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[Role of neoadjuvant rectal score in prognosis and adjuvant chemotherapy decision-making in locally advanced rectal cancer following neoadjuvant short-course radiotherapy and consolidation chemotherapy]. ZHONGHUA ZHONG LIU ZA ZHI [CHINESE JOURNAL OF ONCOLOGY] 2024; 46:335-343. [PMID: 38644269 DOI: 10.3760/cma.j.cn112152-20231024-00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Objectives: To assess the prognostic impact of the neoadjuvant rectal (NAR) score following neoadjuvant short-course radiotherapy and consolidation chemotherapy in locally advanced rectal cancer (LARC), as well as its value in guiding decisions for adjuvant chemotherapy. Methods: Between August 2015 and August 2018, patients were eligible from the STELLAR phase III trial (NCT02533271) who received short-course radiotherapy plus consolidation chemotherapy and for whom the NAR score could be calculated. Based on the NAR score, patients were categorized into low (<8), intermediate (8-16), and high (>16) groups. The Kaplan-Meier method, log rank tests, and multivariate Cox proportional hazard regression models were used to evaluate the impact of the NAR score on disease-free survival (DFS). Results: Out of the 232 patients, 24.1%, 48.7%, and 27.2% had low (56 cases), intermediate (113 cases), and high NAR scores (63 cases), respectively. The median follow-up period was 37 months, with 3-year DFS rates of 87.3%, 68.3%, and 53.4% (P<0.001) for the low, intermediate, and high NAR score groups. Multivariate analysis demonstrated that the NAR score (intermediate NAR score: HR, 3.10, 95% CI, 1.30-7.37, P=0.011; high NAR scores: HR=5.44, 95% CI, 2.26-13.09, P<0.001), resection status (HR, 3.00, 95% CI, 1.64-5.52, P<0.001), and adjuvant chemotherapy (HR, 3.25, 95% CI, 2.01-5.27, P<0.001) were independent prognostic factors for DFS. In patients with R0 resection, the 3-year DFS rates were 97.8% and 78.0% for those with low and intermediate NAR scores who received adjuvant chemotherapy, significantly higher than the 43.2% and 50.6% for those who did not (P<0.001, P=0.002). There was no significant difference in the 3-year DFS rate (54.2% vs 53.3%, P=0.214) among high NAR score patients, regardless of adjuvant chemotherapy. Conclusions: The NAR score is a robust prognostic indicator in LARC following neoadjuvant short-course radiotherapy and consolidation chemotherapy, with potential implications for subsequent decisions regarding adjuvant chemotherapy. These findings warrant further validation in studies with larger sample sizes.
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CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only. J Chem Inf Model 2024; 64:2807-2816. [PMID: 37252890 DOI: 10.1021/acs.jcim.3c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Anticancer peptides (ACPs) recently have been receiving increasing attention in cancer therapy due to their low consumption, few adverse side effects, and easy accessibility. However, it remains a great challenge to identify anticancer peptides via experimental approaches, requiring expensive and time-consuming experimental studies. In addition, traditional machine-learning-based methods are proposed for ACP prediction mainly depending on hand-crafted feature engineering, which normally achieves low prediction performance. In this study, we propose CACPP (Contrastive ACP Predictor), a deep learning framework based on the convolutional neural network (CNN) and contrastive learning for accurately predicting anticancer peptides. In particular, we introduce the TextCNN model to extract the high-latent features based on the peptide sequences only and exploit the contrastive learning module to learn more distinguishable feature representations to make better predictions. Comparative results on the benchmark data sets indicate that CACPP outperforms all the state-of-the-art methods in the prediction of anticancer peptides. Moreover, to intuitively show that our model has good classification ability, we visualize the dimension reduction of the features from our model and explore the relationship between ACP sequences and anticancer functions. Furthermore, we also discuss the influence of data set construction on model prediction and explore our model performance on the data sets with verified negative samples.
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StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides. Bioinformatics 2024; 40:btae057. [PMID: 38305458 PMCID: PMC10904144 DOI: 10.1093/bioinformatics/btae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
MOTIVATION Diabetes is a chronic metabolic disorder that has been a major cause of blindness, kidney failure, heart attacks, stroke, and lower limb amputation across the world. To alleviate the impact of diabetes, researchers have developed the next generation of anti-diabetic drugs, known as dipeptidyl peptidase IV inhibitory peptides (DPP-IV-IPs). However, the discovery of these promising drugs has been restricted due to the lack of effective peptide-mining tools. RESULTS Here, we presented StructuralDPPIV, a deep learning model designed for DPP-IV-IP identification, which takes advantage of both molecular graph features in amino acid and sequence information. Experimental results on the independent test dataset and two wet experiment datasets show that our model outperforms the other state-of-art methods. Moreover, to better study what StructuralDPPIV learns, we used CAM technology and perturbation experiment to analyze our model, which yielded interpretable insights into the reasoning behind prediction results. AVAILABILITY AND IMPLEMENTATION The project code is available at https://github.com/WeiLab-BioChem/Structural-DPP-IV.
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Expression and Significance of BCCIP and Glutathione Peroxidase 4 in Clear Cell Renal Cell Carcinoma. Bull Exp Biol Med 2024; 176:363-368. [PMID: 38342812 DOI: 10.1007/s10517-024-06025-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 02/13/2024]
Abstract
In this retrospective study involving 112 patients with clear cell renal cell carcinoma (ccRCC), we analyzed clinical significance and prognostic value of the expression of BCCIP protein interacting with BRCA2 and CDKN1A and glutathione peroxidase 4 (GPX4). The expressions of mRNA and the corresponding proteins were evaluated using reverse transcription PCR and immunohistochemistry. In comparison with control samples of renal peritumoral tissue, the expressions of BCCIP and its mRNA in the tumor tissues were significantly down-regulated, while the expressions of GPX4 and the corresponding mRNA were significantly up-regulated. The down-regulation of BCCIP expression was closely related to histological grade, TNM stage, and lymph node metastasis (p<0.05). The GPX4 overexpression was closely related to tumor size, TNM stage, and the presence of distant metastasis. The Kaplan-Meier survival analysis showed that tumor size, TNM stage, lymph node metastasis, distant metastasis, expressions of BCCIP and GPX4 correlated with progression-free survival (p<0.05). Multivariate Cox regression showed that down-regulation of BCCIP expression and overexpression of GPX4, TNM stage, and distant metastasis were independent prognostic factors of progression-free survival. Thus, down-regulation of BCCIP expression and overexpression of GPX4 are indicatives of progression of ccRCC with poor prognosis. Hence, the control of expression of these proteins can be considered as a novel target for the treatment of ccRCC.
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Myokines and Biomarkers of Frailty in Older Inpatients with Undernutrition: A Prospective Study. J Frailty Aging 2024; 13:82-90. [PMID: 38616363 DOI: 10.14283/jfa.2024.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
BACKGROUND Population aging might increase the prevalence of undernutrition in older people, which increases the risk of frailty. Numerous studies have indicated that myokines are released by skeletal myocytes in response to muscular contractions and might be associated with frailty. This study aimed to evaluate whether myokines are biomarkers of frailty in older inpatients with undernutrition. METHODS The frailty biomarkers were extracted from the Gene Expression Omnibus and Genecards datasets. Relevant myokines and health-related variables were assessed in 55 inpatients aged ≥ 65 years from the Peking Union Medical College Hospital prospective longitudinal frailty study. Serum was prepared for enzyme-linked immunosorbent assay using the appropriate kits. Correlations between biomarkers and frailty status were calculated by Spearman's correlation analysis. Multiple linear regression was performed to investigate the association between factors and frailty scores. RESULTS The prevalence of frailty was 13.21%. The bioinformatics analysis indicated that leptin, adenosine 5'-monophosphate-activated protein kinase (AMPK), irisin, decorin, and myostatin were potential biomarkers of frailty. The frailty group had significantly higher concentrations of leptin, AMPK, and MSTN than the robust group (p < 0.05). AMPK was significantly positively correlated with frailty (p < 0.05). The pre-frailty and frailty groups had significantly lower concentrations of irisin than the robust group (p < 0.05), whereas the DCN concentration did not differ among the groups. Multiple linear regression suggested that the 15 factors influencing the coefficients of association, the top 50% were the ADL score, MNA-SF score, serum albumin concentration, urination function, hearing function, leptin concentration, GDS-15 score, and MSTN concentration. CONCLUSIONS Proinflammatory myokines, particularly leptin, myostatin, and AMPK, negatively affect muscle mass and strength in older adults. ADL and nutritional status play major roles in the development of frailty. Our results confirm that identification of frailty relies upon clinical variables, myokine concentrations, and functional parameters, which might enable the identification and monitoring of frailty.
