Ranking Plant Network Nodes Based on Their Centrality Measures

A Controllability Reinforcement Learning Method for Pancreatic Cancer Biomarker Identification

Pancreatic cancer is one of the most malignant cancers with rapid progression and poor prognosis. The use of transcriptional data can be effective in finding new biomarkers for pancreatic cancer. Many network-based methods used to identify cancer biomarkers are proposed, among which the combination of network controllability appears. However, most of the existing methods do not study RNA, rely on priori and mutations information, or can only achieve classification tasks. In this study, we propose a method combined Relational Graph Convolutional Network and Deep Q-Network called RDDriver to identify pancreatic cancer biomarkers based on multi-layer heterogeneous transcriptional regulation network. Firstly, we construct a regulation network containing long non-coding RNA, microRNA, and messenger RNA. Secondly, Relational Graph Convolutional Network is used to learn the node representation. Finally, we use the idea of Deep Q-Network to build a model, which score and prioritize each RNA with the Popov-Belevitch-Hautus criterion. We train RDDriver on three small simulated networks, and calculate the average score after applying the model parameters to the regulation networks separately. To demonstrate the effectiveness of the method, we perform experiments for comparison between RDDriver and other eight methods based on the approximate benchmark of three types cancer drivers RNAs.

Exploring the Impact of Hand Dominance on Laparoscopic Surgical Skills Development Using Network Models

BACKGROUND

Laparoscopic surgery demands high precision and skill, necessitating effective training protocols that account for factors such as hand dominance. This study investigates the impact of hand dominance on the acquisition and proficiency of laparoscopic surgical skills, utilizing a novel assessment method that combines Network Models and electromyography (EMG) data.

METHODS

Eighteen participants, comprising both medical and non-medical students, engaged in laparoscopic simulation tasks, including peg transfer and wire loop tasks. Performance was assessed using Network Models to analyze EMG data, capturing muscle activity and learning progression. The NASA Task Load Index (TLX) was employed to evaluate subjective task demands and workload perceptions.

RESULTS

Our analysis revealed significant differences in learning progression and skill proficiency between dominant and non-dominant hands, suggesting the need for tailored training approaches. Network Models effectively identified patterns of skill acquisition, while NASA-TLX scores correlated with participants' performance and learning progression, highlighting the importance of considering both objective and subjective measures in surgical training.

CONCLUSIONS

The study underscores the importance of hand dominance in laparoscopic surgical training and suggests that personalized training protocols could enhance surgical precision, efficiency, and patient outcomes. By leveraging advanced analytical techniques, including Network Models and EMG data analysis, this research contributes to optimizing clinical training methodologies, potentially revolutionizing surgical education and improving patient care.

Integrated Systems Biology Pipeline to Compare Co-Expression Networks in Plants and Elucidate Differential Regulators

To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic, and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. The coordination and integration of all these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. In this study, we describe a reproducible protocol POTFUL (pant co-expression transcription factor regulators), implemented in Python 3, for integrating co-expression and transcription factor target protein networks to infer gene regulation.