A non-negative spike-and-slab lasso generalized linear stacking prediction modeling method for high-dimensional omics data.

BACKGROUND: High-dimensional omics data are increasingly utilized in clinical and public health research for disease risk prediction. Many previous sparse methods have been proposed that using prior knowledge, e.g., biological group structure information, to guide the model-building process. However, these methods are still based on a single model, offen leading to overconfident inferences and inferior generalization. RESULTS: We proposed a novel stacking strategy based on a non-negative spike-and-slab Lasso (nsslasso) generalized linear model (GLM) for disease risk prediction in the context of high-dimensional omics data. Briefly, we used prior biological knowledge to segment omics data into a set of sub-data. Each sub-model was trained separately using the features from the group via a proper base learner. Then, the predictions of sub-models were ensembled by a super learner using nsslasso GLM. The proposed method was compared to several competitors, such as the Lasso, grlasso, and gsslasso, using simulated data and two open-access breast cancer data. As a result, the proposed method showed robustly superior prediction performance to the optimal single-model method in high-noise simulated data and real-world data. Furthermore, compared to the traditional stacking method, the proposed nsslasso stacking method can efficiently handle redundant sub-models and identify important sub-models. CONCLUSIONS: The proposed nsslasso method demonstrated favorable predictive accuracy, stability, and biological interpretability. Additionally, the proposed method can also be used to detect new biomarkers and key group structures.

A novel non-negative Bayesian stacking modeling method for Cancer survival prediction using high-dimensional omics data.

BACKGROUND: Survival prediction using high-dimensional molecular data is a hot topic in the field of genomics and precision medicine, especially for cancer studies. Considering that carcinogenesis has a pathway-based pathogenesis, developing models using such group structures is a closer mimic of disease progression and prognosis. Many approaches can be used to integrate group information; however, most of them are single-model methods, which may account for unstable prediction. METHODS: We introduced a novel survival stacking method that modeled using group structure information to improve the robustness of cancer survival prediction in the context of high-dimensional omics data. With a super learner, survival stacking combines the prediction from multiple sub-models that are independently trained using the features in pre-grouped biological pathways. In addition to a non-negative linear combination of sub-models, we extended the super learner to non-negative Bayesian hierarchical generalized linear model and artificial neural network. We compared the proposed modeling strategy with the widely used survival penalized method Lasso Cox and several group penalized methods, e.g., group Lasso Cox, via simulation study and real-world data application. RESULTS: The proposed survival stacking method showed superior and robust performance in terms of discrimination compared with single-model methods in case of high-noise simulated data and real-world data. The non-negative Bayesian stacking method can identify important biological signal pathways and genes that are associated with the prognosis of cancer. CONCLUSIONS: This study proposed a novel survival stacking strategy incorporating biological group information into the cancer prognosis models. Additionally, this study extended the super learner to non-negative Bayesian model and ANN, enriching the combination of sub-models. The proposed Bayesian stacking strategy exhibited favorable properties in the prediction and interpretation of complex survival data, which may aid in discovering cancer targets.

Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation.

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear 'Bartlett' (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

Osimertinib successfully combats EGFR-negative glioblastoma cells by inhibiting the MAPK pathway.

