Medical image registration via neural fields.

Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to domain shift. Here we present a new neural network based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural networks to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic mini-batch gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. NIR is evaluated on two 3D MR brain scan datasets, demonstrating highly competitive performance in terms of both registration accuracy and regularity. Compared to traditional optimization-based methods, our approach achieves better results in shorter computation times. In addition, our methods exhibit performance on a cross-dataset registration task, compared to the pre-trained learning-based methods.

Inflammation Links Cardiac Injury and Renal Dysfunction: A Cardiovascular Magnetic Resonance Study.

Background: Inflammation is essential in cardiorenal syndrome, however there is still a lack of evidence proving the interaction between cardiac injury, renal dysfunction and the inflammatory response. This study aimed to illustrate the association between renal dysfunction and cardiac injury with a specific focus on the role of inflammation. Methods: A single-center, retrospective study included patients with heart failure admitted to the cardiovascular department from September 2019 to April 2022. Patients received cardiovascular magnetic resonance (CMR) imaging (T1 mapping and late gadolinium enhancement (LGE)). Demographic, creatinine and native T1 were analyzed using pearson correlation, linear regression and adjusted for confounders. Interaction and subgroup analysis were performed. Results: Finally, 50 validated heart failure (HF) patients (age 58.5 ± 14.8 years; 78.0% men) were included. Cardiac global native T1 for the high estimated glomeruar filtration rate (eGFR) group was 1117.0 ± 56.6 ms, and for the low eGFR group was 1096.5 ± 61.8 ms. Univariate analysis identified global native T1 ( ß = 0.16, 95% confidence interval (CI): 0.04-0.28, p = 0.014) and C-reactive protein (CRP) ( ß = 0.30, 95% CI: 0.15-0.45, p < 0.001) as determinants of creatinine. Multivariable linear regression analysis identified global native T1 ( ß = 0.12, 95% CI: 0.01-0.123, p = 0.040) as a determinant of creatinine while age and diabetes were adjusted. Significant interactions between CRP and global native T1 in relation to creatinine level (p for interaction = 0.005) were identified. Conclusions: Kidney dysfunction was associated with cardiac injury and inflammation, respectively. The interaction between myocardial injury and kidney dysfunction is contingent on the severity of the inflammatory response. Further studies were needed to identify the mechanisms of the inflammatory response in cardiorenal syndrome.

Assessing breast disease with deep learning model using bimodal bi-view ultrasound images and clinical information.

Breast cancer is the second leading cause of carcinoma-linked death in women. We developed a multi-modal deep-learning model (BreNet) to differentiate breast cancer from benign lesions. BreNet was constructed and trained on 10,108 images from one center and tested on 3,762 images from two centers in three steps. The diagnostic ability of BreNet was first compared with that of six radiologists; a BreNet-aided scheme was constructed to improve the diagnostic ability of the radiologists; and the diagnosis of real-world radiologists' scheme was then compared with the BreNet-aided scheme. The diagnostic performance of BreNet was superior to that of the radiologists (area under the curve [AUC]: 0.996 vs. 0.841). BreNet-aided scheme increased the pooled AUC of the radiologists from 0.841 to 0.934 for reviewing images, and from 0.892 to 0.934 in the real-world test. The use of BreNet significantly enhances the diagnostic ability of radiologists in the detection of breast cancer.

Seamounts generate efficient active transport loops to nourish the twilight ecosystem.

Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary in situ observations focusing on a shallow seamount in the oligotrophic ocean. The findings show that the seamount's topography interferes with the oceanic current to generate lee waves, effectively enhancing the nutrient supply to the euphotic layer downstream of the seamount. This continuous supply enhances phytoplankton biomass and subsequently the grazing and diurnal vertical migration of zooplankton, rapidly transporting the augmented phytoplankton biomass to the aphotic layer. Unlike the cyclonic eddies that move in the upper ocean, seamounts stand at fixed locations creating a more efficient and steady active transport loop. This active transport loop connects the euphotic and twilight zones, potentially conveying nourishment to benthic ecosystems to create stereoscopic oases in the oligotrophic ocean.

Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers.

The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. To aid the exploration of these factors, we introduced EpiOut, an algorithm to identify chromatin accessibility outliers that are regions exhibiting divergent accessibility from the population baseline in a single or few samples. Annotation of accessible regions with histone chromatin immunoprecipitation sequencing and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is available at github.com/uci-cbcl/EpiOut.

Identification of a pathogenic SMCHD1 variant in a Chinese patient with bosma arhinia microphthalmia syndrome: a case report.

