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Introduction: Arteriovenous fistula (AVF) dysfunction is a prevalent complication among maintenance hemodialysis patients. However, the factors influencing AVF patency remain unclear. To address this, we conducted a study aimed at identifying factors contributing to AVF dysfunction in this patient population., Methods: The study compared clinical data, vascular calcification score, and laboratory data focusing on blood cell composition and coagulation in 100 maintenance hemodialysis patients in whom an AVF had been inserted from January through September of 2022. The patients were divided into a group in which the AVF functioned without issues and a group in which the AVF was dysfunctional, defined as not able to provide a blood flow of greater than 200 mL/min., Findings: Patients in the 2 groups (56 in the dysfunctional AVF group and 44 in the group with satisfactory AVF function) were similar demographically. Compared with the normally functioning AVF group, the AVF dysfunction group exhibited significantly higher Agatston calcium scores (20.5 [1.28, 298] median [Q1, Q3] vs. 1.14 [0.00, 11.6]; p = 0.01), elevated triglyceride levels (1.1 [0.6, 1.2] mmol/L vs. 0.5 [0.3, 0.8]; p < 0.01), increased prothrombin activity (113 ± 22.1% vs. 99.4 ± 23.1; p < 0.01), lower prothrombin time (10.4 [9.8, 10.8] s vs. 11.0 [10.3, 11.5]; p < 0.01), higher red blood cell (RBC) counts (3.5 ± 0.7 · 10 12 /L vs. 3.0 ± 0.7; p < 0.01), and elevated hemoglobin levels (98.0 ± 21.8 g/L vs. 84.9 ± 24.2; p < 0.01). Higher C-reactive protein (20.2 [3.3, 20.2] mg/L vs. 17.8 [6.2, 17.8]; p = 0.01) and procalcitonin levels (0.9 [0.4, 0.9] ng/mL vs. 0.5 [0.2, 0.7]; p < 0.01) were also noted. Logistic regression analysis indicated that platelet/lymphocyte ratio, monocyte/lymphocyte ratio, and RBC count were factors associated with AVF dysfunction. Increased monocyte/lymphocyte ratio and RBC count correlated with higher risk, while a higher platelet/lymphocyte ratio was associated with lower risk., Discussion: Arteriovenous fistula dysfunction in maintenance hemodialysis patients is associated with higher proportions of specific hematological parameters, particularly elevated RBC count, and altered platelet/lymphocyte and monocyte/lymphocyte ratios., (© 2024 International Society for Hemodialysis.)

Introduction: This study aimed to evaluate the characteristics and prognostic factors for coronavirus disease 2019 (COVID-19) patients on maintenance hemodialysis (HD)., Methods: All admitted HD patients who were infected with SARS-CoV-2 from December 1, 2022, to January 31, 2023, were included. Patients with pneumonia were further classified into the mild, moderate, severe, and critical illness. Clinical symptoms, laboratory results, radiologic findings, treatment, and clinical outcomes were collected. Independent risk factors for progression to critical disease and in-hospital mortality were determined by the multivariate regression analysis. The receiver operating characteristic analysis with the area under the curve was used to evaluate the predictive performance of developing critical status and in-hospital mortality., Results: A total of 182 COVID-19 patients with HD were included, with an average age of the 61.55 years. Out of the total, 84 (46.1%) patients did not have pneumonia and 98 (53.8%) patients had pneumonia. Among patients with pneumonia, 48 (49.0%) had moderate illness, 26 (26.5%) severe illness, and 24 (24.5%) critical illness, respectively. Elder age [HR (95% CI): 1.07 (1.01-1.13), p &lt;0.01], increased levels of lactate dehydrogenase (LDH) [1.01 (1.003-1.01), p &lt;0.01], and C-reactive protein (CRP) [1.01 (1.00-1.01), p = 0.04] were risk factors for developing critical illness. Elder age [1.11 (1.03-1.19), p = 0.01], increased procalcitonin (PCT) [1.07 (1.02-1.12), p = 0.01], and LDH level [1.004 (1-1.01), p = 0.03] were factors associated with increased risk of in-hospital mortality., Conclusion: Age, CRP, PCT, and LDH can be used to predict negative clinical outcomes for HD patients with COVID-19 pneumonia., (© 2023 S. Karger AG, Basel.)

