Comprehensive analysis of lung adenocarcinoma: Unveiling differential gene expression, survival-linked genes, subtype stratification, and immune landscape implications.

This study offers a detailed exploration of lung adenocarcinoma (LUAD), addressing its heterogeneity and treatment challenges through a multi-faceted analysis that includes gene expression, genetic subtyping, pathway analysis, immune assessment, and drug sensitivity. It identifies 165 genes with significant expression differences and 46 genes associated with survival, revealing insights into oxidative stress and autophagy. LUAD samples were divided into three subtypes using consensus clustering on these 46 genes, with distinct survival outcomes. Gene Set Enrichment Analysis (GSEA) on HALLMARK gene sets indicated pathway variations with survival implications. The immune landscape, analyzed using the CIBERSORT algorithm, showed different immune cell distributions across subtypes, with the first subtype exhibiting a better immune environment and survival prospects. Advanced machine learning techniques developed a risk model from a set of four genes, effectively categorizing patients into high and low-risk groups, validated through external datasets and analyses. This model linked lower risk scores to better clinical stages, with a higher mutation rate and potential immunotherapy benefits observed in the high-risk group. Drug sensitivity assessments highlighted varied treatment responses between risk groups, suggesting avenues for personalized therapy. This comprehensive analysis enhances the understanding of LUAD's molecular and clinical nuances, offering valuable insights for tailored treatment approaches.

Effect of fission defects on tensile strength of U3Si2 Σ5(210) grain boundary from first-principles calculations.

U3Si2 is regarded as a promising accident tolerant fuel (ATF) to replace the commercial fuel UO2; however, grain boundary (GB) embrittlement of U3Si2 caused by irradiation-induced defect segregation remains to be clarified. In this work, the U3Si2 Σ5(210) symmetrically tilted GB is taken as a representative to elucidate the individual effect of xenon (Xe) and vacancy on the tensile strength and failure of GBs using first-principles calculations. Compared with the predicted segregation energies of defects at the most energetically favourable positions of GBs, Si vacancy (VSi) has a much stronger preference to segregate to GBs than that of Xe substitution on the Si sublattice (XeSi). Moreover, the strengthening/embrittlement potency of GBs with single vacancy/Xe is evaluated using the first-principles-based uniaxial tensile test. Although both VSi and XeSi yield a weakening effect on the strength of the U3Si2 Σ5(210) GB, such defective GBs exhibit significantly stronger interface strengths compared to the corresponding defects segregated to the UO2 Σ3(111) GB. The underlying mechanism of strength change of U3Si2 GBs is discussed in terms of charge analysis. Our results can provide a fundamental understanding of the mechanical behavior of irradiated GBs from an atomic perspective.

The genomic and evolutionary landscapes of anaplastic thyroid carcinoma.

Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.

Roles of entrapped bubbles in methanogenic granules under oscillating pressure: Respiration and embolization for intra-granular transport.

Anaerobic granular sludge plays a pivotal role in the treatment of concentrated organic wastewater. However, previous studies on intra- granular transport have generally overlooked lung-like respiration that expedites transport in response to fluctuating pressure. This study explored the activities of calcified and normal granules under simulated hydrostatic pressure oscillations. The results revealed a significant enhancement in the bioactivity of calcified granules under oscillating pressure, contrasting with the comparatively lower bioactivity observed in normal granules. The hypothesis posited that the gas pockets in calcified granules facilitated respiration as the functional structure. The presence of tiny bubbles exhibited a propensity for inducing clogging, thereby diminishing the capillary connectivity essential for substrate diffusion. The proposed respiration and embolization concepts decipher the distinct roles of entrapped bubbles in the granular bioactivity across diverse fluid states. This study offers valuable insights into the impact of fluidization on microscopic transport within granule-based bed reactors.

A single-center retrospective study on epidemiological and Traditional Chinese Medicine syndrome characteristics of 21010 patients with reflux/heartburn symptoms.

