Benchmarking Retrieval-Augmented Generation for Medicine

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine.Comment: Homepage: https://teddy-xionggz.github.io/benchmark-medical-rag

Biomedical Question Answering: A Survey of Approaches and Challenges

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into 5 distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and discuss some potential future directions to explore.Comment: In submission to ACM Computing Survey

The Application of Social Characteristic and L1 Optimization in the Error Correction for Network Coding in Wireless Sensor Networks

One of the remarkable challenges about Wireless Sensor Networks (WSN) is how to transfer the collected data efficiently due to energy limitation of sensor nodes. Network coding will increase network throughput of WSN dramatically due to the broadcast nature of WSN. However, the network coding usually propagates a single original error over the whole network. Due to the special property of error propagation in network coding, most of error correction methods cannot correct more than C/2 corrupted errors where C is the max flow min cut of the network. To maximize the effectiveness of network coding applied in WSN, a new error-correcting mechanism to confront the propagated error is urgently needed. Based on the social network characteristic inherent in WSN and L1 optimization, we propose a novel scheme which successfully corrects more than C/2 corrupted errors. What is more, even if the error occurs on all the links of the network, our scheme also can correct errors successfully. With introducing a secret channel and a specially designed matrix which can trap some errors, we improve John and Yi’s model so that it can correct the propagated errors in network coding which usually pollute exactly 100% of the received messages. Taking advantage of the social characteristic inherent in WSN, we propose a new distributed approach that establishes reputation-based trust among sensor nodes in order to identify the informative upstream sensor nodes. With referred theory of social networks, the informative relay nodes are selected and marked with high trust value. The two methods of L1 optimization and utilizing social characteristic coordinate with each other, and can correct the propagated error whose fraction is even exactly 100% in WSN where network coding is performed. The effectiveness of the error correction scheme is validated through simulation experiments

The patient-related factors in revision procedures on tibia of patients with osteogenesis imperfecta treated with the Peter-Williams nail

Abstract Objective To investigate the patient-related factors that affect the revision rate for the tibia in patients with osteogenesis imperfecta treated with the Peter-Williams nail, and to explore the relationship between the risk factors and complications postsurgery. Methods We retrospectively analysed the data of 211 patients (93 females (44.08%) and 118 males (55.92%)) with osteogenesis imperfecta treated with Peter-Williams. The factors affecting surgical revision were analysed by performing binary logistic regression. Then, a total of 211 patients with type III, type I or type IV OI were divided into five groups according to the results of regression. Statistical comparison of these groups was performed to further investigate the relationship between patient-related factors and revision procedures. Statistical comparison was also performed to analyse the relationship between the classification and postoperative complications. Results Among the 211 patients who underwent surgery, 40 had type I OI, 109 had type IV OI, and 62 had type III OI. Binary logistic regression revealed that the classification (OR = 3.32, 95% CI 1.06–10.39, P = 0.039) and initial operation age (OR = 0.83, 95% CI 0.76–0.92, P < 0.001) were significantly correlated with revision procedures. In type III patients, the initial operation age was significantly correlated with revision procedures (P < 0.001), and the revision rate was lower in patients aged 9 to12 years (P = 0.001). In type I and IV patients, the initial operation age was not significantly correlated with revision procedures (P = 0.281). Classification had a significant effect on postoperative deformity (P = 0.003). Conclusions The study reported that the age of initial surgery and classification were the influencing factors affecting the revision procedures of tibia in patients with osteogenesis imperfecta treated with the Peter-Williams nail. In patients with type III disease, the revision rate was lower individuals aged 9–12 years old, and a higher incidence of postoperative deformity was observed

Altered Functional Connectivity in Children with ADHD Revealed by Scalp EEG: An ERP Study

Attention deficit hyperactivity disorder (ADHD) is one of the most common neurodevelopmental brain disorders in childhood. Despite extensive researches, the neurobiological mechanism underlying ADHD is still left unveiled. Since the deficit functions, such as attention, have been demonstrated in ADHD, in our present study, based on the oddball P3 task, the corresponding electroencephalogram (EEG) of both healthy controls (HCs) and ADHD children was first collected. And we then not only focused on the event-related potential (ERP) evoked during tasks but also investigated related brain networks. Although an insignificant difference in behavior was found between the HCs and ADHD children, significant electrophysiological differences were found in both ERPs and brain networks. In detail, the dysfunctional attention occurred during the early stage of the designed task; as compared to HCs, the reduced P2 and N2 amplitudes in ADHD children were found, and the atypical information interaction might further underpin such a deficit. On the one hand, when investigating the cortical activity, HCs recruited much stronger brain activity mainly in the temporal and frontal regions, compared to ADHD children; on the other hand, the brain network showed atypical enhanced long-range connectivity between the frontal and occipital lobes but attenuated connectivity among frontal, parietal, and temporal lobes in ADHD children. We hope that the findings in this study may be instructive for the understanding of cognitive processing in children with ADHD

Additional file 1 of Plasma exosomes improve peripheral neuropathy via miR-20b-3p/Stat3 in type I diabetic rats

Additional file 1: Figure S1. The diabetic model was successfully constructed after STZ injection. Figure S2. Internalization of plasma exosomes of sciatic nerve in NC rats. Figure S3. Biological distribution of plasma exosomes in vivo. Figure S4. Effects of plasma exosomes on RSC96 and DRG cells. Figure S5. Effects of plasma exosomes on RSC96 and DRG cells. Figure S6. Statistical analysis of pstat3/stat3. Figure S7. Characterization of ageing plasma exosomes. Figure S8. Ageing-exos did not improve nerve damage caused by high glucose. Figure S9. Ageing-exos augments the motor and sensory innervation of the targets. Table S1. Random blood glucose and total cholesterol levels after exosome treatment. Table S2. Random blood glucose and total cholesterol levels after miR-20b-3p agomir treatment. Table S3. Sequence information used in the article. Table S4. Reagent information used in the article

Long-Acting Heterodimeric Paclitaxel–Idebenone Prodrug-Based Nanomedicine Promotes Functional Recovery after Spinal Cord Injury

After spinal cord injury (SCI), successive systemic administration of microtubule-stabilizing agents has been shown to promote axon regeneration. However, this approach is limited by poor drug bioavailability, especially given the rapid restoration of the blood–spinal cord barrier. There is a pressing need for long-acting formulations of microtubule-stabilizing agents in treating SCI. Here, we conjugated the antioxidant idebenone with microtubule-stabilizing paclitaxel to create a heterodimeric paclitaxel–idebenone prodrug via an acid-activatable, self-immolative ketal linker and then fabricated it into chondroitin sulfate proteoglycan-binding nanomedicine, enabling drug retention within the spinal cord for at least 2 weeks and notable enhancement in hindlimb motor function and axon regeneration after a single intraspinal administration. Additional investigations uncovered that idebenone can suppress the activation of microglia and neuronal ferroptosis, thereby amplifying the therapeutic effect of paclitaxel. This prodrug-based nanomedicine simultaneously accomplishes neuroprotection and axon regeneration, offering a promising therapeutic strategy for SCI