Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon gamma-related gene signature based on anti-tumor immunity predicts glioma patient prognosis

Background: Glioma is the most common primary tumor of the central nervous system. The conventional glioma treatment strategies include surgical excision and chemo- and radiation-therapy. Interferon Gamma (IFN-γ) is a soluble dimer cytokine involved in immune escape of gliomas. In this study, we sought to identify IFN-γ-related genes to construct a glioma prognostic model to guide its clinical treatment. Methods: RNA sequences and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA) and the China Glioma Genome Atlas (CGGA). Using univariate Cox analysis and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm, IFN-γ-related prognostic genes were selected to construct a risk scoring model, and analyze its correlation with the clinical features. A high-precision nomogram was drawn to predict prognosis, and its performance was evaluated using calibration curve. Finally, immune cell infiltration and immune checkpoint molecule expression were analyzed to explore the tumor microenvironment characteristics associated with the risk scoring model. Results: Four out of 198 IFN-γ-related genes were selected to construct a risk score model with good predictive performance. The expression of four IFN-γ-related genes in glioma tissues was significantly increased compared to normal brain tissue (p < 0.001). Based on ROC analysis, the risk score model accurately predicted the overall survival rate of glioma patients at 1 year (AUC: The Cancer Genome Atlas 0.89, CGGA 0.59), 3 years (AUC: TCGA 0.89, CGGA 0.68), and 5 years (AUC: TCGA 0.88, CGGA 0.70). Kaplan-Meier analysis showed that the overall survival rate of the high-risk group was significantly lower than that of the low-risk group (p < 0.0001). Moreover, high-risk scores were associated with wild-type IDH1, wild-type ATRX, and 1P/19Q non-co-deletion. The nomogram predicted the survival rate of glioma patients based on the risk score and multiple clinicopathological factors such as age, sex, pathological grade, and IDH Status, among others. Risk score and infiltrating immune cells including CD8 T-cell, resting CD4 memory T-cell, regulatory T-cell (Tregs), M2 macrophages, resting NK cells, activated mast cells, and neutrophils were positively correlated (p < 0.05). In addition, risk scores closely associated with expression of immune checkpoint molecules such as PD-1, PD-L1, CTLA-4, LAG-3, TIM-3, TIGIT, CD48, CD226, and CD96. Conclusion: Our risk score model reveals that IFN-γ -associated genes are an independent prognostic factor for predicting overall survival in glioma, which is closely associated with immune cell infiltration and immune checkpoint molecule expression. This model will be helpful in predicting the effectiveness of immunotherapy and survival rate in patients with glioma.
Genome-wide analysis of the Populus trichocarpa laccase gene family and functional identification of PtrLAC23

Introduction Biofuel is a kind of sustainable, renewable and environment friendly energy. Lignocellulose from the stems of woody plants is the main raw material for “second generation biofuels”. Lignin content limits fermentation yield and is therefore a major obstacle in biofuel production. Plant laccase plays an important role in the final step of lignin formation, which provides a new strategy for us to obtain ideal biofuels by regulating the expression of laccase genes to directly gain the desired lignin content or change the composition of lignin. Methods Multiple sequence alignment and phylogenetic analysis were used to classify PtrLAC genes; sequence features of PtrLACs were revealed by gene structure and motif composition analysis; gene duplication, interspecific collinearity and Ka/Ks analysis were conducted to identify ancient PtrLACs; expression levels of PtrLAC genes were measured by RNA-Seq data and qRT-PCR; domain analysis combine with cis-acting elements prediction together showed the potential function of PtrLACs. Furthermore, Alphafold2 was used to simulate laccase 3D structures, proLAC23::LAC23-eGFP transgenic Populus stem transects were applied to fluorescence observation. Results A comprehensive analysis of the P. trichocarpa laccase gene (PtLAC) family was performed. Some ancient PtrLAC genes such as PtrLAC25, PtrLAC19 and PtrLAC41 were identified. Gene structure and distribution of conserved motifs clearly showed sequence characteristics of each PtrLAC. Combining published RNA-Seq data and qRT-PCR analysis, we revealed the expression pattern of PtrLAC gene family. Prediction results of cis-acting elements show that PtrLAC gene regulation was closely related to light. Through above analyses, we selected 5 laccases and used Alphafold2 to simulate protein 3D structures, results showed that PtrLAC23 may be closely related to the lignification. Fluorescence observation of proLAC23::LAC23-eGFP transgenic Populus stem transects and qRT-PCR results confirmed our hypothesis again. Discussion In this study, we fully analyzed the Populus trichocarpa laccase gene family and identified key laccase genes related to lignification. These findings not only provide new insights into the characteristics and functions of Populus laccase, but also give a new understanding of the broad prospects of plant laccase in lignocellulosic biofuel production.
Optimization of multi-temporal generation scheduling in power system under elevated renewable penetrations: A review