OBJECTIVE: To provide a basis for the clinical identification of true and false reflux, integrated traditional Chinese and Western medicine, and psychosomatic treatment, we conducted a retrospective study of the etiology and epidemiological and Traditional Chinese Medicine (TCM) syndrome characteristics of patients with reflux/heartburn symptoms. METHODS: The 210 10 patients with reflux/heartburn treated at Tianjin Nankai Hospital from January 1, 2016, to December 31, 2019, were divided into four groups according to their pathogenesis. Sex, age, course of disease, incidence rate, gastroscopy, 24-h pH-impedance, esophageal manometry, Hamilton Anxiety Scale (HAMA) / Hamilton Depression Scale (HAMD) score, 8-week proton pump inhibitor (PPI) treatment effect, and TCM syndrome characteristics were statistically analyzed. RESULTS: A total of 21010 patients (8864 men and 12146 women), with reflux/heartburn symptoms were screened, including 6284 (29.9%) patients with reflux esophagitis (RE), 10427 (49.6%) patients with non-erosive reflux esophagitis (NERD), 2430 (11.6%) patients with reflux hypersensitivity (RH), and 1870 (8.9%) patients with functional heartburn (FH). The incidence of the disease was higher in women than in men (0.0001). The ranking of the incidence of anxiety and depression in these four groups was FH>RH>NERD>RE ( 0.0001). There were more women than men in the groups with anxiety and more men than women in the groups with depression ( 0.0001), and there was no significant difference in the distribution of anxiety and depression between men and women ( 0.5689). There were significant differences in TCM syndrome characteristics between NERD, RE, and functional esophageal diseases ( 0.01). The highest proportion of functional esophageal disease TCM symptoms was stagnation and phlegm obstruction syndrome (36.16%), and there was no significant difference between RH and FH. The effective rates of PPI treatment at 8 weeks in patients in the RE, NERD, RH, and FH groups were 89%, 72%, 54%, and 0%, respectively. RE was classified into grades A, B, C, and D according to the Los Angeles grading system. The ranking of the incidence of these four grades was A>B>C>D ( 0.0001). The effective rates of PPI treatment at 8 weeks were 91%, 81%, 69%, and 63% in patients with grade A, B, C, and D RE, respectively ( 0.0001). The highest proportion of TCM syndrome types of NERD and RE was the stagnated heat syndrome in the liver and stomach syndrome, 38.99% and 33.90%, respectively. CONCLUSION: Reflux/heartburn symptoms are relatively common in middle-aged women, and NERD is the most common etiology, followed by RE, RH, and FH. The most common TCM syndrome characteristics in NERD and RE were stagnated heat syndrome in the liver and stomach syndrome, and stagnation and phlegm obstruction syndrome in functional esophageal diseases. Most patients with reflux/heartburn symptoms also experienced anxiety and depression.

Understanding xenon and vacancy behavior in UO2, UN and U3Si2: a comparative DFT+U study.

Extensive attention has been paid to accident tolerant fuels (ATFs), such as uranium mononitride (UN) and uranium sesquisilicide (U3Si2), which are regarded as potential candidates to replace uranium dioxide (UO2) in light-water reactors (LWRs). However, the thermodynamic behavior of fission gas atoms in these fuels that can quantitatively affect the burnup characteristics of ATFs needs to be explored. To this end, systematic density functional calculations on the energetic properties of xenon (Xe)-vacancy complexes in UO2, UN and U3Si2 are performed with the GGA+U approach as well as the corrected chemical potential. The stabilities of Xe-vacancy clusters, including interstitial trap site (IS), mono-, bi- and tri-atomic vacancies, are thoroughly assessed. The formation energies of vacancy complexes indicate that they are more likely to form vacancy cluster defects and their complexes with Xe in UO2 and to generate mono-atomic vacancy and Xe-vacancy complexes in both UN and U3Si2. Xe can be strictly confined by the trap sites in UO2 and UN, and yet in U3Si2, it prefers to move to the centre of a large free volume trap site. The strong solubility of Xe in U3Si2 indicates the excellent storage capacity of fission gas products in the matrix. Overall, this work provides comprehensive insights into the origins of the interplay between Xe and vacancies as well as the thermodynamic behavior of defects in uranium-based fuels.

Early Assessment of Chemotherapy Response in Advanced Non-Small Cell Lung Cancer with Circulating Tumor DNA.