Glioblastoma (GBM) patients have extremely poor prognoses, and currently no effective treatment available including surgery, radiation, and chemotherapy. MAPK-interacting kinases (MNK1/2) as the downstream of the MAPK-signaling pathway regulate protein synthesis in normal and tumor cells. Research has shown that targeting MNKs may be an effective strategy to treat GBM. In this study we investigated the antitumor activity of osimertinib, an FDA-approved epidermal growth factor receptor (EGFR) inhibitor, against patient-derived primary GBM cells. Using high-throughput screening approach, we screened the entire panel of FDA-approved drugs against primary cancer cells derived from glioblastoma patients, found that osimertinib (3 µM) suppressed the proliferation of a subset (10/22) of EGFR-negative GBM cells (>50% growth inhibition). We detected the gene expression difference between osimertinib-sensitive and -resistant cells, found that osimertinib-sensitive GBM cells displayed activated MAPK-signaling pathway. We further showed that osimertinib potently inhibited the MNK kinase activities with IC50 values of 324 nM and 48.6 nM, respectively, against MNK1 and MNK2 kinases; osimertinib (0.3-3 µM) dose-dependently suppressed the phosphorylation of eukaryotic translation initiation factor 4E (eIF4E). In GBM patient-derived xenografts mice, oral administration of osimertinib (40 mg· kg-1 ·d-1, for 18 days) significantly suppressed the tumor growth (TGI = 74.5%) and inhibited eIF4E phosphorylation in tumor cells. Given the fact that osimertinib could cross the blood-brain barrier and its toxicity was well tolerated in patients, our results suggest that osimertinib could be a new and effective drug candidate for the EGFR-negative GBM patients.

Interleukin-22 Plays a Protective Role by Regulating the JAK2-STAT3 Pathway to Improve Inflammation, Oxidative Stress, and Neuronal Apoptosis following Cerebral Ischemia-Reperfusion Injury.

The interleukins (ILs) are a pluripotent cytokine family that have been reported to regulate ischemic stroke and cerebral ischemia/reperfusion (I/R) injury. IL-22 is a member of the IL-10 superfamily and plays important roles in tissue injury and repair. However, the effects of IL-22 on ischemic stroke and cerebral I/R injury remain unclear. In the current study, we provided direct evidence that IL-22 treatment decreased infarct size, neurological deficits, and brain water content in mice subjected to cerebral I/R injury. IL-22 treatment remarkably reduced the expression of inflammatory cytokines, including IL-1ß, monocyte chemotactic protein- (MCP-) 1, and tumor necrosis factor- (TNF-) α, both in serum and the ischemic cerebral cortex. In addition, IL-22 treatment also decreased oxidative stress and neuronal apoptosis in mice after cerebral I/R injury. Moreover, IL-22 treatment significantly increased Janus tyrosine kinase (JAK) 2 and signal transducer and activator of transcription (STAT) 3 phosphorylation levels in mice and PC12 cells, and STAT3 knockdown abolished the IL-22-mediated neuroprotective function. These findings suggest that IL-22 might be exploited as a potential therapeutic agent for ischemic stroke and cerebral I/R injury.

Silencing IL12p35 Promotes Angiotensin II-Mediated Abdominal Aortic Aneurysm through Activating the STAT4 Pathway.

Background and Purpose. Abdominal aortic aneurysm (AAA) is a chronic inflammatory disorder and the important causes of death among men over the age of 65 years. Interleukin-12p35 (IL12p35) is an inflammatory cytokine that participates in a variety of inflammatory diseases. However, the role of IL12p35 in the formation and development of AAA is still unknown. Experimental Approach. Male apolipoprotein E-deficient (Apoe-/-) mice were generated and infused with 1.44 mg/kg angiotensin II (Ang II) per day. We found that IL12p35 expression was noticeably increased in the murine AAA aorta and isolated aortic smooth muscle cells (SMCs) after Ang II stimulation. IL12p35 silencing promoted Ang II-induced AAA formation and rupture in Apoe-/- mice. IL12p35 silencing markedly increased the expression of inflammatory cytokines, including IL-1ß, IL-6, and tumor necrosis factor-α (TNF-α), in both the serum and AAA aorta. Additionally, IL12p35 silencing exacerbated SMC apoptosis in Apoe-/- mice after Ang II infusion. IL12p35 silencing significantly increased signal transducer and activator of transcription (STAT) 4 phosphorylation levels in AAA mice, and STAT4 knockdown abolished the IL12p35-mediated proinflammatory response and SMC apoptosis. Interpretation. Silencing IL12p35 promotes AAA formation by activating the STAT4 pathway, and IL12p35 may serve as a novel and promising therapeutic target for AAA treatment.

Overexpression of TrpC5 promotes tumor metastasis via the HIF-1α-Twist signaling pathway in colon cancer.

