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Neoplasia (New York, N.Y.) Jun 2024Cancer of unknown primary (CUP) is a rare type of metastatic cancer in which the origin of the tumor is unknown. Since the treatment strategy for patients with...
Cancer of unknown primary (CUP) is a rare type of metastatic cancer in which the origin of the tumor is unknown. Since the treatment strategy for patients with metastatic tumors depends on knowing the primary site, accurate identification of the origin site is important. Here, we developed an image-based deep-learning model that utilizes a vision transformer algorithm for predicting the origin of CUP. Using DNA methylation dataset of 8,233 primary tumors from The Cancer Genome Atlas (TCGA), we categorized 29 cancer types into 18 organ classes and extracted 2,312 differentially methylated CpG sites (DMCs) from non-squamous cancer group and 420 DMCs from squamous cell cancer group. Using these DMCs, we created organ-specific DNA methylation images and used them for model training and testing. Model performance was evaluated using 394 metastatic cancer samples from TCGA (TCGA-meta) and 995 samples (693 primary and 302 metastatic cancers) obtained from 20 independent external studies. We identified that the DNA methylation image reveals a distinct pattern based on the origin of cancer. Our model achieved an overall accuracy of 96.95 % in the TCGA-meta dataset. In the external validation datasets, our classifier achieved overall accuracies of 96.39 % and 94.37 % in primary and metastatic tumors, respectively. Especially, the overall accuracies for both primary and metastatic samples of non-squamous cell cancer were exceptionally high, with 96.79 % and 96.85 %, respectively.
PubMed: 38943996
DOI: 10.1016/j.neo.2024.101021 -
Computer Methods and Programs in... Jun 2024Atrial fibrillation (AF) is the most common cardiac arrhythmia, inducing accelerated and irregular beating. Beside well-known disabling symptoms - such as palpitations,...
BACKGROUND AND OBJECTIVE
Atrial fibrillation (AF) is the most common cardiac arrhythmia, inducing accelerated and irregular beating. Beside well-known disabling symptoms - such as palpitations, reduced exercise tolerance, and chest discomfort - there is growing evidence that an alteration of deep cerebral hemodynamics due to AF increases the risk of vascular dementia and cognitive impairment, even in the absence of clinical strokes. The alteration of deep cerebral circulation in AF represents one of the least investigated among the possible mechanisms. Lenticulostriate arteries (LSAs) are small perforating arteries mainly departing from the middle cerebral artery (MCA) and susceptible to small vessel disease, which is one of the mechanisms of subcortical vascular dementia development. The purpose of this study is to investigate the impact of different LSAs morphologies on the cerebral hemodynamics during AF.
METHODS
By combining a computational fluid dynamics (CFD) analysis of LSAs with 7T high-resolution magnetic resonance imaging (MRI), we performed different CFD-based multivariate regression analyses to detect which geometrical and morphological vessel features mostly affect AF hemodynamics in terms of wall shear stress. We exploited 17 cerebral 7T-MRI derived LSA vascular geometries extracted from 10 subjects and internal carotid artery data from validated 0D cardiovascular-cerebral modeling as inflow conditions.
RESULTS
Our results revealed that few geometrical variables - namely the size of the MCA and the bifurcation angles between MCA and LSA - are able to satisfactorily predict the AF impact. In particular, the present study indicates that LSA morphologies exhibiting markedly obtuse LSA-MCA inlet angles and small MCA size downstream of the LSA-MCA bifurcation may be more prone to vascular damage induced by AF.
CONCLUSIONS
The present MRI-based computational study has been able for the first time to: (i) investigate the net impact of LSAs vascular morphologies on cerebral hemodynamics during AF events; (ii) detect which combination of morphological features worsens the hemodynamic response in the presence of AF. Awaiting necessary clinical confirmation, our analysis suggests that the local hemodynamics of LSAs is affected by their geometrical features and some LSA morphologies undergo greater hemodynamic alterations in the presence of AF.
PubMed: 38943985
DOI: 10.1016/j.cmpb.2024.108303 -
Computer Methods and Programs in... Jun 2024Recent advancements in brain-computer interface (BCI) technology have seen a significant shift towards incorporating complex decoding models such as deep neural networks...