The traditional power generation mix and the geographical distribution of units have faced structural reform with the increasing renewables. The existing scheduling schemes confront the optimization challenges of multi-source collaborative and multi-temporal coordination. This paper reviews the optimization of generation scheduling in power systems with renewables integration in different time scales, which are medium- and long-term, short-term and real-time, respectively. First, the scheduling model and method are summarized. The connections and differences of the multi-source mathematic model with uncertainty, as well as the market mechanism, including thermal power, hydroelectric power, wind power, solar energy, and energy storage, are also indicated. Second, the scheduling algorithm and approach are sorted out from the two dimensions of certainty and uncertainty. The innovation and difference in algorithm between the traditional scheduling and the scheduling problem with renewables are presented. Meanwhile, the interaction and coupling relationship among the different time scales are pointed out in each section. The challenges and shortcomings of current research and references future directions are also provided for dispatchers.
Internal structure of intonational categories: The (dis)appearance of a perceptual magnet effect

The question of whether intonation events are speech categories like phonemes and lexical tones has long been a puzzle in prosodic research. In past work, researchers have studied categoricality of pitch accents and boundary tones by examining perceptual phenomena stemming from research on phoneme categories (i.e., intonation boundary effects—peaks in discrimination sensitivity at category boundaries, perceptual magnet effects—sensitivity minima near the best exemplar or prototype of a category). Both lines of research have yielded mixed results. However, boundary effects are not necessarily related to categoricality of speech. Using improved methodology, the present study examines whether pitch accents have domain-general internal structure of categories by testing the perceptual magnet effect. Perceived goodness and discriminability of re-synthesized productions of Dutch rising pitch accent (L*H) were evaluated by native speakers of Dutch in three experiments. The variation between these stimuli was quantified using a polynomial-parametric modeling approach. A perceptual magnet effect was detected: (1) rated “goodness” decreased as acoustic-perceptual distance relative to the prototype increased (Experiment 1), and (2) equally spaced items far from the prototype were more frequently discriminated than equally spaced items in the neighborhood of the prototype (Experiment 2). These results provide first evidence for internal structure of pitch accents, similar to that found in color and phoneme categories. However, the discrimination accuracy gathered here was lower than that reported for phonemes. The discrimination advantage in the neighborhood far from the prototype disappeared when participants were tested on a very large number of stimuli (Experiment 3), similar to findings on phonemes and different from findings for lexical tones in neutral network simulations of distributional learning. These results suggest a more transient nature of the perceptual magnet effect in the perception of pitch accents and arguably weaker categoricality of pitch accents, compared to that of phonemes and in particular of lexical tones.
Ubiquitin-binding site 1 of pathogenic ataxin-3 regulates its toxicity in Drosophila models of Spinocerebellar Ataxia Type 3