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MolCAP: Molecular Chemical reActivity Pretraining and prompted-finetuning enhanced molecular representation learning. Comput Biol Med 2023; 167:107666. [PMID: 37956623 DOI: 10.1016/j.compbiomed.2023.107666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Molecular representation learning (MRL) is a fundamental task for drug discovery. However, previous deep-learning (DL) methods focus excessively on learning robust inner-molecular representations by mask-dominated pretraining frameworks, neglecting abundant chemical reactivity molecular relationships that have been demonstrated as the determining factor for various molecular property prediction tasks. Here, we present MolCAP to promote MRL, a graph-pretraining Transformer based on chemical reactivity (IMR) knowledge with prompted finetuning. Results show that MolCAP outperforms comparative methods based on traditional molecular pretraining frameworks, in 13 publicly available molecular datasets across a diversity of biomedical tasks. Prompted by MolCAP, even basic graph neural networks are capable of achieving surprising performance that outperforms previous models, indicating the promising prospect of applying reactivity information to MRL. In addition, manually designed molecular templets are potential to uncover the dataset bias. All in all, we expect our MolCAP to gain more chemical meaningful insights for the entire process of drug discovery.
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Generation of the iPSC line FINi002-A from a male Parkinson's disease patient carrying compound heterozygous mutations in the PRKN gene. Stem Cell Res 2023; 73:103211. [PMID: 37890334 DOI: 10.1016/j.scr.2023.103211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The most common cause of autosomal recessive familial Parkinson's disease (PD) are mutations in the PRKN/PARK2 gene encoding an E3 ubiquitin protein-ligase PARKIN. We report the generation of an iPSC cell line from the fibroblasts of a male PD patient carrying a common missense variant in exon 7 (p.Arg275Trp), and a 133 kb deletion encompassing exon 8, using transiently-present Sendai virus. The established line displays typical human primed iPSC morphology and expression of pluripotency-associated markers, normal karyotype without SNP array-detectable copy number variations and can give rise to derivatives of all three embryonic germ layers. We envisage the usefulness of this iPSC line, carrying a common and well-studied missense mutation in the RING1 domain of the PARKIN protein, for the elucidation of PARKIN-dependent mechanisms of PD using in vitro and in vivo models.
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MicroRNA-206 Contributes to the Progression of Preeclampsia by Suppressing the Viability and Mobility of Trophocytes via the Inhibition of AGTR1. Physiol Res 2023; 72:597-606. [PMID: 38015759 PMCID: PMC10751052 DOI: 10.33549/physiolres.935131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/09/2023] [Indexed: 01/05/2024] Open
Abstract
The development of preeclampsia (PE) is associated with the impaired trophoblast motility. MicroRNAs (miRs) contribute to the modulation of trophoblast invasion. In the current study, the role of miR-206/AGTR1 in the TNF-alpha-induced invasion defect of trophoblasts was explored. The levels of miR-206 and ATGR1 in clinical placenta tissues were investigated. Trophoblasts were treated with TNF-alpha, and the levels of miR-206 and ATGR1 were modulated. Changes in cell viability, invasion, and inflammation in trophoblasts were detected. The level of miR-206 was induced, while the level of AGTR1 was suppressed in placenta tissues. In in vitro assays, TNF-alpha suppressed viability, induced inflammatory response, inhibited invasion, upregulated miR-206, and down-regulated AGTR1. The inhibited expression of miR-206 or the overexpression of AGTR1 counteracted the effects of TNF-alpha, indicating the key role of the miR-206/AGTR1 in progression of PE. Collectively, miR-206 suppressed viability, induced inflammatory response, and decreased invasion of trophoblasts by inhibiting AGTR1.
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Phase I dose escalation and expansion study of golidocitinib, a highly selective JAK1 inhibitor, in relapsed or refractory peripheral T-cell lymphomas. Ann Oncol 2023; 34:1055-1063. [PMID: 37673210 DOI: 10.1016/j.annonc.2023.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Relapsed or refractory peripheral T-cell lymphomas (r/r PTCLs) are a group of rare and aggressive diseases that lack effective therapies. Constitutive activation of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is reported to be associated with PTCLs. Golidocitinib is an oral, potent JAK1 selective inhibitor evaluated in a phase I/II multinational study in patients with r/r PTCLs. PATIENTS AND METHODS Patients with r/r PTCLs were eligible. The primary objectives were to assess safety and tolerability of golidocitinib and to define its recommended phase II dose (RP2D). The secondary objectives were to evaluate its antitumor activity and pharmacokinetics (PK). RESULTS A total of 51 patients were enrolled and received golidocitinib treatment at 150 or 250 mg once daily (QD). The median prior lines of therapies were 2 (range: 1-8). Golidocitinib was tolerated at both doses tested, while a higher incidence of serious adverse events and dose modifications at 250 mg were observed. The most common grade ≥3 drug-related treatment-emergent adverse events were neutropenia (27.5%) and thrombocytopenia (11.8%). An objective response rate of 39.2% and a complete response rate of 21.6% were observed. With median follow-up time of 14.7 and 15.9 months, the median duration of response (DoR) and progression-free survival were 8.0 and 3.3 months, respectively. Based on these data, 150 mg QD was defined as the RP2D. Golidocitinib demonstrated a favorable PK profile as an oral agent. Biomarker analysis suggested a potential correlation between JAK/STAT pathway aberrations and clinical activity of golidocitinib. CONCLUSIONS In this phase I study, golidocitinib demonstrated an acceptable safety profile and encouraging antitumor efficacy in heavily pretreated patients with r/r PTCLs. These results support the initiation of the multinational pivotal study in patients with r/r PTCLs.
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Retrosynthesis prediction with an interpretable deep-learning framework based on molecular assembly tasks. Nat Commun 2023; 14:6155. [PMID: 37788995 PMCID: PMC10547708 DOI: 10.1038/s41467-023-41698-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Automating retrosynthesis with artificial intelligence expedites organic chemistry research in digital laboratories. However, most existing deep-learning approaches are hard to explain, like a "black box" with few insights. Here, we propose RetroExplainer, formulizing the retrosynthesis task into a molecular assembly process, containing several retrosynthetic actions guided by deep learning. To guarantee a robust performance of our model, we propose three units: a multi-sense and multi-scale Graph Transformer, structure-aware contrastive learning, and dynamic adaptive multi-task learning. The results on 12 large-scale benchmark datasets demonstrate the effectiveness of RetroExplainer, which outperforms the state-of-the-art single-step retrosynthesis approaches. In addition, the molecular assembly process renders our model with good interpretability, allowing for transparent decision-making and quantitative attribution. When extended to multi-step retrosynthesis planning, RetroExplainer has identified 101 pathways, in which 86.9% of the single reactions correspond to those already reported in the literature. As a result, RetroExplainer is expected to offer valuable insights for reliable, high-throughput, and high-quality organic synthesis in drug development.
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Prognostic Role and Time Varying Failure Hazard of Neoadjuvant Rectal (NAR) Scores in the Stellar Randomized Phase 3 Trial. Int J Radiat Oncol Biol Phys 2023; 117:S105. [PMID: 37784277 DOI: 10.1016/j.ijrobp.2023.06.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study examined the prognostic role of the neoadjuvant rectal (NAR) score on disease-free survival (DFS) in the STELLAR phase III trial and assessed time-varying failure hazard. MATERIALS/METHODS The study included patients from the STELLAR trial who underwent total mesorecta excision and had calculable NAR scores. Chi-square tests were used to analyze the distribution of demographic information, treatment information, and NAR scores. Kaplan-Meier and Cox regression analyses assessed DFS, while smoothed hazard plots evaluated hazard variations. RESULTS Of 461 patients, 231 received total neoadjuvant therapy (TNT) and 229 received concurrent chemoradiotherapy (CRT). With a median follow-up of 37 months, 3-year DFS rates for low, intermediate, and high NAR scores were 86.2%, 72.671.8%, and 53.153.6%, respectively (P <0.001). In the TNT group, rates for the corresponding NAR score groups were 87.3%, 67.6%, and 52.4% while in the CRT group, rates were 84.7%, 76.0%, and 53.4% (both P <0.001). Multivariate analysis showed NAR scores as independent prognostic factors for DFS (intermediate vs. low, hazard ratio (HR) = 2.452.55, 95% confidence interval (CI): 1.347 - 4.4675, P <0.003; high vs. low, HR = 4.2668, 95% CI: 2.5133 - 8.727.79, P <0.001). The DFS hazardrisk rates for different NAR score groups initially increased and then decreased, peaking in the second year with rates of 5.04.6%, 11.62%, and 21.52% for low, intermediate, and high NAR scores, respectively. After the fourth year, the high NAR score still had a higher failure hazardrisk (12.5%), while the intermediate and low NAR score had a lower relapse hazardrisk (<3%). CONCLUSION The NAR score was a strong prognostic factor for DFS in the STELLAR trial, irrespective of TNT or CRT modalities. Hazard variations at different NAR score levels offer insights for personalized monitoring and warrant further investigation in clinical trials using NAR scores as endpoints. (NCT02533271).
