Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms

Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
The Influence of Self-Esteem and Psychological Flexibility on Medical College Students' Mental Health: A Cross-Sectional Study

Background Mental health problems has become a major public health issue among medical students. Self-esteem and psychological flexibility were important associated factors for mental health, but their relations have not been discussed in medical students. The present study aimed to assess the status of mental health problems among medical students and identified whether psychological flexibility had a mediating role in the effects of self-esteem on the top three most common psychological symptoms. Methods A total of 810 undergraduate students from 18 classes comprised in the sample. Nine dimensions of psychological symptoms was assessed by the Symptom Checklist-90-revised (SCL-90-R). Self-esteem was measured by the Self-esteem Scale (SES) and psychological flexibility was evaluated by the Acceptance and Action Questionnaire 2nd Edition (AAQ-II) and Cognitive Fusion Questionnaire (CFQ-F). Univariate analysis and logistic regression analysis were used to determine the relationship among the top three common psychological symptoms, self-esteem, psychological flexibility, and participants' characteristics. The mediating effect of psychological flexibility between self-esteem and psychological symptoms was detected by bootstrap method. Results 57.8% of the medical undergraduate students reported positive at least one of the nine psychological symptom dimensions assessed by the SCL-90-R and 13.8% of students had moderate or more severe symptoms. The symptoms of obsessive-compulsiveness, interpersonal sensitivity, and depression were the three most common psychological symptoms among the medical students. Meanwhile, self-esteem and psychological flexibility were negatively associated to the symptoms of obsessive-compulsiveness, interpersonal sensitivity, and depression. And, almost 50% effects of self-esteem on these three symptoms in medical students exert indirect effects through psychological flexibility. Conclusions Psychological distress was quite common in the Chinese medical students. The three most common psychological symptoms were successively obsessive-compulsiveness, interpersonal sensitivity, and depression. Low self-esteem and psychological inflexibility might be the risk factors for these top three symptoms, and psychological flexibility might play a mediating role in the effects of self-esteem on these psychological symptoms.
Safety and Efficacy of PD-1/PD-L1 Inhibitors in Cancer Patients With Preexisting Autoantibodies

Background Programmed cell death protein-1/programmed cell death ligand-1 (PD-1/PD-L1) inhibitors therapy is now a routine scheme in cancers. However, the effect of preexisting autoantibodies on the safety and efficacy of PD-1/PD-L1 inhibitors in cancer patients is not well understood. Methods The present retrospective cohort study evaluated the safety and efficacy of PD-1/PD-L1 inhibitors in patients with preexisting autoantibodies. Patients who received PD-1/PD-L1 inhibitors in the Department of Medical Oncology, Peking Union Medical College Hospital between November 2017 and August 2021 were reviewed. Results 67 (37.9%) of the 177 patients, 27 (20.3%) of the 133 patients, and 16 (11.0%) of 146 patients who received PD-1/PD-L1 inhibitors were positive for ANA, anti-Ro52, and antithyroid antibodies, respectively. Preexisting ANA and anti-Ro52 antibody were not associated with the increased risk of immune-related adverse events (irAEs), while thyroid dysfunction was more frequent in patients with positive antithyroid antibody (75.0% versus 13.8%, p < 0.001). The median progression-free survival (PFS, 13.1 versus 7.0 months, p = 0.015) was significantly longer in the ANA-positive patients, while the median overall survival (OS, 14.5 versus 21.8 months, p = 0.67) did not differ significantly between the ANA-positive and ANA-negative groups. Moreover, the preexisting anti-Ro52 and antithyroid antibodies were not significantly associated with PFS and OS. Conclusions The presence of ANA and anti-Ro52 antibody were not associated with a higher risk of irAEs, whereas patients positive for antithyroid antibody should monitor closely immune-related thyroid dysfunction. Preexisting ANA might be a predictor of longer PFS, while anti-Ro52 and antithyroid antibodies had no significant effect on survival outcomes in patients receiving PD-1/PD-L1 inhibitors therapy.
A Clinical-Radiomics Nomogram Based on the Apparent Diffusion Coefficient (ADC) for Individualized Prediction of the Risk of Early Relapse in Advanced Sinonasal Squamous Cell Carcinoma: A 2-Year Follow-Up Study