Arteriovenous fistula (AVF) is the first choice of vascular access in hemodialysis (HD) patients. However, the correlations between patient factors and the arteriovenous fistula patency remain unclear. Therefore, our study investigates the risk factors associated with AVF dysfunction in HD patients. A total of 233 end-stage renal disease (ESDR) patients who met the study inclusion criteria in the Nephrology Department of Hunan Provincial People's Hospital between December 2020 and June 2022 were included in this study. The baseline demographic, clinical and laboratory parameters were collected at the time of AVF creation and analyzed. Of the 233 ESRD patients, 146 (62.7%) were male and the mean age was 56.11 ± 12.14 (21-82) years. The patients were followed for a median time of 14 months. Kaplan-Meier analysis showed a 6-, 12- and 24-month post-placement survival of 87.1%, 82.8% and 80.7%, respectively. Univariate Cox regression analysis revealed weight (HR, 1.03; P = 0.03) as a predictor for the loss of vascular access functionality. In addition, multivariate Cox regression analysis further demonstrated that sex (HR, 3.41; P = 0.03), weight (HR 1.08; P < 0.01) and phosphorus level (HR: 3.03; P = 0.01) are independent risk factors for AVF dysfunction. AVF dysfunction is highly associated with several risk factors including weight, phosphorus level, and sex. Positive intervention strategies targeting these potential factors, such as weight loss or oral phosphate binders could improve the long-term success of AVF., (© 2023. The Author(s).)

Obesity-related glomerulopathy (ORG) is an independent risk factor for chronic kidney disease and even progression to end-stage renal disease. Efforts have been undertaken to elucidate the mechanisms underlying the development of ORG and substantial advances have been made in the treatment of ORG, but relatively little is known about cell-specific changes in gene expression. To define the transcriptomic landscape at single-cell resolution, we analyzed kidney samples from four patients with ORG and three obese control subjects without kidney disease using single-cell RNA sequencing. We report for the first time that immune cells, including T cells and B cells, are decreased in ORG patients. Further analysis indicated that SPP1 was significantly up-regulated in T cells and B cells. This gene is related to inflammation and cell proliferation. Analysis of differential gene expression in glomerular cells (endothelial cells, mesangial cells, and podocytes) showed that these cell types were mainly enriched in genes related to oxidative phosphorylation, cell adhesion, thermogenesis, and inflammatory pathways (PI3K-Akt signaling, MAPK signaling). Furthermore, we found that the podocytes of ORG patients were enriched in genes related to the fluid shear stress pathway. Moreover, an evaluation of cell-cell communications revealed that there were interactions between glomerular parietal epithelial cells and other cells in ORG patients, with major interactions between parietal epithelial cells and podocytes. Altogether, our identification of molecular events, cell types, and differentially expressed genes may facilitate the development of new preventive or therapeutic approaches for ORG., (© 2023 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.)

Heparin-induced thrombocytopenia (HIT) is a severe, potentially life-threatening adverse drug reaction. It is an antibody-mediated process involving platelet activation. Heparin and low-molecular-weight heparin (LMWH) are routinely used in uremic patients undergoing hemodialysis. Here, we report a case of HIT that occurred in a hemodialysis patient after she switched from heparin to the LMWH nadroparin for anticoagulation during hemodialysis. The clinical features, incidence, mechanism, and treatment of HIT are discussed.

Background: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus and a common cause of end-stage kidney disease. The incidence of DKD is rising worldwide and associated with increased morbidity and premature mortality, indicating an urgent need to further explore the underlying pathogenesis and potential biomarkers. Exosomes are nanoscale vesicles secreted by all cell types that play an essential role in cellular homeostasis and intercellular communications by transferring molecular cargoes between different cells., Summary: Emerging evidence indicates that exosomes are both a crucial signaling mediator and a potential biomarker of DKD. On the one hand, exosomes released by various kidney resident cells facilitate the cell-cell crosstalk as a contributing factor in DKD; on the other hand, exosomes can be detected from urine and blood and have emerged as promising noninvasive biomarkers for DKD., Key Messages: Herein, we highlight the recent advances in research on the role of exosomes from different kidney resident cells in DKD. We further discuss the potential use of urine exosomes as biomarkers and therapeutic agents., Competing Interests: The authors have no conflicts of interest to declare., (© 2023 The Author(s). Published by S. Karger AG, Basel.)

