Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between depressive symptoms and diagnosis of diabetes and its complications: A network analysis in electronic health records

Objectives Diabetes and its complications are commonly associated with depressive symptoms, and few studies have investigated the diagnosis effect of depressive symptoms in patients with diabetes. The present study used a network-based approach to explore the association between depressive symptoms, which are annotated from electronic health record (EHR) notes by a deep learning model, and the diagnosis of type 2 diabetes mellitus (T2DM) and its complications. Methods In this study, we used anonymous admission notes of 52,139 inpatients diagnosed with T2DM at the first affiliated hospital of Nanjing Medical University from 2008 to 2016 as input for a symptom annotation model named T5-depression based on transformer architecture which helps to annotate depressive symptoms from present illness. We measured the performance of the model by using the F1 score and the area under the receiver operating characteristic curve (AUROC). We constructed networks of depressive symptoms to examine the connectivity of these networks in patients diagnosed with T2DM, including those with certain complications. Results The T5-depression model achieved the best performance with an F1-score of 91.71 and an AUROC of 96.25 compared with the benchmark models. The connectivity of depressive symptoms in patients diagnosed with T2DM (p = 0.025) and hypertension (p = 0.013) showed a statistically significant increase 2 years after the diagnosis, which is consistent with the number of patients diagnosed with depression. Conclusion The T5-depression model proposed in this study can effectively annotate depressive symptoms in EHR notes. The connectivity of annotated depressive symptoms is associated with the diagnosis of T2DM and hypertension. The changes in the network of depressive symptoms generated by the T5-depression model could be used as an indicator for screening depression.
A review of agroforestry, precision agriculture, and precision livestock farming—The case for a data-driven agroforestry strategy

Agroforestry can be defined as an agroecosystem whereby soil is used holistically and synergistically by various stakeholders including farmers, livestock, and plants. As such, agroforestry offers numerous benefits that include conservation of biodiversity, regulation of pests and diseases, increased quality of soil, air and water, efficient cycling of nutrients, and resilience to climate change. Review of published studies in agroforestry shows however that research in this area could benefit from increased real-time, spatial and temporal measurements. This situation is to be contrasted with that of precision agriculture in monocultures and precision livestock farming where progress made in sensor systems has attracted considerable research interest. It is advocated in this review article that wireless sensor networks could also significantly impact agroforestry through the monitoring of the local real-time interactions that occur between the various components constituting agroforestry systems. This review article proposes therefore the new field of data-driven agroforestry which lies at the intersection of precision agriculture, precision livestock farming, permaculture, and agroforestry. Data-driven agroforestry has the potential to not only help farmers harness the interactions between the different components of an agroforestry system to their advantage but also shine light on fundamental interactions between soil, plants, trees, and livestock while offering a sustainable agricultural method beneficial to all agroforestry stakeholders.
Spatial and seasonal characteristics of dissolved heavy metals in the seawater of Beibu Gulf, the Northern South China Sea

Heavy metal contaminations in the marine environment are of considerable attention because of their high potential ecological effects and public concern for human health. However, the influencing factors for the large-scale distributions of heavy metals in Beibu Gulf, a newly developing industry and port in South China, are still unclear due to the lack of large-scale investigation. Here, a total of 871 samples in the 127 stations in the seawater of Beibu Gulf during spring, summer, fall and winter in 2020-2021 were analyzed for dissolved heavy metal concentrations and physicochemical parameters. The concentrations of heavy metals in the Beibu Gulf ranked following the order of Zn > Cu > Cr > As > Pb > Hg > Cd. Compared to other regions, the concentrations of Hg were at relatively higher levels, which were mainly influenced by the input of the transportation of water masses from the local and other regions; whereas the other heavy metals were at relatively lower levels. Seasonally variations in the concentrations of heavy metals were observed in the gulf, which is mainly influenced by human activities (i.e., shipping and mariculture activities) and seasonally hydrological conditions. Seasonal changes in the spatial distribution of heavy metals have been found in the gulf. The higher concentrations of heavy metals mainly occurred in the coastal bays or areas in summer whereas the higher concentrations were observed in the offshore areas during the other three seasons. This is mainly related to the seasonal changes of the water masses that affect the seawater of Beibu Gulf, which exhibits the dominant contribution of coastal current from the northern Beibu Gulf in summer, and the dominant contribution of west-Guangdong coastal current and SCS water during the other three seasons. The potential ecological risk index revealed that Hg is the main ecological risk factor in the gulf, and the heavy metal contamination in the gulf seems to be noticeable. This study highlights the seasonal changes of the water masses that affect the seawater of Beibu Gulf greatly affecting the large-scale distributions of heavy metals in the gulf.
An integrated metabolome and transcriptome approach reveals the fruit flavor and regulatory network during jujube fruit development