Purpose To develop and validate a nomogram model combining radiomic features and clinical characteristics to preoperatively predict the risk of early relapse (ER) in advanced sinonasal squamous cell carcinomas (SNSCCs). Methods A total of 152 SNSCC patients (clinical stage III-IV) who underwent diffusion-weighted imaging (DWI) were included in this study. The training cohort included 106 patients assessed at the headquarters of our hospital using MR scanner 1. The testing cohort included 46 patients assessed at the branch of our hospital using MR scanner 2. Least absolute shrinkage and selection operator (LASSO) regression was applied for feature selection and radiomic signature (radscore) construction. Multivariable logistic regression analysis was applied to identify independent predictors. The performance of the model was evaluated using the area under the receiver operating characteristic curve (AUC), calibration curve and decision curve analysis (DCA). Furthermore, the patients were classified into high- or low-risk ER subgroups according to the optimal cutoff value of the nomogram using X-tile. The recurrence-free survival probability (RFS) of each subgroup was assessed. Results ER was noted in 69 patients. The radscore included 8 selected radiomic features. The radscore, T stage and surgical margin were independent predictors. The nomogram showed better performance (AUC = 0.92) than either the radscore or the clinical factors in the training cohort (P < 0.050). In the testing cohort, the nomogram showed better performance (AUC = 0.92) than the clinical factors (P = 0.016) and tended to show better performance than the radscore (P = 0.177). The nomogram demonstrated good calibration and clinical utility. Kaplan-Meier analysis showed that the 2-year RFS rate for low-risk patients was significantly greater than that for high-risk patients in both the training and testing cohorts (P < 0.001). Conclusions The ADC-based radiomic nomogram model is potentially useful in predicting the risk of ER in advanced SNSCCs.
Transcriptome-Wide Characterization of Seed Aging in Rice: Identification of Specific Long-Lived mRNAs for Seed Longevity

Various long-lived mRNAs are stored in seeds, some of which are required for the initial phase of germination and are critical to seed longevity. However, the seed-specific long-lived mRNAs involved in seed longevity remain poorly understood in rice. To identify these mRNAs in seeds, we first performed aging experiment with 14 rice varieties, and categorized them as higher longevity (HL) and lower longevity (LL) rice varieties in conventional rice and hybrid rice, respectively. Second, RNA-seq analysis showed that most genes showed similar tendency of expression changes during natural and artificial aging, suggesting that the effects of these two aging methods on transcription are comparable. In addition, some differentially expressed genes (DEGs) in the HL and LL varieties differed after natural aging. Furthermore, several specific long-lived mRNAs were identified through a comparative analysis of HL and LL varieties after natural aging, and similar sequence features were also identified in the promoter of some specific long-lived mRNAs. Overall, we identified several specific long-lived mRNAs in rice, including gibberellin receptor gene GID1, which may be associated with seed longevity.
Effects of Dietary Indole-3-carboxaldehyde Supplementation on Growth Performance, Intestinal Epithelial Function, and Intestinal Microbial Composition in Weaned Piglets

