Deep learning-based localization algorithms on fluorescence human brain 3D reconstruction: a comparative study using stereology as a reference.

3D reconstruction of human brain volumes at high resolution is now possible thanks to advancements in tissue clearing methods and fluorescence microscopy techniques. Analyzing the massive data produced with these approaches requires automatic methods able to perform fast and accurate cell counting and localization. Recent advances in deep learning have enabled the development of various tools for cell segmentation. However, accurate quantification of neurons in the human brain presents specific challenges, such as high pixel intensity variability, autofluorescence, non-specific fluorescence and very large size of data. In this paper, we provide a thorough empirical evaluation of three techniques based on deep learning (StarDist, CellPose and BCFind-v2, an updated version of BCFind) using a recently introduced three-dimensional stereological design as a reference for large-scale insights. As a representative problem in human brain analysis, we focus on a 4 -cm 3 portion of the Broca's area. We aim at helping users in selecting appropriate techniques depending on their research objectives. To this end, we compare methods along various dimensions of analysis, including correctness of the predicted density and localization, computational efficiency, and human annotation effort. Our results suggest that deep learning approaches are very effective, have a high throughput providing each cell 3D location, and obtain results comparable to the estimates of the adopted stereological design.

Experiences of physiotherapists considering virtual reality for shoulder rehabilitation: A focus group study.

Introduction: Shoulder pain is common and associated with substantial morbidity. Different treatment strategies are being prescribed with equivocal results. Virtual reality (VR) is a novel technology and emerging research suggests that VR may be a promising alternative to current treatments. Prior to effectiveness research or any large-scale introduction, VR-applications require appropriate scrutiny including feasibility- and acceptability of clinicians and patients. Therefore, the aim of this study was to collect experiences of physiotherapists after using immersive VR. Methods: A qualitative interpretive design was used to explore physiotherapists' experiences related to the use of VR for people with shoulder symptoms. 17 physiotherapists were asked to use VR at home for five days prior to a focus group interview. Data from the focus group interviews were analyzed using a six-phase process of thematic analysis. Results: Three main themes were identified, each divided into subthemes. The main themes were: 1. VR as an extension of contemporary physiotherapy care: physiotherapists were positive about the potential of VR and its applicability in daily care. 2. Physiotherapist uncertainties of future care using VR: participants expressed concerns about their professional identity, particularly as patients engage in independent home exercises. 3. Physiotherapist's requirements for implementation of VR: participants shared their needs for evidence regarding the effectiveness and parameters such as frequency, dosage and intensity of the VR intervention. Conclusion: Physiotherapists were positive about VR as an intervention tool. However, they felt more knowledge is needed about parameters of VR. The findings of this study inform researchers and technology developers about optimal design of interventions and applications using VR.

Optical Clearing and Labeling for Light-sheet Fluorescence Microscopy in Large-scale Human Brain Imaging.

Despite the numerous clearing techniques that emerged in the last decade, processing postmortem human brains remains a challenging task due to its dimensions and complexity, which make imaging with micrometer resolution particularly difficult. This paper presents a protocol to perform the reconstruction of volumetric portions of the human brain by simultaneously processing tens of sections with the SHORT (SWITCH - H2O2 - Antigen Retrieval - 2,2'-thiodiethanol [TDE]) tissue transformation protocol, which enables clearing, labeling, and sequential imaging of the samples with light-sheet fluorescence microscopy (LSFM). SHORT provides rapid tissue clearing and homogeneous multi-labeling of thick slices with several neuronal markers, enabling the identification of different neuronal subpopulations in both white and grey matter. After clearing, the slices are imaged via LSFM with micrometer resolution and in multiple channels simultaneously for a rapid 3D reconstruction. By combining SHORT with LSFM analysis within a routinely high-throughput protocol, it is possible to obtain the 3D cytoarchitecture reconstruction of large volumetric areas at high resolution in a short time, thus enabling comprehensive structural characterization of the human brain.

Segmentation of supragranular and infragranular layers in ultra-high resolution 7T ex vivo MRI of the human cerebral cortex.

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Leveraging recent advancements in ultra-high resolution ex vivo MRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers in ex vivo MRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphere ex vivo scans at 120 µm, we propose a multi-resolution U-Nets framework (MUS) that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation, while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.

