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General General

The connectome of an insect brain.

In Science (New York, N.Y.)

Brains contain networks of interconnected neurons and so knowing the network architecture is essential for understanding brain function. We therefore mapped the synaptic-resolution connectome of an entire insect brain (Drosophila larva) with rich behavior, including learning, value computation, and action selection, comprising 3016 neurons and 548,000 synapses. We characterized neuron types, hubs, feedforward and feedback pathways, as well as cross-hemisphere and brain-nerve cord interactions. We found pervasive multisensory and interhemispheric integration, highly recurrent architecture, abundant feedback from descending neurons, and multiple novel circuit motifs. The brain's most recurrent circuits comprised the input and output neurons of the learning center. Some structural features, including multilayer shortcuts and nested recurrent loops, resembled state-of-the-art deep learning architectures. The identified brain architecture provides a basis for future experimental and theoretical studies of neural circuits.

Winding Michael, Pedigo Benjamin D, Barnes Christopher L, Patsolic Heather G, Park Youngser, Kazimiers Tom, Fushiki Akira, Andrade Ingrid V, Khandelwal Avinash, Valdes-Aleman Javier, Li Feng, Randel Nadine, Barsotti Elizabeth, Correia Ana, Fetter Richard D, Hartenstein Volker, Priebe Carey E, Vogelstein Joshua T, Cardona Albert, Zlatic Marta

2023-Mar-10

General General

A study of autoencoders as a feature extraction technique for spike sorting.

In PloS one ; h5-index 176.0

Spike sorting is the process of grouping spikes of distinct neurons into their respective clusters. Most frequently, this grouping is performed by relying on the similarity of features extracted from spike shapes. In spite of recent developments, current methods have yet to achieve satisfactory performance and many investigators favour sorting manually, even though it is an intensive undertaking that requires prolonged allotments of time. To automate the process, a diverse array of machine learning techniques has been applied. The performance of these techniques depends however critically on the feature extraction step. Here, we propose deep learning using autoencoders as a feature extraction method and evaluate extensively the performance of multiple designs. The models presented are evaluated on publicly available synthetic and real "in vivo" datasets, with various numbers of clusters. The proposed methods indicate a higher performance for the process of spike sorting when compared to other state-of-the-art techniques.

Ardelean Eugen-Richard, Coporîie Andreea, Ichim Ana-Maria, Dînșoreanu Mihaela, Mureșan Raul Cristian

2023

General General

A Pilot Study of Plantar Mechanics Distributions and Fatigue Profiles after Running on a Treadmill: Using a Support Vector Machine Algorithm.

In Journal of healthcare engineering

The treadmill is widely used in running fatigue experiments, and the variation of plantar mechanical parameters caused by fatigue and gender, as well as the prediction of fatigue curves by a machine learning algorithm, play an important role in providing different training programs. This experiment aimed to compare changes in peak pressure (PP), peak force (PF), plantar impulse (PI), and gender differences of novice runners after they were fatigued by running. A support vector machine (SVM) was used to predict the fatigue curve according to the changes in PP, PF, and PI before and after fatigue. 15 healthy males and 15 healthy females completed two runs at a speed of 3.3 m/s ± 5% on a footscan pressure plate before and after fatigue. After fatigue, PP, PF, and PI decreased at hallux (T1) and second-fifth toes (T2-5), while heel medial (HM) and heel lateral (HL) increased. In addition, PP and PI also increased at the first metatarsal (M1). PP, PF, and PI at T1 and T2-5 were significantly higher in females than in males, and metatarsal 3-5 (M3-5) were significantly lower in females than in males. The SVM classification algorithm results showed the accuracy was above average level using the T1 PP/HL PF (train accuracy: 65%; test accuracy: 75%), T1 PF/HL PF (train accuracy: 67.5%; test accuracy: 65%), and HL PF/T1 PI (train accuracy: 67.5%; test accuracy: 70%). These values could provide information about running and gender-related injuries, such as metatarsal stress fractures and hallux valgus. Application of the SVM to the identification of plantar mechanical features before and after fatigue. The features of the plantar zones after fatigue can be identified and the learned algorithm of plantar zone combinations with above-average accuracy (T1 PP/HL PF, T1 PF/HL PF, and HL PF/T1 PI) can be used to predict running fatigue and supervise training. It provided an important idea for the detection of fatigue after running.

Liu Qian, Chen Hairong, Thirupathi Anand, Yang Meimei, Baker Julien S, Gu Yaodong

2023

General General

Assessing the effects of therapeutic combinations on SARS-CoV-2 infected patient outcomes: A big data approach.

In PloS one ; h5-index 176.0

BACKGROUND : The COVID-19 pandemic has demonstrated the need for efficient and comprehensive, simultaneous assessment of multiple combined novel therapies for viral infection across the range of illness severity. Randomized Controlled Trials (RCT) are the gold standard by which efficacy of therapeutic agents is demonstrated. However, they rarely are designed to assess treatment combinations across all relevant subgroups. A big data approach to analyzing real-world impacts of therapies may confirm or supplement RCT evidence to further assess effectiveness of therapeutic options for rapidly evolving diseases such as COVID-19.