Recent advancements in brain-computer interface (BCI) technology have seen a significant shift towards incorporating complex decoding models such as deep neural networks (DNNs) to enhance performance. These models are particularly crucial for sophisticated tasks such as regression for decoding arbitrary movements. However, these BCI models trained and tested on individual data often face challenges with limited performance and generalizability across different subjects. This limitation is primarily due to a tremendous number of parameters of DNN models. Training complex models demands extensive datasets. Nevertheless, group data from many subjects may not produce sufficient decoding performance because of inherent variability in neural signals both across individuals and over time METHODS: To address these challenges, this study proposed a transfer learning approach that could effectively adapt to subject-specific variability in cortical regions. Our method involved training two separate movement decoding models: one on individual data and another on pooled group data. We then created a salience map for each cortical region from the individual model, which helped us identify the input's contribution variance across subjects. Based on the contribution variance, we combined individual and group models using a modified knowledge distillation framework. This approach allowed the group model to be universally applicable by assigning greater weights to input data, while the individual model was fine-tuned to focus on areas with significant individual variance RESULTS: Our combined model effectively encapsulated individual variability. We validated this approach with nine subjects performing arm-reaching tasks, with our method outperforming (mean correlation coefficient, r = 0.75) both individual (r = 0.70) and group models (r = 0.40) in decoding performance. In particular, there were notable improvements in cases where individual models showed low performances (e.g., r = 0.50 in the individual decoder to r = 0.61 in the proposed decoder) CONCLUSIONS: These results not only demonstrate the potential of our method for robust BCI, but also underscore its ability to generalize individual data for broader applicability.
PubMed: 38943984
DOI: 10.1016/j.cmpb.2024.108294 -
Comparative Biochemistry and... Jun 2024Rainbow trout (Oncorhynchus mykiss) is an economically significant freshwater-farmed fish worldwide, and the frequent outbreaks of infectious hematopoietic necrosis...
Rainbow trout (Oncorhynchus mykiss) is an economically significant freshwater-farmed fish worldwide, and the frequent outbreaks of infectious hematopoietic necrosis (IHN) in recent years have gravely compromised the healthy growth of the rainbow trout aquaculture industry. Fish skin is an essential immune barrier against the invasion of external pathogens, but it is poorly known about the role of circRNAs in rainbow trout skin. Therefore, we examined the expression profiles of circRNAs in rainbow trout skin following IHNV infection using RNA-seq. A total of 6607 circRNAs were identified, of which 34 circRNAs were differentially expressed (DE) and these DE circRNA source genes were related to immune-related pathways such as Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, Cytokine-cytokine receptor interaction, ubiquitin mediated proteolysis, and ferroptosis. We used qRT-PCR, Sanger sequencing, and subcellular localization to validate the chosen DE circRNAs, confirming their localization and expression patterns in rainbow trout skin. Further, 12 DE circRNAs were selected to construct the circRNA-miRNA-mRNA regulatory network, finding one miRNA could connect one or more circRNAs and mRNAs, and some miRNAs were reported to be associated with antiviral immunity. The functional prediction findings revealed that novel_circ_002779 and novel_circ_004118 may act as sponges for miR-205-z and miR-155-y to regulate the expression of target genes TLR8 and PIK3R1, respectively, and participated in the antiviral immune responses in rainbow trout. These results shed light on the immunological mechanism of circRNAs in rainbow trout skin and offer fundamental information for further research on the innate immune system and breeding rainbow trout resistant to disease.
PubMed: 38943979
DOI: 10.1016/j.cbd.2024.101277 -
International Journal of Surgery Case... May 2024Primary intracranial neuroendocrine tumors (NETs) are exceedingly rare, often posing diagnostic challenges, particularly in non-secreting variants. These tumors may...
INTRODUCTION AND IMPORTANCE
Primary intracranial neuroendocrine tumors (NETs) are exceedingly rare, often posing diagnostic challenges, particularly in non-secreting variants. These tumors may initially present with nonspecific symptoms, leading to delayed diagnosis and potential neurological complications.