Physiotherapist beliefs and perspectives on virtual reality supported rehabilitation for the management of musculoskeletal shoulder pain: A focus group study.

BACKGROUND: Virtual Reality (VR) is an immersive computer-generated environment that provides a multi-sensory experience for the user. Modern technology allows the user to explore and interact with the virtual environment, offering opportunities for rehabilitation. The use of immersive VR in the management of musculoskeletal shoulder pain is relatively new and research is required to demonstrate its feasibility and effectiveness in this field. AIM: The aims of this study were, firstly, to explore physiotherapists' beliefs and perspectives of immersive VR as a platform for rehabilitation in patients with musculoskeletal shoulder pain, secondly, to identify potential barriers and facilitators to using VR in a musculoskeletal setting and thirdly, to gain insight from clinicians that would inform the development of a VR intervention for the rehabilitation of musculoskeletal shoulder pain. METHODS: This study used qualitative descriptive design methodology. A series of three focus group interviews were carried out, via Microsoft Teams. Physiotherapists received an Oculus Quest™ headset to use at home prior to the focus group interviews. A six-phase process of reflexive thematic analysis was carried out to identify themes within the data. Atlas Ti Qualitative Data Analysis software was used to facilitate thematic analysis. RESULTS: Five themes were identified within the data. They reflected physiotherapists beliefs that VR provides novel opportunities for shoulder rehabilitation and may offer new avenues for managing movement-related fear and improving concordance with rehabilitation. However, barriers related to safety and practical considerations associated with using VR were also identified in the final themes. CONCLUSION: These findings provide valuable insight into clinician acceptability of immersive VR as a platform for rehabilitation and the need for further research to answer the questions posed by physiotherapists in the current study. This research will contribute to human-centered design of VR-supported interventions for managing musculoskeletal shoulder pain.

3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy.

The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H2O2-antigen Retrieval-TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.

Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques.

The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.

Adverse outcomes in COVID-19 and diabetes: a retrospective cohort study from three London teaching hospitals.

INTRODUCTION: Patients with diabetes mellitus admitted to hospital with COVID-19 have poorer outcomes. However, the drivers of poorer outcomes are not fully elucidated. We performed detailed characterization of patients with COVID-19 to determine the clinical and biochemical factors that may be drivers of poorer outcomes. RESEARCH DESIGN AND METHODS: This is a retrospective cohort study of 889 consecutive inpatients diagnosed with COVID-19 between March 9 and April 22, 2020 in a large London National Health Service Trust. Unbiased multivariate logistic regression analysis was performed to determine variables that were independently and significantly associated with increased risk of death and/or intensive care unit (ICU) admission within 30 days of COVID-19 diagnosis. RESULTS: 62% of patients in our cohort were of non-white ethnic background and the prevalence of diabetes was 38%. 323 (36%) patients met the primary outcome of death/admission to the ICU within 30 days of COVID-19 diagnosis. Male gender, lower platelet count, advancing age and higher Clinical Frailty Scale (CFS) score (but not diabetes) independently predicted poor outcomes on multivariate analysis. Antiplatelet medication was associated with a lower risk of death/ICU admission. Factors that were significantly and independently associated with poorer outcomes in patients with diabetes were coexisting ischemic heart disease, increasing age and lower platelet count. CONCLUSIONS: In this large study of a diverse patient population, comorbidity (ie, diabetes with ischemic heart disease; increasing CFS score in older patients) was a major determinant of poor outcomes with COVID-19. Antiplatelet medication should be evaluated in randomized clinical trials among high-risk patient groups.

Physiotherapist beliefs and perspectives on virtual reality-supported rehabilitation for the assessment and management of musculoskeletal shoulder pain: a focus group study protocol.

