Miracle-dz/UniFAR-FTUs huggingface dataset:
Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades

Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118–134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123–139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
Overcoming Resistance to Checkpoint Inhibitors: Natural Killer Cells in Non-Small Cell Lung Cancer

Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatments over the last 10 years, with even increasing indications in many neoplasms. Non-small cell lung cancer (NSCLC) is considered highly immunogenic, and ICIs have found a wide set of applications in this area, in both early and advanced lines of treatment, significantly changing the prognosis of these patients. Unfortunately, not all patients can benefit from the treatment, and resistance to ICIs can develop at any time. In addition to T lymphocytes, which are the major target, a variety of other cells present in the tumor microenvironment (TME) act in a complex cross-talk between tumor, stromal, and immune cells. An imbalance between activating and inhibitory signals can shift TME from an “anti-” to a “pro-tumorigenic” phenotype and vice versa. Natural killer cells (NKs) are able to recognize cancer cells, based on MHC I (self and non-self) and independently from antigen presentation. They represent an important link between innate and adaptive immune responses. Little data are available about the role of pro-inflammatory NKs in NSCLC and how they can influence the response to ICIs. NKs express several ligands of the checkpoint family, such as PD-1, TIGIT, TIM-3, LAG3, CD96, IL1R8, and NKG2A. We and others have shown that TME can also shape NKs, converting them into a pro-tumoral, pro-angiogenic “nurturing” phenotype through “decidualization. ” The features of these NKs include expression of CD56, CD9, CD49a, and CXCR3; low CD16; and poor cytotoxicity. During ICI therapy, tumor-infiltrating or associated NKs can respond to the inhibitors or counteract the effect by acting as pro-inflammatory. There is a growing interest in NKs as a promising therapeutic target, as a basis for adoptive therapy and chimeric antigen receptor (CAR)-NK technology. In this review, we analyzed current evidence on NK function in NSCLC, focusing on their possible influence in response to ICI treatment and resistance development, addressing their prognostic and predictive roles and the rationale for exploiting NKs as a tool to overcome resistance in NSCLC, and envisaging a way to repolarize decidual NK (dNK)-like cells in lung cancer.
Latent Profile Analysis of Positive Solitude During the Recurrent Outbreak of COVID-19

The current study aimed to identify latent profiles of positive solitude during the recurrent outbreak of COVID-19 among Chinese adults. A total of 902 adults from China completed the questionnaires. We found five different profiles of positive solitude: low positive solitude group, medium-low positive solitude group, quietness positive solitude group, medium-high positive solitude group, and high positive solitude group. Positive and negative affect were significantly different from the five profiles. In addition, gender had different effects on different positive solitude profiles. The results of the study provide a new perspective to understand the positive solitude of Chinese adults during the recurrent outbreak of COVID-19 by using the people-centered approach.
Validation of the Peruvian Spanish Version of the Stress and Anxiety to Viral Epidemics-6 Scale to Measure Viral Anxiety of Medical Students During COVID-19

Introduction The COVID-19 pandemic has created academic problems for Peruvian medical students leading to anxiety and depression. Hence, validated scales, such as the Stress and Anxiety to Viral Epidemics-6 items (SAVE-6), are required to identify and propose interventions to improve mental health. We aimed to perform a psychometric validation of the Peruvian version of SAVE-6 on medical students during the COVID-19 pandemic in Lima, Peru, in 2022. Methods A total of 260 medical students at National University of San Marcos (UNMSM) participated in an online survey in January 2022. We collected sociodemographic characteristics and classified psychiatric symptoms using SAVE-6, the Generalized Anxiety Disorder-7 items (GAD-7) scale, and the Patient Health Questionnaire-9 items (PHQ-9). We performed confirmatory and parallel factor analysis to examine the validity of the Peruvian Spanish version of SAVE-6. Results We explored the reliability and validity of SAVE-6 and SAVE-6 after excluding item 5, since factor loading of item 5 is too low. Both scales showed good internal consistencies (Cronbach's α = 0.780 and.82 and McDonald's Ω = 0.792 and.829, respectively). Furthermore, SAVE-6 after excluding item 5 showed good convergent validity with GAD-7 (r = 0.224, p <.001) and PHQ-9 (r = 0.217, p <.001). Consequently, instead of the full SAVE-6, SAVE-6 excluding item 5 proved to be reliable and valid enough to assess the anxiety of Peruvian medical students during the pandemic. Conclusion The Peruvian Spanish SAVE-6 scale excluding item 5, rather than the full SAVE-6, can be applied to measure viral anxiety of medical students in Peru with good validity and reliability.
Children's Positive and Negative Emotional Responses to an HIV Disclosure Study in South Africa

