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FIGURE 1 in Morphological and histometric features of the caudal kidney in piranha Pygocentrus nattereri (Characiformes: Serrasalmidae)
FIGURE 1 | Macroscopic view of the caudal kidney in Pygocentrus nattereri. A. The typical anatomical position of the organ, ventrally situated on to vertebra column. Two branches (arrowhead) in the cranial portion are divided by the renal arterial (asterisk). The ureters (arrows) emerge from the middle portion of the organ extending to the caudal region. B. Ventral view after dissection of the peritoneum membranes; a vertebral vascular groove can be observed (arrow); Ca, caudal portion. C. Dorsal view with a prominent vertebral groove (sulcus arteriae vertebralis, arrow). Scale bars = 1 cm.
FIGURE 2 in Morphological and histometric features of the caudal kidney in piranha Pygocentrus nattereri (Characiformes: Serrasalmidae)
FIGURE 2 | Histological cross-sections of the caudal kidney in Pygocentrus nattereri highlighting the vascular features. A. Low magnification showing the typical aspect of the kidney parenchyma; segments of blood vessels (BV) are diffusely recognized in all regions; some granulomatous formations are often found (circles in black). HE, scale bar = 200 µm. B. Capillary network from larger vessels spread throughout the parenchyma (arrows) supplying the lymphohematopoietic areas (L); note an immature renal corpuscle (RC) near a capillary branch. HE, scale bar = 50 µm. C. Some RC are usually viewed very closed to larger vessels (V), proximal (PT) and distal tubules (DT); note the brush edge (arrowhead), a characteristic of PT. PAS, scale bar = 50 µm. D. A branch of the renal vein (V) near an RC; a thin collagen bundle can be seen surrounding the vessel. TM, scale bar = 50 µm. E. and F. Represents arterial irrigation of the RC, which demonstrate a thick collagenous layer (asterisk); in E., a large arteria (A) with a branch toward the glomerular area (arrow); in F., an arteriole (A) alongside an RC showing a slightly collagenous marking and Bowman's space (arrow); TM, E., scale bar = 50 µm; D., scale bar = 10 µm.
FIGURE 4 in Morphological and histometric features of the caudal kidney in piranha Pygocentrus nattereri (Characiformes: Serrasalmidae)
FIGURE 4 | Intracellular and intraluminal deposits in the caudal kidney of Pygocentrus natteri. A. Cross-section of proximal tubules showing intracytoplasmic single or multi droplets hyaline deposits in epithelial cells (arrows); HE, scale bar = 10 µm. B. Collecting duct presenting a luminal melanogenic macrophage; leukocyte cells often infiltrate the muscularis layer peripherally to the epithelial cells or enter the luminal space (arrows); HE, scale bar = 50 µm. C. Collecting tubule with an abundant luminal accumulation of melanogenic macrophages; HE, scale bar = 50 µm. D. Melanogenic macrophages and epithelial cells of a collecting duct; the cell's basophilic luminal border indicates a degenerative process (arrow); HE, scale bar = 10 µm. E. Area of focal necrosis involving the collecting duct epithelium with melanogenic macrophage infiltrate (arrowhead); hyaline deposits in the cytoplasm of tubular epithelial cells (asterisk) are observed; HE, scale bar = 50 µm.
FIGURE 6 in Morphological and histometric features of the caudal kidney in piranha Pygocentrus nattereri (Characiformes: Serrasalmidae)
FIGURE 6 | Frequency of hemosiderin and lipofuscin in the caudal kidney melanomacrophages centers (MMC) of Pygocentrus natteri. A. Frequency of area of pigments in tissue of female and male (mean, bars = epm). Differences between substances was observed (*), P = 0.006. B. Histological section stained with Perl's method for ferric iron for hemosiderin detection (arrow). C. Histological sections stained with Schmorl's solution for lipofuscin detection (arrow); scale bars = 50 µm.
Data used in analyses of Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells"
<p>CosMx 1000-plex data and R code from childhood-onset lupus nephris samples, generated for the article Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells".</p>
Fig. 4 in Histopathology of gills, kidney and liver of a Neotropical fish caged in an urban stream
Fig. 4. Photomicrographs of the liver of P. lineatus caged in Cambé stream. a) normal hepatic tissue, showing hepatocytes with granular cytoplasm (*) and central and round nucleus (arrow); b) hepatocytes with irregular shaped nucleus (black arrows), eosinophilic granules in the cytoplasm (arrowheads) and nuclear hypertrophy (*); c) bile stagnation (arrows); d) nuclear degeneration (arrows) and cytoplasmic degeneration (*); e) melanomacrophages aggregate, close to a vessel (white arrow) and cytoplasmic vacuolation (*); f) hepatic tissue showing focal necrosis (white arrow). Scale bar 10 mm, H.E.