CASE REPORT
We present the case of a 33-year-old male admitted with a one-year history of progressively worsening headache accompanied by acute left ptosis and diplopia. Initial examination revealed left eye ptosis and hypotropia, indicative of third and fourth cranial nerve paralysis. Cavoscopy revealed a mild anterior wall bulge of the sphenoid with normal mucosa. MRI imaging unveiled an expansive clival process extending towards the sellar region and left cavernous sinus, completely occupying the sphenoid sinus and exerting mass effect on the pituitary stalk. Hormonal assays were within reference ranges, ruling out a hormonally-active tumor. Endoscopic endonasal surgery for biopsy revealed a low-grade neuroendocrine tumor positive for cytokeratin AE1/AE2, chromogranin A, synaptophysin, and beta-catenin, with a Ki-67-labeling index <2 %. Somatostatin receptor scintigraphy confirmed intense hyper fixation of the tracer in the sphenoidal tumor, supporting its neuroendocrine origin. The patient declined surgical intervention after informed consent, opting for C1 somatostatin analogs prior to radiotherapy. One-year follow-up demonstrated symptom stability with no tumor progression.
CLINICAL DISCUSSION
To this day, no consensus among reports concerning the optimal management of these cases. Imaging assessment is crucial to validate the primary nature of the tumor and to exclude any distant localization. Various therapeutic modalities, such as surgery, radiotherapy, and somatostatin analogs, should be considered based on the specific characteristics and extent of the tumor.
CONCLUSION
Our case is a clear reminder that neuroendocrine tumors should be considered as a differential diagnosis for skull base neoplasms.
PubMed: 38943936
DOI: 10.1016/j.ijscr.2024.109750 -
Translational Oncology Jun 2024Tumor derived Extracellular vesicles (EVs) in circulating system may contain tumor-specific markers, and EV detection in body fluids could become an important tool for...
Tumor derived Extracellular vesicles (EVs) in circulating system may contain tumor-specific markers, and EV detection in body fluids could become an important tool for early tumor diagnosis, prognosis assessment. Meningiomas are the most common benign intracranial tumors, few studies have revealed specific protein markers for meningiomas from patients' body fluids. In this study, using proximity labeling technology and non-tumor patient plasma as a control, we detected protein levels of EVs in plasma samples from meningioma patients before and after surgery. Through bioinformatics analysis, we discovered that the levels of EV count and protein count in meningioma patients were significantly higher than those in healthy controls, and were significantly decreased postoperatively. Among EV proteins in meningioma patients, the levels of MUC1, SIGLEC11, E-Cadherin, KIT, and TASCTD2 were found not only significantly elevated than those in healthy controls, but also significantly decreased after tumor resection. Moreover, using publicly available GEO databases, we verified that the mRNA level of MUC1, SIGLEC11, and CDH1 in meningiomas were significantly higher in comparison with normal dura mater tissues. Additionally, by analyzing human meningioma specimens collected in this study, we validated the protein levels of MUC1 and SIGLEC11 were significantly increased in WHO grade 2 meningiomas and were positively correlated with tumor proliferation levels. This study indicates that meningiomas secret EV proteins into circulating system, which may serve as specific markers for diagnosis, malignancy predicting and tumor recurrent assessment.
PubMed: 38943923
DOI: 10.1016/j.tranon.2024.102046 -
Clinical Psychology Review Jun 2024Personal recovery represents a paradigm shift in mental healthcare. Validated self-report outcome measures (PROMs) are needed to facilitate the transformation towards... (Review)
Review
BACKGROUND
Personal recovery represents a paradigm shift in mental healthcare. Validated self-report outcome measures (PROMs) are needed to facilitate the transformation towards recovery-oriented practices and services. Objectives were to identify published measures and analyze their measurement properties using a standardized methodology.
METHODS
Following the COSMIN guidelines, we conducted a systematic review of personal recovery PROMs in serious mental illness. The MEDLINE, PMC, PsycINFO, PsycARTICLES, PBSC and Scopus electronic databases were searched for articles published between May 2012 and February 2024. Full-text articles from a previous systematic review were also examined.
RESULTS
91 studies were included in the review, describing 25 PROMs. Ten of them had not been identified in previous reviews. Quality of evidence was globally poor for most PROM measurement properties. Very little evidence was found for cross-cultural validity, measurement invariance, measurement error and criterion validity. The Recovery Assessment Scale and Questionnaire about the Process of Recovery showed the strongest evidence for sufficient psychometric data on a wide range of measurement properties.
CONCLUSIONS
Several personal recovery measures are now available. While research is still needed to enhance their validity on some psychometric properties, the current tools appear sufficient to cover most research and clinical needs.