The benefits of HIV status disclosure to children is widely cited. However, few studies have reported how children respond to the process in a longitudinal fashion. This paper describes children's responses, as documented by healthcare providers (HCPs), during a longitudinal disclosure study conducted at Chris Hani Baragwanath Academic Hospital in Soweto, South Africa. Two HCPs facilitating disclosure recorded observations of 30 participating children (60% female), aged 7-13 years. Participants attended an average of six disclosure counseling sessions over 78 weeks. Observations documented by HCPs included the child's behavior and expressed emotions during the disclosure counseling sessions. The data was analyzed using content analysis. Mixed responses were observed in children who received full disclosure (27/30), with more children responding with strong negative emotions (16/27). However, 10 of those responded well to reassurance, and emotionally improved over subsequent sessions. Improvements were also observed in the communication and relationship between caregivers and children (17/30). Although most children understood the disclosure content (17/30), many were avoidant of the topic of HIV (16/30). With the understanding of the complex range of emotions elicited by HIV disclosure, we can better prepare HCPs on what to anticipate and train caregivers to further manage negative responses post-disclosure. This in turn may lead to more positive experiences of disclosure and the child's healthy acceptance of their HIV status.
How Does Perceived Support for Innovation Lead to Deviant Innovation Behavior of Knowledge Workers? A Moderated Mediation Framework

Many studies concerning deviant innovation behavior mainly focus on the influence of personality differences or leadership styles, and there is a lack of attention given to internal cognitive factors related to actors. Therefore, the purpose of this paper is to examine the internal mechanism of perceived support for innovation on deviant innovation behavior. A two-wave study was conducted among 393 knowledge workers from 10 knowledge-intensive enterprises in the People's Republic of China. Model 4 and Model 14 from SPSS macro PROCESS are used to test the mediating effect of innovation commitment and the moderating effect of threatened self-identity, respectively. The findings suggest that perceived support for innovation can significantly predict deviant innovation behavior; innovation commitment fully mediates the relationship between perceived support for innovation and deviant innovation behavior; public threat to self-identity plays a moderating role in the relationship between innovation commitment and deviant innovation behavior; and public threat to self-identity moderates the mediating effect of innovation commitment on perceived support for innovation and deviant innovation behavior. This study enriches the research on antecedent variables of deviant innovation behavior, and highlights the important role of situational factors on the whole mechanism.
Integrative Analysis Identifies Cell-Type-Specific Genes Within Tumor Microenvironment as Prognostic Indicators in Hepatocellular Carcinoma

Background Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, but effective early detection and prognostication methods are lacking. Methods The Cox regression model was built to stratify the HCC patients. The single-cell RNA sequencing data analysis and gene set enrichment analysis were employed to investigate the biological function of identified markers. PLCB1 gain- or loss-of-function experiments were performed, and obtained HCC samples were analyzed using quantitative real-time PCR and immunohistochemistry assay to validate the biological function of identified markers. Results In this study, we developed a model using optimized markers for HCC recurrence prediction. Specifically, we screened out 8 genes through a series of data analyses, and built a multivariable Cox model based on their expression. The risk stratifications using the Eight-Gene Cox (EGC) model were closely associated with the recurrence-free survivals (RFS) in both training and three validation cohorts. We further demonstrated that this risk stratification could serve as an independent predictor in predicting HCC recurrence, and that the EGC model could outperform other models. Moreover, we also investigated the cell-type-specific expression patterns of the eight recurrence-related genes in tumor microenvironment using single-cell RNA sequencing data, and interpreted their functional roles from correlation and gene set enrichment analyses, in vitro and in vivo experiments. Particularly, PLCB1 and SLC22A7 were predominantly expressed in malignant cells, and they were predicted to promote angiogenesis and to help maintain normal metabolism in liver, respectively. In contrast, both FASLG and IL2RB were specifically expressed in T cells, and were highly correlated with T cell marker genes, suggesting that these two genes might assist in maintaining normal function of T cell-mediated immune response in tumor tissues. Conclusion In conclusion, the EGC model and eight identified marker genes could not only facilitate the accurate prediction of HCC recurrence, but also improve our understanding of the mechanisms behind HCC recurrence.
Predictors of Recurrence and Survival in Cancer Patients With Pericardial Effusion Requiring Pericardiocentesis