As a microbial tryptophan metabolite, indole-3-carboxaldehyde (ICA) has been suggested to confer benefits to host, such as regulation of intestinal barrier function. This study aimed to elucidate the role of ICA in modulating intestinal homeostasis via using a weaned pig model. Twenty-four weaned piglets were randomly allocated into three groups: the control group (a basal diet), ICA100 group (the basal diet supplemented with 100 mg/kg ICA), and ICA200 group (the basal diet supplemented with 200 mg/kg ICA). The experiment lasted 14 d, and pigs from the control and ICA100 groups were slaughtered. The results showed no significant differences in the average daily gain (ADG) and average daily feed intake (ADFI) among the three groups (P > 0.05). However, the ICA100 group had a lower feed to gain ratio (F:G) (P < 0.05). Dietary ICA supplementation did not alter the villus height, crypt depth, and villus height/crypt depth ratio in the small intestine, and did not change the intestinal permeability and antioxidant parameters (P > 0.05). Intriguingly, ICA treatment significantly increased the jejunal, ileal and colonic indexes in piglets (P < 0.05). Besides, the expression of proliferating cell nuclear antigen (PCNA) in the intestine was up-regulated by ICA treatment. Moreover, in vitro experiments demonstrated that 15 μM ICA significantly accelerated the proliferation activity of IPEC-J2 cells, and increased the expression of the ICA receptor aryl hydrocarbon receptor (AHR) and the proliferation markers PCNA and Cyclin D1 (P < 0.05). In addition, dietary ICA supplementation modulated the intestinal flora, increasing the richness estimators and diversity index, decreasing the abundances of phylum Fibrobacterota and genera Alloprevotella, Prevotella, and Parabacteroides, and enriching the abundance of genera Butyrivibrio. These data reveal a beneficial role for the microbial metabolite ICA on intestinal epithelial proliferation, rather than intestinal barrier function, in weaned piglets.
Serum Cytokines Predict the Severity of Coronary Artery Disease Without Acute Myocardial Infarction

Introduction Various cytokines were involved in the process of atherosclerosis, and their serum levels were correlated with coronary artery disease (CAD) to varying degrees. However, there were limited reports about the correlation between serum cytokines and the severity of coronary atherosclerotic lesion in patients with non-acute myocardial infarction (AMI). The purpose of this study was to investigate the relationship between serum cytokines and the severity of CAD, and identify the predictors of severe CAD in patients suspected to have CAD but AMI had been ruled out. Methods A total of 502 patients who had suspected CAD and underwent coronary angiography were enrolled. The serum levels of IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IL-17, TNF-α, IFN-α,and IFN-γ were determined by multiplexed particle-based flow cytometric assays technology. And the severity of CAD was evaluated by Gensini score (GS). Results The serum levels of IL-4, IL-12p70, IL-17, and IFN-α were significantly lower in the severe CAD group (GS≥30) than those in the non-severe CAD group (GS < 30). And IL-12p70 and IL-17 were negatively correlated with the severity of CAD. Multivariate logistic regression analyses demonstrated that two serum cytokines (IL-12p70 and IL-17), one clinical protective factor (HDL-C), and two clinical risk factors (gender and diabetes) were the independent predictors of severe CAD. ROC curve analysis showed that multivariate mode combined these predictors had a good performance in predicting severe CAD. Conclusion The combination of serum cytokines (IL-12p70 and IL-17) and clinical risk factors (HDL-C, gender, and diabetes) may help identify patients with more severe coronary artery lesions from those with suspected CAD but not AMI, and may contribute to guiding the risk stratification for patients with chest discomfort in health care facilities without sufficient medical resources (especially cardiac catheterization resources).
Clinical Outcomes and Microbiological Characteristics of Sequence Type 11 Klebsiella pneumoniae Infection

