Treatment outcomes and risk factors of patients with intracranial germ cell tumour with choriocarcinoma element or ß-HCG level higher than 500 IU/L.

BACKGROUND: In previous studies, patients with intracranial germ cell tumour (iGCT) with pure choriocarcinoma or mixed germ cell tumours with choriocarcinoma element showed similar dismal prognoses, with median overall survival (OS) of 22 months and 1-year survival rate of approximately 60%. However, these conclusions need to be updated because radiotherapy, which is the mainstay for this disease, was not applied in a number of patients. Additionally, prognostic factors need to be explored in this population. METHODS: Clinical data of patients with iGCTs with histologically confirmed choriocarcinoma element or beta-human chorionic gonadotropin (ß-HCG) > 500 IU/L were collected from the archives of our institution and retrospectively studied. RESULTS: A total of 76 patients were eligible for this study. Except for two early deaths, all patients received radiotherapy (craniospinal irradiation [CSI], n = 23; non-CSI, n = 51). The median follow-up duration for the entire series was 63 months (range, 6-188 months). The 5-year event-free survival (EFS) and OS rates were 81.5% and 84.1%, respectively. Among patients who did not have early death or progressive disease after induction chemotherapy, multivariate analysis revealed that chemotherapy cycles (> 4 vs. ≤ 4) (hazard ratio [HR] for EFS 0.144, p = 0.020; HR for OS 0.111, p = 0.028) and ß-HCG levels (> 3000 IU/L vs. ≤ 3000 IU/L) (HR for EFS 4.342, p = 0.059; HR for OS 6.614, p = 0.033) were independent factors for survival. CONCLUSIONS: Patients with iGCTs with choriocarcinoma element or ß-HCG > 500 IU/L showed improved survival with radiotherapy-based treatments. Additional chemotherapy cycles could result in additional survival benefits. Patients with ß-HCG level > 3000 IU/L had poorer prognosis.

Time-dependent risk of atopic dermatitis following nontyphoidal Salmonella infection.

BACKGROUND: The pathogenesis of atopic dermatitis (AD) remains unclear. Nontyphoidal Salmonella (NTS) infection might trigger immune-mediated reactions. We aimed to examine NTS and the risk of subsequent AD. METHODS: From 2002 to 2015, eligible patients (aged 0-100 years) with NTS were identified. NTS and non-NTS groups were matched at a 1:10 ratio on age and sex. We utilized conditional multivariable Cox proportional hazard models to estimate the adjusted hazard ratio (aHR) and 95% confidence interval (CI) for AD development. Subgroup analyses were conducted based on age, sex, and severity of NTS infection. We utilized landmark analysis to explore the time-dependent hazard of AD following NTS. RESULTS: In the NTS group (N = 6624), 403 developed AD. After full adjustment of demographics and comorbidities, the NTS group had a higher risk of AD than the reference group (aHR = 1.217, 95% CI = 1.096-1.352). Age-stratified analysis revealed that NTS group exhibited an elevated risk compared to the reference group, particularly among those aged 13-30 years (aHR = 1.25, 95% CI = 1.017-1.559), individuals aged 31-50 years (aHR = 1.388, 95% CI = 1.112-1.733), those aged 51-70 years (aHR = 1.301, 95% CI = 1.008-1.679), and individuals aged 71 years and over (aHR = 1.791, 95% CI = 1.260-2.545). Severe NTS was associated with a higher risk of AD than the reference group (aHR = 2.411, 95% CI = 1.577-3.685). Landmark analysis showed generally consistent findings. CONCLUSIONS: Minimizing exposure to NTS infection may represent a prospective strategy for averting the onset and progression of atopic dermatitis.

The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase.

Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD+ reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding.

Computational drug repositioning and drug-target prediction have become essential tasks in the early stage of drug discovery. In previous studies, these two tasks have often been considered separately. However, the entities studied in these two tasks (i.e., drugs, targets, and diseases) are inherently related. On one hand, drugs interact with targets in cells to modulate target activities, which in turn alter biological pathways to promote healthy functions and to treat diseases. On the other hand, both drug repositioning and drug-target prediction involve the same drug feature space, which naturally connects these two problems and the two domains (diseases and targets). By using the wisdom of the crowds, it is possible to transfer knowledge from one of the domains to the other. The existence of relationships among drug-target-disease motivates us to jointly consider drug repositioning and drug-target prediction in drug discovery. In this paper, we present a novel approach called iDrug, which seamlessly integrates drug repositioning and drug-target prediction into one coherent model via cross-network embedding. In particular, we provide a principled way to transfer knowledge from these two domains and to enhance prediction performance for both tasks. Using real-world datasets, we demonstrate that iDrug achieves superior performance on both learning tasks compared to several state-of-the-art approaches. Our code and datasets are available at: https://github.com/Case-esaC/iDrug.