Monitoring treatment efficacy early during therapy could enable a change in treatment to improve patient outcomes. We report an early assessment of response to treatment in advanced NSCLC using a plasma-only strategy to measure changes in ctDNA levels after one cycle of chemotherapy. Plasma samples were collected from 92 patients with Stage IIIB-IV NSCLC treated with first-line chemo- or chemoradiation therapies in an observational, prospective study. Retrospective ctDNA analysis was performed using next-generation sequencing with a targeted 198-kb panel designed for lung cancer surveillance and monitoring. We assessed whether changes in ctDNA levels after one or two cycles of treatment were associated with clinical outcomes. Subjects with ≤50% decrease in ctDNA level after one cycle of chemotherapy had a lower 6-month progression-free survival rate (33% vs. 58%, HR 2.3, 95% CI 1.2 to 4.2, log-rank p = 0.009) and a lower 12-month overall survival rate (25% vs. 70%, HR 4.3, 95% CI 2.2 to 9.7, log-rank p < 0.001). Subjects with ≤50% decrease in ctDNA level after two cycles of chemotherapy also had shorter survival. Using non-invasive liquid biopsies to measure early changes in ctDNA levels in response to chemotherapy may help identify non-responders before standard-of-care imaging in advanced NSCLC.

[Comparison between charged aerosol detector and evaporative light scattering detector for analysis of sugar in Zhusheyong Yiqi Fumai and study on accuracy of methods].

Evaporative light scattering detector(ELSD) and charged aerosol detector(CAD) methods were established in this study for the content determination of four kinds of sugars in Zhusheyong Yiqi Fumai(YQFM), and the factors affecting the accuracy of CAD methods were discussed. HPLC-ELSD chromatographic separation was performed on a Shodex Asahipak NH2 P-50 column with acetonitrile-water(75∶25)as the mobile phase, with a flow rate of 0.8 mL·min~(-1), drift tube temperature of 80 ℃. The analysis by HPLC-CAD was performed on the same column with acetonitrile-water as mobile phase for gradient elution, with a flow rate of 0.8 mL·min~(-1), a neb temperature of 45 ℃, and power function(PF) of 1.3. The samples of YQFM were detected by ELSD and CAD respectively. It was found that YQFM was composed of fructose, glucose, sucrose and maltose. The linear relationship of the two methods was good, and the recoveries, reproducibility and stability of these four kinds of sugars measured by the two methods satisfied the requirements of methodology. Both CAD and ELSD detectors were accurate and reliable in detecting saccharides components in YQFM. In addition, it was revealed in this study for the first time that the PF parameter of CAD had an important influence on the accuracy of sugar determination and acted as the key parameter of CAD method. It was also found that for CAD, a non-linear detector, there was no significant difference between the results of linear regression and logarithmic regression.

Complex foot deformities associated with lower limb deformities: a new therapeutic strategy for simultaneous correction using Ilizarov procedure together with osteotomy and soft tissue release.

AIM: The aim of the current study is to introduce a new therapeutic strategy for simultaneous correction of complex foot deformities (CFD) and the associated lower limb deformities (LLD) by using Ilizarov technique with osteotomy and soft tissue procedure and to report its early clinical results. METHODS: A retrospective review of CFD associated with LLD simultaneous correction utilizing the Ilizarov procedure together with osteotomy and soft tissue balance from 2015 to 2019 was conducted. RESULTS: Thirty-two patients were followed for an average of 42.8 months. The mean external fixation time (EFT) was 6.5 months. The mean healing index (HI) was 1.7 months/cm. At the time of fixator removal, plantigrade feet were achieved in all patient and lower limb deformities were corrected. No recurrence of the deformities occurred. The mean LLRS AIM score was improved from 7.5 to 0.3. At the final follow-up, the ASAMI-Paley score was graded as excellent in all limbs in the aspect of bone results, and functional results were defined as excellent in 29 (90.6%) limbs and good in 3 (9.4%) limbs. The mean modified Dimeglio score was significantly improved from 7.2 to 1.3. No deep infection of the osteotomy site or nonunion was noted in the current study. CONCLUSION: The therapeutic strategy by using the Ilizarov procedure together with osteotomy and soft tissue balance is a safe and effective way to simultaneously correct CFD and LLD. LEVEL OF EVIDENCE: Level IV, retrospective case series.

Assessment of a Highly Curated Somatic Oncology Database to Aid in the Interpretation of Clinically Important Variants in Next-Generation Sequencing Results.