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The Short-Term Efficacy and Safety of Induction Chemotherapy Combined with PD-1 Inhibitor or Anti-EGFR in Locoregionally Advanced Nasopharyngeal Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:e635. [PMID: 37785894 DOI: 10.1016/j.ijrobp.2023.06.2036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study aimed to investigate the short-term efficacy and safety of induction chemotherapy (IC) combined with PD-1 inhibitor or anti-EGFR in the treatment of locoregionally advanced nasopharyngeal carcinoma (LA-NPC). MATERIALS/METHODS We retrospectively reviewed the clinical data of 206 patients with LA-NPC, including IC combined with anti-PD1 (57 patients), IC combined with anti-EGFR (28 patients), and IC alone (121 patients). The short-term efficacy was assessed at the end of IC and one month after overall treatment. According to the RECIST v1.1, the short-term efficacy of cervical lymph nodes and primary nasopharynx foci was divided into complete remission (CR), partial remission (PR), stable disease (SD), and progressive disease (PD). The overall response (ORR) was defined as the sum of CR and PR. Acute toxicities were graded according to the CTCAE v5.0. One-way analysis of variance (ANOVA) was used to compare differences in the numerical variables among groups. Fisher Freeman-Halton test or Pearson Chi-square test was used to compare classified variables. RESULTS The ORR rates of primary nasopharynx foci in IC, anti-EGFR, and anti-PD1 group were 68.60%, 67.9%, and 94.7%, respectively, and the corresponding rates of ORR in cervical lymph nodes were 78.5%, 71.4%, and 93.0%, respectively. There was a statistical difference in the ORR between the three groups. Further analysis showed that after IC or overall treatment, the CR rate of primary nasopharynx foci in the anti-PD1 group was significantly higher than the other two groups. The most common adverse effects were hematotoxicity, gastrointestinal toxicity, and transaminase elevation. However, there were no statistical differences in the frequency of any common adverse effects between the three groups. CONCLUSION The addition of anti-PD1 based on IC significantly improved the short-term efficacy of LA-NPC and toxicities were tolerable.
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Early Cardiotoxicity in Patients Receiving Hypofractionated Radiotherapy after Breast Conserving Surgery: Analysis of a Prospective Study. Int J Radiat Oncol Biol Phys 2023; 117:e169. [PMID: 37784775 DOI: 10.1016/j.ijrobp.2023.06.1008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) To evaluate the early cardiotoxicity of hypofractionated radiotherapy (HFRT) in patients with left-sided breast cancer after breast-conserving surgery, and to investigate the correlation between cardiotoxicity and cardiac dose. MATERIALS/METHODS A total of 103 women from 2017 to 2018 who received left-sided whole-breast with or without regional nodal irradiation either using deep inspiration breath-hold (DIBH) or free-breathing (FB) technique were prospectively enrolled. N-terminal pro-B-type natriuretic peptide (NT-proBNP), electrocardiogram, and radionuclide myocardial perfusion imaging were conducted before and after HFRT. Logistic regression analyses were performed to determine the association of cancer treatment, cardiac dose, and cardiovascular risk factors with cardiotoxic effects. RESULTS The mean dose (Dmean) of the heart, left anterior descending coronary artery (LAD), left ventricular (LV), and right ventricular (RV) in all patients was 403 cGy, 1685 cGy, 627 cGy, and 444 cGy, respectively. In comparison to FB, DIBH significantly reduced cardiac dose (heart Dmean 250 cGy vs. 570 cGy, LAD Dmean 1250 cGy vs. 2170 cGy, LV Dmean 420 cGy vs. 850 cGy, RV Dmean 260 cGy vs. 650 cGy; all p<0.001). With a median follow-up of 49 months (range, 2-65 months), no patients had clinical cardiac abnormalities or cardiac-related symptoms, but 42 (41%) patients had subclinical cardiac events. Among them, 41 were electrocardiogram changes, and one had LV ejection fraction decreased by 10% compared with the baseline level. Twenty-five (60%) recovered during follow-up, of which 17 (40%) experienced subclinical changes only once. The mean value of NT-proBNP did not change significantly before and after HFRT. In univariate analyses, DIBH technique significantly decreased the risk of subclinical cardiac events compared with FB (OR 0.31, 95% CI 0.14-0.71; p = 0.006); however, higher mean doses of heart and LV, anthracycline-based chemotherapy, obesity, and hypertension were associated with increased risk of subclinical cardiac events (all p<0.05). CONCLUSION Early subclinical cardiac damage after HFRT in left-sided breast cancer is dose-related, and mostly manageable and reversible without medical intervention.
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Cost-Effectiveness of Short-Course Radiotherapy Based Total Neoadjuvant Therapy for Locally Advanced Rectal Cancer in China. Int J Radiat Oncol Biol Phys 2023; 117:e356-e357. [PMID: 37785230 DOI: 10.1016/j.ijrobp.2023.06.2439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The phase III STELLAR (NCT02533271) trial demonstrated that four cycles of chemotherapy after short-course radiotherapy (SCRT-TNT) were not inferior to the standard care of long-course concurrent radiotherapy (LCRT) in patients with locally advanced rectal cancer (LARC). This study assessed the cost-effectiveness of SCRT-TNT versus LCRT in locally advanced rectal cancer in China on the basis of the STELLAR trial. MATERIALS/METHODS A Markov model was used to synthesize the healthcare costs and benefits of LARC patients based on results from the STELLAR trial. The model assumes that LARC who meet the inclusion criteria of the STELLAR trial experience four possible states: No Evidence of Disease (NED), locally recurrence, distant metastases, or any death from rectal cancer or other unrelated causes, where local recurrence continues to be classified as resectable and unresectable. The transition status period is 3 month, and 5 years is used to calculate direct medical costs and health benefits. The probabilities of states transition after SCRT-TNT or LCRT were derived from the results of the STELLAR trial and previous published article (Table.1). Costs were evaluated from the Chinese payer's perspective reported in early 2022 US dollars (US$1 = 6.78 Chinese Yuan). Sensitivity analyses were performed for key variables. Cost-effectiveness was evaluated using the incremental cost-effectiveness ratio and net monetary benefits. Effectiveness was defined as quality-adjusted life-years (QALYs). Willingness-to-pay (WTP) threshold was set at $43500/QALY. Data were collected from October 3, 2020, to September 20, 2021, and analyzed from November 15, 2020, to October 25, 2021. RESULTS During the 5-year horizon, for the base case scenario, SCRT-TNT incurred a lower total cost and higher QALYs compared with LCCRT. The total cost was $65767 and QALYs were 1.77 for SCRT-TNT; for LCCRT, the total cost was $72802 and QALYs were 1.64. This resulted in an ICER of -$ 55470.69 per QALY. Therefore, SCRT-TNT was a cost-saving and dominating treatment strategy compared with LCRT. Sensitivity analysis showed that ICERs were most sensitive to the parameters of distant metastases risk after treatment. CONCLUSION SCRT-TNT in locally advanced rectal cancer can be a cost-effective alternative to LCRT in China, and should be considered in appropriately selected patients.
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Prospective Efficacy of Two Cycles Toripalimab Plus Induction Chemotherapy in T4 or N3 Locoregionally Advanced Nasopharyngeal Carcinoma: A Retrospective and Mechanistic Study. Int J Radiat Oncol Biol Phys 2023; 117:S70. [PMID: 37784558 DOI: 10.1016/j.ijrobp.2023.06.377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Gemcitabine-cisplatin (GP) as the most commonly used induction chemotherapy is the standard first-line systemic treatment for advanced nasopharyngeal carcinoma. However, the toxicity of three cycles induction chemotherapy following on chemoradiotherapy remains a pertinent issue. Additional monoclonal antibody against human programmed death-1 (PD-1) has shown promising efficacy in recurrent or metastatic nasopharyngeal carcinoma. MATERIALS/METHODS In this study, we compared three cycles of gemcitabine and cisplatin as classical induction chemotherapy with two cycles of induction chemotherapy plus toripalimab, and then both groups treated with the similar concurrent chemoradiotherapy. Patients with locoregionally advanced nasopharyngeal carcinoma staging T4 or N3 were randomly assigned in a 1:1 ratio to receive gemcitabine (at a dose of 1 g per square meter of body-surface area on days 1 and 8) plus cisplatin (80 mg per square meter on day 1-3), administered every 3 weeks for three cycles, or GP combined with toripalimab (at a dose of 240mg) for two cycles. The primary end point was recurrence-free survival (i.e., freedom from disease recurrence [distant metastasis or locoregional recurrence] or death from any cause) in the intention-to-treat population. Secondary end points included overall survival, treatment adherence, and safety. RESULTS A total of 60 patients were included in the trial (30 patients in the toripalimab combined induction chemotherapy group and another 30 in the standard-therapy group). Among 60 patients evaluable for response assessment after induction therapy, all patients had overall response in combined group, including 10 patients (30%) with complete response (CR) in the primary tumor site. 21 patients (70%) were evaluated as partial response (PR) in the standard induction chemotherapy, and another 9 patients were assessed as SDa. At a median follow-up of 27.6 months, the 6-months, 1-, 2-year recurrence-free survival was 100% vs 86.7%, 100% vs 80%, 93% vs 70% in the toripalimab combined induction chemotherapy group and standard-therapy group (stratified hazard ratio for recurrence or death, 0.62; 95% confidence interval [CI], 0.38 to 0.87; P = 0.001). Overall survival at 2 years was 93.3% and 100%, respectively (stratified hazard ratio for death, 0.53; 95% CI, 0.29 to 0.79). The incidence of acute adverse events of grade 3 or 4 was 76.8% in the standard-induction chemotherapy group and 56% in the standard-therapy group, with a higher incidence of neutropenia, thrombocytopenia, anemia, nausea, and vomiting in the induction chemotherapy group. The incidence of grade 3 or 4 late toxic effects was 10.2% in the induction chemotherapy group and 10.4% in the combined-therapy group. CONCLUSION Two cycles of toripalimab combined with induction chemotherapy of and CCRT shows excellent distant metastatic control with acceptable safety, which is a new promising and effective systemic therapy regimen for high-risk of metastatic NPC patients.