The fruit flavor is a key economic value attribute of jujube. Here we compared metabolomes and transcriptomes of “Mazao” (ST) and “Ping’anhuluzao” (HK) with unique flavors during fruit development. We identified 437 differential metabolites, mainly sugars, acids, and lipids. Fructose, glucose, mannose and citric acid, and malic acid are the determinants of sugar and acid taste of jujube fruit. Based on the transcriptome, 16,245 differentially expressed genes (DEGs) were identified, which were involved in “glucosyltransferase activity,” “lipid binding,” and “anion transmembrane transporter activity” processes. Both transcriptome and metabolome showed that developmental stages 2 and 3 were important transition periods for jujube maturation. Based on WGCNA and gene-metabolite correlation analysis, modules, and transcription factors (ZjHAP3, ZjTCP14, and ZjMYB78) highly related to sugar and acid were identified. Our results provide new insights into the mechanism of sugar and acid accumulation in jujube fruit and provide clues for the development of jujube with a unique flavor.
Cardiovascular manifestations identified by multi-modality imaging in patients with long COVID

Background The possibility of permanent cardiovascular damage causing cardiovascular long COVID has been suggested; however, data are insufficient. This study investigated the prevalence of cardiovascular disorders, particularly in patients with cardiovascular long COVID using multi-modality imaging. Methods A total of 584 patients admitted to the hospital due to COVID-19 between January 2020 and September 2021 were initially considered. Upon outpatient follow-up, 52 (9%) were suspected to have cardiovascular long COVID, had complaints of chest pain, dyspnea, or palpitations, and were finally enrolled in this study. This study is registered with the Japanese University Hospital Medical Information Network (UMIN 000047978). Results Of 52 patients with long COVID who were followed up in the outpatient clinic for cardiovascular symptoms, cardiovascular disorders were present in 27% (14/52). Among them, 15% (8/52) had myocardial injury, 8% (4/52) pulmonary embolisms, and 4% (2/52) both. The incidence of a severe condition (36% [5/14] vs. 8% [3/38], p = 0.014) and in-hospital cardiac events (71% [10/14] vs. 24% [9/38], p = 0.002) was significantly higher in patients with cardiovascular disorders than in those without. A multivariate logistic regression analysis revealed that a severe condition (OR, 5.789; 95% CI 1.442–45.220; p = 0.017) and in-hospital cardiac events (OR, 8.079; 95% CI 1.306–25.657; p = 0.021) were independent risk factors of cardiovascular disorders in cardiovascular long COVID patients. Conclusions Suspicion of cardiovascular involvement in patients with cardiovascular long COVID in this study was approximately 30%. A severe condition during hospitalization and in-hospital cardiac events were risk factors of a cardiovascular sequalae in CV long COVID patients.
Labor market situation of refugees in Europe: The role of individual and contextual factors