Fig. 3 in Histopathology of gills, kidney and liver of a Neotropical fish caged in an urban stream
Fig. 3. Photomicrographs of the kidney of P. lineatus caged in Cambé stream. a) normal renal corpuscle showing the glomerulus and the Bowman's space well defined (arrow), proximal tubules (*), distal tubules (arrowheads); b) glomerular expansion and absence of the Bowman's space (arrow) and tubule cells with hypertrophied nucleus (arrowheads); c) tubule starting the regeneration process (white arrow), occlusion of the tubular lumen (black arrows) and cloudy swelling degeneration (*); d) detail of 2 tubules with hyaline droplets degeneration (*). Scale bar 10 mm, H.E.
Fig. 1 in Histopathology of gills, kidney and liver of a Neotropical fish caged in an urban stream
Fig. 1. Map showing the region of Londrina city (Paraná State), where the in situ tests were carried out at the reference site (Apertados stream), and the sites at Cambé stream (A, B and C).
Figure 1 in The origin of vertebrates: a hypothesis based on kidney development
Figure 1. Schematic drawing of the excretory apparatus in the 'protovertebrate' (A), in higher annelids (B), and in an advanced developmental stage in 'protovertebrates' (C, modified detail from A). Note that the peritoneal fold in (C) is still open towards the coelom on the left side, whereas it is already closed in a later stage (right side), thus forming a separate nephric chamber. Both conditions can be found in the pronephros of extant lower vertebrates. Abbreviations: AO, dorsal aorta; CC, coelomic cavity; DC, dorsal chorda; DV, dorsal vessel; GT, glomerular tuft; IN, intestine; MN, metanephridium; NC, neural chord; NP, nephroporus; PC, pronephric chamber; PF, peritoneal fold; SS, segmental septum; UD, urinary duct.
Data files for manuscript "Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study"
<p>#2021-09-19<br> #Summary<br> This ZIP-file contains the Excel files used for all analyses for the manuscript "Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study".</p> <p><br> #File structure<br> README.txt This README file.<br> File S1 ("FileS1_GCKD-ADTKD.cohort.xlsx") Cohort characteristics, sequencing quality parameters and fingerprinting results.<br> File S2 ("FileS2_GCKD-ADTKD.content.xlsx") Sequencing panel design/ content with information on gene domains used for Figure 2.<br> File S3 ("FileS3_GCKD-ADTKD.variants.xlsx") Information on small variants, CNVs and MUC1 analyses (SNaPshot and adVNTR).<br> File S4 ("FileS4_GCKD-ADTKD.simulation.xlsx") Curated variant and individual data from the Groopman study with results of the simulation for Figure 4.</p> <p><br> #Files and checksums<br> 2D6184BC145987D3EE2E0DC6873DDDDB ./README.txt<br> 10EE4C3C9D9ED6417647F26A09583820 ./FileS1_GCKD-ADTKD.cohort.xlsx<br> 9F95661845215FB7875EB053F887AB36 ./FileS2_GCKD-ADTKD.content.xlsx<br> 2AC19FBC6103CB48905F64716428AE5B ./FileS3_GCKD-ADTKD.variants.xlsx<br> 2D6184BC145987D3EE2E0DC6873DDDDB ./FileS4_GCKD-ADTKD.simulation.xlsx</p>
Data from: Age estimation using methylation-sensitive high-resolution melting (MS-HRM) in both healthy felines and those with chronic kidney disease
<p>Age is an important ecological tool in wildlife conservation. However, it is difficult to estimate in most animals, including felines — most of whom are endangered. Here, we developed the first DNA methylation-based age-estimation technique — as an alternative to current age-estimation methods — for two feline species that share a relatively long genetic distance with each other: domestic cat (<i>Felis catus</i>; 79 blood samples) and an endangered <i>Panthera</i>, the snow leopard (<i>Panthera uncia</i>; 11 blood samples). We measured the methylation rates of two gene regions <span>using </span>methylation-sensitive high-resolution melting (MS-HRM). Domestic cat age was estimated with a mean absolute deviation (MAD) of 3.83 years. Health conditions influenced accuracy of the model. Specifically, the models built on cats with chronic kidney disease (CKD) had lower accuracy than those built on healthy cats. The snow leopard-specific model (i.e. the model that resets the model settings for snow leopards) had a better accuracy (MAD = 2.10 years) than that obtained on using the domestic cat model directly. This implies that our markers could be utilised across species, although changing the model settings when targeting different species could lead to better estimation accuracy. The snow leopard-specific model also successfully distinguished between sexually immature and mature individuals.</p>