Background: Crescent formation is rare in primary membranous nephropathy (MN). The mechanism of crescent formation is unknown and the treatments are tentative., Patient Concerns: A 71-year-old woman presented with nephrotic syndrome, hematuria, and rapidly progressive kidney dysfunction., Diagnosis: Kidney biopsy was performed, and the diagnosis was MN in combination with crescentic glomerulonephritis. Circulating anti-PLA2R was detected of a high level., Interventions: The patient received rituximab besides corticosteroids., Outcomes: The patient achieved complete remission of proteinuria and recovery of kidney function., Conclusion: Our case suggests that there is a pathologic feature of MN and crescents in the absence of known immunologic factors as well as rituximab could serve as an effective cure and could be considered in serious MN conditions., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2022 the Author(s). Published by Wolters Kluwer Health, Inc.)

Background: Autophagy is a highly regulated and evolutionarily conserved process in eukaryotes which is responsible for protein and organelle degradation. Although this process was described over 60 years ago, the selective autophagy of mitochondria (mitophagy) was recently coined in 2005. Research on the topic of mitophagy has made rapid progress in the past decade, which proposed to play critical roles in human health and disease. This study aimed to visualize the scientific outputs and research trends of mitophagy. Methods: Articles and reviews related to the topic of mitophagy were retrieved from the Web of Science Core Collection on 30 November 2021. Two kinds of software (CiteSpace and VOSviewer) were used to perform a visualized analysis of countries/regions, institutions, authors, journals, references, and keywords. Results: From 2005 to 2021, total 5844 publications on mitophagy were identified for final analysis. The annual number of publications grew yearly over the past 17 years. United States (N = 2025) and Chinese Academy of Sciences is the leading country and institute (N = 112) ranked by the number of publications, respectively. The most productive author was Jun Ren (N = 38) and Derek P. Narendra obtained the most co-cited times (2693 times). The journals with the highest output and the highest co-citation frequency were Autophagy (N = 208) and Journal of Biological Chemistry (co-citation: 17226), respectively. Analyses of references and keywords suggested that "mechanism of mitochondrial quality control", "molecule and signaling pathway in mitophagy", and "mitophagy related diseases" were research hotspots, and parkin-mediated mitophagy and its roles in skeletal muscle and inflammation-related diseases may be the frontiers of future research. Conclusion: Although mitophagy research has flourished and attracted attention from all over the world, the regional imbalance in the development of mitophagy research was observed. Our results provided a comprehensive global research landscape of mitophagy from 2005- 2021 from a perspective of bibliometrics, which may serve as a reference for future mitophagy studies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Li, Yin, Yang, Yang, Chen, Liang, Zhang and Xie.)

Background: Mitochondrial biogenesis and dysfunction are associated with renal tubular epithelial cell injury and the pathophysiological development of diabetic nephropathy (DN). Adiponectin (APN) is a plasma hormone protein specifically secreted by adipocytes. In the present study, we studied the effects of APN on mitochondrial biogenesis and function in renal tubular epithelial cells and examined the mechanisms underlying its actions., Materials: A rat model of type 2 diabetes mellitus (T2DM) was established using streptozotocin (STZ), and an NRK-52E culture model exposed to high glucose was also used. We found that APN treatment alleviated kidney histopathological injury in T2DM rats, reduced fasting blood glucose (FBG) and postprandial blood glucose (PBG) levels, maintained stable animal weight, promoted cell viability, inhibited apoptosis and the formation of autophagosomes, and also increased mitochondrial mass, mitochondrial DNA (mtDNA) content and mitochondrial membrane potential (MMP) in vivo and in vitro., Results: We found that the expression of AdipoR1/CREB/PGC-1α/TFAM pathway proteins and respiratory chain complex subunits CO1, CO2, CO3, ATP6 and ATP8 were significantly increased after APN treatment. We also found that inhibition of cAMP response element binding protein (CREB) weakened the effects of APN in NRK-52E cells treated with high glucose. Coimmunoprecipitation experiments showed that AdipoR1 interacted with CREB., Conclusion: APN promoted mitochondrial biogenesis and function in renal tubular epithelial cells by regulating the AdipoR1/CREB/PGC-1α/TFAM pathway. APN has the potential to serve as an effective drug for the treatment of DN., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest., (Copyright © 2021 Elsevier Inc. All rights reserved.)

