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View article: cGAS-STING pathway reprograms macrophage polarization and is highly expressed in responding tumors after neoadjuvant immunotherapy in head and neck carcinoma
cGAS-STING pathway reprograms macrophage polarization and is highly expressed in responding tumors after neoadjuvant immunotherapy in head and neck carcinoma Open
Given the critical role of the cGAS-STING pathway in antitumor immunity, this study investigates the functional role of STING in head and neck squamous cell carcinoma (HNSCC) to evaluate the therapeutic potential of STING agonists. Analysi…
View article: AI-powered spatiotemporal imputation and prediction of chlorophyll-a concentration in coastal ecosystems
AI-powered spatiotemporal imputation and prediction of chlorophyll-a concentration in coastal ecosystems Open
Predicting spatiotemporal Chlorophyll-a (Chl_a) distributions is essential for diagnosing and analysing productivity and ecosystem health of coastal oceans. Yet, current tools remain inadequate for prognosing marine ecosystems through pred…
View article: Roles of parental stress and children’s emotional skills on behavioral responses: evidence from NSCH parent reports
Roles of parental stress and children’s emotional skills on behavioral responses: evidence from NSCH parent reports Open
Introduction Early self-regulation is a crucial predictor of how well preschoolers respond to challenging, frustrating, and distracting situations. Examining the mediating role of contextual and individual factors provides insight into how…
View article: SARS-CoV-2 damages cardiomyocyte mitochondria and implicates long COVID-associated cardiovascular manifestations
SARS-CoV-2 damages cardiomyocyte mitochondria and implicates long COVID-associated cardiovascular manifestations Open
Our findings demonstrate a profound impact of SARS-CoV-2 on mitochondrial integrity, shedding light on the cardiovascular implications of Long COVID.
View article: AI-powered spatiotemporal imputation and prediction of chlorophyll-a concentration in coastal ecosystems
AI-powered spatiotemporal imputation and prediction of chlorophyll-a concentration in coastal ecosystems Open
Predicting spatiotemporal Chlorophyll-a (Chl_a) distributions is essential for diagnosing and analyzing productivity and ecosystem health of coastal oceans. Yet, current tools remain inadequate for diagnosing and prognosing marine ecosyste…
View article: TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction
TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction Open
Motivation Cryo-electron tomography (cryo-ET) has revolutionized our ability to observe structures from the subcellular to the atomic level in their native states. Achieving high-resolution reconstruction involves collecting tilt series at…
View article: Construction and Implementation of Human-Machine Collaborative Practice Teaching Mode Based on AI – Take the “Python and Web Crawler” Lesson as an Example
Construction and Implementation of Human-Machine Collaborative Practice Teaching Mode Based on AI – Take the “Python and Web Crawler” Lesson as an Example Open
With the rapid development of information technology, artificial intelligence technology gradually penetrates the field of education, providing new possibilities for the innovation of teaching mode. The traditional teaching mode often has …
View article: UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs Open
Automatic single particle picking is a critical step in the data processing pipeline of cryo-electron microscopy structure reconstruction. In recent years, several deep learning-based algorithms have been developed, demonstrating their pot…
View article: Evaluation of emotion classification schemes in social media text: an annotation-based approach
Evaluation of emotion classification schemes in social media text: an annotation-based approach Open
The AHP evaluation result shows that Ekman's scheme had the highest score. The multi-dimensional scaling (MDS) analysis shows that Ekman, Plutchik, and the Seven Emotions are relatively similar. We analyzed Ekman's six basic emotions in re…
View article: SARS-CoV-2 Damages Cardiomyocytes Mitochondria and Implicates Long COVID-associated Cardiovascular Manifestations
SARS-CoV-2 Damages Cardiomyocytes Mitochondria and Implicates Long COVID-associated Cardiovascular Manifestations Open
Our study investigates the persistent cardiovascular symptoms observed in individuals long after contracting SARS-CoV-2, a condition commonly referred to as “Long COVID”, which has significantly affected millions globally. We meticulously …
View article: MitoStructSeg: mitochondrial structural complexity resolution via adaptive learning for cross-sample morphometric profiling
MitoStructSeg: mitochondrial structural complexity resolution via adaptive learning for cross-sample morphometric profiling Open