Reevaluating the mechanism of excitation energy regulation in iron-starved cyanobacteria.

This paper presents spectroscopic investigations of IsiA, a chlorophyll a-binding membrane protein produced by cyanobacteria grown in iron-deficient environments. IsiA, if associated with photosystem I, supports photosystem I in light harvesting by efficiently transferring excitation energy. However, if separated from photosystem I, IsiA exhibits considerable excitation quenching observed as a substantial reduction of protein-bound chlorophyll a fluorescence lifetime. Previous spectroscopic studies suggested that carotenoids are involved in excitation energy dissipation and in addition play a second role in this antenna complex by supporting chlorophyll a in light harvesting by absorbing in the spectral range inaccessible for chlorophyll a and transferring excitation to chlorophylls. However, this investigation does not support these proposed roles of carotenoids in this light harvesting protein. This study shows that carotenoids do not transfer excitation energy to chlorophyll a. In addition, our investigations do not support the hypothesis that carotenoids are quenchers of the excited state of chlorophyll a in this protein complex. We propose that quenching of chlorophyll a fluorescence in IsiA is maintained by pigment-protein interaction via electron transfer from an excited chlorophyll a to a cysteine residue, an excitation quenching mechanism that was recently proposed to regulate the light harvesting capabilities of the bacteriochlorophyll a-containing Fenna-Mathews-Olson protein from green sulfur bacteria.

9- and 13-Hydroxy-octadecadienoic acids (9+13 HODE) are inversely related to granulocyte colony stimulating factor and IL-6 in runners after 2h running.

This study utilized a pro-inflammatory exercise mode to explore potential linkages between increases in 9- and 13-hydroxy-octadecadienoic acid (9+13 HODE) and biomarkers for inflammation, oxidative stress, and muscle damage. Male (N=10) and female (N=10) runners ran at ∼70% VO2max for 1.5h followed by 30min of downhill running (-10%). Blood samples were taken pre-run and immediately-, 1-h-, and 24-h post-run, and analyzed for 9+13 HODE, F2-isoprostanes, six cytokines, C-reactive protein (CRP), creatine kinase (CK), and myoglobin (MYO). Gender groups performed at comparable relative heart rate and oxygen consumption levels during the 2-h run. All outcome measures increased post-run (time effects, P⩽0.001), with levels near pre-run levels by 24h except for CRP, CK, MYO, and delayed onset of muscle soreness (DOMS). Plasma 9+13 HODE increased 314±38.4% post-run (P<0.001), 77.3±15.8% 1-h post-run (P<0.001), and 40.6±16.4% 24-h post-exercise (P=0.024), and F2-isoprostanes increased 50.8±8.9% post-run (P<0.001) and 19.0±5.3% 1-h post-run (P=0.006). Post-run increases were comparable between genders for all outcomes except for 9+13 HODE (interaction effect, P=0.024, post-run tending higher in females), IL-10 (P=0.006, females lower), and DOMS (P=0.029, females lower). The pre-to-post-run increase in 9+13 HODEs was not related to other outcomes except for plasma granulocyte colony stimulating factor (GCSF) (r=-0.710, P<0.001) and IL-6 (r=-0.457, P=0.043). Within the context of this study, exercise-induced increases in 9+13 HODEs tended higher in females, and were not related to increases in F2-isoprostanes, muscle damage, or soreness. The negative relationships to GCSF and IL-6 suggest a linkage between 9+13 HODES and exercise-induced neutrophil chemotaxis, degranulation, and inflammation.

miR-130a can predict response to temozolomide in patients with glioblastoma multiforme, independently of O6-methylguanine-DNA methyltransferase.

BACKGROUND: Currently, O6-methylguanine-DNA methyltransferase(MGMT) promoter methylation is the most convincing predictive biomarker for temozolomide (TMZ) response in patients with glioblastoma multiforme (GBM). However, technical obstacles prevent this biomarker from being applied widely. On the other hand, microRNAs (miRNAs) are easily investigated in the clinical setting using quantitative real-time polymerase chain reactions. This study aimed to identify miRNAs that could serve as predictive biomarkers for TMZ response. METHODS: The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases were used to investigate the significance of associations between miRNA expression and overall survival (OS) in TMZ-treated patients with GBM. Cytotoxicity assays were used to validate the miRNAs' roles in the response of glioma cells to TMZ. Biological insights concerning the miRNAs were explored using gene set enrichment analysis (GSEA) and gene ontology (GO) analysis. RESULTS: miR-130a was found to be significantly associated with OS in TMZ-treated patients from TCGA and the CGGA. In contrast, miR-130a appeared to be unassociated with OS in patients who only received radiotherapy. The TMZ cytotoxicity assay showed that miR-130a over-expression could sensitize response to TMZ in glioma cells. GSEA and GO analysis indicated that lower miR-130a could generate a more extensive response to oxidative stress, which in turn could elevate Ape1 and mediate resistance to TMZ. In vitro experiment verified that cells with lower miR-130a express higher Ape1 under oxidative stress. CONCLUSIONS: Our data suggested that miR-130a could be a predictive marker for TMZ response in patients with GBM, independently of the mechanism by which MGMT acts as a biomarker. miR-130a could serve as a guide for treatment strategy selection in cases of GBM.