The scoring of crescents (Cs) was recently added to the Oxford classification for IgA nephropathy (IgAN). Because of the short-term use of the C score in clinical practice, its validity and applicability need to be verified. We, retrospectively, analyzed the clinicopathological data of 144 primary IgAN patients diagnosed at our hospital from March 2017 to March 2019 and with complete ≥6-month follow-up data. We found that the C score was positively correlated with the Lee's classification in the assessment of renal pathological changes and significantly correlated with increased proteinuria and decreased estimated glomerular filtration rate. Univariate Cox regression analysis showed an association of C formation with IgAN prognosis, and multivariate Cox regression indicated Cs as an independent prognosis factor. The optimal proportion of Cs for prognosis prediction by the receiver operating characteristic curve was 11%. Kaplan-Meier survival curve revealed a significantly decreased renal survival rate in patients with C proportions ≥11%. Further multivariate Cox regression analysis confirmed that the C proportion ≥11% is an independent risk factor for poor prognosis of IgAN patients. Our findings demonstrate that Cs are independently related to the prognosis of patients with IgAN, and the proportion of Cs ≥11% is an independent risk factor for poor outcomes., Competing Interests: Conflict of interest: All the authors have declared no competing interests., (© 2022 Ying Chen et al., published by De Gruyter.)

Aim: High glucose (HG) induces the production of transforming growth factor (TGF)-β and reactive oxygen species, which further activates JAK/STAT signaling and promotes the synthesis of matrix proteins, contributes to the pathophysiological processes of diabetic nephropathy. This study aims to investigate the protection role of vitamin D (VD) in the kidney in high glucose condition., Methods: Rat glomerular mesangial cells were cultured in high glucose medium, with or without VD or VD receptor (VDR) siRNAs treatment. The levels of TGF-β and fibronectin were detected by qRT-PCR, immunoblotting and enzyme-linked immunosorbent assay (ELISA). The levels of phosphorylated JAK2, STAT1 and STAT3, and JAK/STAT signaling downstream genes were examined by immunoblotting and qRT-PCR., Results: In rat glomerular mesangial cells, VD treatment can repress the tyrosine phosphorylation of JAK2, STAT1 and STAT3. VD inhibited TGF-β and fibronectin expression which was rescued by vitamin d receptor (VDR) siRNA and STATs inhibitor perficitinib. The JAK/STAT signaling downstream protein coding genes including SOCS1, SOCS3 and type IV collagen were repressed by VD. Meanwhile, the expression of non-coding RNAs such as miR-181a, miR-181b, was repressed by VD, and the expression of miR-34a and Let-7b was upregulated by VD., Conclusion: Vitamin D (VD) treatment inhibits the function of HG on fibronectin production through regulating JAK/STAT pathway. These results provide direct evidences that VD protects glomerular mesangial cells from high glucose-induced injury through repressing JAK/STAT signaling, which has the potential for clinical DN treatment.