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Lymphocyte Count Kinetics and the Effect of Different Radiotherapy Techniques on Radiation-Induced Lymphopenia in Patients with Breast Cancer Receiving Hypofractionated Postmastectomy Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e216-e217. [PMID: 37784888 DOI: 10.1016/j.ijrobp.2023.06.1112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiation-induced lymphopenia (RIL) is associated with poor prognosis in solid tumors. This study aimed to describe the lymphocyte kinetics in patients with breast cancer receiving hypofractionated postmastectomy radiotherapy (RT) and to investigate the association of different RT techniques with RIL. MATERIALS/METHODS We assessed 607 patients who received hypofractionated postmastectomy RT for breast cancer in our prospective clinical database from 8 hospitals. All patients received irradiation to the chest wall and supraclavicular fossa. RT techniques included integrated RT with the photon-based intensity modulated techniques to irradiate all target volumes (integrated RT) and a hybrid approach combining photon irradiation to supraclavicular nodes and electron irradiation to the chest wall (hybrid RT). Peripheral lymphocyte counts (PLC) were tested prior to RT (baseline), weekly during RT, at 1, 2 weeks, 3, 6 months after RT, and then every 6 months. Grade 3+ RIL was defined as PLC nadir during RT of <0.5 ×103/ml. Mean PLC was compared by the t test. Univariate, multivariate, and propensity score matching (PSM) analyses were used to evaluate the effect of different RT techniques on grade 3+ RIL. RESULTS During RT, 121 (19.9%) of patients had grade 3+ RIL. The PLC started to recover at 1 week and reached baseline levels 1 year after RT. A greater proportion of the patients treated with the integrated RT (90/269, 33.5%) developed grade 3+ PLC compared with those receiving hybrid RT (31/338, 9.2%, P < 0.001). After conducting PSM, multivariate analyses showed lower baseline PLC (HR = 0.15, P<0.001) and RT technique (the integrated RT vs. hybrid RT, HR = 4.76, P<0.001) were independent risk factors for grade 3+ RIL. The PLC in patients receiving the integrated RT after RT were higher than that in those receiving hybrid RT (p<0.05). CONCLUSION RT technique affect the risk of and recovery from RIL, which may impact survival. Choosing appropriate RT technique to minimize RIL might be considered to benefit their outcomes.
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Dose-Volume Predictors for Radiation Esophagitis in Breast Cancer Patients Undergoing Hypofractionated Regional Nodal Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e211-e212. [PMID: 37784878 DOI: 10.1016/j.ijrobp.2023.06.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiation esophagitis (RE) is often overlooked in breast cancer radiotherapy. This study aimed to assess the incidence and dose-volume predictors of RE in breast cancer patients undergoing hypofractionated regional nodal irradiation (RNI). MATERIALS/METHODS Eligible patients were included who received intensity-modulated radiotherapy (RT) at the chest wall, the supraclavicular/infraclavicular fossa, level II axilla, and/or the internal mammary chain after mastectomy. The prescribed dose was 43.5 Gy in 15 fractions. The dose constraint for the esophagus was maximum dose <48 Gy. RE was evaluated weekly during RT and at 1 and 2 weeks, followed by 3 and 6 months after RT, and was graded according to the Common Toxicity Criteria for Adverse Events v3.0. The esophagus was contoured from the lower border level of the cricoid cartilage to the lower margin of the aortic arch. Esophageal total volume, mean dose (Dmean), maximum dose (Dmax), and the relative and absolute volumes receiving at least 5-45 Gy by 5 Gy increments (RV5-RV45 and AV5-AV45) were evaluated. Univariable and multivariable logistics regression analyses were performed to determine risk factors for RE, and receiver operating characteristic curves were obtained to identify the thresholds of esophageal dosimetric parameters. RESULTS In total, 298 patients were included between May 8, 2020 and January 5, 2022 (minimum post-RT follow-up: 6 months). A total of 153 (51.3%) patients had left-sided breast cancer and 145 (48.7%) patients received internal mammary nodal irradiation (IMNI). Grade 2 and 3 RE incidence was 40.9% (122/298) and 0.3% (1/298), respectively. No grade 4 or 5 RE was observed. All RE cases resolved within 1 month after RT, and the median duration of RE was 3 weeks (range, 1-5). Based on univariable analyses, tumor laterality (p < .001), IMNI (p = .056) and esophageal Dmean, Dmax, RV10-RV40, and AV10-AV40 were risk factors of ≥grade 2 RE. Esophageal RV10-RV40 and AV35-AV40 were significantly associated with the risk of ≥grade 2 RE after adjusting for tumor laterality and IMNI. Based on multivariable analyses, RV25 and AV35 were optimum dose-volume predictors for ≥grade 2 RE at thresholds 20% for RV25 (35.9% vs. 60.9%, p = .04) and 0.27 mL for AV35 (31.0% vs. 54.6%, p = .04). CONCLUSION RE is common in breast cancer patients undergoing hypofractionated RNI. With the same esophageal contouring standard, maintaining the upper esophageal V25 at <20% and V35 at <0.27 mL may decrease the risk of RE and improve the quality of life of patients.
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Quality Assurance in a Phase III, Multicenter, Randomized Trial of POstmastectomy radioThErapy in Node posiTive Breast Cancer with or without Internal mAmmary nodaL Irradiation (POTENTIAL): A Planning Dummy Run. Int J Radiat Oncol Biol Phys 2023; 117:S97. [PMID: 37784615 DOI: 10.1016/j.ijrobp.2023.06.431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) To report the planning dummy run results of the POstmastectomy radioThErapy in Node posiTive breast cancer with or without Internal mAmmary nodaL irradiation (POTENTIAL) trial-a multicenter, randomized, phase 3 trial-to evaluate postmastectomy radiotherapy, with or without internal mammary nodal irradiation, for patients with high-risk breast cancer. MATERIALS/METHODS All participating institutions were provided the contours of the dummy run case, and they generated radiotherapy (RT) plans per protocol guidelines. The plans were reviewed and feedback were provided by the quality assurance team, after which the institutions resubmitted revised plans. The information on beams arrangement, skin flash, inhomogeneity corrections, and protocol compliance was assessed both in the primary and final submission. RESULTS Theplans from 26 institutions were included in the analysis. A number of major deviations were found in the primary submission, such as less strict constraint on organs at risk (OARs) V5Gy, and no application of chest wall skin flash. The protocol compliance rates of the dose coverage for the planning target volume of the chest wall (PTVcw), PTV of supra/infraclavicular fossa plus axilla levels I, II, III (PTVsc+ax), and PTV of the IMN region (PTVim) were all significantly improved in the final submission compared with those in the primary submission, which were 96.2% vs. 69.2%, 100% vs. 76.9%, and 88.4% vs. 53.8, respectively. For OARs, the protocol compliance rates of heart Dmean, left anterior descending coronary artery V40Gy, ipsilateral lung V5Gy, and stomach V5Gy were significantly improved. CONCLUSION All major deviations were corrected and protocol compliance was significantly improved and of high level in the final submission. Moreover, the variations were reduced. Therefore, a planning dummy run was essential to guarantee good RT plan quality and inter-institutional consistency for multicenter trials.
