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1.
BMC Psychiatry ; 24(1): 414, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38834981

ABSTRACT

BACKGROUND: Fostering empathy has been continuously emphasized in the global medical education. Empathy is crucial to enhance patient-physician relationships, and is associated with medical students' academic and clinical performance. However, empathy level of medical students in China and related influencing factors are not clear. METHODS: This was a cross-sectional study among medical students in 11 universities. We used the Jefferson Scale of Empathy Student-version of Chinese version to measure empathy level of medical students. Factors associated with empathy were identified by the univariate and multivariate logistic regression analyses. Based on the variables identified above, the nomogram was established to predict high empathy probability of medical students. Receiver operating characteristic curve, calibration plot and decision curve analysis were used to evaluate the discrimination, calibration and educational utility of the model. RESULTS: We received 10,901 samples, but a total of 10,576 samples could be used for further analysis (effective response rate of 97.02%). The mean empathy score of undergraduate medical students was 67.38 (standard deviation = 9.39). Six variables including gender, university category, only child or not, self-perception doctor-patient relationship in hospitals, interest of medicine, Kolb learning style showed statistical significance with empathy of medical students (P < 0.05). Then, the nomogram was established based on six variables. The validation suggested the nomogram model was well calibrated and had good utility in education, as well as area under the curve of model prediction was 0.65. CONCLUSIONS: We identify factors influencing empathy of undergraduate medical students. Moreover, increasing manifest and hidden curriculums on cultivating empathy of medical students may be needed among medical universities or schools in China.


Subject(s)
Education, Medical, Undergraduate , Empathy , Physician-Patient Relations , Students, Medical , Humans , Students, Medical/psychology , Students, Medical/statistics & numerical data , Cross-Sectional Studies , Male , Female , China , Young Adult , Adult , Nomograms
2.
Wei Sheng Yan Jiu ; 53(3): 427-434, 2024 May.
Article in Chinese | MEDLINE | ID: mdl-38839584

ABSTRACT

OBJECTIVE: To investigate the association between long-term fine particulate matter(PM_(2.5)) exposure and the risk of chronic kidney disease(CKD) in people with abnormal metabolism syndrome(MS) components. METHODS: Based on health checkup data from a hospital in Beijing, a retrospective cohort study was used to collect annual checkup data from 2013-2019. A questionnaire was used to obtain information on demographic characteristics and lifestyle habits. We measured blood pressure, height, weight, waist circumference, concentrations of triglycerides(TG), fasting glucose, and high-density lipoprotein cholesterol(HDL-C). Longitude and latitude were also extracted from the addresses of the study subjects for pollutant exposure data estimation. Logistic regression models were used to explore the estimated effect of long-term PM_(2.5) exposure on the risk of CKD prevalence in people with abnormal MS components. Two-pollutant and multi-pollutant models were developed to test the stability of these result. Subgroup analysis was conducted based on age, the presence of MS, individual MS component abnormalities, and dual-component MS abnormalities. RESULTS: The study included 1540 study subjects with abnormal MS components at baseline, 206 with CKD during the study period. The association between long-term PM_(2.5) exposure and increased risk of CKD in people with abnormal MS fractions was statistically significant, with a 2.26-fold increase in risk of CKD for every 10 µg/m~3 increase in PM_(2.5) exposure(OR=3.26, 95% CI 2.72-3.90). The result in the dual-pollutant models and multi-pollutant models suggested that the association between long-term PM_(2.5) exposure and increased risk of CKD in people with abnormal MS fractions remained stable after controlling for contemporaneous confounding by other air pollutants. The result of subgroup analysis revealed that individuals aged 45 or older, without MS, with TG<1.7 mmol/L, HDL-C≥1.04 mmol/L, without hypertension, and with central obesity and high blood sugar had a stronger association between PM_(2.5) exposure and CKD-related health effects. CONCLUSION: Long-term exposure to PM_(2.5) may increase the risk of CKD in people with abnormal MS components. More attention should be paid to middle-aged and elderly people aged ≥45 years, people with central obesity and hyperglycemia.


