-
STAR Protocols Jun 2024Drug resistance is currently the biggest challenge in cancer chemotherapy. Here, we present a protocol to develop a chemotherapy drug screening process by constructing a...
Drug resistance is currently the biggest challenge in cancer chemotherapy. Here, we present a protocol to develop a chemotherapy drug screening process by constructing a cancer prognostic model (PM) using public databases. We describe steps for downloading code and data, preparing the expression matrix and metadata for analysis, screening modeling genes, and constructing a PM. We then detail procedures for constructing predictive websites for cancer patients' survival based on their age, tumor stage, gene expression levels, and risk scores. For complete details on the use and execution of this protocol, please refer to Bai et al..
PubMed: 38943649
DOI: 10.1016/j.xpro.2024.103158 -
Modern Pathology : An Official Journal... Jun 2024As around 25-30% of classical Hodgkin Lymphoma (cHL) patients with advanced stages do not respond to standard therapies, the tumor microenvironment (TME) of cHL is one...
As around 25-30% of classical Hodgkin Lymphoma (cHL) patients with advanced stages do not respond to standard therapies, the tumor microenvironment (TME) of cHL is one avenue that may be explored with the aim of improving risk stratification. CD4+ T cells are thought to be one of the main cell types in the TME. However, few immune signatures have been studied, and many of these lack related spatial data. Thus, our aim is to spatially resolve the CD4+ T cell subtypes that influence cHL outcome, depicting new immune signatures or transcriptional patterns that are in crosstalk with the tumor cells. This study was conducted using the Nanostring GeoMx DSP technology, based on the selection of distinct functional areas of patients' tissues followed by the gene-expression profiling. The goals were to assess the differences in CD4+ T cell populations between tumor-rich and immune-predominant areas defined by different CD30 and PD-L1 expression levels and to seek correlations with clinical metadata. Our results depict a complex map of CD4+ T cells with different functions and differentiation states that are enriched at distinct locations, the flux of cytokines and chemokines that could be related to these, and the specific relationships with the clinical outcome.
PubMed: 38936478
DOI: 10.1016/j.modpat.2024.100551 -
Life (Basel, Switzerland) May 2024The differential diagnosis of atypical melanocytic skin lesions localized on palms and soles represents a diagnostic challenge: indeed, this spectrum encompasses...
Pattern Analysis of Benign and Malignant Atypical Melanocytic Skin Lesions of Palms and Soles: Variations of Dermoscopic Features According to Anatomic Site and Personal Experience.
The differential diagnosis of atypical melanocytic skin lesions localized on palms and soles represents a diagnostic challenge: indeed, this spectrum encompasses atypical nevi (AN) and early-stage melanomas (EN) displaying overlapping clinical and dermoscopic features. This often generates unnecessary excisions or delayed diagnosis. Investigations to date were mostly carried out in specific populations, focusing either on acrolentiginous melanomas or morphologically typical acquired nevi. To investigate the dermoscopic features of atypical melanocytic palmoplantar skin lesions (aMPPLs) as evaluated by variously skilled dermatologists and assess their concordance; to investigate the variations in dermoscopic appearance according to precise location on palms and soles; to detect the features with the strongest association with malignancy/benignity in each specific site. A dataset of 471 aMPPLs-excised in the suspect of malignancy-was collected from 10 European Centers, including a standardized dermoscopic picture (17×) and lesion/patient metadata. An anatomical classification into 17 subareas was considered, along with an anatomo-functional classification considering pressure/friction, (4 macroareas). A total of 156 participants (95 with less than 5 years of experience in dermoscopy and 61 with ≥than 5 years) from 17 countries performed a blinded tele-dermoscopic pattern analysis over 20 cases through a specifically realized web platform. A total of 37,440 dermoscopic evaluations were obtained over 94 (20%) EM and 377 (80%) AN. The areas with the highest density of EM compared to AN were the heel (40.3% EM/aMPPLs) of the sole and the "fingers area" (33%EM/aMPPLs) of the palm, both characterized by intense/chronic traumatism/friction. Globally, the recognition rates of 12 dermoscopic patterns were non statistically different between 95 dermatology residents and 61 specialists: aMPPLs in the plantar arch appeared to be the most "difficult" to diagnose, the was poorly recognized and patterns often misinterpreted. Regarding the aMPPL of the "heel area", the ( = 0.014) and ( = 0.001) significantly discriminated benign cases, while ( = 0.002) and ( = 0.025) malignant ones. In aMPPLs of the "plantar arch", the ( = 0.012) was significant for benignity and , or for malignancy. In palmar lesions, no data were significant in the discrimination between malignant and benign aMPPLs. This study highlights that (i) the pattern analysis of aMPPLs is challenging for both experienced and novice dermoscopists; (ii) the histological distribution varies according to the anatomo-functional classification; and (iii) different dermoscopic patterns are able to discriminate malignant from benign aMPPLs within specific plantar and palmar areas.
