Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Soil aridification and desertification are particularly prominent in China’s karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H2O2), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4. 1.13, E3.2. 1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.
Downregulation of miR-211-5p Promotes Carboplatin Resistance in Human Retinoblastoma Y79 Cells by Affecting the GDNF–LIF Interaction

Purpose To investigate the role of the miR-211-5p-GDNF signaling pathway in carboplatin resistance of retinoblastoma Y79 cells and what factors it may be affected by. Methods A carboplatin-resistant retinoblastoma cell line (Y79R) was established in vitro. RNA-seq and microRNA-seq were constructed between Y79 and Y79R cells. RNA interference, RT-PCR, Western blot (WB), and flow cytometry were used to verify the expression of genes and proteins between the two cell lines. The TargetScan database was used to predict the microRNAs that regulate the target genes. STING sites and Co-Immunoprecipitation (COIP) were used to study protein–protein interactions. Results GDNF was speculated to be the top changed gene in the drug resistance in Y79R cell lines. Moreover, the speculation was verified by subsequent RT-PCR and WB results. When the expression of GDNF was knocked down, the IC50 of the Y79R cell line significantly reduced. GDNF was found to be the target gene of miR-211-5p. Downregulation of miR-211-5p promotes carboplatin resistance in human retinoblastoma Y79 cells. MiR-211-5p can regulate the expression of GDNF. Our further research also found that GDNF can bind to LIF which is also a secreted protein. Conclusion Our results suggest that downregulation of miR-211-5p promotes carboplatin resistance in human retinoblastoma Y79 cells, and this process can be affected by GDNF–LIF interaction. These results can provide evidence for the reversal of drug resistance of RB.
Influence of Elevated Temperatures on Resistance Against Phoma Stem Canker in Oilseed Rape

Cultivar resistance is an important tool in controlling pathogen-related diseases in agricultural crops. As temperatures increase due to global warming, temperature-resilient disease resistance will play an important role in crop protection. However, the mechanisms behind the temperature-sensitivity of the disease resistance response are poorly understood in crop species and little is known about the effect of elevated temperatures on quantitative disease resistance. Here, we investigated the effect of temperature increase on the quantitative resistance of Brassica napus against Leptosphaeria maculans. Field experiments and controlled environment inoculation assays were done to determine the influence of temperature on R gene-mediated and quantitative resistance against L. maculans; of specific interest was the impact of high summer temperatures on the severity of phoma stem canker. Field experiments were run for three consecutive growing seasons at various sites in England and France using twelve winter oilseed rape breeding lines or cultivars with or without R genes and/or quantitative resistance. Stem inoculation assays were done under controlled environment conditions with four cultivars/breeding lines, using avirulent and virulent L. maculans isolates, to determine if an increase in ambient temperature reduces the efficacy of the resistance. High maximum June temperature was found to be related to phoma stem canker severity. No temperature effect on stem canker severity was found for the cultivar ES Astrid (with only quantitative resistance with no known R genes). However, in the controlled environmental conditions, the cultivar ES Astrid had significantly smaller amounts of necrotic tissue at 20°C than at 25°C. This suggests that, under a sustained temperature of 25°C, the efficacy of quantitative resistance is reduced. Findings from this study show that temperature-resilient quantitative resistance is currently available in some oilseed cultivars and that efficacy of quantitative resistance is maintained at increased temperature but not when these elevated temperatures are sustained for a long period.
The Effect of Feedstock Concentration on the Microbial Community Dynamics During Textile Waste Composting

In this study, the effect of initial feedstock concentration on the microbial community structure and dynamics during textile waste composting processes was investigated using the next-generation sequencing approach. For this, three mixtures were prepared with different textile waste concentrations mixed with green waste and paper and cardboard waste for composting, to choose the proportion that will provide a mature final compost. A comprehensive characterization of the microbial communities associated with different textile waste concentrations during composting was achieved. It was noted that by increasing the concentration of textile waste, microbial communities (bacterial and fungal) change. Genera and species belonging to Actinobacteria, Firmicutes, Chloroflexia, Rozellomycota, Mortierellomycota, Aphelidiomycota, Ascomycota, and Mucoromycota were the most abundant in the mixtures containing either 40 or 60% of textile waste, whereas some of the species were absent at 80% of textile waste in the mix; this difference was also reflected by their enzymatic activities. Generally, these phyla are associated with composting, and they play a major role in recalcitrant molecular decaying. Ultimately, it can be concluded that the shift most likely occurred in microbial communities during composting probably owing to the interaction between changes in the nutrient concentration and microbial communities. This investigation proves that the concentration of textile waste significantly affects the microbial communities and demonstrates that a high concentration of textile waste is not suitable to grant a good maturity of compost.
Identification of a Novel Survival-Related circRNA–miRNA–mRNA Regulatory Network Related to Immune Infiltration in Liver Hepatocellular Carcinoma

