A deep learning method to predict bacterial ADP-ribosyltransferase toxins.

MOTIVATION: ADP-ribosylation is a critical modification involved in regulating diverse cellular processes, including chromatin structure regulation, RNA transcription, and cell death. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent virulence factors that orchestrate the manipulation of host cell functions to facilitate bacterial pathogenesis. Despite their pivotal role, the bioinformatic identification of novel bARTTs poses a formidable challenge due to limited verified data and the inherent sequence diversity among bARTT members. RESULTS: We proposed a deep learning-based model, ARTNet, specifically engineered to predict bARTTs from bacterial genomes. Initially, we introduced an effective data augmentation method to address the issue of data scarcity in training ARTNet. Subsequently, we employed a data optimization strategy by utilizing ART-related domain subsequences instead of the primary full sequences, thereby significantly enhancing the performance of ARTNet. ARTNet achieved a Matthew's correlation coefficient (MCC) of 0.9351 and an F1-score (macro) of 0.9666 on repeated independent test datasets, outperforming three other deep learning models and six traditional machine learning models in terms of time efficiency and accuracy. Furthermore, we empirically demonstrated the ability of ARTNet to predict novel bARTTs across domain superfamilies without sequence similarity. We anticipate that ARTNet will greatly facilitate the screening and identification of novel bARTTs from bacterial genomes. AVAILABILITY AND IMPLEMENTATION: ARTNet is publicly accessible at http://www.mgc.ac.cn/ARTNet/. The source code of ARTNet is freely available at https://github.com/zhengdd0422/ARTNet/.

Pan-Cancer Proteomics Analysis Reveals Wiskott-Aldrich Syndrome Protein as a Potential Regulator of Programmed Death-Ligand 1.

The programmed death-ligand 1 (PD-L1) is a key mediator of immunosuppression in the tumor microenvironment. The expression of PD-L1 in cancer cells is useful for the clinical determination of an immune checkpoint blockade (ICB). However, the regulatory mechanism of the PD-L1 abundance remains incompletely understood. Here, we integrated the proteomics of 52 patients with solid tumors and examined immune cell infiltration to reveal PD-L1-related regulatory modules. Wiskott-Aldrich syndrome protein (WASP) was identified as a potential regulator of PD-L1 transcription. In two independent cohorts containing 164 cancer patients, WASP expression was significantly associated with PD-L1. High WASP expression contributed to immunosuppressive cell composition, including cells positive for immune checkpoints (PD1, CTLA4, TIGIT, and TIM3), FoxP3+ Treg cells, and CD163+ tumor-associated macrophages. Overexpression of WASP increased, whereas knockdown of WASP decreased the protein level of PD-L1 in cancer cells without alteration of PD-L1 protein stability. The WASP-mediated cell migration and invasion were markedly attenuated by the silence of PD-L1. Collectively, our data suggest that WASP is a potential regulator of PD-L1 and the WASP/PD-L1 axis is responsible for cell migration and an immunosuppressive microenvironment.

Immune cell patterns before and after neoadjuvant immune checkpoint blockade combined with chemoradiotherapy in locally advanced esophageal squamous cell carcinoma.

BACKGROUND: Neoadjuvant immune checkpoint blockade (ICB) combined with chemoradiotherapy offers high pathologic complete response (pCR) rate for patients with locally advanced esophageal squamous cell carcinomas (ESCC). But the dynamic tumor immune microenvironment modulated by such neoadjuvant therapy remains unclear. PATIENTS AND METHODS: A total of 41 patients with locally advanced ESCC were recruited. All patients received neoadjuvant toripalimab combined with concurrent chemoradiotherapy. Matched pre- and post-treatment tissues were obtained for fluorescent multiplex immunohistochemistry (mIHC) and IHC analyses. The densities and spatial distributions of immune cells were determined by HALO modules. The differences of immune cell patterns before and after neoadjuvant treatment were investigated. RESULTS: In the pre-treatment tissues, more stromal CD3 + FoxP3 + Tregs and CD86+/CD163 + macrophages were observed in patients with residual tumor existed in the resected lymph nodes (pN1), compared with patients with pCR. The majority of macrophages were distributed in close proximity to tumor nest in pN1 patients. In the post-treatment tissues, pCR patients had less CD86 + cell infiltration, whereas higher CD86 + cell density was significantly associated with higher tumor regression grades (TRG) in non-pCR patients. When comparing the paired pre- and post-treatment samples, heterogeneous therapy-associated immune cell patterns were found. Upon to the treatment, CD3 + T lymphocytes were slightly increased in pCR patients, but markedly decreased in non-pCR patients. In contrast, a noticeable increase and a less obvious decrease of CD86 + cell infiltration were respectively depicted in non-pCR and pCR patients. Furthermore, opposite trends of the treatment-induced alterations of CD8 + and CD15 + cell infiltrations were observed between pN0 and pN1 patients. CONCLUSIONS: Collectively, our data demonstrate a comprehensive picture of tumor immune landscape before and after neoadjuvant ICB combined with chemoradiotherapy in ESCC. The infiltration of CD86 + macrophage may serve as an unfavorable indicator for neoadjuvant toripalimab combined with chemoradiotherapy.