The paper sheds light on the patterns of labor market integration of refugees in Western countries, who arrived primarily during the 2015–2016 mass refugee migration. Its major focus lies on the role of individual and contextual factors responsible for refugees' success in the labor market. At the host country level, the extent of permeability along the ethnic lines and the welcome of reception—both on the part of the majority population and the part of the established minorities—constitute further essential moderators of refugees' labor market success. This comprehensive literature overview draws on the flourishing body of research in Europe and beyond and discusses commonalities and differences across refugee origins and destinations while paying particular attention to the time trends and meaningful heterogeneities along with refugees' socio-demographic characteristics. We conclude by identifying major avenues for future research.
A novel neutrophil extracellular trap signature to predict prognosis and immunotherapy response in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant cancers, and patients with HNSCC possess early metastases and poor prognosis. Systematic therapies (including chemotherapy, targeted therapy, and immunotherapy) are generally applied in the advanced/late stages of HNSCC, but primary and acquired resistance eventually occurs. At present, reliable biomarkers to predict the prognosis of HNSCC have not been completely identified. Recent studies have shown that neutrophil extracellular traps (NETs) are implicated in cancer progression, metastasis and cancer immune response, and NET-related gene signatures are associated with the prognosis of patients with several human cancers. To explore whether NET-related genes play crucial roles in HNSCC, we have performed systematic analysis and reported several findings in the current study. Firstly, we identified seven novel NET-related genes and developed a NET-score signature, which was highly associated with the clinicopathological and immune traits of the HNSCC patients. Then, we, for the first time, found that NIFK was significantly upregulated in HNSCC patient samples, and its levels were significantly linked to tumor malignancy and immune status. Moreover, functional experiments confirmed that NIFK was required for HNSCC cell proliferation and metastasis. Altogether, this study has identified a novel NET-score signature based on seven novel NET-related genes to predict the prognosis of HNSCC and NIFK has also explored a new method for personalized chemo-/immuno-therapy of HNSCC.
Entrepreneurship education on entrepreneurial intention: The moderating role of the personality and family economic status

This study investigates the impact of entrepreneurship education on college students’ entrepreneurial intentions, as well as the moderating effects of personality and family economic status on the relationship between entrepreneurship education and entrepreneurial intention, respectively. We tested our hypotheses using a sample of college students in Tianjin, China, and analyzed the data of 326 questionnaires containing validated measures. The results show that entrepreneurship education has a positive impact on college students’ entrepreneurial intentions; proactive personality negatively moderates this relationship; and family economic status positively moderates it. However, the moderating effect of narcissistic personality has not been verified. This study is unique and innovative as it brings new insights to this stream of literature by introducing the roles of the personality and family economic status in the relationship between entrepreneurship education and entrepreneurial intention. Our analysis provides important empirical evidence about the negative moderating effect of proactive personality and the positive moderating effect of family economic status on the relationship between entrepreneurship education and entrepreneurial intention, introducing insights into the heterogeneity of the effect of entrepreneurship education.
Epidemiological characteristics an outbreak of ST11 multidrug-resistant and hypervirulent Klebsiella pneumoniae in Anhui, China

Klebsiella pneumoniae has become a primary threat to global health because of its virulence and resistance. In 2015, China reported multidrug-resistant (MDR) and hypervirulent K. pneumoniae (hvKp) isolates. The emergence of MDR-hvKp poses a significant threat to public health. We collected 76 MDR K. pneumoniae isolates from the same hospital, of which there were a total of six MDR-hvKp isolates. We performed multilocus sequence typing (MLST) and capsular typing, whole genome sequencing, comparative genome analysis, and phylogenetic analysis as well as phenotypic experiments, including growth curves, mucoviscosity assay, Galleria mellonella infection model, human whole blood survival, and human neutrophil bactericidal assay to further characterize the samples. We identified six large plasmids carrying extended spectrum β-lactamase (ESBL) genes or carbapenemase genes (blaCTX–M–65, blaKPC–2, blaSHV–12, blaSHV–158), 9 plasmids containing other drug resistance genes, and 7 hypervirulence plasmids carrying rmpA and rmpA2 in ST11 MDR-hvKp isolates. Some of these plasmids were identical, whereas others differed only by insertion elements. In addition, we identified a plasmid, p21080534_1, that carries hypervirulence genes (iucABCD, iutA, rmpA2), a carbapenemase gene (blaKPC–2), and an ESBL gene (blaSHV–12), as well as MDR-hvKp 21072329, which did not carry rmpA or rmpA2, but exhibited hypervirulence and hypermucoviscosity. ST11 MDR-hvKp derived from hypervirulence and multidrug resistance plasmids not only causes significant treatment difficulties, but also represents an unprecedented challenge to public health. Therefore, urgent measures are needed to limit further spread.
Substrate specificity of branched chain amino acid aminotransferases: The substitution of glycine to serine in the active site determines the substrate specificity for α-ketoglutarate