Aim This study investigated the factors predicting survival and the recurrence of pericardial effusion (PE) requiring pericardiocentesis (PCC) in patients with cancer. Materials and Methods We analyzed the data of patients who underwent PCC for large PEs from 2010 to 2020 at The University of Texas MD Anderson Cancer Center. The time to the first recurrent PE requiring PCC was the interval from the index PCC with pericardial drain placement to first recurrent PE requiring drainage (either repeated PCC or a pericardial window). Univariate and multivariate Fine-Gray models accounting for the competing risk of death were used to identify predictors of recurrent PE requiring drainage. Cox regression models were used to identify predictors of death. Results The study cohort included 418 patients with index PCC and pericardial drain placement, of whom 65 (16%) had recurrent PEs requiring drainage. The cumulative incidences of recurrent PE requiring drainage at 12 and 60 months were 15.0% and 15.6%, respectively. Younger age, anti-inflammatory medication use, and solid tumors were associated with an increased risk of recurrence of PE requiring drainage, and that echocardiographic evidence of tamponade at presentation and receipt of immunotherapy were associated with a decreased risk of recurrence. Factors predicting poor survival included older age, malignant effusion on cytology, non-use of anti-inflammatory agents, non-lymphoma cancers and primary lung cancer. Conclusion Among cancer patients with large PEs requiring drainage, young patients with solid tumors were more likely to experience recurrence, while elderly patients and those with lung cancer, malignant PE cytology, and non-use of anti-inflammatory agents showed worse survival.
Exploring the Relationship Between Organizational Culture Types and Knowledge Management Processes: A Meta-Analytic Path Analysis

This study investigated the relationship between organizational culture types according to Competing Values Framework (Clan, Adhocracy, Market, Hierarchy) and Knowledge Management Processes (Creation, Dissemination, Storage, Application) using meta-analytic path analysis. To produce the necessary pooled correlation matrix for model testing, we used the univariate (r) approach to carry out two additional meta-analyzes. Based on data collected from several research databases, we extracted the paired correlation coefficients (r) among knowledge management processes (k = 32, N = 6835) then the inter-correlations between knowledge management processes and culture types (k = 7, N = 865). The findings revealed that no particular culture type has a stronger effect on all KM processes. Clan, Adhocracy and Market have significant but varying effects on Knowledge Management processes. Notably, the clan is more associated with knowledge creation, while Adhocracy has a greater effect on knowledge application, and market has a stronger effect on knowledge dissemination and storage. However, hierarchical culture has an insignificant effect on knowledge creation and the lowest effects on the rest of Knowledge Management processes. Therefore, the study concluded that knowledge management success is determined by developing a balanced portfolio of cultural traits from clan, adhocracy and market cultures.
How Stress Can Change Our Deepest Preferences: Stress Habituation Explained Using the Free Energy Principle

People who habituate to stress show a repetition-induced response attenuation—neuroendocrine, cardiovascular, neuroenergetic, and emotional—when exposed to a threatening environment. But the exact dynamics underlying stress habituation remain obscure. The free energy principle offers a unifying account of self-organising systems such as the human brain. In this paper, we elaborate on how stress habituation can be explained and modelled using the free energy principle. We introduce habituation priors that encode the agent’s tendency for stress habituation and incorporate them in the agent’s decision-making process. Using differently shaped goal priors—that encode the agent’s goal preferences—we illustrate, in two examples, the optimising (and thus habituating) behaviour of agents. We show that habituation minimises free energy by reducing the precision (inverse variance) of goal preferences. Reducing the precision of goal priors means that the agent accepts adverse (previously unconscionable) states (e.g., lower social status and poverty). Acceptance or tolerance of adverse outcomes may explain why habituation causes people to exhibit an attenuation of the stress response. Given that stress habituation occurs in brain regions where goal priors are encoded, i.e., in the ventromedial prefrontal cortex and that these priors are encoded as sufficient statistics of probability distributions, our approach seems plausible from an anatomical-functional and neuro-statistical point of view. The ensuing formal and generalisable account—based on the free energy principle—further motivate our novel treatment of stress habituation. Our analysis suggests that stress habituation has far-reaching consequences, protecting against the harmful effects of toxic stress, but on the other hand making the acceptability of precarious living conditions and the development of the obese type 2 diabetes mellitus phenotype more likely.
The Value of Hepatic Scintigraphy in the Diagnosis of Biliary Atresia

Introduction Biliary Atresia (BA) requires prompt diagnosis and surgical intervention to optimize its outcome. The aim of this study was to evaluate the accuracy of EHIDA in distinguishing between BA and other causes of cholestatic jaundice. Methods This was a retrospective study of all patients who underwent EHIDA in a tertiary center from 1997 to 2019. The sensitivity, specificity, Negative Predictive Value (NPV) and Positive Predictive Value (PPV) of EHIDA were evaluated. Factors that can potentially affect its accuracy were also analyzed. Results During the study period, 93 patients aged 10 to 110 days with cholestasis and suspected BA underwent EHIDA. The sensitivity and NPV were 91.2 and 85.3% while specificity and PPV were 80.6 and 88.1%. These results suggested that EHIDA is suboptimal in both diagnosing or excluding BA. Out of 59 patients who showed no tracer activities in the intestines after 24 h, 56 were subjected to surgical exploration and 52 (92.9%) were eventually diagnosed BA. The accuracy of EHIDA scan were different by the maturity of the patient, age at testing and severity of cholestasis. Conclusions EHIDA has a limited accuracy and surgical exploration remains the gold standard to establish the diagnosis of BA. Potential confounding factors that may affect the accuracy of EHIDA were identified but require further studies with larger sample sizes to validate.
Age-Related Increase of Collagen/Fibrin Deposition and High PAI-1 Production in Human Nasal Polyps