Graphene-to-substrate energy transfer through out-of-plane longitudinal acoustic phonons.

Practically, graphene is often deposited on substrates. Given the major substrate-induced modification of properties and considerable energy transfer at the interface, the graphene-substrate interaction has been widely discussed. However, the proposed mechanisms were restricted to the two-dimensional (2D) plane and interface, while the energy conduction in the third dimension is hardly considered. Herein, we disclose the transfer of energy perpendicular to the interface of the combined system of the 2D graphene and the 3D base. More precisely, our observation of the energy dissipation of optically excited graphene via emitting out-of-plane longitudinal acoustic phonon into the substrate is presented. By applying nanoultrasonic spectroscopy with a piezoelectric nanolayer embedded in the substrate, we found that under photoexcitation by a femtosecond laser pulse graphene can emit longitudinal coherent acoustic phonons (CAPs) with frequencies over 1 THz into the substrate. In addition, the waveform of the CAP pulse infers that the photocarriers and sudden lattice heating in graphene caused modification of graphene-substrate bond and consequently generated longitudinal acoustic phonons in the substrate. The direct observation of this unexplored graphene-to-substrate vertical energy transfer channel can bring new insights into the understanding of the energy dissipation and limited transport properties of supported graphene.

Alteration of bile acid metabolism in the rat induced by chronic ethanol consumption.

Our understanding of the bile acid metabolism is limited by the fact that previous analyses have primarily focused on a selected few circulating bile acids; the bile acid profiles of the liver and gastrointestinal tract pools are rarely investigated. Here, we determined how chronic ethanol consumption altered the bile acids in multiple body compartments (liver, gastrointestinal tract, and serum) of rats. Rats were fed a modified Lieber-DeCarli liquid diet with 38% of calories as ethanol (the amount equivalent of 4-5 drinks in humans). While conjugated bile acids predominated in the liver (98.3%), duodenum (97.8%), and ileum (89.7%), unconjugated bile acids comprised the largest proportion of measured bile acids in serum (81.2%), the cecum (97.7%), and the rectum (97.5%). In particular, taurine-conjugated bile acids were significantly decreased in the liver and gastrointestinal tract of ethanol-treated rats, while unconjugated and glycine-conjugated species increased. Ethanol consumption caused increased expression of genes involved in bile acid biosynthesis, efflux transport, and reduced expression of genes regulating bile acid influx transport in the liver. These results provide an improved understanding of the systemic modulations of bile acid metabolism in mammals through the gut-liver axis.

IDH-mutant grade 4 astrocytoma: a comparison integrating the clinical, pathological, and survival features between primary and secondary patients.

OBJECTIVE: IDH-mutant grade 4 astrocytomas (AIDHmut/G4) are divided into primary de novo (pAIDHmut/G4) and secondary with a history of prior lower-grade gliomas (LGGs; sAIDHmut/G4). The mutational spectrum and DNA methylation patterns are homogeneous within de novo pAIDHmut/G4 and evolved sAIDHmut/G4, but the two groups have different diagnoses, management, and outcomes. This study sought to systematically compare the clinical, pathological, and survival characteristics between them. METHODS: Of the 871 grade 4 astrocytomas with data for IDH mutation, 698 (80.1%) were primary and 173 (19.9%) were secondary. Of the 698 primary tumors, 103 (14.8%) were pAIDHmut/G4, and of the 173 secondary tumors, 108 (62.4%) were sAIDHmut/G4. Clinical, pathological, and survival features were compared between pAIDHmut/G4 and sAIDHmut/G4. Multivariate analyses were performed to identify prognostic factors. RESULTS: Patients with sAIDHmut/G4 had significantly shorter median overall survival (OS; 11.8 vs 34.2 months, hazard ratio [HR] 2.69, 95% confidence interval [CI] 1.367-5.306, p = 0.004) and progression-free survival (PFS; 8.5 vs 24.3 months, HR 2.83, 95% CI 1.532-5.235, p = 0.001) than patients with pAIDHmut/G4. In patients with sAIDHmut/G4, resection status and chemotherapy were independent prognostic factors for OS and PFS; in patients with pAIDHmut/G4, LGG component, resection status, and O6-methylguanine DNA methyltransferase promoter methylation were independent prognostic factors. The therapeutic strategies of LGGs did not influence survival of patients with sAIDHmut/G4, but patients who had not received radiotherapy or chemotherapy when they were diagnosed with LGGs were found to benefit from radiotherapy or chemotherapy when they progressed to sAIDHmut/G4. CONCLUSIONS: The different clinical characteristics, survival, and risk factors between sAIDHmut/G4 and pAIDHmut/G4 provide a reference to guide treatment decisions in AIDHmut/G4.

Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.

Background: Alzheimer's disease (AD), a progressive neurodegenerative disorder, continues to increase in prevalence without any effective treatments to date. In this context, knowledge graphs (KGs) have emerged as a pivotal tool in biomedical research, offering new perspectives on drug repurposing and biomarker discovery by analyzing intricate network structures. Our study seeks to build an AD-specific knowledge graph, highlighting interactions among AD, genes, variants, chemicals, drugs, and other diseases. The goal is to shed light on existing treatments, potential targets, and diagnostic methods for AD, thereby aiding in drug repurposing and the identification of biomarkers. Results: We annotated 800 PubMed abstracts and leveraged GPT-4 for text augmentation to enrich our training data for named entity recognition (NER) and relation classification. A comprehensive data mining model, integrating NER and relationship classification, was trained on the annotated corpus. This model was subsequently applied to extract relation triplets from unannotated abstracts. To enhance entity linking, we utilized a suite of reference biomedical databases and refine the linking accuracy through abbreviation resolution. As a result, we successfully identified 3,199,276 entity mentions and 633,733 triplets, elucidating connections between 5,000 unique entities. These connections were pivotal in constructing a comprehensive Alzheimer's Disease Knowledge Graph (ADKG). We also integrated the ADKG constructed after entity linking with other biomedical databases. The ADKG served as a training ground for Knowledge Graph Embedding models with the high-ranking predicted triplets supported by evidence, underscoring the utility of ADKG in generating testable scientific hypotheses. Further application of ADKG in predictive modeling using the UK Biobank data revealed models based on ADKG outperforming others, as evidenced by higher values in the areas under the receiver operating characteristic (ROC) curves. Conclusion: The ADKG is a valuable resource for generating hypotheses and enhancing predictive models, highlighting its potential to advance AD's disease research and treatment strategies.

Self-Reinforced PTLG Copolymer with Shish Kebab Structures and a Bionic Surface as Bioimplant Materials for Tissue Engineering Applications.

Green and biodegradable materials with great mechanical properties and biocompatibility will offer new opportunities for next-generation high-performance biological materials. Herein, the novel oriented shish kebab crystals of a novel poly(trimethylene carbonate-lactide-glycolide) (PTLG) vascular stent are first reported to be successfully fabricated through a feasible solid-state drawing process to simultaneously enhance the mechanical performance and biocompatibility. The crystal structure of this self-reinforced vascular stent was transformed from spherulites to a shish kebab crystal, which indicates the mechanical interlocking effect and prevents the lamellae from slipping with a significant improvement of mechanical strength to 333 MPa. Meanwhile, it is different from typical biomedical polymers with smooth surface structures, and the as-obtained PTLG vascular stent exhibits a bionic surface morphology with a parallel micro groove and ridge structure. These ridges and grooves were attributed to the reorganization of cytoskeleton fiber bundles following the direction of blood flow shear stress. The structure and parameters of these morphologies were highly similar to the inner surface of blood vessels of the human, which facilitates cell adhesion growth to improve its proliferation, differentiation, and activity on the surface of PTLG.

Novel molecular subtypes of intracranial germ cell tumors expand therapeutic opportunities.

BACKGROUND: Intracranial germ cell tumors (IGCTs) are a rare group of malignancies that are clinically classified as germinomas and nongerminomatous germ cell tumors (NGGCTs). Previous studies have found that somatic mutations involving the mitogen-activated protein kinase/mTOR signaling pathway are common early events. However, a comprehensive genomic understanding of IGCTs is still lacking. METHODS: We established a cohort including over 100 IGCTs and conducted genomic and transcriptomic sequencing. RESULTS: We identified novel recurrent driver genomic aberrations, including USP28 truncation mutations and high-level copy number amplification of KRAS and CRKL caused by replication of extrachromosomal DNA. Three distinct subtypes associated with unique genomic and clinical profiles were identified with transcriptome analysis: Immune-hot, MYC/E2F, and SHH. Both immune-hot and MYC/E2F were predominantly identified in germinomas and shared similar mutations involving the RAS/MAPK signaling pathway. However, the immune-hot group showed an older disease onset age and a significant immune response. MYC/E2F was characterized by a younger disease onset age and increased genomic instability, with a higher proportion of tumors showing whole-genome doubling. Additionally, the SHH subtype was mostly identified in NGGCTs. CONCLUSIONS: Novel genomic aberrations and molecular subtypes were identified in IGCTs. These findings provide molecular basis for the potential introduction of new treatment strategies in this setting.