METHODS : Gradient Boosted Decision Tree, Deep and Convolutional Neural Network classifiers were implemented and trained on the National COVID Cohort Collaborative (N3C) data repository to predict the patients' outcome of death or discharge. Models leveraged the patients' characteristics, the severity of COVID-19 at diagnosis, and the calculated proportion of days on different treatment combinations after diagnosis as features to predict the outcome. Then, the most accurate model is utilized by eXplainable Artificial Intelligence (XAI) algorithms to provide insights about the learned treatment combination impacts on the model's final outcome prediction.

RESULTS : Gradient Boosted Decision Tree classifiers present the highest prediction accuracy in identifying patient outcomes with area under the receiver operator characteristic curve of 0.90 and accuracy of 0.81 for the outcomes of death or sufficient improvement to be discharged. The resulting model predicts the treatment combinations of anticoagulants and steroids are associated with the highest probability of improvement, followed by combined anticoagulants and targeted antivirals. In contrast, monotherapies of single drugs, including use of anticoagulants without steroid or antivirals are associated with poorer outcomes.

CONCLUSIONS : This machine learning model by accurately predicting the mortality provides insights about the treatment combinations associated with clinical improvement in COVID-19 patients. Analysis of the model's components suggests benefit to treatment with combination of steroids, antivirals, and anticoagulant medication. The approach also provides a framework for simultaneously evaluating multiple real-world therapeutic combinations in future research studies.

Moradi Hamidreza, Bunnell H Timothy, Price Bradley S, Khodaverdi Maryam, Vest Michael T, Porterfield James Z, Anzalone Alfred J, Santangelo Susan L, Kimble Wesley, Harper Jeremy, Hillegass William B, Hodder Sally L

2023

General General

EHRDiff: Exploring Realistic EHR Synthesis with Diffusion Models

ArXiv Preprint

Electronic health records (EHR) contain vast biomedical knowledge and are rich resources for developing precise medicine systems. However, due to privacy concerns, there are limited high-quality EHR data accessible to researchers hence hindering the advancement of methodologies. Recent research has explored using generative modelling methods to synthesize realistic EHR data, and most proposed methods are based on the generative adversarial network (GAN) and its variants for EHR synthesis. Although GAN-style methods achieved state-of-the-art performance in generating high-quality EHR data, such methods are hard to train and prone to mode collapse. Diffusion models are recently proposed generative modelling methods and set cutting-edge performance in image generation. The performance of diffusion models in realistic EHR synthesis is rarely explored. In this work, we explore whether the superior performance of diffusion models can translate to the domain of EHR synthesis and propose a novel EHR synthesis method named EHRDiff. Through comprehensive experiments, EHRDiff achieves new state-of-the-art performance for the quality of synthetic EHR data and can better protect private information in real training EHRs in the meanwhile.

Hongyi Yuan, Songchi Zhou, Sheng Yu

2023-03-10

Public Health Public Health

Determinants of COVID-19 vaccine hesitancy among students and parents in Sentinel Schools Network of Catalonia, Spain.

In PloS one ; h5-index 176.0

Vaccine hesitancy is defined as a delay in acceptance of vaccines despite its availability, caused by many determinants. Our study presents the key reasons, determinants and characteristics associated with COVID-19 vaccine acceptability among students over 16 years and parents of students under 16 years and describe the COVID-19 vaccination among students in the settings of sentinel schools of Catalonia, Spain. This is a cross-sectional study that includes 3,383 students and the parents between October 2021 and January 2022. We describe the student's vaccination status and proceed a univariate and multivariate analysis using a Deletion Substitution Addition (DSA) machine learning algorithm. Vaccination against COVID-19 reached 70.8% in students under 16 years and 95.8% in students over 16 years at the end of the study project. The acceptability among unvaccinated students was 40.9% and 20.8% in October and January, respectively, and among parents was proportionally higher among students aged 5-11 (70.2%) in October and aged 3-4 (47.8%) in January. The key reason to not vaccinate themselves, or their children, were concern about side effects, insufficient research about the effect of the vaccine in children, rapid development of vaccines, necessity for more information and previous infection by SARS-CoV-2. Several variables were associated with refusal end hesitancy. For students, the main ones were risk perception and use of alternative therapies. For parents, the age of students, sociodemographic variables, socioeconomic impact related to the pandemic, and use of alternative therapies were more evident. Monitoring vaccine acceptance and refusal among children and their parents has been important to understand the interaction between different multilevel determinants and we hope it will be useful to improve public health strategies for future interventions in this population.

Ganem Fabiana, Folch Cinta, Colom-Cadena Andreu, Bordas Anna, Alonso Lucia, Soriano-Arandes Antoni, Casabona Jordi

2023