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CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Brief Bioinform 2023; 24:bbad352. [PMID: 37861173 DOI: 10.1093/bib/bbad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/29/2023] [Accepted: 09/17/2023] [Indexed: 10/21/2023] Open
Abstract
NcRNA-encoded small peptides (ncPEPs) have recently emerged as promising targets and biomarkers for cancer immunotherapy. Therefore, identifying cancer-associated ncPEPs is crucial for cancer research. In this work, we propose CoraL, a novel supervised contrastive meta-learning framework for predicting cancer-associated ncPEPs. Specifically, the proposed meta-learning strategy enables our model to learn meta-knowledge from different types of peptides and train a promising predictive model even with few labeled samples. The results show that our model is capable of making high-confidence predictions on unseen cancer biomarkers with only five samples, potentially accelerating the discovery of novel cancer biomarkers for immunotherapy. Moreover, our approach remarkably outperforms existing deep learning models on 15 cancer-associated ncPEPs datasets, demonstrating its effectiveness and robustness. Interestingly, our model exhibits outstanding performance when extended for the identification of short open reading frames derived from ncPEPs, demonstrating the strong prediction ability of CoraL at the transcriptome level. Importantly, our feature interpretation analysis discovers unique sequential patterns as the fingerprint for each cancer-associated ncPEPs, revealing the relationship among certain cancer biomarkers that are validated by relevant literature and motif comparison. Overall, we expect CoraL to be a useful tool to decipher the pathogenesis of cancer and provide valuable information for cancer research. The dataset and source code of our proposed method can be found at https://github.com/Johnsunnn/CoraL.
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PLPMpro: Enhancing promoter sequence prediction with prompt-learning based pre-trained language model. Comput Biol Med 2023; 164:107260. [PMID: 37557052 DOI: 10.1016/j.compbiomed.2023.107260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
Abstract
The promoter region, positioned proximal to the transcription start sites, exerts control over the initiation of gene transcription by modulating the interaction with RNA polymerase. Consequently, the accurate recognition of promoter regions represents a critical focus within the bioinformatics domain. Although some methods leveraging pre-trained language models (PLMs) for promoter prediction have been proposed, the full potential of such PLMs remains largely untapped. In this study, we introduce PLPMpro, a model that capitalizes on prompt-learning and the pre-trained language model to enhance the prediction of promoter sequences. PLPMpro effectively harnesses the prompt learning paradigm to fully exploit the inherent capacities of the PLM, resulting in substantial improvements in prediction performance. Experiment results unequivocally demonstrate the efficacy of prompt learning in bolstering the capabilities of the pre-trained model. Consequently, PLPMpro surpasses both typical pre-trained model-based methods for promoter prediction and typical deep learning methods. Furthermore, we conduct various experiments to meticulously scrutinize the effects of different prompt learning settings and different numbers of soft modules on the model performance. More importantly, the interpretation experiment reveals that the pre-trained model captures biological semantics. Collectively, this research imparts a novel perspective on the optimal utilization of PLMs for addressing biological problems.
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Rm-LR: A long-range-based deep learning model for predicting multiple types of RNA modifications. Comput Biol Med 2023; 164:107238. [PMID: 37515874 DOI: 10.1016/j.compbiomed.2023.107238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
Recent research has highlighted the pivotal role of RNA post-transcriptional modifications in the regulation of RNA expression and function. Accurate identification of RNA modification sites is important for understanding RNA function. In this study, we propose a novel RNA modification prediction method, namely Rm-LR, which leverages a long-range-based deep learning approach to accurately predict multiple types of RNA modifications using RNA sequences only. Rm-LR incorporates two large-scale RNA language pre-trained models to capture discriminative sequential information and learn local important features, which are subsequently integrated through a bilinear attention network. Rm-LR supports a total of ten RNA modification types (m6A, m1A, m5C, m5U, m6Am, Ψ, Am, Cm, Gm, and Um) and significantly outperforms the state-of-the-art methods in terms of predictive capability on benchmark datasets. Experimental results show the effectiveness and superiority of Rm-LR in prediction of various RNA modifications, demonstrating the strong adaptability and robustness of our proposed model. We demonstrate that RNA language pretrained models enable to learn dense biological sequential representations from large-scale long-range RNA corpus, and meanwhile enhance the interpretability of the models. This work contributes to the development of accurate and reliable computational models for RNA modification prediction, providing insights into the complex landscape of RNA modifications.
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[Research progress of cell therapy in hereditary pulmonary alveolar proteinosis]. ZHONGHUA JIE HE HE HU XI ZA ZHI = ZHONGHUA JIEHE HE HUXI ZAZHI = CHINESE JOURNAL OF TUBERCULOSIS AND RESPIRATORY DISEASES 2023; 46:730-734. [PMID: 37402667 DOI: 10.3760/cma.j.cn112147-20230107-00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Hereditary pulmonary alveolar proteinosis (hPAP) is a rare interstitial lung disease caused by mutation in CSF2RA/CSF2RB, characterized by the deposition of pulmonary surfactant due to the alveolar macrophage dysfunction. The whole lung lavage can effectively alleviate the symptoms but is associated with potential complications. Cell therapy is a novel approach with advances that provide a new therapeutic strategy for the treatment of hPAP.
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[Research progress on the relation and related mechanism of night shift work and cardiovascular disease]. ZHONGHUA LAO DONG WEI SHENG ZHI YE BING ZA ZHI = ZHONGHUA LAODONG WEISHENG ZHIYEBING ZAZHI = CHINESE JOURNAL OF INDUSTRIAL HYGIENE AND OCCUPATIONAL DISEASES 2023; 41:475-480. [PMID: 37400414 DOI: 10.3760/cma.j.cn121094-20220420-00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Cardiovascular disease is a class of diseases involving the heart or blood vessels, which accounts for about one-third of all deaths worldwide each year. Unhealthy diet, lack of physical activity, smoking and excessive alcohol consumption are all risk factors for cardiovascular disease. With the increasing number of night shift workers, the number of patients with cardiovascular disease has increased, and night shift work has gradually become a risk factor of cardiovascular disease. At present, the mechanism of cardiovascular disease caused by night shift work is still unclear. This review summarizes the relationship between night shift work and cardiovascular disease and its related biochemical indicators, and discusses the research on related mechanisms.
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[Current status of diagnosis and treatment of chronic lymphocytic leukemia in China: A national multicenter survey research]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:380-387. [PMID: 37550187 PMCID: PMC10440613 DOI: 10.3760/cma.j.issn.0253-2727.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 08/09/2023]
Abstract
Objective: To understand the current status of diagnosis and treatment of chronic lymphocytic leukemia (CLL) /small lymphocytic lymphoma (SLL) among hematologists, oncologists, and lymphoma physicians from hospitals of different levels in China. Methods: This multicenter questionnaire survey was conducted from March 2021 to July 2021 and included 1,000 eligible physicians. A combination of face-to-face interviews and online questionnaire surveys was used. A standardized questionnaire regarding the composition of patients treated for CLL/SLL, disease diagnosis and prognosis evaluation, concomitant diseases, organ function evaluation, treatment selection, and Bruton tyrosine kinase (BTK) inhibitor was used. Results: ①The interviewed physicians stated that the proportion of male patients treated for CLL/SLL is higher than that of females, and the age is mainly concentrated in 61-70 years old. ②Most of the interviewed physicians conducted tests, such as bone marrow biopsies and immunohistochemistry, for patient diagnosis, in addition to the blood test. ③Only 13.7% of the interviewed physicians fully grasped the initial treatment indications recommended by the existing guidelines. ④In terms of cognition of high-risk prognostic factors, physicians' knowledge of unmutated immunoglobulin heavy-chain variable and 11q- is far inferior to that of TP53 mutation and complex karyotype, which are two high-risk prognostic factors, and only 17.1% of the interviewed physicians fully mastered CLL International Prognostic Index scoring system. ⑤Among the first-line treatment strategy, BTK inhibitors are used for different types of patients, and physicians have formed a certain understanding that BTK inhibitors should be preferentially used in patients with high-risk factors and elderly patients, but the actual use of BTK inhibitors in different types of patients is not high (31.6%-46.0%). ⑥BTK inhibitors at a reduced dose in actual clinical treatment were used by 69.0% of the physicians, and 66.8% of the physicians had interrupted the BTK inhibitor for >12 days in actual clinical treatment. The use of BTK inhibitors is reduced or interrupted mainly because of adverse reactions, such as atrial fibrillation, severe bone marrow suppression, hemorrhage, and pulmonary infection, as well as patients' payment capacity and effective disease progression control. ⑦Some differences were found in the perceptions and behaviors of hematologists and oncologists regarding the prognostic assessment of CLL/SLL, the choice of treatment options, the clinical use of BTK inhibitors, etc. Conclusion: At present, a gap remains between the diagnosis and treatment of CLL/SLL among Chinese physicians compared with the recommendations in the guidelines regarding the diagnostic criteria, treatment indications, prognosis assessment, accompanying disease assessment, treatment strategy selection, and rational BTK inhibitor use, especially the proportion of dose reduction or BTK inhibitor discontinuation due to high adverse events.