In cancer cells, intracellular Ca2+ homeostasis is altered, and this is involved in tumor initiation, progression, and metastasis. However, little is known about the underlying mechanisms. Here, we report that transient receptor potential channel 5 (TrpC5), a receptor-activated non-selective Ca2+ channel, is correlated with tumor metastasis in colon cancer patients. Moreover, in colon cancer cells, overexpression of TrpC5 caused a robust rise in the concentration of ([Ca2+]i), decreased E-cadherin, and increased mesenchymal biomarker expression, then promoted cell migration, invasion, and proliferation. Interestingly, we found that TrpC5 mediated hypoxia-inducible factor 1α (HIF-1α) expression, activating Twist to promote the epithelial-mesenchymal transition (EMT). Notably, patients with high expression of TrpC5 displayed poorer overall and metastasis-free survival. Taken together, our findings demonstrate that TrpC5 induces the EMT through the HIF-1α-Twist signaling pathway to promote tumor metastasis in colon cancer.

Association of spontaneous abortion with bipolar disorder and major depression based on inverse probability treatment weighting of multigroup propensity scores: Evidence from the UK Biobank.

BACKGROUND: Few studies have explored the association between the number of SAs and bipolar disorder and major depression (BDMD). This study aims to investigate the association between SA and BDMD, and the possible dose-response relationship between them. METHODS: We conducted a cross-sectional study of 13,200 female UK Biobank participants. Participants were classified into BDMD and no-BDMD groups based on their BDMD status. The number of SAs was grouped into non-SA, occasional SA (OSA), and recurrent SA (RSA). Baseline characteristics of the three groups were balanced using inverse probability treatment weighting (IPTW) based on propensity scores. The three-knots restricted cubic spline regression model was utilized to assess the dose-response relationship between the number of SAs and BDMD. RESULTS: The IPTW-adjusted multivariate logistic regression revealed that SA was an independent risk factor for BDMD, with adjusted OR of 1.12 (95 % CI: 1.07-1.19) and 1.32 (95 % CI: 1.25-1.40) in the OSA and RSA groups, respectively. The strength of this association amplified as the number of SAs (P for trend <0.001). There was a nonlinear relationship between the number of SAs and the risk of BDMD, with an approximately inverted L-shaped curve. LIMITATIONS: The information of the SA and BDMD status relied on self-reported by volunteers, and the study sample was mostly of European descent. CONCLUSIONS: Women who reported experiencing multiple SAs are more likely to have BDMD. Therefore, it is imperative to provide psychological care and interventions for women in the postpartum period.

Adverse event profile of CGRP monoclonal antibodies: findings from the FDA adverse event reporting database.

BACKGROUND: Four CGRP Monoclonal Antibodies (mAbs) have been approved for migraine prophylaxis by the Food and Drug Administration (FDA) since 2018. However, there are concerns about the safety of these four drugs for real-world use. OBJECTIVE: To compare the adverse event profiles of four CGRP-mAbs with FAERS data. METHODS: The study was based on records from the FAERS database. Only reports containing one of the active ingredients with CGRP-mAbs were included in this study. Disproportionality analyses including but not limited to reporting odds ratio (ROR) and information components (IC) were conducted to identify drug-AE associations. RESULTS: In total, 58110 reports were identified for CGRP-mAbs. 80 overlapping signals were disproportionately reported. They affected a range of organs and systems, including the gastrointestinal and cardiovascular systems, skin, and hair. Additionally, the rare cardiovascular adverse events were significantly different among the four CGRP-mAbs. CONCLUSION: We identified numerous shared underlying signals (overlapping signals) for CGRP-mAbs as suspected drugs in multiple systems and organs. The unlabeled common signals may indicate potential safety issues. In addition, the underlying safety signals varied among the four CGRP-mAbs, particularly in the cardiovascular system, and further studies are needed to confirm these associations and the potential clinical implications.

Development and validation of a cuproptosis-related prognostic model for acute myeloid leukemia patients using machine learning with stacking.