Spinocerebellar Ataxia Type 3 (SCA3) is a member of the family of polyglutamine (polyQ) diseases that are caused by anomalous CAG triplet repeat expansions in several genes. SCA3 results from abnormal polyQ expansion in the deubiquitinase (DUB), ataxin-3 (Atxn3). To understand the role of the different domains of mutant Atxn3 on its pathogenicity, with the hope that they can be explored for therapeutic interventions, we have systematically studied their individual and collective effects on its toxicity. One such domain is ubiquitin-binding site 1 (UbS1) on the catalytic domain of Atxn3; UbS1 is necessary for the enzymatic activity of Atxn3. Here, we investigated the importance of UbS1 on the toxicity of pathogenic Atxn3. We generated transgenic Drosophila melanogaster lines that express polyQ-expanded Atxn3 with and without a functional UbS1. We found that mutating UbS1 markedly exacerbates the toxicity of pathogenic Atxn3. Additional studies indicated that UbS1 regulates the toxicity of Atxn3 not by affecting its aggregation or sub-cellular localization, but by impacting its role in ubiquitin processing. Our findings provide additional insights into the role of Atxn3’s domains in the pathogenicity of SCA3.
Retrospective analysis of longitudinal melanonychia: A Chinese experience

Objective We aimed to analyze the clinical and histopathologic characteristics of longitudinal melanonychia (LM), explore the differences between adults and children, and propose some recommendations. Methods Data on pigmentation, lentigo, subungual melanoma (SUM), and nail matrix nevus (NMN) were acquired for comparison. Results Lesions on thumbs in the children’s group were significantly fewer (p = 0.006) than in adults. Lesions on little fingers in children were more than in adults; the difference was statistically significant (p = 0.025). The widths of bands in adults were wider than in children (p < 0.001), and the duration and width were positively correlated (r = 0.474). There was more pigmentation in adults than in children; the difference was statistically significant (p = 0.005). NMN was reported in 56.1% children and 34.3% adults; the difference was statistically significant (p = 0.005). Adults had six SUM cases, whereas none in children; the difference was statistically significant (p = 0.006). The recurrence rate in adults was significantly higher than in children (p = 0.019). Conclusion The widths of bands increase with the course, indicating that LM may be progressive. The four pathological types have different distributions with age, and each type requires different treatment. The lower recurrence rate in children suggests that LM needs diagnosis and appropriate treatment as soon as possible.
Gardnerella subgroup dominant microbiomes are associated with divergent cervicovaginal immune responses in a longitudinal cohort of Kenyan women

Most cervicovaginal microbiome-immunology studies to date have relied on 16S rDNA microbial profiling which does not resolve the molecular subgroups of Gardnerella, believed to be central to the pathogenesis of bacterial vaginosis (BV) and subsequent risk of HIV acquisition. Here we used the cpn60 universal target which in addition to other microbial taxa, resolves four Gardnerella subgroups, for cervicovaginal microbial profiling in a longitudinal cohort of Kenyan women to examine associations with cellular and soluble markers of inflammation and HIV susceptibility. Participants (N = 41) were sampled, contributing 362 samples for microbiome analysis. All non-Lactobacillus dominant microbial communities were associated with high pro-inflammatory cytokine levels. Divergent associations were observed among different Gardnerella subgroup dominated communities with respect to the chemokine IP-10. Specifically, Gardnerella subgroup A dominant and polymicrobial communities were associated with reduced concentrations of IP-10 in adjusted linear mixed models (p<0.0001), compared to microbial communities dominated by Lactobacillus (non-iners) species. However, these associations did not translate to significant differences in the proportion or absolute number of CCR5, HLA-DR and CD38 expressed on cervical CD4+ T- cells. These findings suggest that some associations between Gardnerella subgroup dominant microbiomes and mucosal immunity differ and are relevant for the study of BV-pathogenesis and understanding the mechanisms of BV-associated HIV risk.
Investigating the effects of gender and scaffolding in developing preschool children’s computational thinking during problem-solving with Bee-Bots