Subject(s)
Environmental Exposure , Metabolic Syndrome , Particulate Matter , Renal Insufficiency, Chronic , Humans , Renal Insufficiency, Chronic/etiology , Renal Insufficiency, Chronic/epidemiology , Metabolic Syndrome/etiology , Metabolic Syndrome/epidemiology , Female , Male , Particulate Matter/adverse effects , Particulate Matter/analysis , Middle Aged , Retrospective Studies , Environmental Exposure/adverse effects , Air Pollutants/adverse effects , Air Pollutants/analysis , Adult , Cohort Studies , Risk Factors , Beijing/epidemiology , Aged , Surveys and Questionnaires , Logistic Models
3.
Int J Neurosci ; : 1-15, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38738478

ABSTRACT

BACKGROUND: Sciatica is a phrase used to describe radiating leg discomfort. The most common cause is lumbar disc herniation (LDH), which is considered to start in the nucleus pulposus. Advancements in lipidomics and metabolomics have unveiled the complex role of fatty acid metabolism (FAM) in both healthy and pathological states. However, the specific roles of fatty acid metabolism-related genes (FAMGs) in shaping therapeutic approaches, especially in LDH, remain largely unexplored and are a subject of ongoing research. METHODS: The junction of the weighted correlation network analysis (WGCNA) test with 6 FAMGs enabled the finding of FAMGs. Gene set variation analysis (GSVA) was used to identify the possible biological activities and pathways of FAMGs. LASSO was used to determine diagnostic effectiveness of the four FAMGs in diagnosing LDH. GSE124272, GSE147383, GSE150408, and GSE153761 were utilized to confirm the levels of expression of four FAMGs. RESULTS: Four FAMGs were discovered [Acyl-CoA Thioesterase 4 (ACOT4), Cytochrome P450 Family 4 Subfamily A Member 11 (CYP4A11), Acyl-CoA Dehydrogenase Long Chain (ACADL), Enoyl-CoA Hydratase and 3-Hydroxyacyl CoA Dehydrogenase (EHHADH)] For biological function analysis, mhc class ib receptor activity, response to thyroxine, response to l phenylalanine derivative were emphasized. CONCLUSIONS: FAMGs can help with prognosis and immunology, and provide evidence for fatty acid metabolism-related targeted therapeutics. In LDH, FAMGs and their interactions with immune cells might be therapeutic targets.

4.
Plant Physiol Biochem ; 211: 108695, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38744088

ABSTRACT

The presence of sugar in plant tissue can lead to an increase in the osmotic pressure within cells, a decrease in the freezing point of plants, and protection against ice crystal damage to the tissue. Trehalose is closely related to sucrose, which comprises the largest proportion of sugar and has become a hot topic of research in recent years. Our previous studies have confirmed that a key trehalose synthesis gene, TaTPS11, from the cold-resistant winter wheat DM1, could enhance the cold resistance of plants by increasing sugar content. However, the underlying mechanism behind this phenomenon remains unclear. In this study, we cloned TaTPS11-6D, edited TaTPS11-6D using CRISPR/Cas9 technology and transformed 'Fielder' to obtain T2 generation plants. We screened out OE3-3 and OE8-7 lines with significantly higher cold resistance than that of 'Fielder' and Cri 4-3 edited lines with significantly lower cold resistance than that of 'Fielder'. Low temperature storage limiting factors were measured for OE3-3, OE8-7 and Cri 4-3 treated at different temperatures.The results showed that TaTPS11-6D significantly increased the content of sugar in plants and the transfer of sugar from source to storage organs under cold conditions. The TaTPS11-6D significantly increased the levels of salicylic, jasmonic, and abscisic acids while also significantly decreasing the level of gibberellic acid. Our research improves the model of low temperature storage capacity limiting factor.


