responses in maize plants. Our results demonstrated that parasitism had cascading effects on microbial associates across trophic levels and also highlighted that insect gut bacteria may contribute to complex interrelationships among parasitoids, herbivores, and plants.
RhoA/ROCK-YAP/TAZ Axis Regulates the Fibrotic Activity in Dexamethasone-Treated Human Trabecular Meshwork Cells

High intraocular pressure (IOP) is a major risk factor for glaucoma, a leading cause of irreversible blindness. Abnormal fibrotic activity in the human trabecular meshwork (HTM) cells is considered to be partly responsible for the increased resistance of aqueous humor outflow and IOP. This study aimed to identify the fibrotic pathways using integrated bioinformatics and further elucidate their mechanism of regulating fibrotic activity in dexamethasone (DEX)-treated HTM cells. Microarray datasets from the GEO database were obtained and analyzed by GEO2R. Bioinformatics analyses, including GO and KEGG analyses, were performed to explore biological functions and signaling pathways of differentially expressed genes (DEGs). The fibrotic pathways and targets were determined by western blot, RT-qPCR, or immunofluorescence staining. The cellular elastic modulus was measured using an atomic force microscope. A total of 204 DEGs, partly enriched in fibrotic activity (collagen-containing ECM, fibroblast activation) and Rap1, Ras, TGF-β, and Hippo pathways, were identified. Experimental results showed that DEX induced fibrotic activity and regulated the expression of RhoA/ROCK in HTM cells. Similarly, the constitutively active RhoA (RhoAG14V) also promoted the fibrotic activity of HTM cells. Mechanistically, RhoAG14V induced the expression and nuclear translocation of YAP/TAZ to produce CTGF. Moreover, inhibition of ROCK or YAP decreased the expression of Collagen I and α-SMA proteins induced by DEX or RhoAG14V in HTM cells. In conclusion, these results indicate that RhoA/ROCK-YAP/TAZ axis plays a crucial role in regulating the fibrotic activity of DEX-treated HTM cells.
Expression Profiles and Functional Characterization of Chemosensory Protein 15 (HhalCSP15) in the Brown Marmorated Stink Bug Halyomorpha halys

Chemosensory proteins (CSPs) have been identified in the sensory tissues of various insect species and are believed to be involved in chemical communication in insects. However, the physiological roles of CSPs in Halyomorpha halys, a highly invasive insect species, are rarely reported. Here, we focused on one of the antennal CSPs (HhalCSP15) and determined whether it was involved in olfactory perception. Reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qRT-PCR) analysis showed that HhalCSP15 was enriched in nymph and male and female adult antennae, indicating its possible involvement in the chemosensory process. Fluorescence competitive binding assays revealed that three of 43 natural compounds showed binding abilities with HhalCSP15, including β-ionone (Ki=11.9±0.6μM), cis-3-hexen-1-yl benzoate (Ki=10.5±0.4μM), and methyl (2E,4E,6Z)-decatrienoate (EEZ-MDT; Ki=9.6±0.8μM). Docking analysis supported the experimental affinity for the three ligands. Additionally, the electrophysiological activities of the three ligands were further confirmed using electroantennography (EAG). EEZ-MDT is particularly interesting, as it serves as a kairomone when H. halys forages for host plants. We therefore conclude that HhalCSP15 might be involved in the detection of host-related volatiles. Our data provide a basis for further investigation of the physiological roles of CSPs in H. halys, and extend the olfactory function of CSPs in stink bugs.
Evidence and Potential Mechanisms of Jin-Gui Shen-Qi Wan as a Treatment for Type 2 Diabetes Mellitus: A Systematic Review and Meta-Analysis

Background: Type 2 diabetes mellitus (T2DM) is a subtype of diabetes mellitus characterized by progressive dysfunction of β-cell insulin secretion and insulin resistance. Jīn-Guì Shèn-Qì Wán (JGSQW) has for many years been widely used in clinical practice as a treatment for T2DM. However, its effect remains unknown. Objectives: This study aims to summarize the clinical evidence of the effect of JGSQW on glucose and lipid metabolism in T2DM and the potential mechanisms underlying this effect. Methods: Six databases were searched without language or publication status restrictions. Data were extracted to a predefined template for synthesis. Results: Fourteen studies with 1586 participants were included in this meta-analysis. All 14 studies were judged to be at high risk of bias. JGSQW is safe for T2DM patients. Pooled results indicated that combination treatment results in a reduction in glycated hemoglobin (HbA1c) (mean difference (MD) −0.49%; 95% CI −0.67 to −0.31), fasting blood glucose (FBG) (MD −0.84; 95% CI −1.19 to −0.49), and 2-hour postprandial glucose 2hBG (MD −1.38; 95% CI −1.60 to −1.16). No significant difference in glucose metabolism was observed between JGSQW and hypoglycemic agents. The available evidence was insufficient to determine the effects on lipid metabolism. Sensitivity analyses indicated that these results were robust. Conclusion: By combining the available evidence, we found that JGSQW is safe for T2DM patients. Compared with hypoglycemic agents alone, combination treatment with JGSQW enhances the effect on glucose metabolism in patients with T2DM. We found no difference in the efficacy of JGSQW alone compared to hypoglycemic agents alone. In terms of lipid metabolism, the current evidence is insufficient and too inconsistent for us to draw firm conclusions, so further studies are needed.