Immune checkpoint molecule TIGIT regulates kidney T cell functions and mediates acute kidney injury
<p>This dataset includes the single cell RNA-seq data associated with the publication listed in the title (abstract below).<br> <br> CellRanger.zip contains the raw transcript counts as produced by CellRanger. There is one folder per sample. The samples are indicated by the folder name (e.g. KO_Ctrl). <br> <br> We have also included .h5ad files that contain of cells that passed quality control, as described in the manuscript.<br> <br> adTIGIT_raw_031422.h5ad contains all passing cells and the raw counts, as well as cell annotations ('celltype')<br> <br> adTIGIT_Tonly_091421.h5ad contains only T cells, .X contains the normalized data and T-cell sub-type ('cluster').<br> <br> Abstract: T cells mediate pathologic and reparative processes during acute kidney injury (AKI) but exact mechanisms regulating kidney T cell functions are unclear. This study identified upregulation of the novel immune checkpoint molecule, TIGIT, on mouse and human kidney T cells following AKI. TIGIT-expressing kidney T cells produced proinflammatory cytokines and had effector and central memory phenotype. Kidney Tregs were predominantly TIGIT+ and reduced after ischemia reperfusion (IR) injury. TIGIT deficient mice had protection from both ischemic and nephrotoxic AKI. Single cell RNA sequencing led to discovery of possible downstream targets of TIGIT. TIGIT mediates AKI pathophysiology, is a promising target for developing AKI therapy, and is being increasingly studied in human cancer therapy trials.</p>
Fourier Ptychography of kidney tissues
<p>Beyond conventional microscopy: observing Kidney tissues by means of Fourier Ptychography -</p> <p>Fourier Ptychography (FP) phase contrast image of a 3 µm thick unstained renal tissue slide and FP phase contrast image of the same region after staining with H&E. The previous images are compared with the corresponding H&E bright image captured by conventional microcopy of the same region on a different section. Moreover, we report a FP phase contrast image of a 10 µm thick unstained renal tissue slide, which has been obtained by stitching 16 FP fields of view to image a big portion of the kidney tissue slide under analysis.</p>
Dataset related to article "Imaging the kidney with an unconventional scanning electron microscopy technique: analysis of the subpodocyte space in diabetic mice".
<p><strong>Datasets:</strong></p> <p><strong>Table 1_Systemic parameters.xlsx </strong>- dataset related to the systemic parameters. These data are presented in Table 1. </p> <p><strong>Figure 6_Morphometric analysis.xlsx </strong>- dataset related to the morphometric characterization of the subpodocyte space and podocytes. These data are presented in Figure 6. </p> <p><strong>Abstract of the manuscript</strong></p> <p>Transmission electron microscopy (TEM) remains the gold standard for renal histopathological diagnoses, given its higher resolving power compared to light microscopy. However, it imposes several limitations on pathologists, including longer sample preparation time and a small observation area. To overcome these, we introduced a scanning electron microscopy (SEM) technique for imaging resin-embedded semi-thin sections of renal tissue. We developed a rapid tissue preparation protocol for experimental models and human biopsies which, alongside SEM digital imaging acquisition of secondary electrons (SE-SEM), enables fast electron microscopy examination, with a resolution similar to that achieved by TEM. We used this unconventional SEM imaging approach to investigate the subpodocyte space (SPS) in BTBR <em>ob/ob</em> mice with type 2 diabetes. Analysis of semi-thin sections with secondary electrons revealed that the SPS had expanded in volume and covered large areas of the glomerular basement membrane, forming wide spaces between the podocyte body and underlying filtering membrane. Our results show that SE-SEM is a valuable tool for imaging the kidney at the ultrastructural level, filling the magnification gap between light microscopy and TEM, and reveal that in diabetic mice the SPS is larger than in normal controls, which is associated with podocyte damage and impaired kidney function.</p>