Shoulder pain accounts for a large proportion of musculoskeletal disorders and years lived with disability. Musculoskeletal shoulder pain is challenging to manage and while research evidence suggests that exercise should be a cornerstone of shoulder pain rehabilitation, the exact type and dosage of exercise is unclear. Adherence is a barrier to successful outcomes with exercise-based management of musculoskeletal pain, especially for those with co-morbidities, high pain levels and reported boredom associated with competing prescribed exercise. Virtual reality (VR) may offer an effective platform for rehabilitation of musculoskeletal shoulder pain. Virtual Reality has been shown to be effective for management of acute and chronic pain conditions, for delivering education around various health conditions, and for supporting rehabilitation of neurological conditions. Therefore, it is possible that VR may have a role in the delivery of exercise and education for individuals with musculoskeletal shoulder pain. VR intervention design should involve several steps and begin with establishing early acceptability from users as to the suitability of the technology in clinical practice as well as potential barriers and facilitators to using the technology successfully. This study will therefore aim to explore physiotherapists beliefs and perspectives of immersive VR as a platform for assessment and rehabilitation in patients with musculoskeletal shoulder pain. Further, this study will inform the development of a VR intervention for use in the rehabilitation of musculoskeletal shoulder pain. A series of online focus groups will be conducted with physiotherapists in Ireland using a qualitative descriptive approach to data analysis. A six-phase process of data analysis will be carried out to identify important patterns and themes within the data. The current study will be the first to explore clinician's perspectives on the role of VR in musculoskeletal practice.

Significance of ambulatory blood pressure monitoring in assessment of potential living kidney donors.

The most recent British Transplant Society (BTS) guidelines recommend that office blood pressure (BP) monitoring in living donors is sufficient for the assessment of hypertension (HTN) and those with BP >140/90 should be further assessed using ambulatory BP monitoring (ABPM). ABPM can detect diurnal and nocturnal variation in BP, thus it can identify masked HTN. The aim of the current study is to assess reliability of ABPM vesus office BP monitoring for assessment in living kidney donors. Office and ABPM of all potential kidney donors at a single center from April 2009 to March 2017 were retrospectively reviewed and compared. Age, sex, body mass index, kidney function, and echocardiography results were collected and analyzed. Two hundred and sixteen kidney donors were stratified based on their BP readings into four groups; group 1 (masked HTN: normotensive in office and hypertensive in ABPM), group 2 (sustained normotension: normotensive in office and in ABPM), group 3 (sustained HTN: hypertensive in office and in ABPM), group 4 (white-coat HTN: hypertensive in office and normotensive in ABPM). Thirteen percent of patients were diagnosed with masked HTN. Office systolic BP monitoring was significantly higher in patients older than 50 years old compared to other younger populations. However, this significant difference in systolic BP was diminished when assessment with ABPM was performed. In conclusion, ABPM is a reliable modality for the identification of masked HTN and white coat HTN. Masked HTN is correlated with increased risk of end organ damage and risk of death in potential kidney donors. Transplant physicians cannot rely solely on office BP monitoring in the assessment of potential living kidney donors. ABPM should be integral part of routine assessment of potential living kidney donors.

A new method for sudden mechanical perturbation with axial load, to assess postural control in sitting and standing.

Sudden application of load along a sagittal or coronal axis has been used to study trunk stiffness, but not axial (vertical) load. This study introduces a new method for sudden-release axial load perturbation. Prima facie validity was supported by comparison with standard mechanical systems. We report the response of the human body to axial perturbation in sitting and standing and within-day repeatability of measures. Load of 20% of body weight was released from light contact onto the shoulders of 22 healthy participants (10 males). Force input was measured via force transducers at shoulders, output via a force plate below the participant, and kinematics via 3-D motion capture. System identification was used to fit data from the time of load release to time of peak load-displacement, fitting with a 2nd-order mass-spring-damper system with a delay term. At peak load-displacement, the mean (SD) effective stiffness measured with this device for participants in sitting was 12.0(3.4)N/mm, and in standing was 13.3(4.2)N/mm. Peak force output exceeded input by 44.8 (10.0)% in sitting and by 30.4(7.9)% in standing. Intra-class correlation coefficients for within-day repeatability of axial stiffness were 0.58 (CI: -0.03 to 0.83) in sitting and 0.82(0.57-0.93) in standing. Despite greater degrees of freedom in standing than sitting, standing involved lesser time, downward displacement, peak output force and was more repeatable in defending upright postural control against the same axial loads. This method provides a foundation for future studies of neuromuscular control with axial perturbation.