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DrugormerDTI: Drug Graphormer for drug-target interaction prediction. Comput Biol Med 2023; 161:106946. [PMID: 37244151 DOI: 10.1016/j.compbiomed.2023.106946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/29/2023] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
Drug-target interactions (DTI) prediction is a crucial task in drug discovery. Existing computational methods accelerate the drug discovery in this respect. However, most of them suffer from low feature representation ability, significantly affecting the predictive performance. To address the problem, we propose a novel neural network architecture named DrugormerDTI, which uses Graph Transformer to learn both sequential and topological information through the input molecule graph and Resudual2vec to learn the underlying relation between residues from proteins. By conducting ablation experiments, we verify the importance of each part of the DrugormerDTI. We also demonstrate the good feature extraction and expression capabilities of our model via comparing the mapping results of the attention layer and molecular docking results. Experimental results show that our proposed model performs better than baseline methods on four benchmarks. We demonstrate that the introduction of Graph Transformer and the design of residue are appropriate for drug-target prediction.
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[NKD1 promotes glucose uptake in colon cancer cells by activating YWHAE transcription]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:585-589. [PMID: 37202194 DOI: 10.12122/j.issn.1673-4254.2023.04.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
OBJECTIVE Bo investigate the regulatory relationship between NKD1 and YWHAE and the mechanism of NKD1 for promoting tumor cell proliferation. METHODS HCT116 cells transfected with pcDNA3.0-NKD1 plasmid, SW620 cells transfected with NKD1 siRNA, HCT116 cells with stable NKD1 overexpression (HCT116-NKD1 cells), SW620 cells with nkd1knockout (SW620-nkd1-/- cells), and SW620-nkd1-/- cells transfected with pcDNA3.0-YWHAE plasmid were examined for changes in mRNA and protein expression levels of YWHAE using qRT-PCR and Western blotting. Chromatin immunoprecipitation (ChIP) assay was used to detect the binding of NKD1 to the promoter region of YWHAE gene. The regulatory effect of NKD1 on YWHAE gene promoter activity was analyzed by dual-luciferase reporter gene assay, and the interaction between NKD1 and YWHAE was analyzed with immunofluorescence assay. The regulatory effect of NKD1 on glucose uptake was examined in the tumor cells. RESULTS In HCT116 cells, overexpression of NKD1 significantly enhanced the expression of YWHAE at both the mRNA and protein levels, while NKD1 knockout decreased its expression in SW620 cells (P < 0.001). ChIP assay showed that NKD1 protein was capable of binding to the YWHAE promoter sequence; dual luciferase reporter gene assay showed that NKD1 overexpression (or knockdown) in the colon cancer cells significantly enhanced (or reduced) the transcriptional activity of YWHAE promoter (P < 0.05). Immunofluorescence assay demonstrated the binding of NKD1 and YWHAE proteins in colon cancer cells. NKD1 knockout significantly reduced glucose uptake in colon cancer cells (P < 0.01), while YWHAE overexpression restored the glucose uptake in NKD1-knockout cells (P < 0.05). CONCLUSION NKD1 protein activates the transcriptional activity of YWHAE gene to promote glucose uptake in colon cancer cells.
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Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206151. [PMID: 36794291 PMCID: PMC10104664 DOI: 10.1002/advs.202206151] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Accurately predicting peptide secondary structures remains a challenging task due to the lack of discriminative information in short peptides. In this study, PHAT is proposed, a deep hypergraph learning framework for the prediction of peptide secondary structures and the exploration of downstream tasks. The framework includes a novel interpretable deep hypergraph multi-head attention network that uses residue-based reasoning for structure prediction. The algorithm can incorporate sequential semantic information from large-scale biological corpus and structural semantic information from multi-scale structural segmentation, leading to better accuracy and interpretability even with extremely short peptides. The interpretable models are able to highlight the reasoning of structural feature representations and the classification of secondary substructures. The importance of secondary structures in peptide tertiary structure reconstruction and downstream functional analysis is further demonstrated, highlighting the versatility of our models. To facilitate the use of the model, an online server is established which is accessible via http://inner.wei-group.net/PHAT/. The work is expected to assist in the design of functional peptides and contribute to the advancement of structural biology research.
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220P Comparison of efficacy and safety of platinum-based chemotherapy as first-line therapy between B3 thymoma and thymic carcinoma. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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A234 PARASITIC INFECTION MIMICKING CROHN'S DISEASE: AN UNUSUAL PRESENTATION OF LOWER GASTROINTESTINAL SCHISTOSOMIASIS. J Can Assoc Gastroenterol 2023. [PMCID: PMC9991126 DOI: 10.1093/jcag/gwac036.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Background Chronic intestinal schistosomiasis (CIS) is a disease caused in humans by infection with one of seven schistosome species. These species are predominantly found in Africa, South America, and East Asia. Symptoms of CIS include abdominal pain, anorexia, weight loss and diarrhea. In cases of large parasitic burden, overt gastrointestinal bleeding can occur. To our knowledge there are only three other cases of CIS mimicking Crohn's Disease that have been published in the literature. In each of these cases, this was associated with ileal disease, perianal fistulas, or both. Purpose We present the first case of CIS in North America that mimicked Crohn's Disease on imaging with no associated ileal or visible perianal disease. Method Case report of a patient presenting to a tertiary care hospital in Edmonton, Alberta. Result(s) A 47 year old man who recently immigrated from Eritrea presented to the emergency department in June 2020 with red blood per rectum. Digital rectum exam revealed small external hemorrhoids. He was discharged with a plan for outpatient abdominal CT scan and colonoscopy. He presented again to the emegency department in January 2021 where he complained of back pain exacerbated by bowel movements productive for small, hard stool. He also began seeing white discharge mixed with his stool. His back pain, white discharge, and blood-streaked bowel movements persisted for over a year, and he developed perianal pain that was exacerbated by valsalva. A CT scan of the abdomen/pelvis revealed extensive soft tissue swelling in the anorectal region, extraluminal gas, and a 15mm fluid collection adjacent to the coccyx. A diagnosis of fistulizing Crohn's Disease was suspected. A digital rectal exam and colonoscopy were performed September 19, 2022 which revealed small hemorrhoids but otherwise endoscopically normal colonic and ileal mucosa. Biopsies from the rectum revealed eosinophilic granulomas associated with parasitic ova; a diagnosis of schistosomiasis was made. Image ![]()
Conclusion(s) CIS is a rare diagnosis in North America. It is unusual for this disease entity to present is a mimic of fistulizing Crohn's Disease. This case report reminds the clinician that a high index of suspicion in patients presenting from endemic regions is required to make this diagnosis. Please acknowledge all funding agencies by checking the applicable boxes below None Disclosure of Interest None Declared
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High prevalence of vertebral deformity in tumor-induced osteomalacia associated with impaired bone microstructure. J Endocrinol Invest 2023; 46:487-500. [PMID: 36097315 DOI: 10.1007/s40618-022-01918-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/02/2022] [Indexed: 10/14/2022]
Abstract
PURPOSE Patients with tumor-induced osteomalacia (TIO) often suffer from irreversible height loss due to vertebral deformity. However, the prevalence of vertebral deformity in TIO patients varies among limited studies. In addition, the distribution and type of vertebral deformity, as well as its risk factors, remain unknown. This study aimed to identify the prevalence, distribution, type and risk factors for vertebral deformity in a large cohort of TIO patients. METHODS A total of 164 TIO patients were enrolled in this retrospective study. Deformity in vertebrae T4-L4 by lateral thoracolumbar spine radiographs was evaluated according to the semiquantitative method of Genant. Bone microstructure was evaluated by trabecular bone score (TBS) and high-resolution peripheral QCT (HR-pQCT). RESULTS Ninety-nine (99/164, 60.4%) patients had 517 deformed vertebrae with a bimodal pattern of distribution (T7-9 and T11-L1), and biconcave deformity was the most common type (267/517, 51.6%). Compared with patients without vertebral deformity, those with vertebral deformity had a higher male/female ratio, longer disease duration, more height loss, lower serum phosphate, higher bone turnover markers, lower TBS, lower areal bone mineral density (aBMD), lower peripheral volumetric BMD (vBMD) and worse microstructure. Lower trabecular vBMD and worse trabecular microstructure in the peripheral bone and lower spine TBS were associated with an increased risk of vertebral deformity independently of aBMD. After adjusting for the number of deformed vertebrae, we found little difference in clinical indexes among the patients with different types of vertebral deformity. However, we found significant correlations of clinical indexes with the number of deformed vertebrae and the spinal deformity index. CONCLUSION We reported a high prevalence of vertebral deformity in the largest cohort of TIO patients and described the vertebral deformity in detail for the first time. Risk factors for vertebral deformity included male sex, long disease duration, height loss, abnormal biochemical indexes and bone impairment. Clinical manifestation, biochemical indexes and bone impairment were correlated with the number of deformed vertebrae and degree of deformity, but not the type of deformity.