To date, the coronavirus disease 2019 (COVID-19) has a worldwide distribution. Risk factors for mortality in critically ill patients, especially detailed self-evaluation indicators and laboratory-examination indicators, have not been well described. In this paper, a total of 192 critically ill patients (142 were discharged and 50 died in the hospital) with COVID-19 were included. Self-evaluation indicators including demographics, baseline characteristics, and symptoms and detailed lab-examination indicators were extracted. Data were first compared between survivors and nonsurvivors. Multivariate pattern analysis (MVPA) was performed to identify possible risk factors for mortality of COVID-19 patients. MVPA achieved a relatively high classification accuracy of 93% when using both self-evaluation indicators and laboratory-examination indicators. Several self-evaluation factors related to COVID-19 were highly associated with mortality, including age, duration (time from illness onset to admission), and the Barthel index (BI) score. When the duration, age increased by 1 day, 1 year, BI decreased by 1 point, the mortality increased by 3.6%, 2.4%, and 0.9% respectively. Laboratory-examination indicators including C-reactive protein, white blood cell count, platelet count, fibrin degradation products, oxygenation index, lymphocyte count, and d-dimer were also risk factors. Among them, duration was the strongest predictor of all-cause mortality. Several self-evaluation indicators that can simply be obtained by questionnaires and without clinical examination were the risk factors of all-cause mortality in critically ill COVID-19 patients. The prediction model can be used by individuals to improve health awareness, and by clinicians to identify high-risk individuals., (© 2020 Wiley Periodicals LLC.)

Objective: IgA nephropathy (IgAN) is one of the most common glomerulonephritis in the world, especially in Asian population. IgAN usually progresses slowly, but it is still an important cause of chronic renal failure. IgAN is characterized by abnormal increase of IgA1 level and deposition in mesangium. At present, there is no specific treatment., Materials and Methods: Previous reports have shown that DC cells expressing immunosuppressive factors can significantly reduce the symptoms of arthritis in arthritis models. Indoleamine 2,3-dioxygenase (IDO) is an important tryptophan degrading enzyme and an important factor regulating immunotolerance. DC expressing functional IDO can inhibit effector T cells by consuming essential tryptophan and/or producing toxic metabolites and promoting the differentiation of Treg cells, which exhibits immunosuppressive effect. In this study, we constructed a IgAN mouse model. The mature DC cells overexpressing IDO were induced in vitro and transfused back to IgAN mice to observe their effects on inflammation and renal injury., Results: The results showed that overexpression of IDO did not affect the maturation of DC cells. The proportion of CD3 + CD4 + and CD3 + CD8 + cells decreased significantly and the proportion of CD4 + CD25 + Foxp3 + cells increased significantly in kidney tissue of IgAN mice after the reinfusion of IDO-expressing DC. The contents of IL-2, IL-4, IL-6, and IL-17A in kidney tissue of IgAN mice also decreased significantly, the damage of kidney tissue was alleviated, ACR was decreased, collagen fibre content in kidney tissue was decreased, and IgA deposition in glomerular mesangium was decreased in IgAN mice., Conclusions: It has the potential to treat IgAN by upregulating the expression of IDO in DC cells by genetic engineering and reinfusion into vivo.

Background: Obesity has become a worldwide epidemic, and the incidence of obesity is increasing year by year. Obesity-related nephropathy (ORN) is a common kidney complication of obesity. Long-chain acyl-CoA synthetases-1, (ACSL1), is a key enzyme in the oxidative metabolism of fatty acids in mitochondria and ACSL1 may play a direct role in renal lipid deposition and promote the progress of ORN. In this study, we focus on the renoprotective role of ACSL1 in ORN. Methods: Electron microscopy, immunohistochemical (IHC) staining, Western blot, and real-time PCR were used to detect the expression of ACSL1and Nrf2 in ORN patients, ob/ob mice and palmitic acid (PA)-treated HK-2 cells. Oil red staining and Elisa Kit were used to detect the intracellular FFA and TG contents in ob/ob mice and PA-treated HK-2 cells. Dihydroethidium (DHE) staining and the MDA/SOD measurement were used to detect the ROS production. In order to demonstrate the role of ACSL1 and the interaction between ACSL1 and Nrf2 in ORN, related siRNA and plasmid were transfected into HK-2 cells. Results: More ROS production and renal lipid deposition have been found in ORN patients, ob/ob mice and PA-treated HK-2 cells. Compared with control, all the expression of ACSL1and Nrf2 were down-regulated in ORN patients, ob/ob mice and PA-treated HK-2 cells. The Nrf2 could regulate the expression of ACSL1 and the ACSL1 played the direct role in renal lipid deposition. Conclusions: The Nrf2 is inhibited in ORN, resulting more ROS production and oxidative stress. Increased oxidative stress will suppress the expression of ACSL1, which could increase the intracellular FFA and TG contents, ultimately leading to renal lipid deposition in renal tubulars and accelerating the development of ORN.