Increasing studies have reported that circular RNAs (circRNAs) play critical roles in tumorigenesis and cancer progression. However, the underlying regulatory mechanisms of circRNA-related competing endogenous RNA (ceRNA) in liver hepatocellular carcinoma (LIHC) are still unclear. In the present study, we discovered dysregulated circRNAs through Gene Expression Omnibus (GEO) analysis and validated the expression of the top seven circRNAs with upregulated expression by qRT–PCR and Sanger sequencing. Then, the Cancer-Specific CircRNA Database (CSCD) was used to predict the downstream miRNAs of seven circRNAs, and expression and survival analyses through The Cancer Genome Atlas (TCGA) were performed to identify the key miRNA in LIHC. Thereafter, the hsa_circ_0017264-hsa-miR-195–5p subnetwork was successfully constructed. Subsequently, we predicted downstream target genes of hsa-miR-195–5p with TargetScan, miRDB, and mirtarbase and overlapped them with differentially expressed mRNAs to obtain 21 target genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to predict the biological and functional roles of these target genes. Finally, with Pearson correlation and prognostic value analysis, a survival-related hsa_circ_0017264-hsa-miR-195-5p-CHEK1/CDC25A/FOXK1 axis was established. Gene set enrichment analysis (GSEA) was performed to determine the function of CHEK1/CDC25A/FOXK1 in the ceRNA network. Moreover, immune infiltration analysis revealed that the ceRNA network was markedly associated with the levels of multiple immune cell infiltrates, immune cell biomarkers and immune checkpoints. Overall, the hsa_circ_0017264-hsa-miR-195-5p-CHEK1/CDC25A/FOXK1 network might provide novel insights into the potential mechanisms underlying LIHC onset and progression.
High Genetic Diversity and Rickettsia felis in Pediculus humanus Lice Infesting Mbuti (pygmy people), -Democratic Republic of Congo

Pediculus humanus is an obligate bloodsucking parasite of humans that has two ecotypes, the head louse and the body louse, which share an intimate history of coevolution with their human host. In the present work, we obtained and analysed head and body lice collected from Mbuti pygmies living in the Orientale province of the Democratic Republic of the Congo. Cytochrome b DNA analysis was performed in order to type the six known lice clades (A, D, B, F, C and E). The results revealed the presence of two mitochondrial clades. Clade D was the most frequent (61.7% of 47), followed by clade A (38.3% of 47). Sixteen haplotypes were found in 47 samples, of which thirteen were novel haplotypes, indicating an unusually high genetic diversity that closely mirrors the diversity of their hosts. Moreover, we report for the first time the presence of the DNA of R. felis in three (6.4% of 47) head and body lice belonging to both clades A and D. Additional studies are needed to clarify whether the Pediculus lice can indeed transmit this emerging zoonotic bacterium to their human hosts.
Monitoring of Circulating CAR T Cells: Validation of a Flow Cytometric Assay, Cellular Kinetics, and Phenotype Analysis Following Tisagenlecleucel

Chimeric antigen receptor (CAR) T cell therapy is a potent new treatment option for relapsed or refractory hematologic malignancies. As the monitoring of CAR T cell kinetics can provide insights into the activity of the therapy, appropriate CAR T cell detection methods are essential. Here, we report on the comprehensive validation of a flow cytometric assay for peripheral blood CD19 CAR T cell detection. Further, a retrospective analysis (n = 30) of CAR T cell and B cell levels over time has been performed, and CAR T cell phenotypes have been characterized. Serial dilution experiments demonstrated precise and linear quantification down to 0.05% of T cells or 22 CAR T cell events. The calculated detection limit at 13 events was confirmed with CAR T cell negative control samples. Inter-method comparison with real-time PCR showed appreciable correlation. Stability testing revealed diminished CAR T cell values already one day after sample collection. While we found long-term CAR T cell detectability and B cell aplasia in most patients (12/17), some patients (5/17) experienced B cell recovery. In three of these patients the coexistence of CAR T cells and regenerating B cells was observed. Repeat CAR T cell infusions led to detectable but limited re-expansions. Comparison of CAR T cell subsets with their counterparts among all T cells showed a significantly higher percentage of effector memory T cells and a significantly lower percentage of naïve T cells and T EMRA cells among CAR T cells. In conclusion, flow cytometric CAR T cell detection is a reliable method to monitor CAR T cells if measurements start without delay and sufficient T cell counts are given.
Effects of Supplemental Leucine on Growth, Nutrient Use, and Muscle and Visceral Tissue Mass in Holstein Bull Calves Fed Milk Replacer