Implications of perceived empathy from spouses during pregnancy for health-related quality of life among pregnant women: a cross-sectional study in Anhui, China.

BACKGROUND: Empathy is a critical component of nursing care, impacting both nurses' and patients' outcomes. However, perceived empathy from spouses during pregnancy and its impact on health-related quality of life (HRQoL) are unclear. This study aimed to examine pregnant women's perceived empathy from their spouses and assess the relation of perceived empathy on HRQoL. METHODS: This cross-sectional study, performed in the obstetric clinics or wards of four well-known hospitals in Anhui Province, China, included 349 pregnant women in the second or third trimester; participants were recruited by convenience sampling and enrolled from October to December 2021. A general information questionnaire, the Interpersonal Reactivity Index (IRI), a purpose-designed empathy questionnaire and the Medical Outcomes Study 12-item Short-Form Health Survey (SF-12) were used to evaluate the pregnant women's general information, perceptions of empathy and HRQoL. Data were analysed using SPSS 22 at a threshold of P < 0.05. Descriptive analysis, Pearson correlation analysis, Student's t test, ANOVA, and multiple regression analysis were used for analysis. RESULTS: The pregnant women's total empathy, physical component summary (PCS) and mental component summary (MCS) scores were 41.6 ± 9.0, 41.6 ± 7.6, and 47.7 ± 9.1, respectively. Correlation analysis revealed that the purpose-designed empathy questionnaire items were significantly positively correlated with perspective taking and empathic concern but were not correlated with the personal distress dimension and were only partially correlated with the fantasy dimension. Maternal physical condition during pregnancy, planned pregnancy, and occupational stress were predictors of the PCS score (ß = 0.281, P < 0.01; ß = 0.132, P = 0.02; ß = -0.128, P = 0.02). The behavioural empathy item of our purpose-designed empathy questionnaire and empathic concern were important predictors of the MCS score (ß = 0.127, P = 0.02; ß = 0.158, P < 0.01), as well as other demographic and obstetric information, explaining 22.0% of the variance in MCS scores totally (F = 12.228, P < 0.01). CONCLUSIONS: Pregnant women perceived lower empathy from their spouses and reported lower HRQoL. Perceived empathy, particularly behavioural empathy, may significantly impact pregnant women's MCS scores but has no effect on their PCS scores. Strategies that foster perceived empathy from spouses among pregnant women are essential for facilitating healthy pregnancies and potentially improving maternal and child health.

VFDB 2022: a general classification scheme for bacterial virulence factors.

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.

Knowledge, attitude, and practice of patients with major depressive disorder on exercise therapy.