Our objective is to develop a prognostic model focused on cuproptosis, aimed at predicting overall survival (OS) outcomes among Acute myeloid leukemia (AML) patients. The model utilized machine learning algorithms incorporating stacking. The GSE37642 dataset was used as the training data, and the GSE12417 and TCGA-LAML cohorts were used as the validation data. Stacking was used to merge the three prediction models, subsequently using a random survival forests algorithm to refit the final model using the stacking linear predictor and clinical factors. The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset. In external validation dataset, the corresponding AUCs were 0.741, 0.754 and 0.783. The predictive performance of the model in the external dataset surpasses that of the model simply incorporates all predictors. Additionally, the final model exhibited good calibration accuracy. In conclusion, our findings indicate that the novel prediction model refines the prognostic prediction for AML patients, while the stacking strategy displays potential for model integration.

Association of altitude and frailty in Chinese older adults: using a cumulative frailty index model.

Objective: The population is aging exponentially and the resulting frailty is becoming increasingly evident. We aimed to explore the association between altitude and frailty, and to identify associated factors for frailty. Methods: This is a community-based cross-sectional survey. 1,298 participants aged ≥60 years from three different altitudes were included in the study. To quantify frailty, we constructed a frailty index (FI) and a frailty score (FS). The FI was divided into non-frailty, prefrailty, and frailty. The Odds Ratios and confidence intervals (ORs, 95%CIs) were used to evaluate the association between altitude and FI and FS in multivariate ordinal logistic regression and linear regression. Results: There were 560 (53.1%) participants in the prefrailty and 488 (37.6%) in the frailty group. The FS increased with higher altitude (P for trend <0.001). Multivariate ordinal logistic regression analysis revealed an association between altitude and frailty, OR = 1.91 (95% CI: 1.38-2.64) in mid-high altitude and 2.49 (95% CI:1.40-4.45) in high altitude. The same trend of association was found in the univariate analysis. The FS increased by 1.69 (95% CI: 0.78-2.60) at mid-high altitude and 3.24 (95%CI:1.66-4.81) at high altitude compared to medium altitude. Conclusion: The study indicates that high altitude exposure is an associated factor for frailty in older adults. This association become stronger with higher altitudes. As a result, it is essential to conduct early frailty screening for residents living at high altitudes.

Cav3.2 channel regulates cerebral ischemia/reperfusion injury: a promising target for intervention.

JOURNAL/nrgr/04.03/01300535-202419110-00028/figure1/v/2024-03-08T184507Z/r/image-tiff Calcium influx into neurons triggers neuronal death during cerebral ischemia/reperfusion injury. Various calcium channels are involved in cerebral ischemia/reperfusion injury. Cav3.2 channel is a main subtype of T-type calcium channels. T-type calcium channel blockers, such as pimozide and mibefradil, have been shown to prevent cerebral ischemia/reperfusion injury-induced brain injury. However, the role of Cav3.2 channels in cerebral ischemia/reperfusion injury remains unclear. Here, in vitro and in vivo models of cerebral ischemia/reperfusion injury were established using middle cerebral artery occlusion in mice and high glucose hypoxia/reoxygenation exposure in primary hippocampal neurons. The results showed that Cav3.2 expression was significantly upregulated in injured hippocampal tissue and primary hippocampal neurons. We further established a Cav3.2 gene-knockout mouse model of cerebral ischemia/reperfusion injury. Cav3.2 knockout markedly reduced infarct volume and brain water content, and alleviated neurological dysfunction after cerebral ischemia/reperfusion injury. Additionally, Cav3.2 knockout attenuated cerebral ischemia/reperfusion injury-induced oxidative stress, inflammatory response, and neuronal apoptosis. In the hippocampus of Cav3.2-knockout mice, calcineurin overexpression offset the beneficial effect of Cav3.2 knockout after cerebral ischemia/reperfusion injury. These findings suggest that the neuroprotective function of Cav3.2 knockout is mediated by calcineurin/nuclear factor of activated T cells 3 signaling. Findings from this study suggest that Cav3.2 could be a promising target for treatment of cerebral ischemia/reperfusion injury.