Subject(s)
Cold Temperature , Plant Proteins , Triticum , Triticum/genetics , Triticum/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Gene Expression Regulation, Plant , Trehalose/metabolism , Abscisic Acid/metabolism , Oxylipins/metabolism , Cyclopentanes/metabolism , Gibberellins/metabolism , Sucrose/metabolism
5.
Ann Epidemiol ; 94: 127-136, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38735386

ABSTRACT

BACKGROUND: Previous studies have shown that remnant cholesterol (RC) was associated with cardiovascular disease (CVD) among middle-aged or older adults. However, lack of evidence on long-term exposures to RC and their role in CVD risk among young adults. We thus aimed to explore the association between cumulative RC burden and CVD in young adults. METHODS: We enrolled participants younger than 45 years free of CVD history in the Kailuan Study who completed the first three health examinations from 2006 to 2010. Cumulative RC burden included cumulative RC burden score, time-weighted cumulative RC, exposure duration of high RC, and time course of RC accumulation. The outcome was the incidence of CVD. Cox proportional hazard models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) between cumulative RC burden and CVD risk. RESULTS: A total of 15,219 participants were included (73.70% male, median age 39.13 years). During a median follow-up duration of 8.71 years (interquartile range: 8.4-9.15 years), 502 individuals developed CVD. After adjustment for traditional cardiovascular risk factors, highest risk of CVD was observed in participants with the highest cumulative RC burden score (HR, 1.66; 95% CI, 1.29-2.12), the highest quartile time-weighted cumulative RC (HR,1.50; 95% CI, 1.15-1.96), the longest exposure duration of high RC (HR, 1.71; 95% CI, 1.21-2.42), and those with cumulative RC burden and positive slope (HR, 1.79; 95% CI, 1.35-2.36). CONCLUSIONS: Cumulative RC burden increased the risk of CVD among young adults, suggesting that maintaining low RC levels throughout young adulthood may minimize CVD risk.


Subject(s)
Cardiovascular Diseases , Cholesterol , Humans , Male , Cardiovascular Diseases/epidemiology , Female , Adult , Cholesterol/blood , Incidence , Risk Factors , China/epidemiology , Young Adult , Proportional Hazards Models , Middle Aged , Triglycerides/blood
6.
Blood ; 2024 May 28.
Article in English | MEDLINE | ID: mdl-38805639

ABSTRACT

Loss of long-term hematopoietic stem cell (LT-HSC) function ex vivo hampers the success of clinical protocols reliant on culture. However, the kinetics and mechanisms by which this occurs remain incompletely characterized. Here, through time-resolved scRNA-Seq, matched in vivo functional analysis and the use of a reversible in vitro system of early G1 arrest, we define the sequence of transcriptional and functional events occurring during the first ex vivo division of human LT-HSCs. We demonstrate that the sharpest loss of LT-HSC repopulation capacity happens early on, between 6 and 24 hours of culture, before LT-HSCs commit to cell cycle progression. During this time window, LT-HSCs adapt to the culture environment, limiting global variability in gene expression and transiently upregulating gene networks involved in signaling and stress responses. From 24 hours, LT-HSC progression past early G1 contributes to the establishment of differentiation programmes in culture. However, contrary to current assumptions, we demonstrate that loss of HSC function ex vivo is independent of cell cycle progression. Finally, we show that targeting LT-HSC adaptation to culture by inhibiting early activation of JAK/STAT signaling improves HSC long-term repopulating function ex vivo. Collectively, our study demonstrates that controlling early LT-HSC adaptation to ex vivo culture, for example via JAK inhibition, is of critical importance to improve HSC gene therapy and expansion protocols.

7.
Sci Total Environ ; 934: 173340, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38763201

ABSTRACT

Arsenic release and reduction in anoxic environments can be mitigated or facilitated by biochar amendment. However, the key fractions in biochars and how they control arsenic transformation remain poorly understood. In this study, a biochar produced from pomelo peel was rich in colloids and was used to evaluate the roles of the colloidal and residual fractions of biochar in arsenic transformation in anoxic paddy soil. Bulk biochar showed a markedly higher maximum adsorption capacity for As(III) at 1732 mg/kg than for As(V) at 75.7 mg/kg, mainly because of the colloidal fraction on the surface. When compared with the control and treatments with the colloidal/residual fraction, the addition of bulk biochar facilitated As(V) reduction and release in the soil during days 0-12, but decreased the dissolved As(III) concentration during days 12-20. The colloidal fraction revealed significantly higher electron donating capacity (8.26 µmole-/g) than that of bulk biochar (0.88 µmole-/g) and residual fraction (0.65 µmole-/g), acting as electron shuttle to promote As(V) reduction. Because the colloidal fraction was rich in aliphatic carbon, fulvic acid-like compounds, potassium, and calcium, it favored As(III) adsorption when more As(III) was released, probably via organic-cation-As(III) complexation. These findings provide deeper insight into the role of the colloidal fraction of biochar in controlling anaerobic arsenic transformation, which will be helpful for the practical application of biochar in arsenic-contaminated environments.