BACKGROUND: This study aimed to explore the knowledge, attitude, and practice (KAP) toward exercise therapy of patients with major depressive disorder (MDD). METHODS: This cross-sectional study was conducted at the First Hospital of Shanxi Medical University between April and October 2023 in patients with MDD. A self-designed questionnaire was used to evaluate the KAP (Cronbach's α = 0.787). The minimum-maximum scores were 2-23 for knowledge, 11-55 for attitude, and 7-35 for practice. RESULTS: A total of 494 valid questionnaires were analyzed. The mean KAP dimension scores were 15.39 ± 3.34/23 (66.91%), 36.54 ± 19.33/55 (66.44%), and 19.33 ± 5.22/35 (55.23%), indicating poor knowledge, negative attitude, and weak practice. Multivariable logistic regression analysis showed that female (OR = 0.613, 95%CI: 0.376-1.000, P = 0.050), urban residence (OR = 0.443, 95%CI: 0.259-0.758, P = 0.003), suburban residence (OR = 0.047, 95%CI: 0.016-0.138, P < 0.001), higher income (OR = 3.889-7.928, all P < 0.001), and unclear self-reported depression level (OR = 0.078, 95%CI: 0.027-0.221, P < 0.001) were independently associated with the knowledge scores. Knowledge scores (OR = 1.102, 95%CI: 1.022-1.188, P = 0.011), female gender (OR = 0.437, 95%CI: 0.246-0.776, P = 0.005), city (OR = 0.410, 95%CI: 0.226-0.744, P = 0.003), married (OR = 3.577, 95%CI: 1.751-7.650, P < 0.001), higher income (OR = 0.065-0.392, both P < 0.050), depressive trend (OR = 2.640, 95%CI: 1.110-6.278, P = 0.028), high depression score level (OR = 0.176, 95%CI: 0.104-0.300, P < 0.001), and unclear self-reported depression score (OR = 0.023, 95%CI: 0.007-0.076, P < 0.001) were independently associated with the attitude scores. Finally, knowledge scores (OR = 1.130, 95%CI: 1.051-1.215, P = 0.001), attitude scores (OR = 1.199, 95%CI: 1.124-1.280, P < 0.001), and city (OR = 0.583, 95%CI: 0.352-0.965, P = 0.036) were independently associated with the practice scores. The structural equation modeling analysis showed that knowledge, but not attitude (ß = 0.103, P = 0.092) or practice (ß = 0.034, P = 0.603), influenced the depression level (ß=-0.074, P < 0.001); attitude influenced practice (ß = 0.369, P < 0.001). CONCLUSION: The KAP toward exercise among MDD patients is poor in Shanxi. Females, people living in urban or suburban areas, with lower income, and self-reported unclear depression levels should be targeted by education interventions.

MU variability in CBCT-guided online adaptive radiation therapy.

PURPOSE: CBCT-guided online-adaptive radiotherapy (oART) systems have been made possible by using artificial intelligence and automation to substantially reduce treatment planning time during on-couch adaptive sessions. Evaluating plans generated during an adaptive session presents significant challenges to the clinical team as the planning process gets compressed into a shorter window than offline planning. We identified MU variations up to 30% difference between the adaptive plan and the reference plan in several oART sessions that caused the clinical team to question the accuracy of the oART dose calculation. We investigated the cause of MU variation and the overall accuracy of the dose delivered when MU variations appear unnecessarily large. METHODS: Dosimetric and adaptive plan data from 604 adaptive sessions of 19 patients undergoing CBCT-guided oART were collected. The analysis included total MU per fraction, planning target volume (PTV) and organs at risk (OAR) volumes, changes in PTV-OAR overlap, and DVH curves. Sessions with MU greater than two standard deviations from the mean were reoptimized offline, verified by an independent calculation system, and measured using a detector array. RESULTS: MU variations relative to the reference plan were normally distributed with a mean of -1.0% and a standard deviation of 11.0%. No significant correlation was found between MU variation and anatomic changes. Offline reoptimization did not reliably reproduce either reference or on-couch total MUs, suggesting that stochastic effects within the oART optimizer are likely causing the variations. Independent dose calculation and detector array measurements resulted in acceptable agreement with the planned dose. CONCLUSIONS: MU variations observed between oART plans were not caused by any errors within the oART workflow. Providers should refrain from using MU variability as a way to express their confidence in the treatment planning accuracy. Clinical decisions during on-couch adaptive sessions should rely on validated secondary dose calculations to ensure optimal plan selection.

Circ_0020887 Silencing Combats Hypoxic-Induced Cardiomyocyte Injury in an MiR-370-3p/CYP1B1-Dependent Manner.