A branched chain aminotransferase from Thermoproteus tenax has been identified, cloned, over-expressed and biochemically characterised. A molecular modelling approach has been used to predict the 3D structure allowing its comparison with other related enzymes. This enzyme has high similarity to a previously characterised aminotransferase from Thermoproteus uzoniensis however its substrate specificity shows key differences towards the substrate α-ketoglutarate. Examination of the active sites of the two related enzymes reveals a single amino acid substitution of a glycine residue to a serine residue which could be responsible for this difference. When Gly104 in T. tenax was mutated to a serine residue and the resultant enzyme characterised, this single amino acid change resulted in a dramatic reduction in activity towards α-ketoglutarate with an 18-fold reduction in Vmax and a 20-fold Km increase, resulting in a 370-fold lower catalytic efficiency. Structural comparisons between the two related Thermoproteus enzymes and another branched chain aminotransferase from Geoglobus acetivorans has revealed that the serine residue affects the flexibility of a key loop involved in catalysis. This subtle difference has provided further insight into our understanding of the substrate specificity of these industrially important enzymes.
Neuronal activity-dependent ATP enhances the pro-growth effect of repair Schwann cell extracellular vesicles by increasing their miRNA-21 loading

Functional recovery after peripheral nerve injuries is critically dependent on axonal regeneration. Several autonomous and non-cell autonomous processes regulate axonal regeneration, including the activation of a growth-associated transcriptional program in neurons and the reprogramming of differentiated Schwann cells (dSCs) into repair SCs (rSCs), triggering the secretion of neurotrophic factors and the activation of an inflammatory response. Repair Schwann cells also release pro-regenerative extracellular vesicles (EVs), but is still unknown whether EV secretion is regulated non-cell autonomously by the regenerating neuron. Interestingly, it has been described that nerve activity enhances axonal regeneration by increasing the secretion of neurotrophic factors by rSC, but whether this activity modulates pro-regenerative EV secretion by rSC has not yet been explored. Here, we demonstrate that neuronal activity enhances the release of rSC-derived EVs and their transfer to neurons. This effect is mediated by activation of P2Y receptors in SCs after activity-dependent ATP release from sensory neurons. Importantly, activation of P2Y in rSCs also increases the amount of miRNA-21 present in rSC-EVs. Taken together, our results demonstrate that neuron to glia communication by ATP-P2Y signaling regulates the content of SC-derived EVs and their transfer to axons, modulating axonal elongation in a non-cell autonomous manner.
Cross-sectional associations between cardiorespiratory fitness and NMR-derived metabolic biomarkers in children – the PANIC study