BACKGROUND: Bosma arhinia microphthalmia syndrome (BAMS; MIM603457) is a rare genetic disorder, predominantly autosomal dominant. It is a multi-system developmental disorder characterized by severe hypoplasia of the nose and eyes, and reproductive system defects. BAMS is extremely rare in the world and no cases have been reported in Chinese population so far. Pathogenic variants in the SMCHD1 gene (MIM614982) cause BAMS, while the underlying molecular mechanisms requires further investigation. CASE PRESENTATION: In this study, a Chinese girl who has suffered from congenital absence of nose and microphthalmia was enrolled and subsequently submitted to a comprehensive clinical and genetic evaluation. Whole-exome sequencing (WES) was employed to identify the genetic entity of thisgirl. A heterozygous pathogenic variant, NM_015295, c.1025G > C; p. (Trp342Ser) of SMCHD1 was identified. By performing very detailed physical and genetic examinations, the patient was diagnosed as BAMS. CONCLUSION: This report is the first description of a variant in SMCHD1 in a Chinese patient affected with BAMS.Our study not only furnished valuable genetic data for counseling of BAMS, but also confirmed the diagnosis of BAMS, which may help the management and prognosis for this patient.

Evaluating the effectiveness and feasibility of a digital health intervention to community-based rehabilitation in older adults: A cluster randomized controlled trial study protocol.

Objective: The escalating global aging population underscores the need to effectively manage geriatric diseases, constituting a significant public health concern. Community-based rehabilitation has emerged as a crucial and accessible paradigm for the rehabilitation of older adults. In China, however, the practical implementation of community-based rehabilitation faces formidable challenges, including a dearth of specialized rehabilitation therapists, substantial disparities between demand and supply, and suboptimal satisfaction rates. We aimed to develop a community-based rehabilitation management platform for older adults centered around digital health technology, with the plan to conduct a cluster randomized controlled trial to gather more evidence to explore the best practices and service models of community-based rehabilitation based on digital health technology. Methods: This cluster randomized controlled trial will be conducted in Zunyi City, China. We will recruit 286 adults aged ≥60 years and randomly allocate 20 subdistricts in a 1:1 ratio into either the intervention group, which will use the Rehabilitation Journey application, or the control group, which will be given a Rehabilitation Information Booklet for Older Adults. Both groups will undergo a 12-month rehabilitation management program, encompassing six months of guidance and an additional six months of follow-up through online and offline methods. The evaluation indicators will be assessed at enrollment and at 3rd, 6th, and 12th month. Discussion: This study endeavors to furnish novel insights to develop a tailored community-based rehabilitation management program for older adults, delivering customized, intelligent, and precise rehabilitation services.

Identification of a novel MYO1D variant associated with laterality defects, congenital heart diseases, and sperm defects in humans.

The establishment of left-right asymmetry is a fundamental process in animal development. Interference with this process leads to a range of disorders collectively known as laterality defects, which manifest as abnormal arrangements of visceral organs. Among patients with laterality defects, congenital heart diseases (CHD) are prevalent. Through multiple model organisms, extant research has established that myosin-Id (MYO1D) deficiency causes laterality defects. This study investigated over a hundred cases and identified a novel biallelic variant of MYO1D (NM_015194: c.1531G>A; p.D511N) in a consanguineous family with complex CHD and laterality defects. Further examination of the proband revealed asthenoteratozoospermia and shortened sperm. Afterward, the effects of the D511N variant and another known MYO1D variant (NM_015194: c.2293C>T; p.P765S) were assessed. The assessment showed that both enhance the interaction with ß-actin and SPAG6. Overall, this study revealed the genetic heterogeneity of this rare disease and found that MYO1D variants are correlated with laterality defects and CHD in humans. Furthermore, this research established a connection between sperm defects and MYO1D variants. It offers guidance for exploring infertility and reproductive health concerns. The findings provide a critical basis for advancing personalized medicine and genetic counseling.

Functional and Structural Abnormalities in the Pain Network of Generalized Anxiety Disorder Patients with Pain Symptoms.

Pain symptoms significantly impact the well-being and work capacity of individuals with generalized anxiety disorder (GAD), and hinder treatment and recovery. Despite existing literature focusing on the neural substrate of pain and anxiety separately, further exploration is needed to understand the possible neuroimaging mechanisms of the pain symptoms in GAD patients. We recruited 73 GAD patients and 75 matched healthy controls (HC) for clinical assessments, as well as resting-state functional and structural magnetic resonance imaging scans. We defined a pain-related network through a published meta-analysis, including the insula, thalamus, periaqueductal gray, prefrontal cortex, anterior cingulate cortex, amygdala, and hippocampus. Subsequently, we conducted the regional homogeneity (ReHo) and the gray matter volume (GMV) within the pain-related network. Correlation analysis was then employed to explore associations between abnormal regions and self-reported outcomes, assessed using the Patient Health Questionnaire-15 (PHQ-15) and pain scores. We observed significantly increased ReHo in the bilateral insula but decreased GMV in the bilateral thalamus of GAD compared to HC. Further correlation analysis revealed a positive correlation between ReHo of the left anterior insula and pain scores in GAD patients, while a respective negative correlation between GMV of the bilateral thalamus and PHQ-15 scores. In summary, GAD patients exhibit structural and functional abnormalities in pain-related networks. The enhanced ReHo in the left anterior insula is correlated with pain symptoms, which might be a crucial brain region of pain symptoms in GAD.