To determine the effects of leucine supplementation on body weight (BW), tissue mass, nutrient digestibility, the concentration of serum amino acids (AAs) and metabolites, and protein abundance of elongation initiation factor 4E (eIF4E) in skeletal muscle, 23 Holstein bull calves (43. 3 ± 1.16 kg; 11.3 ± 0.57 days of age) fed milk replacer at 2.5% of body weight (BW; dry matter basis) were used in a randomized complete block design. Leucine was supplemented at 0, 0.4, 0.6, or 0.8 g Leu/kg BW per day for 28 d. Data were analyzed using the MIXED procedure of SAS. Leucine supplementation did not affect calf BW (P = 0.73), and digestibility of nitrogen (P = 0.21), organic matter (P = 0.28), and dry matter (P = 0.28). Masses proportional to BW of the pancreas (P = 0.04), omasum (P < 0.01), and spleen (P = 0.01) were quadratically affected by treatment where tissue mass decreased at 0.4 g Leu/kg BW and increased at 0.6 and 0.8 g Leu/kg BW. Semitendinosus mass proportional to BW tended (P = 0.07) to be quadratically affected, as tissue mass increased at 0.4 g Leu/kg BW, and decreased at 0.6 and 0.8 g Leu/kg BW. Serum Leu concentration increased linearly (P = 0.002; day × time × treatment) across days and after feedings with increased supplemental Leu. Increasing supplemental Leu linearly decreased serum Ala (P < 0.01), Arg (P = 0.04), Ile (P = 0.02), Met (P < 0.01), and Pro (P = 0.05) concentrations, and quadratically affected serum Glu (P = 0.04) and Lys (P = 0.03) concentrations where serum Glu and Lys concentrations were decreased at 0.4 g Leu/kg BW and increased at 0.6 and 0.8 g Leu/kg BW. There was no effect of treatment on protein abundance of eIF4E in semitendinosus or longissimus dorsi. These data indicate that supplemental Leu did not influence ADG and nitrogen retention in calves fed milk replacer. However, changes in serum AA concentrations and tissue masses proportional to BW suggest that supplementation of Leu at lower levels could increase the use of AA for non-visceral tissue growth.
Comprehensive Analysis of the Tumor Immune Microenvironment Landscape in Glioblastoma Reveals Tumor Heterogeneity and Implications for Prognosis and Immunotherapy

Background Glioblastoma (GBM) is a fatal brain tumor with no effective treatment. The specific GBM tumor immune microenvironment (TIME) may contribute to resistance to immunotherapy, a tumor therapy with great potential. Thus, an in-depth understanding of the characteristics of tumor-infiltrating immune cells is essential for exploring biomarkers in GBM pathogenesis and immunotherapy. Methods We estimated the relative abundances of 25 immune cell types in 796 GBM samples using single sample gene set enrichment analysis (ssGSEA). Unsupervised clustering was used to identify different GBM-associated TIME immune cell infiltration (GTMEI) patterns. The GTMEIscore system was constructed with principal component analysis (PCA) to determine the immune infiltration pattern of individual tumors. Results We revealed three distinct GTMEI patterns with different clinical outcomes and modulated biological pathways. We developed a scoring system (GTMEIscore) to determine the immune infiltration pattern of individual tumors. We comprehensively analyzed the genomic characteristics, molecular subtypes and clinicopathological features as well as proteomic, phosphoproteomic, acetylomic, lipidomic and metabolomic properties associated with the GTMEIscore and revealed many novel dysregulated pathways and precise targets in GBM. Moreover, the GTMEIscore accurately quantified the immune status of many other cancer types. Clinically, the GTMEIscore was found to have significant potential therapeutic value for chemotherapy/radiotherapy, immune checkpoint inhibitor (ICI) therapy and targeted therapy. Conclusions For the first time, we employed a multilevel and multiplatform strategy to construct a multidimensional molecular map of tumors with different immune infiltration patterns. These results may provide theoretical basises for identifying more effective predictive biomarkers and developing more effective drug combination strategies or novel immunotherapeutic agents for GBM.
Factors Associated With Experiences of Fear, Anxiety, Depression, and Changes in Sleep Pattern During the COVID-19 Pandemic Among Adults in Nigeria: A Cross-Sectional Study