Objective Cardiorespiratory fitness has been inversely associated with cardiovascular risk across the lifespan. Some studies in adults suggest that higher cardiorespiratory fitness is associated with cardioprotective metabolite profile, but the evidence in children is lacking. Therefore, we investigated the cross-sectional association of cardiorespiratory fitness with serum nuclear magnetic resonance derived metabolic biomarkers in children. Methods A population sample of 450 children aged 6–8 years was examined. Cardiorespiratory fitness was assessed by a maximal exercise test on a cycle ergometer and quantified as maximal power output normalised for lean body mass assessed by dual-energy X-ray absorbtiometry. Serum metabolites were assessed using a high throughput nuclear magnetic resonance platform. The data were analysed using linear regression analyses adjusted for age and sex and subsequently for body fat percentage (BF%) assessed by DXA. Results Cardiorespiratory fitness was directly associated with high density lipoprotein (HDL) cholesterol (β=0.138, 95% CI=0.042 to 0.135, p=0.005), average HDL particle diameter (β=0.102, 95% CI=0.004 to 0.199, p=0.041), and the concentrations of extra-large HDL particles (β=0.103, 95% CI=0.006 to 0.201, p=0.038), large HDL particles (β=0.122, 95% CI=0.025 to 0.220, p=0.014), and medium HDL particles (β=0.143, 95% CI=0.047 to 0.239, p=0.004) after adjustment for age and sex. Higher cardiorespiratory fitness was also associated with higher concentrations of ApoA1 (β=0.145, 95% CI=0.047 to 0.242, p=0.003), glutamine (β=0.161, 95% CI=0.064 to 0.257, p=0.001), and phenylalanine (β=0.187, 95% CI=0.091 to 0.283, p<0.001). However, only the direct associations of cardiorespiratory fitness with the concentrations of HDL cholesterol (β=0.114, 95% CI=0.018 to 0.210, p=0.021), medium HDL particles (β=0.126, 95% CI=0.030 to 0.223, p=0.010), ApoA1 (β=0.126, 95% CI=0.030 to 0.223, p=0.011), glutamine (β=0.147, 95% CI=0.050 to 0.224, p=0.003), and phenylalanine (β=0.217, 95% CI=0.122 to 0.311, p<0.001) remained statistically significant after further adjustment for BF%. Conclusions Higher cardiorespiratory fitness was associated with a cardioprotective biomarker profile in children. Most associations were independent of BF% suggesting that the differences in serum metabolites between children are driven by cardiorespiratory fitness and not adiposity.
COVID-19 in unvaccinated patients with inborn errors of immunity—polish experience

At the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, patients with inborn errors of immunity (IEI) appeared to be particularly vulnerable to a severe course of the disease. It quickly turned out that only some IEI groups are associated with a high risk of severe infection. However, data on the course of Coronavirus Disease 2019 (COVID-19) in patients with IEI are still insufficient, especially in children; hence, further analyses are required. The retrospective study included 155 unvaccinated people with IEI: 105 children and 50 adults (67.7% and 32.3%, respectively). Male patients dominated in the study group (94 people, 60.6%). At least two comorbidities were found in 50 patients (32.3%), significantly more often in adults (56% vs. 21%). Adult patients presented significantly more COVID-19 symptoms. Asymptomatic and mildly symptomatic course of COVID-19 was demonstrated in 74.8% of the entire group, significantly more often in children (88.6% vs. 46%). Moderate and severe courses dominated in adults (54% vs. 11.4%). Systemic antibiotic therapy was used the most frequently, especially in adults (60% vs. 14.3%). COVID-19-specific therapy was used almost exclusively in adults. In the whole group, complications occurred in 14.2% of patients, significantly more often in adults (30% vs. 6.7%). In the pediatric group, there were two cases (1.9%) of multisystem inflammatory syndrome in children. Deaths were reported only in the adult population and accounted for 3.9% of the entire study group. The death rate for all adults was 12%, 15.4% for adults diagnosed with common variable immunodeficiency, 12.5% for those with X-linked agammaglobulinemia, and 21.4% for patients with comorbidity. The results of our study imply that vaccinations against COVID-19 should be recommended both for children and adults with IEI. Postexposure prophylaxis and early antiviral and anti-SARS-CoV-2 antibody-based therapies should be considered in adults with IEI, especially in those with severe humoral immune deficiencies and comorbidity.