Targeting circular RNA has been a novel approach to preventing and limiting acute myocardial infarction (AMI). Here, we planned to investigate the role and mechanism of circ_0020887 in AMI progression.Hypoxic injury in human cardiomyocytes (AC16) was measured using cell counting kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, flow cytometry, and colorimetric assay kits. RNA and protein expressions were determined using real-time quantitative PCR and western blotting. Direct interplay between RNAs was determined using dual-luciferase reporter, RNA pull-down, and RIP assays.In the plasma and hypoxia-induced AC16 cells of patients with AMI, circ_0020887 and miR-370-3p were upregulated and downregulated, respectively, concomitant with the upregulation of cytochrome P450 1B1 (CYP1B1). Circ_0020887 interference could inhibit hypoxia-induced AC16 cell apoptosis, oxidative stress, and inflammatory response. Circ_0020887 could sponge miR-370-3p, and miR-370-3p could target CYP1B1. The inhibition effect of circ_0020887 knockdown on hypoxia-induced AC16 cell injury could be reversed by the miR-370-3p inhibitor. Besides, CYP1B1 overexpression also overturned the suppressive effect of miR-370-3p on hypoxia-induced AC16 cell apoptosis, oxidative stress, and inflammatory response.In conclusion, circ_0020887 regulated the miR-370-3p/CYP1B1 axis to regulate hypoxia-induced cardiomyocyte injury, confirming that circ_0020887 might promote cardiomyocyte injury.

Biallelic CLCN2 mutations cause retinal degeneration by impairing retinal pigment epithelium phagocytosis and chloride channel function.

CLCN2 encodes a two-pore homodimeric chloride channel protein (CLC-2) that is widely expressed in human tissues. The association between Clcn2 and the retina is well-established in mice, as loss-of-function of CLC-2 can cause retinopathy in mice; however, the ocular phenotypes caused by CLCN2 mutations in humans and the underlying mechanisms remain unclear. The present study aimed to define the ocular features and reveal the pathogenic mechanisms of CLCN2 variants associated with retinal degeneration in humans using an in vitro overexpression system, as well as patient-induced pluripotent stem cell (iPSC)-derived retinal pigment epithelium (RPE) cells and retinal organoids (ROs). A patient carrying the homozygous c.2257C > T (p.R753X) nonsense CLCN2 mutation was followed up for > 6 years. Ocular features were comprehensively characterized with multimodality imaging and functional examination. The patient presented with severe bilateral retinal degeneration with loss of photoreceptor and RPE. In vitro, mutant CLC-2 maintained the correct subcellular localization, but with reduced channel function compared to wild-type CLC-2 in HEK293T cells. Additionally, patient iPSC-derived RPE cells carrying the CLCN2 mutation exhibited dysfunctional ClC-2 chloride channels and outer segment phagocytosis. Notably, these functions were rescued following the repair of the CLCN2 mutation using the CRISPR-Cas9 system. However, this variant did not cause significant photoreceptor degeneration in patient-derived ROs, indicating that dysfunctional RPE is likely the primary cause of biallelic CLCN2 variant-mediated retinopathy. This study is the first to establish the confirmatory ocular features of human CLCN2-related retinal degeneration, and reveal a pathogenic mechanism associated with biallelic CLCN2 variants, providing new insights into the cause of inherited retinal dystrophies.

Survival benefits associated with being adherent and having longer persistence to adjuvant hormone therapy across up to five years among U.S. Medicare population with breast cancer.

PURPOSE: To assess associations between adherence to and persistence with adjuvant hormone therapy and mortality among older women with breast cancer. METHODS: The surveillance, epidemiology, and end results data linked with U.S. Medicare claims was used. This study included older women diagnosed with stage I-III hormone receptor-positive breast cancer from 2009 through 2017. Adherence was defined as having proportion of days covered (PDC) ≥ 0.80. Persistence was defined as having no discontinuation, i.e., no break of ≥ 180 continuous days. Length of persistence was calculated as time from therapy initiation to discontinuation. Cox models with time-dependent covariates were used to assess associations between adherence and persistence with mortality. RESULTS: This study included 25,796 women. Adherence rates were 78.1 percent, 75.2 percent, 72.4 percent, 70.0 percent, and 61.5 percent from year 1 to year 5 after hormone therapy initiation. Persistence rates were 87.5 percent, 81.7 percent, 77.1 percent, 72.9 percent, and 68.9 percent through cumulative intervals of 1 year up to 5 years. Adherence was associated with all-cause mortality but not associated with breast cancer-specific mortality. Persistent women had lower risk of all-cause mortality and breast cancer-specific mortality. Each additional year of persistence had additional contributions to survival benefits (11% decreased risk of all-cause mortality and 37% decreased risk of breast cancer-specific mortality). CONCLUSION: This study confirms the detrimental effect of nonadherence to adjuvant hormone therapy across up to 5 years on all-cause survival in older U.S. women. It also reveals the survival benefits associated with having longer persistence across up to 5 years.