Shunt-Dependent Post-Traumatic Hydrocephalus: Predictors and Long-Term Functional Outcomes.

INTRODUCTION: As a disorder of the brain in adults and children, traumatic brain injury (TBI) is considered the major cause of mortality and morbidity. As a serious complication of TBI, post-traumatic hydrocephalus (PTH) is commonly identified and significantly associated with neurocognitive impairment, motor dysfunction, and growth impairment. The long-term functional outcomes after shunt dependence are totally not clear. METHODS: This study included 6279 patients between 2012 and 2022. To identify the unfavorable functional outcomes and the PTH-related factors, we carried out univariable logistic regression analyses. To identify the occurrence time of PTH, we conducted the log-rank test and Kaplan-Meier analysis. RESULTS: Mean patient age was 51.03 ± 22.09 years. Of the 6279 patients with TBI, 327 developed PTH (5.2%). Several PTH development-associated factors, such as intracerebral hematoma, diabetes, longer initial hospital stay, craniotomy, low GCS (Glasgow Coma Scale), EVD (external ventricular drain), and DC (decompressive craniectomy) (p < 0.01), were identified. We also analyzed the factors of unfavorable outcomes after TBI including > 80 years, repeated operations, hypertension, EVD, tracheotomy, and epilepsy (p < 0.01). Ventriculoperitoneal shunt (VPS) itself is not an independent factor of the unfavorable outcome but shunt complication is a strong independent factor of unfavorable outcome (p < 0.05). CONCLUSION: We should emphasize the practices that can minimize the risks of shunt complications. Additionally, the rigorous radiographic and clinical surveillance will benefit those patients at high risk of developing PTH. TRIAL REGISTRATION: ClinicalTrials.gov identifier, ChiCTR2300070016.

Association between total bilirubin and gender-specific incidence of fundus arteriosclerosis in a Chinese population: a retrospective cohort study.

To investigate the gender-specific relationship between total bilirubin (TBIL) and fundus arteriosclerosis in the general population, and to explore whether there is a dose-response relationship between them. In a retrospective cohort study, 27,477 participants were enrolled from 2006 to 2019. The TBIL was divided into four groups according to the quartile. The Cox proportional hazards model was used to estimate the HRs with 95% CIs of different TBIL level and fundus arteriosclerosis in men and women. The dose-response relationship between TBIL and fundus arteriosclerosis was estimated using restricted cubic splines method. In males, after adjusting for potential confounders, the Q2 to Q4 level of TBIL were significantly associated with the risk of fundus arteriosclerosis. The HRs with 95% CIs were 1.217 (1.095-1.354), 1.255 (1.128-1.396) and 1.396 (1.254-1.555), respectively. For females, TBIL level was not associated with the incidence of fundus arteriosclerosis. In addition, a linear relationship between TBIL and fundus arteriosclerosis in both genders (P < 0.0001 and P = 0.0047, respectively). In conclusion, the incidence of fundus arteriosclerosis is positively correlated with serum TBIL level in males, but not in females. In addition, there was a linear dose-response relationship between TBIL and incidence of fundus arteriosclerosis.

Sex-specific association of serum uric acid trajectories with risk of incident retinal arteriosclerosis in Chinese population: A population-based longitudinal study.