Background Sequence type 11 (ST11) Klebsiella pneumoniae (Kp) is highly prevalent in China and is a typical sequence type among KPC-producing isolates. This study aimed to evaluate the clinical outcomes and microbiological features of ST11 Kp infections. Methods A retrospective cohort study was conducted at Peking University Third Hospital from January 2017 to March 2021. Clinical data were collected from medical records. Antimicrobial susceptibility testing and string tests were performed. Whole-genome sequencing was used to analyze the capsular serotypes, detect virulence-associated genes, and perform multilocus sequence typing. The risk of all-cause mortality in ST11 Kp-infected patients was compared to that in non-ST11 Kp-infected patients. Results From 139 patients infected with Kp, 49 ST11 Kp (35.3%) strains were isolated. The Charlson comorbidity index in the ST11 group was higher than that in the non-ST11 group (3.94 ± 1.59 vs. 2.41 ± 1.54, P = 0.001). A greater number of ST11 Kp-infected patients required ICU admission (46.9 vs. 16.7%, P < 0.001) and mechanical ventilation (28.6 vs. 10.0%, P = 0.005). All ST11 isolates presented a multidrug-resistant (MDR) phenotype, and twenty-nine (59.2%) hypervirulent Kp (hvKp) were identified. Twenty-four ST11 strains presented with hypermucoviscosity. The presence of capsular types K47 and K64 was frequent in the ST11 Kp strains (P < 0.001). The key virulence-associated genes rmpA, rmpA2, iucA, iroB, and peg344 were present in 26.5, 42.9, 59.2, 0, and 26.5% of the isolates, respectively, in the ST11 group. Twenty-one ST11 isolates harbored the combination of iucA+rmpA2. The 30-day mortality rate and sequential organ failure assessment (SOFA) score were significantly higher in ST11 Kp-infected patients than in non-ST11 Kp-infected patients (P < 0.01). ST11 Kp infection appeared to be an independent risk factor for mortality in ST11 Kp-infected patients. Conclusions A high prevalence of the ST11 clone was found in the hospital, which accounted for elevated antimicrobial resistance and exhibited great molecularly inferred virulence. Patients with ST11 Kp infection had a tendency toward increased 30-day mortality and SOFA scores. ST11 Kp infection was an independent risk factor for mortality, suggesting that enhanced surveillance and management are essential.
Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity

T cell-mediated immunity plays a central role in the control and clearance of intracellular Coxiella burnetii infection, which can cause Q fever. Therefore, we aimed to develop a novel T cell-targeted vaccine that induces pathogen-specific cell-mediated immunity to protect against Q fever in humans while avoiding the reactogenicity of the current inactivated whole cell vaccine. Human HLA class II T cell epitopes from C. burnetii were previously identified and selected by immunoinformatic predictions of HLA binding, conservation in multiple C. burnetii isolates, and low potential for cross-reactivity with the human proteome or microbiome. Epitopes were selected for vaccine inclusion based on long-lived human T cell recall responses to corresponding peptides in individuals that had been naturally exposed to the bacterium during a 2007-2010 Q fever outbreak in the Netherlands. Multiple viral vector-based candidate vaccines were generated that express concatemers of selected epitope sequences arranged to minimize potential junctional neo-epitopes. The vaccine candidates caused no antigen-specific reactogenicity in a sensitized guinea pig model. A subset of the vaccine epitope peptides elicited antigenic recall responses in splenocytes from C57BL/6 mice previously infected with C. burnetii. However, immunogenicity of the vaccine candidates in C57BL/6 mice was dominated by a single epitope and this was insufficient to confer protection against an infection challenge, highlighting the limitations of assessing human-targeted vaccine candidates in murine models. The viral vector-based vaccine candidates induced antigen-specific T cell responses to a broader array of epitopes in cynomolgus macaques, establishing a foundation for future vaccine efficacy studies in this large animal model of C. burnetii infection.
Seasonal, Annual, and Decadal Distribution of Three Rorqual Whale Species Relative to Dynamic Ocean Conditions Off Oregon, USA