Heterogeneous Brain Abnormalities in Schizophrenia Converge on a Common Network Associated With Symptom Remission.

BACKGROUND AND HYPOTHESIS: There is a huge heterogeneity of magnetic resonance imaging findings in schizophrenia studies. Here, we hypothesized that brain regions identified by structural and functional imaging studies of schizophrenia could be reconciled in a common network. STUDY DESIGN: We systematically reviewed the case-control studies that estimated the brain morphology or resting-state local function for schizophrenia patients in the literature. Using the healthy human connectome (n = 652) and a validated technique "coordinate network mapping" to identify a common brain network affected in schizophrenia. Then, the specificity of this schizophrenia network was examined by independent data collected from 13 meta-analyses. The clinical relevance of this schizophrenia network was tested on independent data of medication, neuromodulation, and brain lesions. STUDY RESULTS: We identified 83 morphological and 60 functional studies comprising 7389 patients with schizophrenia and 7408 control subjects. The "coordinate network mapping" showed that the atrophy and dysfunction coordinates were functionally connected to a common network although they were spatially distant from each other. Taking all 143 studies together, we identified the schizophrenia network with hub regions in the bilateral anterior cingulate cortex, insula, temporal lobe, and subcortical structures. Based on independent data from 13 meta-analyses, we showed that these hub regions were specifically connected with regions of cortical thickness changes in schizophrenia. More importantly, this schizophrenia network was remarkably aligned with regions involving psychotic symptom remission. CONCLUSIONS: Neuroimaging abnormalities in cross-sectional schizophrenia studies converged into a common brain network that provided testable targets for developing precise therapies.

Mitochondrial disturbance related to increased caspase-1 of CD4+T cells in HIV-1 infection.

BACKGROUND: In HIV-1 infection, more than 95% of CD4+T cells die of caspase-1 mediated pyroptosis. What governs the increased susceptibility of CD4+T cells to pyroptosis is poorly understood. METHODS: Blood samples were obtained from 31 untreated HIV-infected patients (UNT), 29 antiretroviral therapy treated HIV-infected patients (ART), and 21 healthy control donors (HD). Plasma levels of IL-18 and IL-1ß, caspase-1 expression, mitochondrial mass (MM) and mitochondrial fusion/fisson genes of CD4+T subsets were measured. RESULTS: A significantly higher IL-18 level in plasma and MM level of CD4+T cells were found in HIV-infected patients (UNT and ART) compared to HD, and the MMhigh phenotype was manifested, related to increased caspase-1 expression. Moreover, the increased MM was more pronounced in the early differentiated and inactivated CD4+T cells. However, higher MM was not intrinsically linked to T cell differentiation disorder or excessive activation of the CD4+T cells. Mechanistically, the increased MM was significantly correlated with an elevated level of expression of the mitochondrial fusion gene mitofusin1. CONCLUSION: An increase in MM was associated with heightened sensitivity of CD4+T cells to pyroptosis, even in early differentiated and inactivated CD4+T cells, in patients with HIV-1 infection, regardless of whether patients were on antiretroviral therapy or not. These new revelations have uncovered a previously unappreciated challenge to immune reconstitution with antiretroviral therapy.

A latent class analysis of community-based rehabilitation needs among Chinese older adults: a mixed study protocol.

Background: Geriatric diseases (e.g., chronic diseases and geriatric syndromes) may result in impaired physical performance and a decline in the quality of life. The results of previous studies reported the positive effects of comprehensive community-based rehabilitation (CBR) services on physical and social functioning and psychosocial wellbeing. However, to provide adequate and personalised rehabilitation services, it is essential to understand the needs of the older adults population. There have been no studies on the need for CBR in older adults populations that consider their heterogeneity. Therefore, high-quality studies are required to recognise the heterogeneity and latent classes of CBR needs in older adults population groups. This study aims to identify the heterogeneity of the rehabilitation needs of older adults in the community and explore whether older adults with similar characteristics have similar needs through a cross-sectional survey and latent class analysis (LCA) to provide support for personalised rehabilitation services. Methods: The study is structured into four phases. The first phase will focus on constructing a comprehensive questionnaire to assess rehabilitation needs. In the second phase, a pilot study will be conducted to evaluate the reliability and validity of the completed questionnaire. This step ensures the robustness of the instrument for data collection. The third phase will involve cross-sectional surveys using the finalised questionnaires to collect the necessary data from the targeted population. The fourth phase will focus on conducting LCA to determine the CBR needs of the older adult population. Discussion: The results of this study will provide novel and critical information for a better understanding of the rehabilitation needs, potential categories, and influencing factors of older adults in the community. The study will be conducted in Guizhou Province in western China, where economic and social development is relatively low, and the results will inform and benefit other regions and developing countries facing similar challenges. However, because of the complete social security and rehabilitation service systems in developed areas, our research results may not fully reflect the situation in these areas. Future studies may need to be conducted in places with different levels of social development. Clinical trial registration: https://www.chictr.org.cn/showproj.html?proj=191398, ChiCTR2300071478.