The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression. We show how mapping of gene expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression patterns. We report on recent developments of the eHistology atlas and our use of web-services to support embedding of the online 'The Atlas of Mouse Development' in the context of other resources such as the DMDD mouse phenotype database. In addition, we discuss new developments including a cellular-resolution placental atlas, third-party atlas models, clonal analysis data and a new interactive eLearning resource for developmental processes., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)

A significant proportion of developmental biology data is presented in the form of images at morphologically diverse stages of development. The curation of these datasets presents different challenges to that of sequence/text-based data. Towards this end, the eMouseAtlas project created a digital atlas of mouse embryo development as a means of understanding developmental anatomy and exploring the relationship between genes and development in a spatial context. Using the morphological staging system pioneered by Karl Theiler, the project has generated 3D models of post-implantation mouse development and used them as a spatial framework for the delineation of anatomical components and for archiving in situ gene expression data in the EMAGE database. This has allowed us to develop a unique online resource for mouse developmental biology. We describe here the underlying structure of the resource, as well as some of the tools that have been developed to allow users to mine the curated image data. These tools include our IIP3D/X3DOM viewer that allows 3D visualisation of anatomy and/or gene expression in the context of a web browser, and the eHistology resource that extends this functionality to allow visualisation of high-resolution cellular level images of histology sections. Furthermore, we review some of the informatics aspects of eMouseAtlas to provide a deeper insight into the use of the atlas and gene expression database.

Peritoneal fibrosis resulting from long-term peritoneal dialysis is a major cause of failure of peritoneal ultrafiltration function and main reason of dropout from peritoneal dialysis. Epithelial-mesenchymal transition (EMT) of peritoneal mesochelial cells (HPMCs) is a major contributor of peritoneal fibrosis. Recently, the association between histone acetylation and kinds of fibrosis including liver, lung and kidney fibrosis is well established. Thus, in this study we tried to profile whether histone acetylation is also operates EMT process in HPMCs and what's the regulatory mechanism. We established an EMT model of HPMCs through high glucose treatment. And hyperacetylation of H3 histone was found using western blot in EMT model. After treated with C646, a histone acetyltransferase (HAT) inhibitor, high glucose-induced EMT in HPMCs was counteracted. To further understand the molecular mechanism of C646 rescues high glucose-induced EMT, CHIP-qPCRwas used to examine the modulation of histone H3 acetylation at promoters of series signaling target genes. We found that the H3 acetylation level at TGF-β1 gene promoter was down-regulation by C646 treatment. Moreover, we also found that TGF-β1/Smad3 signaling was blocked. Hence, our results suggest that histone H3 acetylation activated TGF-β1/Smad3 signaling during EMT of HPMCs, and C646 can rescue the mesenchymal phenotype transition. These findings may provide a novel pathogenic mechanism and therapeutic target for peritoneal fibrosis.

EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities.

The EMAGE (Electronic Mouse Atlas of Gene Expression) database (http://www.emouseatlas.org/emage) allows users to perform on-line queries of mouse developmental gene expression. EMAGE data are represented spatially using a framework of 3D mouse embryo models, thus allowing uniquely spatial queries to be carried out alongside more traditional text-based queries. This spatial representation of the data also allows a comparison of spatial similarity between the expression patterns. The data are mapped to the models by a team of curators using bespoke mapping software, and the associated meta-data are curated for accuracy and completeness. The data contained in EMAGE are gathered from three main sources: from the published literature, through large-scale screens and collaborations, and via direct submissions from researchers. There are a variety of ways to query the EMAGE database via the on-line search interfaces, as well as via direct computational script-based queries. EMAGE is a free, on-line, community resource funded by the Medical Research Council, UK.