Background: The impact of serum uric acid (SUA) trajectories on the development of retinal arteriosclerosis is uncertain. The purpose of this study was to identify adult SUA trajectories by sex and determine their association with risk of retinal arteriosclerosis. Methods: In this longitudinal study, 4,324 participants who were aged between 18 and 60 years without retinal arteriosclerosis at or before baseline (from January 1, 2010, through December 31, 2010) were included. Group-based trajectory modeling was used to identify SUA trajectories during the exposure period (from January 1, 2006, through December 31, 2010). Cox proportional-hazards models were applied to evaluate the associations between SUA trajectories and the risk of incident retinal arteriosclerosis during the outcome period (from January 1, 2011, through December 31, 2019). Results: 4 distinct SUA trajectories were identified in both women and men: low, moderate, moderate-high, and high. During a median follow-up of 9.54 years (IQR 9.53-9.56), 97 women and 295 men had developed retinal arteriosclerosis. In the fully adjusted model, a significant association between the moderate-high SUA trajectory group and incidence of retinal arteriosclerosis was observed only in men (HR: 1.76, 95% CI: 1.17-2.65) compared with the low trajectory group, but not in women (HR: 0.77, 95% CI: 0.39-1.52). Also, the high SUA trajectory group had the highest risk with an adjusted HR of 1.81 (95% CI, 1.04-3.17) in men. However, they did not exhibit a substantially increased risk in women. Conclusion: Higher SUA trajectory groups were significantly associated with an increased risk of incident retinal arteriosclerosis in men but not in women.

Predicting monthly hospital outpatient visits based on meteorological environmental factors using the ARIMA model.

Accurate forecasting of hospital outpatient visits is beneficial to the rational planning and allocation of medical resources to meet medical needs. Several studies have suggested that outpatient visits are related to meteorological environmental factors. We aimed to use the autoregressive integrated moving average (ARIMA) model to analyze the relationship between meteorological environmental factors and outpatient visits. Also, outpatient visits can be forecast for the future period. Monthly outpatient visits and meteorological environmental factors were collected from January 2015 to July 2021. An ARIMAX model was constructed by incorporating meteorological environmental factors as covariates to the ARIMA model, by evaluating the stationary [Formula: see text], coefficient of determination [Formula: see text], mean absolute percentage error (MAPE), and normalized Bayesian information criterion (BIC). The ARIMA [Formula: see text] model with the covariates of [Formula: see text], [Formula: see text], and [Formula: see text] was the optimal model. Monthly outpatient visits in 2019 can be predicted using average data from past years. The relative error between the predicted and actual values for 2019 was 2.77%. Our study suggests that [Formula: see text], [Formula: see text], and [Formula: see text] concentration have a significant impact on outpatient visits. The model built has excellent predictive performance and can provide some references for the scientific management of hospitals to allocate staff and resources.

α-Lipoic Acid-Plus Ameliorates Endothelial Injury by Inhibiting the Apoptosis Pathway Mediated by Intralysosomal Cathepsins in an In Vivo and In Vitro Endothelial Injury Model.

α-Lipoic acid-plus (LAP), an amine derivative of α-lipoic acid, has been reported to protect cells from oxidative stress damage by reacting with lysosomal iron and is more powerful than desferrioxamine (DFO). However, the role of LAP in experimental carotid artery intimal injury (CAII) has not yet been well investigated. Therefore, we sought to uncover the role and potential endovascular protective mechanisms of LAP in endothelial injury. In vitro, oxyhemoglobin (OxyHb) stimulation of cultured human umbilical vein endothelial cells (HUVECs) simulated intimal injury. In vivo, balloon compression injury of the carotid artery was used to establish a rat CAII model. We found that the protein levels of cathepsin B/D, ferritin, transferrin receptor (TfR), cleaved caspase-3, and Bax increased in the injured endothelium and HUVECs but were rectified by DFO and LAP treatments, as revealed by western blotting and immunofluorescence staining. Additionally, DFO and LAP decreased oxidative stress levels and endothelial cell necrosis of the damaged endothelium. Moreover, DFO and LAP significantly ameliorated the increased oxidative stress, iron level, and lactic dehydrogenase activity of HUVECs and improved the reduced HUVEC viability induced by OxyHb. More importantly, DFO and LAP significantly reduced mitochondrial damage and were beneficial for maintaining lysosomal integrity, as indicated by acridine orange (AO), Lyso-Tracker Red, JC-1, and ATPB staining in HUVECs. Finally, LAP might offer more significant endovascular protective effects than DFO. Our data suggested that LAP exerted endovascular protective effects by inhibiting the apoptosis signaling pathway mediated by intralysosomal cathepsins by reacting with excessive iron in endothelial lysosomes after intimal injury.