Subject(s)
Arsenic , Charcoal , Soil Pollutants , Soil , Charcoal/chemistry , Arsenic/analysis , Adsorption , Soil/chemistry , Colloids/chemistry , Citrus/chemistry , Environmental Restoration and Remediation/methods
8.
Cell Stem Cell ; 2024 May 13.
Article in English | MEDLINE | ID: mdl-38754428

ABSTRACT

Autophagy is central to the benefits of longevity signaling programs and to hematopoietic stem cell (HSC) response to nutrient stress. With age, a subset of HSCs increases autophagy flux and preserves regenerative capacity, but the signals triggering autophagy and maintaining the functionality of autophagy-activated old HSCs (oHSCs) remain unknown. Here, we demonstrate that autophagy is an adaptive cytoprotective response to chronic inflammation in the aging murine bone marrow (BM) niche. We find that inflammation impairs glucose uptake and suppresses glycolysis in oHSCs through Socs3-mediated inhibition of AKT/FoxO-dependent signaling, with inflammation-mediated autophagy engagement preserving functional quiescence by enabling metabolic adaptation to glycolytic impairment. Moreover, we show that transient autophagy induction via a short-term fasting/refeeding paradigm normalizes glycolytic flux and significantly boosts oHSC regenerative potential. Our results identify inflammation-driven glucose hypometabolism as a key driver of HSC dysfunction with age and establish autophagy as a targetable node to reset oHSC regenerative capacity.

9.
Nat Commun ; 15(1): 4590, 2024 May 30.
Article in English | MEDLINE | ID: mdl-38816360

ABSTRACT

Nasopharyngeal carcinoma (NPC)-mediated immunosuppression within the tumor microenvironment (TME) frequently culminates in the failure of otherwise promising immunotherapies. In this study, we identify tumor-intrinsic FLI1 as a critical mediator in impairing T cell anti-tumor immunity. A mechanistic inquiry reveals that FLI1 orchestrates the expression of CBP and STAT1, facilitating chromatin accessibility and transcriptional activation of IDO1 in response to T cell-released IFN-γ. This regulatory cascade ultimately leads to augmented IDO1 expression, resulting in heightened synthesis of kynurenine (Kyn) in tumor cells. This, in turn, fosters CD8+ T cell exhaustion and regulatory T cell (Treg) differentiation. Intriguingly, we find that pharmacological inhibition of FLI1 effectively obstructs the CBP/STAT1-IDO1-Kyn axis, thereby invigorating both spontaneous and checkpoint therapy-induced immune responses, culminating in enhanced tumor eradication. In conclusion, our findings delineate FLI1-mediated Kyn metabolism as an immune evasion mechanism in NPC, furnishing valuable insights into potential therapeutic interventions.


Subject(s)
Indoleamine-Pyrrole 2,3,-Dioxygenase , Interferon-gamma , Kynurenine , Proto-Oncogene Protein c-fli-1 , STAT1 Transcription Factor , T-Lymphocytes, Regulatory , Tumor Microenvironment , Kynurenine/metabolism , Interferon-gamma/metabolism , Interferon-gamma/immunology , Animals , Proto-Oncogene Protein c-fli-1/metabolism , Proto-Oncogene Protein c-fli-1/genetics , Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism , Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics , Tumor Microenvironment/immunology , Tumor Microenvironment/drug effects , Humans , Mice , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/drug effects , T-Lymphocytes, Regulatory/metabolism , STAT1 Transcription Factor/metabolism , Cell Line, Tumor , Nasopharyngeal Carcinoma/immunology , Nasopharyngeal Carcinoma/metabolism , Nasopharyngeal Carcinoma/genetics , Nasopharyngeal Carcinoma/pathology , Nasopharyngeal Carcinoma/drug therapy , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/drug effects , Mice, Inbred C57BL , Nasopharyngeal Neoplasms/immunology , Nasopharyngeal Neoplasms/metabolism , Nasopharyngeal Neoplasms/pathology , Nasopharyngeal Neoplasms/drug therapy , Nasopharyngeal Neoplasms/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , Tumor Escape/drug effects , Mice, Knockout
10.
iScience ; 27(6): 109869, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38799568