The research community has embraced computational thinking as an essential skill to develop in school and academic settings. Many researchers argue that computational thinking should be developed in the context of programming and robotic activities in all educational levels of education, starting from early childhood education. However, the factors related to developing computational thinking in preschool education are still under study. Furthermore, not too many empirical investigations provide evidence about the development of computational thinking in young children. The present study examined the effects of scaffolding and gender in developing young children’s sequencing and decomposition skills - two of the five skills that constitute computational thinking. The results indicated statistically significant effects about the type of scaffolding on children’s computational thinking in favor of the children assigned to the experimental groups. Lastly, boys outperformed girls on all occasions, indicating that gender effects exist. The authors conclude that researchers need to design teaching interventions in such a way so they have mathemagenic outcomes for all learners irrespective of gender. Finally, the authors conclude with implications and future research directions.
Fractional quantum Hall effect in optical lattices

In this research, we study the bosonic fractional quantum Hall (FQH) states in a system of ultracold bosons in a two-dimensional optical lattice in the presence of a synthetic magnetic field, described by the bosonic Harper–Hofstadter Hamiltonian. We use the cluster Gutzwiller mean-field and exact diagonalization techniques in our work. We obtain incompressible states as ground states at various filling factors similar to those of the FQH states. We focus in particular on the ν = 1/2 FQH state, and it is characterized by the two-point correlation function and the many-body Chern number. We further investigate the effect of dipolar interaction on the ν = 1/2 FQH state. We find that the dipolar interaction stabilizes the FQH state against the competing superfluid state.
The impact of gum-chewing on postoperative ileus following gynecological cancer surgery: A systematic review and meta-analysis of randomized controlled trials

Objective To assess the effect and safety of gum-chewing on the prevention of postoperative ileus after gynecological cancer surgery. Methods We conducted a systematic review of randomized controlled trials (RCTs) published between 2000 and 2022 in English and Chinese, using the EBSCO, Web of Science, Scopus, Cochrane Central Register of Controlled Trials (Cochrane database), PubMed, Medline (via Ovid), Chinese National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database, and Wan Fang databases. A total of 837 studies were screened using Endnote software, and those that met the inclusion criteria were selected for analysis. The main outcome of interest was the incidence of postoperative ileus, and secondary outcomes included time to first flatus, time to first bowel movement, and length of hospital stay. Results Two authors extracted data and performed quality assessment independently. The review included six RCTs with a total of 669 patients. Compared with routine care, gum-chewing could significantly reduce the incidence of postoperative ileus (RR 0.46, 95% CI: 0.30, 0.72, P=0.0006), shorten the time to first flatus (WMD -9.58, 95% CI: -15.04, -4.12, P=0.0006), first bowel movement (WMD -11.31, 95% CI: -21.05, -1.56, P=0.02), and the length of hospital stay (WMD -1.53, 95% CI: -2.08, -0.98, P<0.00001). Conclusions Gum-chewing is associated with early recovery of gastrointestinal function after gynecological cancer surgery and may be an effective and harmless intervention to prevent postoperative ileus. Systemaic review registration https://www.crd. york.ac. uk/prospero/#searchadvanced, identifier CRD42022384346.
Stability analysis and numerical simulation of foundation in old goaf under building load

This study comprehensively analyzes the safety and stability of old goaf under construction engineering based on specific projects using a variety of research methods. The Beijing Mentougou mining area is used as the research background. The methods of field investigation, laboratory testing, engineering drilling, geophysical exploration, theoretical calculation, and numerical simulation are combined to quantitatively analyze the stability of the foundation and ground buildings in old goaf. The influence depth of the building load and height of the caving crack zone are calculated using the “three-zone theory” to judge if the goaf is at risk of activation. Further simulation is conducted using two types of finite element analysis software, which increases the reliability of the numerical analysis. The results demonstrate that uneven subsidence of approximately 100 mm occurs in the buildings and ground surface, and subsidence of approximately 50 mm occurs in the goaf roof. It is also proven that goaf affects the stability of the surrounding rock and building foundation. Finally, a goaf treatment scheme is proposed. The treatment effect is found to be remarkable through field tests and numerical simulations, ensuring the safety and stability of a building foundation. The combination of theoretical calculation and numerical simulation can effectively evaluate the safety and stability of the project under load, and has a strong promotion and application value. The research results meet the needs of engineering practice, and provide a great reference value for the rational utilization of the land above the old goaf in the Mentougou district of Beijing and similar mining cities, which has a good theoretical significance and application prospect.
Dietary oleic acid contributes to the regulation of food intake through the synthesis of intestinal oleoylethanolamide