Efficient feature extraction from highly sparse binary genotype data for cancer prognosis prediction using an auto-encoder.

Genomics involving tens of thousands of genes is a complex system determining phenotype. An interesting and vital issue is how to integrate highly sparse genetic genomics data with a mass of minor effects into a prediction model for improving prediction power. We find that the deep learning method can work well to extract features by transforming highly sparse dichotomous data to lower-dimensional continuous data in a non-linear way. This may provide benefits in risk prediction-associated genotype data. We developed a multi-stage strategy to extract information from highly sparse binary genotype data and applied it for cancer prognosis. Specifically, we first reduced the size of binary biomarkers via a univariable regression model to a moderate size. Then, a trainable auto-encoder was used to learn compact features from the reduced data. Next, we performed a LASSO problem process to select the optimal combination of extracted features. Lastly, we applied such feature combination to real cancer prognostic models and evaluated the raw predictive effect of the models. The results indicated that these compressed transformation features could better improve the model's original predictive performance and might avoid an overfitting problem. This idea may be enlightening for everyone involved in cancer research, risk reduction, treatment, and patient care via integrating genomics data.

Knowledge, attitude, and practice associated with antimicrobial resistance among medical students between 2017 and 2022: A survey in East China.

This study described the knowledge, attitude, practice regarding antimicrobial resistance (AMR) among medical students between 2017 and 2022 in East China. A questionnaire-based survey was conducted with a total of 1,066 respondents. We highlighted that the undergraduates had a significant increase in the knowledge of antimicrobial resistance during the 5 years from 2017 to 2022 (p < 0.001). The majority of the assertions about the AMR were correctly identified by respondents. However, gaps were still observed in the issues of antimicrobial targets and bacterial transmission. In addition, overconfident attitudes and inappropriate behaviors of antimicrobial overuse and misuse were observed in the respondents. A number of 30.2% to 45.2% of the respondents asserted that there is no risk of AMR as long as the antimicrobials are taken correctly, and a proportion of the students (25.3% in 2022; 69.3% in 2017, p < 0.001) declared to buy antimicrobials from friends or family members to treat the same illness. Finally, spearman correlation coefficient was enrolled to compare the correlation of the student's KAP. Results showed that the students' knowledge of antimicrobials had a correlation with attitude (p = 0.0126) and practice (p < 0.001), suggesting that public education on knowledge could influence the behaviors among the medical students. Taken all together, our findings show a need to strengthen the medical students' cogitation on antimicrobial attitude and practice of appropriate usage as an essential strategy to reduce intractable public health problems. Additional curriculum reforms will be needed to add more specific AMR-related lectures to raise awareness amongst medical students in China.

Gliosarcoma: The Distinct Genomic Alterations Identified by Comprehensive Analysis of Copy Number Variations.

Gliosarcoma (GSM), a histologic variant of glioblastoma (GBM), carries a poor prognosis with less than one year of median survival. Though GSM is similar with GBM in most clinical and pathological symptoms, GBM has unique molecular and histological features. However, as the rarity of GSM samples, the genetic information of this tumor is still lacking. Here, we take a comprehensive analysis of DNA copy number variations (CNV) in GBM and GSM. Whole genome sequencing was performed on 21 cases of GBM and 15 cases of GSM. CNVKIT is used for CNV calling. Our data showed that chromosomes 7, 8, 9, and 10 were the regions where CNV frequently happened in both GBM and GSM. There was a distinct CNV signal in chromosome 2 especially in GSM. The pathway enrichment of genes with CNV was suggested that the GBM and GSM shared the similar mechanism of tumor development. However, the CNV of some screened genes displayed a disparate form between GBM and GSM, such as AMP, BEND2, HDAC6, FOXP3, ZBTB33, TFE3, and VEGFD. It meant that GSM was a distinct subgroup possessing typical biomarkers. The pathways and copy number alterations detected in this study may represent key drivers in gliosarcoma oncogenesis and may provide a starting point toward targeted oncologic analysis with therapeutic potential.