ABSTRACT

The core of telomerase consists of the protein subunit telomerase reverse transcriptase (TERT) and the telomerase RNA component (TERC). So far, the role of TERC in cancer development has remained elusive. Here, we found TERC expression elevated in non-small cell lung cancer (NSCLC) tissues, which was associated with disease progression and poor prognosis in patients. Using NSCLC cell lines and xenograft models, we showed that knockdown of TERC caused cell cycle arrest, and inhibition of cell proliferation and migration. Mechanistically, TERC was exported to the cytoplasm by nuclear RNA export factor 1 (NXF1), where it mediated the interaction of TERT with other telomerase subunits. Depletion of TERC hindered the assembly and subsequent nuclear localization of the telomerase complex, preventing TERT from functioning in telomere maintenance and transcription regulation. Our findings suggest that TERC is a potential biomarker for NSCLC diagnosis and prognosis and can be a target for NSCLC treatment.

11.
Arch Gerontol Geriatr ; 124: 105445, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38733919

ABSTRACT

OBJECT: The relationship between sleep duration trajectories and cognitive decline remains uncertain. This study aims to examine the connections between various patterns of sleep duration and cognitive function. METHODS: Group-based trajectory modeling (GBTM) was employed to identify longitudinal trajectories of sleep duration over four-year follow-up period, while considering age, sex and nap duration as adjustments. Logistic regression was utilized to analyze the association between sleep trajectories and cognition, with odds ratios (OR) and 95 % confidence intervals (CI) reported. Subgroup analyses based on various demographic characteristics were conducted to explore potential differences in sleep trajectories and cognitive decline across different population subgroups. RESULTS: A total of 5061 participants were followed for four years, and three sleep duration trajectories were identified: high increasing (n = 2101, 41.6 %), stable increasing (n = 2087, 40.7 %), and low decreasing (n = 873, 17.7 %). After adjustment for basic demographic information, health status, and baseline cognition, the high increasing trajectory was found to be associated with cognitive decline in terms of global cognition (OR:1.52,95 %CI:1.18-1.96), mental intactness (OR:1.36,95 %CI:1.07-1.73) and episodic memory (OR:1.33, 95 %CI:1.05-1.67), as compared to stable increasing trajectory. These associations were particularly prominent among the non-elderly population (≤65 years) and those without depressive symptoms. CONCLUSION: This study suggests that both high increasing and low decreasing sleep duration trajectories are linked to cognitive decline, as compared to the stable increasing trajectory. Long-term attention to changes in sleep duration facilitates early prevention of cognitive decline.

12.
Inj Prev ; 2024 May 20.
Article in English | MEDLINE | ID: mdl-38768979

ABSTRACT

BACKGROUND: Practical interventions of fall prevention are challenging for infants and toddlers. This study aimed to explore specific details of falls that occurred at home for kids 0-3 years old using key information from social media platforms, which provided abundant data sources for fall events. METHODS: We used internet-based search techniques to collect fall events information from 2013 to 2023. The search was restricted and implemented between 1 and 12 April 2023. Online platforms included Baidu, Weibo, WeChat, TikTok, Toutiao and Little Red Book. A qualitative descriptive approach was used to analyse the fall events and major factors, including the fall event time, child age, environmental factors and behavioural characteristics of children and caregivers. RESULTS: We identified 1005 fall injury cases among infants and toddlers. Fall mechanisms included falls from household furniture (71.2%), falls from height (21.4%) and falls on the same level (7.4%). Environmental risk factors mainly consisted of not using or installing bed rails incorrectly, a gap between beds, unstable furniture, slippery ground and windows without guardrails. Behavioural factors included caregivers leaving a child alone, lapsed attention, turning around to retrieve something, misusing baby products, inadequately holding the child and falling asleep with children. Child behavioural factors included walking or running while holding an object in hand or mouth and underdeveloped walking skills. CONCLUSION: Interventions for preventing falls should be designed specifically for Chinese families, especially considering family function in the context of Chinese culture. Social media reports could provide rich information for researchers.