Background Multiple facets of the pandemic can be a source of fear, depression, anxiety and can cause changes in sleep patterns. The aim of this study was to identify health profiles and the COVID-19 pandemic related factors associated with fear, depression, anxiety and changes in sleep pattern in adults in Nigeria. Methods The data for this analysis was extracted from a cross-sectional online survey that collected information about mental health and well-ness from a convenience sample of adults 18 years and above resident in Nigeria from July to December 2020. Study participants were asked to complete an anonymous, closed-ended online questionnaire that solicited information on sociodemographic profile, health profiles (high, moderate and low COVID-19 infection risk profile) including HIV status, COVID-19 status, and self-reported experiences of fear, anxiety, depression and changes in sleep patterns. Results In total, 4,439 participants with mean age of 38.3 (±11.6) years responded to the survey. Factors associated with higher odds of having COVID-19 related fear were health risk (p < 0.05); living with HIV (AOR: 3.88; 95% CI: 3.22–4.69); having COVID-19 symptoms but not tested (AOR: 1.61; 95% CI: 1.30–1.99); having a friend who tested positive to COVID-19 (AOR: 1.28; 95% CI: 1.07–1.53) and knowing someone who died from COVID-19 (AOR: 1.43; 95% CI: 1.24–1.65). The odds of feeling anxious was significantly higher for those with moderate or low health risk profile (p < 0.05); living with HIV (AOR: 1.64; 95% CI: 1.32–2.04); had a friend who tested positive for COVID-19 (AOR: 1.35; 95% CI: 1.08–1.68) or knew someone who died from COVID-19 (AOR: 1.53; 95% CI: 1.28–1.84). The odds of feeling depressed was significantly higher for those with health risk profile (p < 0.05); living with HIV (AOR: 2.49; 95% CI: 1.89–3.28); and respondents who had COVID-19 symptoms but had not taken a test (AOR: 1.41; 95% CI: 1.02–1.94). Factors associated with higher odds of having sleep pattern changes were having moderate and low health risk profiles (p < 0.05). Conclusion The study findings suggest that the pandemic may cause fear, anxiety, depression and changes in sleep patterns differently for people with different health profile, HIV status and COVID-19 status.
Characteristics of Porosity and Permeability of Ultra-High Temperature Perforated Damage Zone in Sandstone Targets

Perforating as a widely-applied stimulation technology is becoming incrementally important in unconventional oil/gas development. It can effectively improve deep-lying high-temperature, high-pressure (HTHP), low-porosity, low-permeability reservoirs, eliminate near-wellbore surface pollution, and increase drainage area. Characteristics of damage zone porosity directly reflect perforating performance. To study porosity and permeability of damage zone in sandstone targets, the paper collected sandstone cores from the 3rd section of the Zhuhai Formation to conduct a simulation experiment for HTHP perforation of large-size targets. After the simulation experiment, an automatic scanner was used to find the planar distribution of the porosity and permeability parameters of the 150°C perforation holes in the cores. The study led to two findings. First, the temperature has a minor effect on the hole depth and diameter in a specified scope. The hole depth decreases as the negative pressure increases and the depth decreases as the effective stress increases. Second, a UHP perforated sandstone target is remarkably zone-specific in planar distribution of the hole porosity and permeability. The damage zone can be divided into the fracture zone, the transition zone, the compaction zone and the undisturbed zone. Besides, the zone permeability damage was quantified. These findings can effectively support research on numerical value simulation for HTHP perforation holes. Besides, they can support HTHP well perforating design and improve near-wellbore permeability enhancement and plug removal.
Risk of Colorectal Cancer in Patients With Irritable Bowel Syndrome: A Meta-Analysis of Population-Based Observational Studies

Background and Aims Evidence on the association between irritable bowel syndrome (IBS) and colorectal cancer (CRC) risk is inconsistent. Therefore, we aimed to examine whether IBS leads to an increased risk for CRC using a systematic review and meta-analysis approach. Methods PubMed, Embase, and Web of Science were systematically searched to identify all relevant literature published through July 30, 2021. The pooled risk ratios (RRs) and corresponding 95% confidence intervals (CIs) for CRC after diagnosis of IBS were computed using random-and fixed-effects models and stratified by age, follow-up time, gender, and study design. The quality of included studies was assessed by the Newcastle-Ottawa scale. Results We included six studies consisting of 1,085,024 participants. Overall, the risk of detecting CRC after the initial IBS diagnosis was significantly higher than non-IBS controls (RR = 1.52, 95% CI: 1.04–2.22, P = 0.032). The peak of elevated risk occurred within the first year of IBS diagnosis (RR = 6.84, 95% CI: 3.70–12.65, P < 0.001), and after 1 year, the risk of CRC was similar to that of the general population (RR = 1.02, 95% CI: 0.88–1.18, P = 0.813). Notably, we found that the RR of CRC was more significant in IBS patients younger than 50 years compared to those older than 50 years (RR = 2.03, 95% CI: 1.17-3.53, P = 0.012 vs. 1.28, 95%CI: 0.94-1.75, P = 0.118, respectively). Gender and study design did not affect the results. Conclusion The risk of CRC within one year of the initial IBS diagnosis was increased approximately six-fold, whereas the long-term risk was not increased. However, current evidence does not support that IBS leads to an increased incidence of CRC, and the early excess risk is more likely attributable to misclassification resulting from overlapping symptoms rather than causation. Clinicians must remain vigilant for the CRC risk in patients younger than 50 years with IBS-like symptoms to avoid delaying necessary screening.