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ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides. BIOINFORMATICS (OXFORD, ENGLAND) 2023; 39:7075544. [PMID: 36897030 PMCID: PMC10027287 DOI: 10.1093/bioinformatics/btad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023]
Abstract
MOTIVATION Plant Small Secreted Peptides (SSPs) play an important role in plant growth, development, and plant-microbe interactions. Therefore, the identification of SSPs is essential for revealing the functional mechanisms. Over the last few decades, machine learning-based methods have been developed, accelerating the discovery of SSPs to some extent. However, existing methods highly depend on handcrafted feature engineering, which easily ignores the latent feature representations and impacts the predictive performance. RESULTS Here, we propose ExamPle, a novel deep learning model using Siamese network and multi-view representation for the explainable prediction of the plant SSPs. Benchmarking comparison results show that our ExamPle performs significantly better than existing methods in the prediction of plant SSPs. Also, our model shows excellent feature extraction ability. Importantly, by utilizing in silicomutagenesis experiment, ExamPle can discover sequential characteristics and identify the contribution of each amino acid for the predictions. The key novel principle learned by our model is that the head region of the peptide and some specific sequential patterns are strongly associated with the SSPs' functions. Thus, ExamPle is expected to be a useful tool for predicting plant SSPs and designing effective plant SSPs. AVAILABILITY AND IMPLEMENTATION Our codes and datasets are available at https://github.com/Johnsunnn/ExamPle.
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[Associations of genetic variations in pyroptosis related genes with acute adverse events in postoperative rectal cancer patients receiving concurrent chemoradiotherapy]. ZHONGHUA ZHONG LIU ZA ZHI [CHINESE JOURNAL OF ONCOLOGY] 2023; 45:146-152. [PMID: 36781235 DOI: 10.3760/cma.j.cn112152-20220622-00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Objective: This study aims to investigate the associations between genetic variations of pyroptosis pathway related key genes and adverse events (AEs) of postoperative chemoradiotherapy (CRT) in patients with rectal cancer. Methods: DNA was extracted from the peripheral blood which was collected from 347 patients before CRT. Sequenom MassARRAY was used to detect the genotypes of 43 haplotype-tagging single nucleotide polymorphisms (htSNPs) in eight pyroptosis genes, including absent in melanoma 2 (AIM2), caspase-1 (CASP1), caspase-4(CASP4), caspase-5 (CASP5), caspase-11 (CASP11), gasdermin D (GSDMD), gasdermin E (GSDME) and NLR family pyrin domain containing 3 (NLRP3). The associations between 43 htSNPs and AEs were evaluated by the odd ratios (ORs) and 95% confidence intervals (CIs) by unconditional logistic regression models, adjusted for sex, age, clinical stage, tumor grade, Karnofsky performance status (KPS), surgical procedure, and tumor location. Results: Among the 347 patients with rectal cancer underwent concurrent CRT with capecitabine after surgery, a total of 101(29.1%) occurred grade ≥ 2 leukopenia. rs11226565 (OR=0.41, 95% CI: 0.21-0.79, P=0.008), rs579408(OR=1.54, 95% CI: 1.03-2.29, P=0.034) and rs543923 (OR=0.63, 95% CI: 0.41-0.98, P=0.040) were significantly associated with the occurrence of grade ≥ 2 leukopenia. One hundred and fifty-six (45.0%) had grade ≥ 2 diarrhea, two SNPs were significantly associated with the occurrence of grade ≥ diarrhea, including CASP11 rs10880868 (OR=0.55, 95% CI: 0.33-0.91, P=0.020) and GSDME rs2954558 (OR=1.52, 95% CI: 1.01-2.31, P=0.050). In addition, sixty-six cases (19.0%) developed grade ≥2 dermatitis, three SNPs that significantly associated with the risk of grade ≥2 dermatitis included GSDME rs2237314 (OR=0.36, 95% CI: 0.16-0.83, P=0.017), GSDME rs12540919 (OR=0.52, 95% CI: 0.27-0.99, P=0.045) and NLRP3 rs3806268 (OR=1.51, 95% CI: 1.03-2.22, P=0.037). There was no significant difference in the association between other genetic variations and AEs of rectal cancer patients (all P>0.05). Surgical procedure and tumor location had great impacts on the occurrence of grade ≥2 diarrhea and dermatitis (all P<0.01). Conclusion: The genetic variants of CASP4, CASP11, GSDME and NLRP3 are associated with the occurrence of AEs in patients with rectal cancer who received postoperative CRT, suggesting they may be potential genetic markers in predicting the grade of AEs to achieve individualized treatment of rectal cancer.
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DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis. Nucleic Acids Res 2023; 51:3017-3029. [PMID: 36796796 PMCID: PMC10123094 DOI: 10.1093/nar/gkad055] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Here, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop-shop web service that enables researchers to develop new deep-learning architectures to answer any biological question. Specifically, given any biological sequence data, DeepBIO supports a total of 42 state-of-the-art deep-learning algorithms for model training, comparison, optimization and evaluation in a fully automated pipeline. DeepBIO provides a comprehensive result visualization analysis for predictive models covering several aspects, such as model interpretability, feature analysis and functional sequential region discovery. Additionally, DeepBIO supports nine base-level functional annotation tasks using deep-learning architectures, with comprehensive interpretations and graphical visualizations to validate the reliability of annotated sites. Empowered by high-performance computers, DeepBIO allows ultra-fast prediction with up to million-scale sequence data in a few hours, demonstrating its usability in real application scenarios. Case study results show that DeepBIO provides an accurate, robust and interpretable prediction, demonstrating the power of deep learning in biological sequence functional analysis. Overall, we expect DeepBIO to ensure the reproducibility of deep-learning biological sequence analysis, lessen the programming and hardware burden for biologists and provide meaningful functional insights at both the sequence level and base level from biological sequences alone. DeepBIO is publicly available at https://inner.wei-group.net/DeepBIO.
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[Interleukin-2 induced T cell kinase deficiency manifested in Epstein-Barr virus-driven hemophagocytic syndrome]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2023; 61:172-174. [PMID: 36720602 DOI: 10.3760/cma.j.cn112140-20220529-00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Baicalein Inhibits the Growth of Transplanted Esophageal Cancer in Mice and the Effect on the Expression of PAK4. Bull Exp Biol Med 2023; 174:478-481. [PMID: 36899200 DOI: 10.1007/s10517-023-05733-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 03/12/2023]
Abstract
We studied the mechanism underlying the effect of baicalein on the growth of transplanted esophageal cancer in NOG mice and its effect on the expression of PAK4. For that purpose, we developed a new model of transplanted esophageal cancer (human esophageal cancer OE19 cells (107 cells/ml) were inoculated to NOG mice). Three experimental groups with transplanted esophageal cancer cells received baicalein in different doses (1, 1.5, and 2 mg/kg). In 32 days, the tumors were resected, and the expression of PAK4 and the level of activated PAK4 were assayed by reverse transcription PCR and Western blotting, respectively. The results showed a dose-depending anti-tumor effect of baicalein on the transplanted esophageal cancer in NOG mice: this effect of baicalein (determined by the size and weight of the tumor) increased with increasing the dose of the substance. Furthermore, the anti-tumor effect of baicalein was also confirmed by reduction of PAK4 expression. Thus, baicalein can inhibit tumor growth by inhibiting activation of PAK4. Therefore, our results showed that baicalein could inhibit the growth of esophageal cancer cells by inhibiting the activity of PAK4, which can be an important mechanism of its antitumor effect.
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SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning. Brief Bioinform 2023; 24:6958502. [PMID: 36562719 DOI: 10.1093/bib/bbac545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cell-penetrating peptides (CPPs) have received considerable attention as a means of transporting pharmacologically active molecules into living cells without damaging the cell membrane, and thus hold great promise as future therapeutics. Recently, several machine learning-based algorithms have been proposed for predicting CPPs. However, most existing predictive methods do not consider the agreement (disagreement) between similar (dissimilar) CPPs and depend heavily on expert knowledge-based handcrafted features. RESULTS In this study, we present SiameseCPP, a novel deep learning framework for automated CPPs prediction. SiameseCPP learns discriminative representations of CPPs based on a well-pretrained model and a Siamese neural network consisting of a transformer and gated recurrent units. Contrastive learning is used for the first time to build a CPP predictive model. Comprehensive experiments demonstrate that our proposed SiameseCPP is superior to existing baseline models for predicting CPPs. Moreover, SiameseCPP also achieves good performance on other functional peptide datasets, exhibiting satisfactory generalization ability.
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The ECRH-Power Upgrade at the Wendelstein 7-X Stellarator. EPJ WEB OF CONFERENCES 2023. [DOI: 10.1051/epjconf/202327704003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The existing ECRH system at W7-X consists of 10 gyrotrons, with output power levels ranging from 0.6 MW up to 1.0 MW each at a frequency of 140 GHz, quasi-optical transmission lines and microwave launchers at the plasma vessel. Compared to other large fusion experiments, W7-X has a relatively low power-to-volume ratio. However high heating power is particularly necessary for achieving high plasma beta values, where the improved confinement of fast ions, one of the optimization criteria of W7-X, can be examined. It is therefore necessary to expand the ECRH systems in several consecutive steps. It is planned to increase the number of gyrotron positions from 10 to 12 and at the same time to evolve the gyrotron output power in several development steps from 1 MW to nominal 1.5 MW and, finally, up to 2 MW. At the same time, the transmission lines will also be upgraded for 2 MW operation. A special effort is also made to improve the reliability of the system by the fast control system.