13.
Article in English | MEDLINE | ID: mdl-38769265

ABSTRACT

Litchi and longan pests significantly affect crop yield and quality. Chemical prevention and control are very effective for production; therefore, it is crucial to study fate assessment and appropriate field efficacy before pesticide application on crops to appropriately assess the health and ecological risks linked with these agents. This study conducted Good Agricultural Practice (GAP) field trials and laboratory experiments to elucidate the dissipation, terminal residues, and efficacy of methoxyfenozide on litchi and longan in six locations throughout China. To detect methoxyfenozide residues on litchi and longan, a QuEChERS/UPLC-MS/MS-based method was designed. The initial methoxyfenozide levels in litchi and longan ranged from 2.21-2.86 to 0.83-0.95 mg kg-1 and indicated half-lives of 5.1-5.3 and 5.3-5.7 days, respectively. After 7 days of foliage treatment, the concentrations of terminal methoxyfenozide residue were 0.78-2.61 and 0.02-1.01 mg kg-1, which were less than the established maximum residue limit for methoxyfenozide in litchi and longan. The chronic (acceptable daily intake = 0.0055-0.0331%) dietary intake risk analysis for methoxyfenozide in longan and litchi indicated acceptable concentrations of terminal residue for the general population. Methoxyfenozide in litchi and longan was readily degraded in first-order kinetics models, the degradation rate on longan was higher than that on litchi, and their dietary risks were negligible to consumers. Two hundred forty grams per liter of methoxyfenozide suspension concentrate (SC) represents a highly efficacious insecticidal dose to control litchi and longan pests and indicates a significant application potential as it is rapidly degraded and linked with reduced post-treatment residue levels.

14.
ACS Omega ; 9(13): 15401-15409, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38585126

ABSTRACT

The addition of antioxidants to rubber is one of the most economical and effective methods for delaying rubber aging. However, antioxidant migration can cause environmental pollution. To address this issue, a new reactive antioxidant was synthesized via the chemical bonding of glycidyl methacrylate (GMA) and p-aminodiphenylamine (PPDA). The product was characterized by Fourier-transform infrared spectroscopy, which confirmed the successful reaction between GMA and PPDA, resulting in a compound with the expected structure. The mixture was then combined with a composite of styrene-butadiene rubber and carbon black. The tensile strength, antioxidant properties, migration, and RPA of the resulting materials were tested and compared with those of the commercial antioxidants N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine, N-isopropyl-N'-phenyl-1,4-phenylenediamine, and poly(1,2-dihydro-2,2,4-trimethylquinoline). After the glycidyl methacrylate antioxidant was grafted onto p-aminodiphenylamine, it became highly compatible with and dispersed in the rubber matrix. The antiaging and antimigration properties of the rubber antioxidants were enhanced without damaging the mechanical properties of the rubber matrix. The short-term and long-term antiaging and antimigration properties of this antioxidant are superior to those of commercially available antioxidants.