PubMed: 38929643
DOI: 10.3390/life14060659 -
Scientific Reports Jun 2024Viral infections pose significant public health challenges, exemplified by the global impact of COVID-19 caused by SARS-CoV-2. Understanding the intricate molecular...
Viral infections pose significant public health challenges, exemplified by the global impact of COVID-19 caused by SARS-CoV-2. Understanding the intricate molecular mechanisms governing virus-host interactions is pivotal for effective intervention strategies. Despite the burgeoning multi-omics data on viral infections, a centralized database elucidating host responses to viruses remains lacking. In response, we have developed a comprehensive database named 'MOI' (available at http://www.fynn-guo.cn/ ), specifically designed to aggregate processed Multi-Omics data related to viral Infections. This meticulously curated database serves as a valuable resource for conducting detailed investigations into virus-host interactions. Leveraging high-throughput sequencing data and metadata from PubMed and Gene Expression Omnibus (GEO), MOI comprises over 3200 viral-infected samples, encompassing human and murine infections. Standardized processing pipelines ensure data integrity, including bulk RNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). MOI offers user-friendly interfaces presenting comprehensive cell marker tables, gene expression data, and epigenetic landscape charts. Analytical tools for DNA sequence conversion, FPKM calculation, differential gene expression, and Gene Ontology (GO)/ Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment enhance data interpretation. Additionally, MOI provides 16 visualization plots for intuitive data exploration. In summary, MOI serves as a valuable repository for researchers investigating virus-host interactions. By centralizing and facilitating access to multi-omics data, MOI aims to advance our understanding of viral pathogenesis and expedite the development of therapeutic interventions.
Topics: Humans; Animals; Mice; COVID-19; SARS-CoV-2; Databases, Genetic; Virus Diseases; High-Throughput Nucleotide Sequencing; Host-Pathogen Interactions; Chromatin Immunoprecipitation Sequencing; Multiomics
PubMed: 38926513
DOI: 10.1038/s41598-024-65629-6 -
GeroScience Jun 2024Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the...
Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.
PubMed: 38922379
DOI: 10.1007/s11357-024-01255-4 -
Nanomaterials (Basel, Switzerland) Jun 2024Pool boiling is essential in many industrial manufacturing applications. In addition, it can become critical in the journey towards improving energy generation... (Review)
Review
Pool boiling is essential in many industrial manufacturing applications. In addition, it can become critical in the journey towards improving energy generation efficiency and accomplishing the goal of net-zero carbon emissions by 2050 via new or traditional power generation applications. The effectiveness of boiling is governed by the bubble cycle. The chemistry and topographical features of the surface being heated have been found to highly impact the boiling performance, such as in the case of pool boiling enhancement when employing hydrophilic and hydrophobic surfaces via nano/micro heater surface modification. Nevertheless, it is questionable how feasible it is to create these surfaces for large-scale applications due to their manufacturing and maintenance cost and complexity. The current work assesses whether the use of nanoparticles in traditional coolants could potentially unlock the mass production of optimised heating surface modification through a metadata literature review analysis. It was discovered that self-assembled layers created as a result of the deposition of nanoparticles in coolants undergoing pool boiling seem to behave most similarly to manufactured hydrophilic surfaces. The creation of enhanced patterned-heat transfer surfaces is shown to be possible via the use of a combination of different nanoparticle suspensions in coolants.
PubMed: 38921888
DOI: 10.3390/nano14121012 -
Journal of Imaging Jun 2024The paper demonstrates a novel methodology for Content-Based Image Retrieval (CBIR), which shifts the focus from conventional domain-specific image queries to more...
The paper demonstrates a novel methodology for Content-Based Image Retrieval (CBIR), which shifts the focus from conventional domain-specific image queries to more complex text-based query processing. Latent diffusion models are employed to interpret complex textual prompts and address the requirements of effectively interpreting the complex textual query. Latent Diffusion models successfully transform complex textual queries into visually engaging representations, establishing a seamless connection between textual descriptions and visual content. Custom triplet network design is at the heart of our retrieval method. When trained well, a triplet network will represent the generated query image and the different images in the database. The cosine similarity metric is used to assess the similarity between the feature representations in order to find and retrieve the relevant images. Our experiments results show that latent diffusion models can successfully bridge the gap between complex textual prompts for image retrieval without relying on labels or metadata that are attached to database images. This advancement sets the stage for future explorations in image retrieval, leveraging the generative AI capabilities to cater to the ever-evolving demands of big data and complex query interpretations.