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Phase II Study of Stereotactic Body Radiation Therapy (SBRT) in Patients with Lung and/or Liver Oligometastases from Colorectal Cancer (CRC): KRAS Gene Status and Metastatic Site Matter. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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EARLY DETECTION OF X-LINKED MOESIN-ASSOCIATED IMMUNE DEFICIENCY ON NEWBORN SCREENING. Ann Allergy Asthma Immunol 2022. [DOI: 10.1016/j.anai.2022.08.879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Comparison of Breast-Conserving Surgery vs. Mastectomy for Patients with Breast Cancer after Neoadjuvant Chemotherapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Development and External Validation of a Nomogram to Predict the Benefit of Regional Node Irradiation in Patients with pT1-2N1M0 Breast Cancer. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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A Decision Support Software for AI-Assisted Decision Making in Response-Adaptive Radiotherapy — An Evaluation Study. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Preliminary Results of a Prospective Phase II Study of Total Neoadjuvant Therapy for Locally Advanced Rectal Cancer. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Radiation-Induced Hypothyroidism in Patients with Breast Cancer after Hypofractionated Radiotherapy: A Prospective Cohort Study. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations. Genome Biol 2022; 23:219. [PMID: 36253864 PMCID: PMC9575223 DOI: 10.1186/s13059-022-02780-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
In this study, we propose iDNA-ABF, a multi-scale deep biological language learning model that enables the interpretable prediction of DNA methylations based on genomic sequences only. Benchmarking comparisons show that our iDNA-ABF outperforms state-of-the-art methods for different methylation predictions. Importantly, we show the power of deep language learning in capturing both sequential and functional semantics information from background genomes. Moreover, by integrating the interpretable analysis mechanism, we well explain what the model learns, helping us build the mapping from the discovery of important sequential determinants to the in-depth analysis of their biological functions.
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1185TiP First-in-human phase I study of ABBV-637 as monotherapy and in combination in patients with relapsed and refractory solid tumors. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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[Outcome comparison between LSA complete reconstruction and partial coverage with endovascular technique for patients with Stanford type B aortic dissection]. ZHONGHUA XIN XUE GUAN BING ZA ZHI 2022; 50:753-760. [PMID: 35982006 DOI: 10.3760/cma.j.cn112148-20220408-00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objectives: To compare the short-term outcomes of branched stentgrafts for left subclavian artery (LSA) revascularization or partial LSA coverage without reconstruction in the treatment of type B aortic dissection with proximal tear close to LSA. Methods: A total of 125 type B aortic dissection patients were treated with thoracic endovascular aortic repair (TEVAR) in Xinqiao Hospital of the Army Medical University from January 2019 to March 2021. Their medical records were reviewed and the outcomes were followed up. According to the different treatment methodologies, the patients were divided into complete LSA coverage with reconstruction group (n=25) and partial LSA coverage without reconstruction group (n=100). The data of baseline characteristics, clinical outcomes, and incidence of postoperative in-hospital adverse events were collected and compared between the two groups. The adverse events during one-year follow-up were also compared between the two groups. Kaplan-Meier analysis and log-rank test were used to compare the cumulative survival rates between groups. Results: Compared with partial LSA coverage group, distance of proximal tear to LSA((8.69±2.32)mm vs. (13.77±1.71) mm) was shorter, in-hospital expenses[175 400(166 000-189 900) yuan vs. 143 700 (138 100-151 800) yuan] was higher, average length of stent [200.00 mm vs. 150.00 (150.00-150.00) mm] and operation time [155.00 (140.00-170.00) min vs. 95.00 (80.00-100.00) min] were longer, and volumes of contrast agent [300.00 (200.00-300.00) ml vs. 200.00 (200.00-300.00) ml] (P<0.05) were higher for patients in the complete LSA coverage with reconstruction group. The incidence of post-operative fever was significantly higher in complete LSA coverage with revascularization group than that in partial LSA partial coverage with reconstruction group (56% vs. 25%, P=0.003). There was no significant difference in the incidences of all-cause death, stroke, endoleak, paraplegia, and LSA branch vessel occlusion between the two groups during follow-up. Kaplan-Meier analysis showed that there was no significant difference in the cumulative survival rates between the two groups (log-rank test: P=0.572 5). Conclusion: The TEVAR with complete LSA revascularization or partial LSA coverage without reconstruction for type B aortic dissection close to LSA are safe and effective with high success rates. There is no significant difference between these two techniques in short-term outcomes.
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First Report of Anthracnose Caused by Colletotrichum sansevieriae on Sansevieria trifasciata var. laurentii in China. PLANT DISEASE 2022; 107:583. [PMID: 35939754 DOI: 10.1094/pdis-03-22-0673-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sansevieria trifasciata var. laurentii (De Wild.) N.E. Brown, commonly known as variegated snake plant or variegated mother-in-law's tongue, is a popular landscape and house plant. In September and October 2019, the obvious leaf spot symptoms were observed on the plants in a 0.2 hm2 of nursery in Qingdao city of China with incidence of 55%. The disease usually starts from the tip or edge of the leaf, initially have slightly water-soaked semi-circular or round brown lesions, which gradually expanded and coalesced into irregular shapes about 3-8 cm in diameter. Grayish brown sunken spots with dark margins that evolve into concentric rings of acervuli which were characteristic of anthracnose, and orange sticky conidial masses were observed under the moist condition. The leaves with typical anthracnose symptoms were collected and deposited in the herbarium of Qingdao agricultural university under accessions no. QDHB074-QDHB087. Subsequently 20 isolates with the same colony and morphological characteristics were obtained from ten diseased leaves by placing surface-sterilized tissue pieces with typical spots on potato dextrose agar (PDA). Colonies are floccose with grayish-white to dark olivaceous gray color, and gray black on the reverse after 14 days at 28°C. Straight conidia [15.0 to 27.5 × 3.5 to 7.0 μm in size (average 18.2 × 6.1 μm) (n = 50)] were cylindrical, aseptate, hyaline, slippery surface, most with one tapering end and the other oval. Setae were black, 185-230 μm in length, with a thin tip and septate in the middle. Appressoria [6.5 to 7.3 × 7.8 to 9.2 μm in size (average 6.8 × 8.1 μm) (n = 15)] were black to dark brown, solitary, spherical with smooth wall. The fungal isolates were identified as Colletotrichum sansevieriae Nakamura (Nakamura et al. 2006), based on the morphological characteristics. To confirm the identification, the internal transcribed spacer (ITS) and calmodulin (CAL) regions of a representative isolate HWL-1016 were amplified by primers ITS1/ITS4 (White et al. 1990) and CMD5/CMD6 (Weir et al. 2012), respectively. The 549 bp ITS (MN922517) and 597 bp CAL (OM994078) sequences had respectively 100% and 99.30% identity with the sequences from holotype species of C. sansevieriae MAFF 239721 (no. NR_152313 and LC180125). Phylogenetic tree based on ITS and CAL sequences respectively or jointly constructed by PAUP4.0 (Swofford 2002) revealed that the fungus in this study clustered with C. sansevieriae isolates (NR_152313, KC790947, HQ433226, JF911349, MN386823). Pathogenicity test of isolate HWL1016 was evaluated on five 3- to 4-month-old potted S. trifasciata var. laurentii under greenhouse conditions (27±2 °C, 16-hr light/8-hr dark photoperiod, 80% relative humidity). Conidial suspension (1×106 conidia/mL) of the isolated fungus from PDA colonies cultured for 15 days and sterile distilled water (as control) were sprayed on pin-pricked surface-sterilized (70% alcohol) leaves of potted plants, respectively. Three replications (three plants) were done for each treatment, and the experiment was repeated twice. The inoculated plants were covered with plastic films for 2 days and obvious water-soaked wounds were observed on the sixth day. After 16 days, the symptoms of the inoculated plants were similar to those in the nursery, with disease incidence reached 100%, while controls remained symptomless. C. sansevieriae was subsequently reisolated from the symptomatic tissues. Anthracnose on S. trifasciata var. laurentii caused by C. sansevieriae has been reported in Australia, Iran, Japan, Malaysia (Kee et al. 2020), South Korea, USA (Talhinhas & Baroncelli 2021), India (Gautam et al. 2012) and Thailand (Li et al. 2020). To our knowledge, this is the first report of C. sansevieriae causing anthracnose on S. trifasciata var. laurentii in China. This study will contribute to guide effective management based on pathogen.
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712 UV-induced reduction in polycomb repression promotes epidermal pigmentation. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Status and future development of Heating and Current Drive for the EU DEMO. FUSION ENGINEERING AND DESIGN 2022. [DOI: 10.1016/j.fusengdes.2022.113159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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