Objective: Our previous studies showed an age-related increased prevalence of nasal polyps (NP) and reduced production of S100A8/9 in elderly patients with chronic rhinosinusitis with NP (CRSwNP). In this study, we investigated an unbiased age-related gene expression profile in CRSwNP subjects and healthy controls, and further identified the differences in their tissue remodeling. Methods: Microarrays using NP and uncinate tissues from health controls (elderly, age ≥65 vs. non-elderly, age 18–49) were performed, and differentially regulated genes were analyzed. Quantitative real-time PCR (qPCR), Immunostaining, Periodic acid-Schiff (PAS), trichrome staining, Western blot, and ELISA were performed for further investigation. Results: Microarrays identified differentially expressed genes according to disease and age; 278 in NP vs. controls, 75 in non-elderly NP vs. non-elderly controls, and 32 in elderly NP vs. elderly controls. qPCR confirmed that the PLAT gene was downregulated and the SERPINB2 gene upregulated in NP vs. controls. The serous glandular cell-derived antimicrobial protein/peptide-related genes such as BPIFB3, BPIFB2, LPO, and MUC7 were remarkably reduced in NP, regardless of age. SERPINE1 gene (plasminogen activator inhibitor-1, PAI-1) expression was significantly increased in elderly NP versus elderly controls. IHC and western blot confirmed significantly decreased production of MUC7 and LPO in NP versus controls. There was a trend of age-related reduction of submucosal gland cells in normal controls. Trichrome and immunofluorescence staining demonstrated an age-related increase of collagen and fibrin deposition in NP, consistent with increased PAI-1 production. Conclusion: This study demonstrated age-related differential glandular remodeling patterns and fibrosis in NP and normal controls. PAI-1 expression was significantly increased in elderly NP versus elderly controls, suggesting PAI-1 as a potential treatment target in elderly NP.
Pup1 QTL Regulates Gene Expression Through Epigenetic Modification of DNA Under Phosphate Starvation Stress in Rice

Cytosine methylation, epigenetic DNA modification, is well known to regulate gene expression. Among the epigenetic modifications, 5-methylcytosine (5-mC) has been one of the extensively studied epigenetic changes responsible for regulating gene expression in animals and plants. Though a dramatic change in 5-mC content is observed at the genome level, the variation in gene expression is generally less than that it is expected. Only less is understood about the significance of 5-mC in gene regulation under P-starvation stress in plants. Using whole-genome bisulfite sequencing of a pair of rice [Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL] genotypes, we could decipher the role of Pup1 on DNA (de)methylation-mediated regulation of gene expression under P-starvation stress. We observed 13–15% of total cytosines to be methylated in the rice genome, which increased significantly under the stress. The number of differentially methylated regions (DMRs) for hypomethylation (6,068) was higher than those (5,279) for hypermethylated DMRs under the stress, particularly in root of NIL-23. Hypomethylation in CHH context caused upregulated expression of 489 genes in shoot and 382 genes in root of NIL-23 under the stress, wherein 387 genes in shoot and 240 genes in root were upregulated exclusively in NIL-23. Many of the genes for DNA methylation, a few for DNA demethylation, and RNA-directed DNA methylation were upregulated in root of NIL-23 under the stress. Methylation or demethylation of DNA in genic regions differentially affected gene expression. Correlation analysis for the distribution of DMRs and gene expression indicated the regulation of gene mainly through (de)methylation of promoter. Many of the P-responsive genes were hypomethylated or upregulated in roots of NIL-23 under the stress. Hypermethylation of gene body in CG, CHG, and CHH contexts caused up- or downregulated expression of transcription factors (TFs), P transporters, phosphoesterases, retrotransposon proteins, and other proteins. Our integrated transcriptome and methylome analyses revealed an important role of the Pup1 QTL in epigenetic regulation of the genes for transporters, TFs, phosphatases, carbohydrate metabolism, hormone-signaling, and chromatin architecture or epigenetic modifications in P-starvation tolerance. This provides insights into the molecular function of Pup1 in modulating gene expression through DNA (de)methylation, which might be useful in improving P-use efficiency or productivity of rice in P-deficient soil.