PubMed: 38921616
DOI: 10.3390/jimaging10060139 -
Journal of the American Medical... Jun 2024To assess the performance of large language models (LLMs) for zero-shot disambiguation of acronyms in clinical narratives.
OBJECTIVE
To assess the performance of large language models (LLMs) for zero-shot disambiguation of acronyms in clinical narratives.
MATERIALS AND METHODS
Clinical narratives in English, German, and Portuguese were applied for testing the performance of four LLMs: GPT-3.5, GPT-4, Llama-2-7b-chat, and Llama-2-70b-chat. For English, the anonymized Clinical Abbreviation Sense Inventory (CASI, University of Minnesota) was used. For German and Portuguese, at least 500 text spans were processed. The output of LLM models, prompted with contextual information, was analyzed to compare their acronym disambiguation capability, grouped by document-level metadata, the source language, and the LLM.
RESULTS
On CASI, GPT-3.5 achieved 0.91 in accuracy. GPT-4 outperformed GPT-3.5 across all datasets, reaching 0.98 in accuracy for CASI, 0.86 and 0.65 for two German datasets, and 0.88 for Portuguese. Llama models only reached 0.73 for CASI and failed severely for German and Portuguese. Across LLMs, performance decreased from English to German and Portuguese processing languages. There was no evidence that additional document-level metadata had a significant effect.
CONCLUSION
For English clinical narratives, acronym resolution by GPT-4 can be recommended to improve readability of clinical text by patients and professionals. For German and Portuguese, better models are needed. Llama models, which are particularly interesting for processing sensitive content on premise, cannot yet be recommended for acronym resolution.
PubMed: 38917444
DOI: 10.1093/jamia/ocae157 -
PloS One 2024Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight...
Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight data management tool that packages metadata with immutable data to promote accessibility, interoperability, and reproducibility. Each dataset is self-contained and does not require metadata to be stored in a centralised system. This decentralised approach means that finding datasets can be difficult. dtool's lookup server, short dserver, as defined by a REST API, makes dtool datasets findable, hence rendering the dtool ecosystem fit for a FAIR data management world. Its simplicity, modularity, accessibility and standardisation via API distinguish dtool and dserver from other solutions and enable it to serve as a common denominator for cross-disciplinary research data management. The dtool ecosystem bridges the gap between standardisation-free data management by individuals and FAIR platform solutions with rigid metadata requirements.
Topics: Software; Data Management; Metadata; Ecosystem; Reproducibility of Results; Internet
PubMed: 38917182
DOI: 10.1371/journal.pone.0306100 -
PloS One 2024This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital...
This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital management of cultural heritage. By introducing an improved Genetic Algorithm (GA), digital management and access efficiency are enhanced, to bring substantial optimization and innovation to the digital management of cultural heritage. Based on the collection of art museums, this study first integrates the collection's images, texts, and metadata with multi-source intelligent information to achieve a more accurate and comprehensive description of digital content. Second, a GA is introduced, and a GA 2 Convolutional Neural Network (GA2CNN) optimization model combining domain knowledge is proposed. Moreover, the convergence speed of traditional GA is improved to adapt to the characteristics of cultural heritage data. Lastly, the Convolutional Neural Network (CNN), GA, and GA2CNN are compared to verify the proposed system's superiority. The results show that in all models, the sample output results' actual value is 2.62, which represents the real data observation results. For sample number 5, compared with the actual value of 2.62, the predicted values of the GA2CNN and GA models are 2.6177 and 2.6313, and their errors are 0.0023 and 0.0113. The CNN model's predicted value is 2.6237, with an error of 0.0037. It can be found that the network fitting accuracy after optimization of the GA2CNN model is high, and the predicted value is very close to the actual value. The digital retrieval system integrated with the GA2CNN model has a good performance in enhancing retrieval efficiency and accuracy. This study provides technical support for the digital organization and display of cultural heritage and offers valuable references for innovative exploration of museum information management in the digital era.
Topics: Museums; Algorithms; Neural Networks, Computer; Information Storage and Retrieval; Art; Humans
PubMed: 38917118
DOI: 10.1371/journal.pone.0305690