Mitochondrial morphology and structural changes are closely associated with metabolic dysfunction and disease progression. However, the structural complexity of mitochondria presents a major challenge for accurate segmentation and analysis…
View article: Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information
Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information Open
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous …
View article: SARS-CoV-2 Phylointeractomics Reveal Functional Evolution of Its Variants Across Susceptible Human Organs
SARS-CoV-2 Phylointeractomics Reveal Functional Evolution of Its Variants Across Susceptible Human Organs Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mainly infects the tissues of the human respiratory, nervous, digestive and urinary systems. Here, we conducted an integrated study of the viral–host protein‒protein interactions…
View article: A Disentangled Representation-Based Multimodal Fusion Framework Integrating Pathomics and Radiomics for KRAS Mutation Detection in Colorectal Cancer
A Disentangled Representation-Based Multimodal Fusion Framework Integrating Pathomics and Radiomics for KRAS Mutation Detection in Colorectal Cancer Open
Kirsten rat sarcoma viral oncogene homolog (namely KRAS) is a key biomarker for prognostic analysis and targeted therapy of colorectal cancer. Recently, the advancement of machine learning, especially deep learning, has greatly promoted th…
View article: Identification of <scp>circRNA</scp>‐disease associations via multi‐model fusion and ensemble learning
Identification of <span>circRNA</span>‐disease associations via multi‐model fusion and ensemble learning Open
Circular RNA (circRNA) is a common non‐coding RNA and plays an important role in the diagnosis and therapy of human diseases, circRNA‐disease associations prediction based on computational methods can provide a new way for better clinical …
View article: FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval Open
The release of AlphaFold2 has sparked a rapid expansion in protein model databases. Efficient protein structure retrieval is crucial for the analysis of structure models, while measuring the similarity between structures is the key challen…
View article: Guest Editorial Computational Mathematics Modeling in Cancer Analysis
Guest Editorial Computational Mathematics Modeling in Cancer Analysis Open
Cancer is a complex disease that can affect any body part. One key feature of cancer is the rapid production of abnormal cells that grow beyond their usual borders and can invade adjoining parts of the body and spread/metastasized to other…
View article: MSTCA-Net: A Novel Impervious Surface Extraction Method Based on a Multistage Transformer
MSTCA-Net: A Novel Impervious Surface Extraction Method Based on a Multistage Transformer Open
The area of impervious surfaces serves as a critical metric to gauge urbanization levels and evaluates ecological health in a given region. However, in some areas with low-density impervious surfaces, these impervious surfaces are often sm…
View article: vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy
vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy Open
Background As software and hardware have developed, so has the scale of research into volume electron microscopy (vEM), leading to ever-increasing resolution. Usually, data collection is followed by image stitching: the same area is subjec…
View article: Realize Generative Yet Complete Latent Representation for Incomplete Multi-View Learning
Realize Generative Yet Complete Latent Representation for Incomplete Multi-View Learning Open
In multi-view environment, it would yield missing observations due to the limitation of the observation process. The most current representation learning methods struggle to explore complete information by lacking either cross-generative v…
View article: Simple but Effective Unsupervised Classification for Specified Domain Images: A Case Study on Fungi Images
Simple but Effective Unsupervised Classification for Specified Domain Images: A Case Study on Fungi Images Open
High-quality labeled datasets are essential for deep learning. Traditional manual annotation methods are not only costly and inefficient but also pose challenges in specialized domains where expert knowledge is needed. Self-supervised meth…
View article: HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing Open
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the number of samples increases, acc…
View article: Source code and data for "trRosettaRNA: automated prediction of RNA 3D structure with transformer network"
Source code and data for "trRosettaRNA: automated prediction of RNA 3D structure with transformer network" Open
Source code for trRosettaRNA