This study evaluated the accuracy of NAVIFY Mutation Profiler, a cloud-based CE-IVD software that aids in interpreting clinically relevant variants detected in somatic oncology next-generation sequencing tests. This tool reports tiered classifications based on different levels of clinical evidence from a highly curated, regularly updated database derived from medical guidelines, drug approvals, and peer-reviewed literature. A retrospective analysis was performed on next-generation sequencing results from 37 lung cancer cases treated with chemotherapy (n = 10), EGFR tyrosine kinase inhibitor (TKI) (n = 5), or ALK TKI (n = 22). Several aspects were assessed, including accuracy of interpretation compared with manual curation, validity of curation content updates over time, and agreement with public databases. For chemotherapy cases with no targetable biomarkers, NAVIFY Mutation Profiler did not identify any targeted therapies. In EGFR and ALK TKI cases, the software associated appropriate targeted therapies and accurately interpreted variant combinations containing drug-resistance variants. Of the nine unique ALK mutations conferring resistance to crizotinib, NAVIFY Mutation Profiler provided correct annotation for all mutations, whereas OncoKB and Catalogue of Somatic Mutations in Cancer indicated crizotinib resistance for eight of nine mutations. For 145 variants analyzed, NAVIFY Mutation Profiler and OncoKB showed substantial agreement (Cohen κ = 0.62) for classifying actionable mutations. Furthermore, NAVIFY Mutation Profiler presented accurate targeted therapies across different regions and remained up-to-date with evolving regional approvals and medical guidelines.

Prevalence of smoking among adolescents in China: an updated systematic review and meta-analysis.

OBJECTIVES: Smoking is a major public health problem worldwide. Estimates for smoking prevalence among adolescents in different regions and in the whole of China are important for the development of public health policies. We conducted a systematic review and meta-analysis to estimate the prevalence of smoking among youth in China. STUDY DESIGN: This is a meta-analysis study. METHODS: English (PubMed, EMBASE) and Chinese (China National Knowledge Internet, WANFANG Data, and CBM) databases were independently searched by two investigators from inception to May 2019. Random effects meta-analysis was conducted to estimate the pooled prevalence of smoking. Subgroup analysis and meta-regression were performed to investigate sources of heterogeneity. This study is registered with PROSPERO, number CRD42019130803. RESULTS: In total, 131 articles were included in the meta-analysis, with a total of 146 studies, involving 684,370 Chinese participants. The total prevalence of smoking among youth in mainland China was 8.17% (95% confidence interval: 6.97-9.45). Subgroup analysis showed that the geographic location and gender could significantly influence the prevalence of smoking. Meta-regression analyses revealed study year, sex ratio (male, %), and response rates did not contribute to the heterogeneity of the results (P-value >0.05). Sensitivity analysis showed that the results were statistically stable. CONCLUSION: This meta-analysis indicates that smoking is common among adolescents in China, and the rate varies between different regions. More practical and effective policies targeting adolescents are urgently needed.

Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors.

Meningiomas account for one-third of all primary brain tumors. Although typically benign, about 20% of meningiomas are aggressive, and despite the rigor of the current histopathological classification system there remains considerable uncertainty in predicting tumor behavior. Here, we analyzed 160 tumors from all 3 World Health Organization (WHO) grades (I through III) using clinical, gene expression, and sequencing data. Unsupervised clustering analysis identified 3 molecular types (A, B, and C) that reliably predicted recurrence. These groups did not directly correlate with the WHO grading system, which classifies more than half of the tumors in the most aggressive molecular type as benign. Transcriptional and biochemical analyses revealed that aggressive meningiomas involve loss of the repressor function of the DREAM complex, which results in cell-cycle activation; only tumors in this category tend to recur after full resection. These findings should improve our ability to predict recurrence and develop targeted treatments for these clinically challenging tumors.

A new deep learning model for assisted diagnosis on electrocardiogram.

In order to enhance the accuracy of computer aided electrocardiogram analysis, we propose a deep learning model called CBRNN to assist diagnosis on electrocardiogram for clinical medical service. It combines two sub networks which are convolutional neural network (CNN) and bi-directional recurrent neural network (BRNN). In the model, CNN with one-dimension convolution is employed to extract features for each lead of ECG, and BRNN is used to fuse features of different leads to represent deeper features. In the training step, we use more than 40 thousand training data and more than 19 thousand validation data to obtain the optimal parameters of the model. Besides, by validating our model on more than CCDD 120,000 real data, it achieves an 87.69% accuracy rate, higher than popular deep learning models such as CNN and ResNet. Our model has better accuracy than state-of-the-art models and it is also slightly higher than the average accuracy of human judgement. It can be served for the first round screening of ECG examination clinical diagnosis.