15.
J Pathol Clin Res ; 10(2): e356, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38602501

ABSTRACT

Anaplastic thyroid carcinoma (ATC) is the most advanced and aggressive thyroid cancer, and poorly differentiated thyroid carcinoma (PDTC) lacks anaplastic histology but has lost architectural and cytologic differentiation. Only a few studies have focused on the genetic relationship between the two advanced carcinomas and coexisting differentiated thyroid carcinomas (DTCs). In the present study, we investigated clinicopathologic features and genetic profiles in 57 ATC and PDTC samples, among which 33 cases had concomitant DTC components or DTC history. We performed immunohistochemistry for BRAF V600E, p53, and PD-L1 expression, Sanger sequencing for TERT promoter and RAS mutations, and fluorescence in situ hybridization for ALK and RET rearrangements. We found that ATCs and PDTCs shared similar gene alterations to their coexisting DTCs, and most DTCs were aggressive subtypes harboring frequent TERT promoter mutations. A significantly higher proportion of ATCs expressed p53 and PD-L1, and a lower proportion expressed PAX-8 and TTF-1, than the coexisting DTCs. Our findings provide more reliable evidence that ATCs and PDTCs are derived from DTCs.


Subject(s)
Adenocarcinoma , Ehlers-Danlos Syndrome , Proline/analogs & derivatives , Thiocarbamates , Thyroid Neoplasms , Humans , B7-H1 Antigen , In Situ Hybridization, Fluorescence , Tumor Suppressor Protein p53/genetics , Thyroid Neoplasms/genetics
16.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38632951

ABSTRACT

In cancer genomics, variant calling has advanced, but traditional mean accuracy evaluations are inadequate for biomarkers like tumor mutation burden, which vary significantly across samples, affecting immunotherapy patient selection and threshold settings. In this study, we introduce TMBstable, an innovative method that dynamically selects optimal variant calling strategies for specific genomic regions using a meta-learning framework, distinguishing it from traditional callers with uniform sample-wide strategies. The process begins with segmenting the sample into windows and extracting meta-features for clustering, followed by using a pre-trained meta-model to select suitable algorithms for each cluster, thereby addressing strategy-sample mismatches, reducing performance fluctuations and ensuring consistent performance across various samples. We evaluated TMBstable using both simulated and real non-small cell lung cancer and nasopharyngeal carcinoma samples, comparing it with advanced callers. The assessment, focusing on stability measures, such as the variance and coefficient of variation in false positive rate, false negative rate, precision and recall, involved 300 simulated and 106 real tumor samples. Benchmark results showed TMBstable's superior stability with the lowest variance and coefficient of variation across performance metrics, highlighting its effectiveness in analyzing the counting-based biomarker. The TMBstable algorithm can be accessed at https://github.com/hello-json/TMBstable for academic usage only.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , High-Throughput Nucleotide Sequencing/methods , Genomics/methods , Genome , Algorithms
18.
Nat Commun ; 15(1): 2827, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38565528

ABSTRACT

Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.


Subject(s)
Bacteriophages , Bacteriophages/genetics , Ecosystem , Phosphorus , Metagenome/genetics , Soil
19.
Microorganisms ; 12(4)2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38674734

ABSTRACT

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and ß diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

20.
Molecules ; 29(8)2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38675680

ABSTRACT

This study presents a method for analyzing dimethomorph residues in lychee using QuEChERS extraction and HPLC-MS/MS. The validation parameters for this method, which include accuracy, precision, linearity, and recovery, indicate that it meets standard validation requirements. Following first-order kinetics, the dissipation dynamic of dimethomorph in lychee was determined to range from 6.4 to 9.2 days. Analysis of terminal residues revealed that residues in whole lychee were substantially greater than those in the pulp, indicating that dimethomorph residues are predominantly concentrated in the peel. When applied twice and thrice at two dosage levels with pre-harvest intervals (PHIs) of 5, 7, and 10 days, the terminal residues in whole lychee ranged from 0.092 to 1.99 mg/kg. The terminal residues of the pulp ranged from 0.01 to 0.18 mg/kg, with the residue ratio of whole lychee to pulp consistently exceeding one. The risk quotient (RQ) for dimethomorph, even at the recommended dosage, was less than one, indicating that the potential for damage was negligible. This study contributes to the establishment of maximum residue limits (MRLs) in China by providing essential information on the safe application of dimethomorph in lychee orchards.


Subject(s)
Litchi , Tandem Mass Spectrometry , Chromatography, High Pressure Liquid/methods , Tandem Mass Spectrometry/methods , Litchi/chemistry , Morpholines/analysis , Pesticide Residues/analysis , Food Contamination/analysis
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