eMouseAtlas (www.emouseatlas.org) is a comprehensive online resource to visualise mouse development and investigate gene expression in the mouse embryo. We have recently deployed a completely redesigned Mouse Anatomy Atlas website (www.emouseatlas.org/emap/ema) that allows users to view 3D embryo reconstructions, delineated anatomy, and high-resolution histological sections. A new feature of the website is the IIP3D web tool that allows a user to view arbitrary sections of 3D embryo reconstructions using a web browser. This feature provides interactive access to very high-volume 3D images via a tiled pan-and-zoom style interface and circumvents the need to download large image files for visualisation. eMouseAtlas additionally includes EMAGE (Edinburgh Mouse Atlas of Gene Expression) (www.emouseatlas.org/emage), a freely available, curated online database of in situ gene expression patterns, where gene expression domains extracted from raw data images are spatially mapped into atlas embryo models. In this way, EMAGE introduces a spatial dimension to transcriptome data and allows exploration of the spatial similarity between gene expression patterns. New features of the EMAGE interface allow complex queries to be built, and users can view and compare multiple gene expression patterns. EMAGE now includes mapping of 3D gene expression domains captured using the imaging technique optical projection tomography. 3D mapping uses WlzWarp, an open-source software tool developed by eMouseAtlas.

Here, we describe the BioMart interface to the eMouseAtlas gene expression database EMAGE. EMAGE is a spatiotemporal database of in situ gene expression patterns in the developing mouse embryo. BioMart provides a generic web query interface and programmable access using web services. The BioMart interface extends access to EMAGE via a powerful method of structuring complex queries and one with which users may already be familiar with from other BioMart implementations. The interface is structured into several data sets providing the user with comprehensive query access to the EMAGE data. The federated nature of BioMart allows scope for integration and cross querying of EMAGE with other similar BioMarts.

We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages (CS) 12-23; approximately 26-56 days post conception (dpc)]. Virtual 3D anatomical models are generated from intact specimens using optical projection tomography (OPT). Using MAPAINT software, selected gene expression data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and/or refine the human anatomical domain boundaries. We have also developed interpolation software that digitally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical domains and ontology are available on the atlas pages along with gene expression data from approximately 100 genes in the HUDSEN Human Spatial Gene Expression Database (http://www.hudsen.org). The aim is that full 3D data will be generated from expression data used to define a more detailed set of anatomical domains linked to a more advanced anatomy ontology and all of these will be available online, contributing to the long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it is generated., (© 2010 The Authors. Journal of Anatomy © 2010 Anatomical Society of Great Britain and Ireland.)

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (approximately 19,000 gene) 'EURExpress' dataset into EMAGE.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spatial methods. Sites of expression are also described using an anatomy ontology and data can be queried using text-based methods. Here we describe recent enhancements to EMAGE which include advances in spatial search methods including: a refined local spatial similarity search algorithm, a method to allow global spatial comparison of patterns in EMAGE and subsequent hierarchical-clustering, and spatial searches across multiple stages of development. In addition, we have extended data access by the introduction of web services and new HTML-based search interfaces, which allow access to data that has not yet been spatially annotated. We have also started incorporating full 3D images of gene expression that have been generated using optical projection tomography (OPT).

Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods.

Background: Anatomy ontologies play an increasingly important role in developing integrated bioinformatics applications. One of the primary relationships between anatomical tissues represented in such ontologies is part-of. As there are a number of ways to divide up the anatomical structure of an organism, each may be represented by more than one valid partonomic (part-of) hierarchy. This raises the issue of how to represent and integrate multiple such hierarchies., Results: In this paper we describe a solution that is based on our work on an anatomy ontology for mouse embryo development, which is part of the Edinburgh Mouse Atlas Project (EMAP). The paper describes the basic conceptual aspects of our approach and discusses strengths and limitations of the proposed solution. A prototype was implemented in Prolog for evaluation purposes., Conclusion: With the proposed name set approach, rather than having to standardise hierarchies, it is sufficient to agree on a suitable set of basic tissue terms and their meaning in order to facilitate the integration of multiple partonomic hierarchies.

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.