Risk factors for lower respiratory tract infection in children with tracheobronchial foreign body aspiration.

The aim of this study was to determine the risk factors for lower respiratory tract infection (LRTI) in children caused by tracheobronchial foreign body aspiration (TFBA).A total of 351 patients were retrospectively reviewed; all patients were diagnosed with TFBA at West China Hospital of Sichuan University from 2015 to 2017. Univariate analyses and multivariate analysis were used.Age (<2 years) (P < .001), type of foreign body (plant) (P < .001), shape of foreign body (nonsmooth) (P < .001), and residence time of foreign body (>7 days) (P = .001) were risk factors for LRTI on univariate analysis. Multivariate analysis showed age (<2 years) (hazard ratio [HR] = 4.457; 95% confidence interval [CI] = 2.031-6.884; P < .001), type of foreign body (plant) (HR = 2.686; 95% CI = 1.577-3.452; P < .001), shape of foreign body (nonsmooth) (HR = 1.649; 95% CI = 1.437-3.663; P < .008), and residence time of foreign body (>7 days) (HR = 1.751; 95% CI = 1.329-3.554; P = .004) were independent risk factors for LRTI. Furthermore, children with LRTI also had longer lengths of hospital stays and antibiotic use than did children without LRTI.Age, plant foreign body, nonsmooth foreign body, and long-term incarceration were all independent risk factors for LRTI in children. These results can help us to select more appropriate intervention times and stratified treatment for children with TFBA.

Integrated Molecular Characterization of Testicular Germ Cell Tumors.

We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance-KIT, KRAS, and NRAS-exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KIT mutations, increased immune infiltration, globally demethylated DNA, and decreased KRAS copy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas.

Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma.

BACKGROUND: Upper urinary tract urothelial cancer (UTUC) may have unique etiologic and genomic factors compared to bladder cancer. OBJECTIVE: To characterize the genomic landscape of UTUC and provide insights into its biology using comprehensive integrated genomic analyses. DESIGN, SETTING, AND PARTICIPANTS: We collected 31 untreated snap-frozen UTUC samples from two institutions and carried out whole-exome sequencing (WES) of DNA, RNA sequencing (RNAseq), and protein analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Adjusting for batch effects, consensus mutation calls from independent pipelines identified DNA mutations, gene expression clusters using unsupervised consensus hierarchical clustering (UCHC), and protein expression levels that were correlated with relevant clinical variables, The Cancer Genome Atlas, and other published data. RESULTS AND LIMITATIONS: WES identified mutations in FGFR3 (74.1%; 92% low-grade, 60% high-grade), KMT2D (44.4%), PIK3CA (25.9%), and TP53 (22.2%). APOBEC and CpG were the most common mutational signatures. UCHC of RNAseq data segregated samples into four molecular subtypes with the following characteristics. Cluster 1: no PIK3CA mutations, nonsmokers, high-grade

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.

Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using next-generation sequencing remains challenging. We develop MuSE ( http://bioinformatics.mdanderson.org/main/MuSE ), Mutation calling using a Markov Substitution model for Evolution, a novel approach for modeling the evolution of the allelic composition of the tumor and normal tissue at each reference base. MuSE adopts a sample-specific error model that reflects the underlying tumor heterogeneity to greatly improve the overall accuracy. We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequencing.

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.

BACKGROUND: Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events. RESULTS: In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data. CONCLUSIONS: ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD's in other cancers and Mendelian diseases.

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

On the basis of multidimensional and comprehensive molecular characterization (including DNA methalylation and copy number, RNA, and protein expression), we classified 894 renal cell carcinomas (RCCs) of various histologic types into nine major genomic subtypes. Site of origin within the nephron was one major determinant in the classification, reflecting differences among clear cell, chromophobe, and papillary RCC. Widespread molecular changes associated with TFE3 gene fusion or chromatin modifier genes were present within a specific subtype and spanned multiple subtypes. Differences in patient survival and in alteration of specific pathways (including hypoxia, metabolism, MAP kinase, NRF2-ARE, Hippo, immune checkpoint, and PI3K/AKT/mTOR) could further distinguish the subtypes. Immune checkpoint markers and molecular signatures of T cell infiltrates were both highest in the subtype associated with aggressive clear cell RCC. Differences between the genomic subtypes suggest that therapeutic strategies could be tailored to each RCC disease subset.