Whale populations recovering from historical whaling are particularly vulnerable to incidental mortality and disturbance caused by growing ocean industrialization. Several distinct populations of rorqual whales (including humpback, blue, and fin whales) migrate and feed off the coast of Oregon, USA where spatial overlap with human activities are on the rise. Effective mitigation of conflicts requires better foundational understanding of spatial and temporal habitat use patterns to inform conservation management. Based on a year-round, multi-platform distance sampling dataset (2016-2021, 177 survey days, 754 groups observed), this study generated density models to describe and predict seasonal distribution of rorqual whales in Oregon. Phenology analysis of sightings revealed a peak of humpback whale and blue whale density over the Oregon continental shelf in August and September respectively, and higher fin whale density in the winter (December). Additionally, we compared rorqual sighting rates across three decades of survey effort (since 1989) and demonstrate that rorqual whales are strikingly more prevalent in the current dataset, including distinct increases of blue and fin whales. Finally, density surface models relating whale densities to static and dynamic environmental variables acquired from data-assimilative ocean models revealed that summer and spring rorqual distribution were influenced by dynamic oceanographic features indicative of active upwelling and frontal zones (respectively 27% and 40% deviance explained). On the continental shelf, blue whales were predicted to occur closer to shore than humpback whales and in the more southern waters off Oregon. Summer and spring rorqual models, and humpback whale models, showed predictive performance suitable for management purposes, assessed through internal cross-validation and comparison to an external dataset (388 groups observed). Indeed, monthly hotspots of high predicted rorqual whale density across multiple years were validated by independent sightings (80% overlap in the summer model). These predictive models lay a robust basis for fine-scale dynamic spatial management to reduce impacts of human activities on endangered populations of rorqual whales in Oregon.
Prognostic Significance of Pretreatment Neutrophil-to-Lymphocyte Ratio, Platelet−to−Lymphocyte Ratio, or Monocyte-to-Lymphocyte Ratio in Endometrial Neoplasms: A Systematic Review and Meta−analysis

Aim Neutrophil–lymphocyte ratio (NLR), platelet–lymphocyte ratio (PLR), or monocyte–lymphocyte ratio (MLR) has been shown to be related to the poor prognosis of cervical cancer, ovarian cancer, breast cancer, and other malignant tumors, but their role in predicting the prognosis of endometrial cancer is still controversial. Therefore, we conducted this meta-analysis to evaluate the effectiveness of NLR more accurately, PLR, or MLR in predicting the prognosis of endometrial cancer (EC). Methods This review systematically searched for relevant publications in databases of the Cochrane Library, PubMed, EMBASE, CNKI, WanFang, VIP, and CBM. Pooled hazard ratios (HR) with 95% confidence intervals (95% CI) were determined and used to explore the association between inflammatory biomarkers (NLR, PLR, and MLR) and overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS) in a random-effects model. We also conducted subgroup analysis and publication bias in this meta-analysis. Stata 12.0 was used for statistical analysis. Results This meta-analysis contained 14 eligible studies including 5,274 patients. Our results showed that NLR or PLR was associated with OS [NLR: HR, 2.51; 95% CI, 1.70–3.71; p <0.001 in univariate analysis (Ua); HR, 1.87; 95% CI, 1.34–2.60; p <0.001 in multivariate analysis (Ma); PLR: HR, 2.50; 95% CI, 1.82–3.43; p <0.001 in Ua; HR, 1.86; 95% CI, 1.22–2.83; p = 0.004 in Ma], but MLR was not associated with OS (HR, 1.44; 95% CI, 0.70–2.95; p = 0.325 in Ua; HR, 1.01; 95% CI, 0.39–2.60; p =0.987 in Ma). A further subgroup analysis found that the correlations were not affected by race, cutoff value, sample size, or treatment. Our meta-analysis showed that NLR or PLR was associated with DFS (NLR: HR, 2.50; 95% CI, 1.38–4.56; p =0.003 in Ua; HR, 2.06; 95% CI, 1.26–3.37, P =0.004 in Ma; PLR: HR, 1.91; 95% CI, 1.30–2.81; p = 0.001 in Ua), and NLR was associated with PFS only in the univariate analysis (HR, 1.71; 95% CI, 1.04–2.81; p =0.035 in Ua; HR, 1.79; 95% CI, 0.65–4.89; P =0.257 in Ma), but MLR was not associated with DFS (HR, 0.36; 95% CI, 0.03–4.13; p =0.409 in Ua). Conclusions Our results indicated that pretreatment NLR and PLR were biomarkers of poor prognosis in patients with endometrial cancer. The results indicated that NLR or PLR was associated with OS and disease-free survival DFS, and NLR was associated with PFS only in univariate analysis, but MLR was not associated with OS or DFS.