Introduction Among the fatty acid ethanolamides (FAEs), oleoylethanolamide (OEA), linoleoylethanolamide (LEA), and palmitoylethanolamide (PEA) are reported to be involved in feeding regulation. In particular, OEA is well characterized as a satiety signal. Following food consumption, OEA is synthesized from oleic acid (OA) via an N-acyl phosphatidylethanolamine-specific phospholipase D-dependent pathway in the gastroenterocytes, and OEA induces satiety by recruiting sensory fibers. Thus, we hypothesized that dietary OA is an important satiety-inducing molecule. However, there has been no direct demonstration of the effect of dietary OA on satiety induction without the influence of the endogenous biosynthesis of OA from stearic acid (SA) or other FAEs. Methods In this study, we used two experimental diets to test our hypothesis: (i) an OA diet (OAD; 38.4 mg of OA/g and 7.2 mg of SA/g) and (ii) a low OA diet (LOAD; 3.1 mg of OA/g and 42.4 mg of SA/g). Results Relative to mice fed the OAD, mice fed the LOAD for two weeks exhibited reduced levels of jejunal OEA but not jejunal LEA and PEA. The LOAD-fed mice showed an increase in food intake and body weight gain. Moreover, LOAD-induced increase in food intake was immediately observed after the switch from the OAD, whereas these effects were diminished by the switch back to the OAD. Furthermore, treatment with OA and OEA diminished the effects of LOAD on food intake. Conclusion Collectively, these results show that dietary OA is a key factor in the reduction of food intake and increase in satiety mediated by OEA signaling.
High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca

Gastrodia elata f.glauca (G. elata) is a commonly used Chinese Medicinal Materials with great medicinal value. The medicinal plant and its endophytic bacteria are a symbiotic whole, and the endophytic bacteria are rich in species, and their metabolites are a treasure trove of natural compounds. However, there is a relative lack of analysis on the diversity, flora composition and network interactions of the endophytic bacteria of G. elata. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to reveal the core microbiota by examining the diversity and community structures of tuber endophytic bacteria in G. elata grown under different regions and exploring the effect of region on its endophytic bacteria. Here, 1,265 endophytic ASVs were found to coexist with G. elata tuber in Guizhou and Hubei. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria and Acdobacteriota. At the family level, the dominant family were Comamonadaceae, Nocardicaece, Xanthobacteraceae, and Burkholderiaceae. At the genus level, Delftia and Rhodococcus were represented the core microbiota in G. elata tuber, which served as the dominant genera that coexisted in all samples tested. Moreover, we found that the beta diversity of endophytic bacteria in G. elata tuber was higher level in the Guizhou region than Hubei region. Overall, this study results to provide a reference for screening active strains and interaction between plants and endophytic bacteria.
Faunal exploitation during the Proto-Zhou period in the Jing River Valley: Evidence from Sunjia and Xitou

This study examines faunal assemblages from the Proto-Zhou sites of Sunjia and Xitou, in the Jing River Valley (Central Shaanxi Province), to address questions concerning the exploitation of different animal resources in the context of the Shang-Zhou dynastic transition in the 11th century BCE. Although the assemblages from Sunjia and Xitou were small and sub-optimally preserved, this study demonstrates that the inclusion of such assemblages is essential to building upon our understanding of the human exploitation of animal resources. Our zooarchaeological analysis shows an increase in husbandry, with pig farming being complemented by extensive caprine and cattle herding. A diversified use of animal resources, and especially the larger number of bovids, could have been prompted by the need for a wider and more efficient exploitation of the immediate environment, in response to growing climatic deterioration, in addition to an increase in interactions with northern pastoral communities. Identified patterns of livestock biometry and relative taxonomic abundance show various degrees of agricultural engagement and a relatively complex livestock economy, suggesting the development of socio-economic complexity in the Jing River Valley in the late second millennium BCE.