PubMed: 38943916
DOI: 10.1016/j.cpr.2024.102459 -
Journal of Hazardous Materials Jun 2024The particle size distribution in tailings notably influences their physical properties and behavior. Despite this, our understanding of how the distribution of tailings...
The particle size distribution in tailings notably influences their physical properties and behavior. Despite this, our understanding of how the distribution of tailings particle sizes impacts in situ pollution and ecological remediation in in-situ environment remains limited. In this study, an iron tailings reservoir was sampled along a particle flow path to compare the pollution characteristic and microbial communities across regions with different particle sizes. The results revealed a gradual reduction in tailings particle size along the flow direction. The predominant mineral composition shifts from minerals such as albite and quartz to layered minerals. Total nitrogen, total organic carbon, and total metal concentrations increased, whereas the acid-generating potential decreased. The region with the finest tailings particle size exhibited the highest microbial diversity, featuring metal-resistant microorganisms such as KD4-96, Micrococcaceae, and Acidimicrobiia. Significant discrepancies were observed in tailings pollution and ecological risks across different particle sizes. Consequently, it is necessary to assess tailings reservoirs pollution in the early stages of remediation before determining appropriate remediation methods. These findings underscore that tailings particle distribution is a critical factor in shaping geochemical characteristics. The responsive nature of the microbial community further validated these outcomes and offered novel insights into the ecological remediation of tailings.
PubMed: 38943882
DOI: 10.1016/j.jhazmat.2024.135024 -
Archives of Oral Biology Jun 2024This study aimed to investigate the correlation between genetic factors and the occurrence and progression of temporomandibular disorders (TMDs) using a comprehensive...
OBJECTIVE
This study aimed to investigate the correlation between genetic factors and the occurrence and progression of temporomandibular disorders (TMDs) using a comprehensive review and meta-analysis.
DESIGN
A comprehensive search was conducted using the ScienceDirect, PubMed, Cochrane Library, Dimensions, and Emerald databases. A reviewer selected the study using modified PICO criteria, considering human subjects with TMDs, comparing different genetic factors among TMD and non-TMD patients, and reporting TMD signs and symptoms as outcomes. The methodological standards of the eligible papers were assessed using the Joanna Briggs Institute (JBI) Critical Appraisal Checklist for Non-randomized Experimental Investigations. Information was collected methodically and examined.
RESULTS
The electronic database search yielded 851 articles, 19 of which were included in this study. The data analysis showed a significant influence of genetic factors, such as polymorphisms and gene differences, on the development of TMD signs and symptoms, such as myofascial pain, chronic pain, and disc displacement. In addition, gene polymorphism significantly influenced TMD development, with an odds ratio of 2.46 (1.93-3.14) and p of 0.00001.
CONCLUSIONS
Genetic factors significantly influenced TMD signs and symptoms, and genetic polymorphisms significantly influenced TMD onset and progression. Further research should be conducted in diverse settings with larger sample sizes to verify and validate these findings.
PubMed: 38943858
DOI: 10.1016/j.archoralbio.2024.106032 -
Biosensors & Bioelectronics Jun 2024The progression of gastric cancer involves a complex multi-stage process, with gastroscopy and biopsy being the standard procedures for diagnosing gastric diseases. This...
Identification of chronic non-atrophic gastritis and intestinal metaplasia stages in the Correa's cascade through machine learning analyses of SERS spectral signature of non-invasively-collected human gastric fluid samples.
The progression of gastric cancer involves a complex multi-stage process, with gastroscopy and biopsy being the standard procedures for diagnosing gastric diseases. This study introduces an innovative non-invasive approach to differentiate gastric disease stage using gastric fluid samples through machine-learning-assisted surface-enhanced Raman spectroscopy (SERS). This method effectively identifies different stages of gastric lesions. The XGBoost algorithm demonstrates the highest accuracy of 96.88% and 91.67%, respectively, in distinguishing chronic non-atrophic gastritis from intestinal metaplasia and different subtypes of gastritis (mild, moderate, and severe). Through blinded testing validation, the model can achieve more than 80% accuracy. These findings offer new possibilities for rapid, cost-effective, and minimally invasive diagnosis of gastric diseases.
PubMed: 38943854
DOI: 10.1016/j.bios.2024.116530