Distributed gene clinical decision support system based on cloud computing

Background: The clinical decision support system can effectively break the limitations of doctors’ knowledge and reduce the possibility of misdiagnosis to enhance health care. The traditional genetic data storage and analysis methods based on stand-alone environment are hard to meet the computational requirements with the rapid genetic data growth for the limited scalability. Methods: In this paper, we propose a distributed gene clinical decision support system, which is named GCDSS. And a prototype is implemented based on cloud computing technology. At the same time, we present CloudBWA which is a novel distributed read mapping algorithm leveraging batch processing strategy to map reads on Apache Spark. Results: Experiments show that the distributed gene clinical decision support system GCDSS and the distributed read mapping algorithm CloudBWA have outstanding performance and excellent scalability. Compared with state-of-the-art distributed algorithms, CloudBWA achieves up to 2.63 times speedup over SparkBWA. Compared with stand-alone algorithms, CloudBWA with 16 cores achieves up to 11.59 times speedup over BWA-MEM with 1 core. Conclusions: GCDSS is a distributed gene clinical decision support system based on cloud computing techniques. In particular, we incorporated a distributed genetic data analysis pipeline framework in the proposed GCDSS system. To boost the data processing of GCDSS, we propose CloudBWA, which is a novel distributed read mapping algorithm to leverage batch processing technique in mapping stage using Apache Spark platform. Keywords: Clinical decision support system, Cloud computing, Spark, Alluxio, Genetic data analysis, Read mappin

RexUIE: A Recursive Method with Explicit Schema Instructor for Universal Information Extraction

Universal Information Extraction (UIE) is an area of interest due to the challenges posed by varying targets, heterogeneous structures, and demand-specific schemas. However, previous works have only achieved limited success by unifying a few tasks, such as Named Entity Recognition (NER) and Relation Extraction (RE), which fall short of being authentic UIE models particularly when extracting other general schemas such as quadruples and quintuples. Additionally, these models used an implicit structural schema instructor, which could lead to incorrect links between types, hindering the model's generalization and performance in low-resource scenarios. In this paper, we redefine the authentic UIE with a formal formulation that encompasses almost all extraction schemas. To the best of our knowledge, we are the first to introduce UIE for any kind of schemas. In addition, we propose RexUIE, which is a Recursive Method with Explicit Schema Instructor for UIE. To avoid interference between different types, we reset the position ids and attention mask matrices. RexUIE shows strong performance under both full-shot and few-shot settings and achieves State-of-the-Art results on the tasks of extracting complex schemas

Precedent-Enhanced Legal Judgment Prediction with LLM and Domain-Model Collaboration

Legal Judgment Prediction (LJP) has become an increasingly crucial task in Legal AI, i.e., predicting the judgment of the case in terms of case fact description. Precedents are the previous legal cases with similar facts, which are the basis for the judgment of the subsequent case in national legal systems. Thus, it is worthwhile to explore the utilization of precedents in the LJP. Recent advances in deep learning have enabled a variety of techniques to be used to solve the LJP task. These can be broken down into two categories: large language models (LLMs) and domain-specific models. LLMs are capable of interpreting and generating complex natural language, while domain models are efficient in learning task-specific information. In this paper, we propose the precedent-enhanced LJP framework (PLJP), a system that leverages the strength of both LLM and domain models in the context of precedents. Specifically, the domain models are designed to provide candidate labels and find the proper precedents efficiently, and the large models will make the final prediction with an in-context precedents comprehension. Experiments on the real-world dataset demonstrate the effectiveness of our PLJP. Moreover, our work shows a promising direction for LLM and domain-model collaboration that can be generalized to other vertical domains

Evaluation of a novel saliva-based epidermal growth factor receptor mutation detection for lung cancer: A pilot study.

BackgroundThis article describes a pilot study evaluating a novel liquid biopsy system for non-small cell lung cancer (NSCLC) patients. The electric field-induced release and measurement (EFIRM) method utilizes an electrochemical biosensor for detecting oncogenic mutations in biofluids.MethodsSaliva and plasma of 17 patients were collected from three cancer centers prior to and after surgical resection. The EFIRM method was then applied to the collected samples to assay for exon 19 deletion and p.L858 mutations. EFIRM results were compared with cobas results of exon 19 deletion and p.L858 mutation detection in cancer tissues.ResultsThe EFIRM method was found to detect exon 19 deletion with an area under the curve (AUC) of 1.0 in both saliva and plasma samples in lung cancer patients. For L858R mutation detection, the AUC of saliva was 1.0, while the AUC of plasma was 0.98. Strong correlations were also found between presurgery and post-surgery samples for both saliva (0.86 for exon 19 and 0.98 for L858R) and plasma (0.73 for exon 19 and 0.94 for L858R).ConclusionOur study demonstrates the feasibility of utilizing EFIRM to rapidly, non-invasively, and conveniently detect epidermal growth factor receptor mutations in the saliva of patients with NSCLC, with results corresponding perfectly with the results of cobas tissue genotyping

Evolution of Cartilage Repair Technology

Articular cartilage plays an important role in daily joint activities. With the aging of the social population, the degenerative cartilage injury and the sports injury caused by inappropriate exercise of young patients, etc., the incidence rate of articular cartilage injury is constantly rising, and the injured patients tend to be younger. Although articular cartilage has its corresponding metabolic activities, it is difficult to recover and regenerate itself once it is damaged due to lack of nerve, blood vessel, and lymphatic tissue Common articular cartilage injuries can be divided into three types according to the degree of injury: partial cartilage injury, full-thickness cartilage injury, and osteochondral defect. If partial cartilage damage and full-thickness cartilage damage are not found and treated in time in the early stage, further deterioration will lead to serious osteochondral defects. After the corresponding subchondral bone injury, the upward invasion of the upper cartilage layer will also cause the overall osteochondral injury. Therefore, whether the osteochondral injury caused by the top-down or the osteochondral injury caused by the bottom-up, it seriously affects the normal activities of human joints. It not only brings great inconvenience to the daily life of patients, but also causes huge economic and psychological burden to patients. At the same time, it also consumes a large number of social public medical resources. Therefore, seeking an effective osteochondral repair strategy is not only the urgent need and hope of the society, but also one of the clinical scientific problems that clinicians and scientists urgently need to solve