Dataset related to: Sirtuin 3 Deficiency Aggravates Kidney Disease in Response to High-Fat Diet through Lipotoxicity-Induced Mitochondrial Damage
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p> </p> <p>Abstract: Sirtuin 3 (SIRT3) is the primary mitochondrial deacetylase that controls the antioxidant<br>pathway and energy metabolism. We previously found that renal Sirt3 expression and activity were<br>reduced in mice with type 2 diabetic nephropathy associated with oxidative stress and mitochondrial<br>abnormalities and that a specific SIRT3 activator improved renal damage. SIRT3 is modulated by<br>diet, and to assess whether Sirt3 deficiency aggravates mitochondrial damage and accelerates kidney<br>disease in response to nutrient overloads, wild-type (WT) and Sirt3-/- mice were fed a high-fat-diet<br>(HFD) or standard diet for 8 months. Sirt3-/- mice on HFD exhibited earlier and more severe<br>albuminuria compared to WT mice, accompanied by podocyte dysfunction and glomerular capillary<br>rarefaction. Mesangial matrix expansion, tubular vacuolization and inflammation, associated with<br>enhanced lipid accumulation, were more evident in Sirt3-/- mice. After HFD, kidneys from Sirt3-/-<br>mice showed more oxidative stress than WT mice, mitochondria ultrastructural damage in tubular<br>cells, and a reduction in mitochondrial mass and energy production. Our data demonstrate that Sirt3<br>deficiency renders mice more prone to developing oxidative stress and mitochondrial abnormalities<br>in response to HFD, resulting in more severe kidney diseases, and this suggests that mitochondria<br>protection may be a method to prevent HFD-induced renal injury.</p>
Dataset related to: Add-On Cyclic Angiotensin-(1-7) with Cyclophosphamide Arrests Progressive Kidney Disease in Rats with ANCA Associated Glomerulonephritis
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p> </p> <p>Abstract: Rapidly progressive crescentic glomerulonephritis associated with anti-neutrophil cytoplasmic antibodies (ANCA-GN) is a major cause of renal failure. Current immunosuppressive therapies are associated with severe side effects, intensifying the need for new therapeutic strategies. The activation of Mas receptor/Angiotensin-(1-7) axis exerted renoprotection in chronic kidney disease.<br> Here, we investigated the effect of adding the lanthionine-stabilized cyclic form of angiotensin-1-7 [cAng-(1-7)] to cyclophosphamide in a rat model of ANCA-GN. At the onset of proteinuria,Wistar Kyoto rats with ANCA-GN received vehicle or a single bolus of cyclophosphamide, with or without daily cAng-(1-7). Treatment with cAng-(1-7) plus cyclophosphamide reduced proteinuria by 85% vs. vehicle, and by 60% vs. cyclophosphamide, and dramatically limited glomerular crescents to less than 10%. The addition of cAng-(1-7) to cyclophosphamide protected against glomerular inflammation and endothelial rarefaction and restored the normal distribution of parietal epithelial cells. Ultrastructural analysis revealed a preserved GBM, glomerular endothelium and podocyte structure, demonstrating that combination therapy provided an additional layer of renoprotection. This study demonstrates that adding cAng-(1-7) to a partially effective dose of cyclophosphamide arrests the progression of renal disease in rats with ANCA-GN, suggesting that cAng-(1-7) could be a novel clinical approach for sparing immunosuppressants.</p>
Automatic Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms - Datasets
<p>Datasets for reproducibility of the results found in Automatic Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms. This study utilized data from the following 4 journals:</p> <p>Lake, B.B. et al. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. Nat Commun 10, 2832 (2019).</p> <p>Liao, J., Yu, Z., Chen, Y. et al. Single-cell RNA sequencing of human kidney. Sci Data 7, 4 (2020).</p> <p>Menon, R. et al. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight 5, e133267 (2020).</p> <p>Wu, H. et al. Single-cell transcriptomics of a human kidney allograft biopsy specimen defines a diverse inflammatory response. J Am Soc Nephrol 29: 2069–2080 (2018).</p> <p>Young, M. D. et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 361, 594–599 (2018).</p>
Safety, Pharmacokinetics, and Preliminary Efficacy of Isatuximab in Patients Awaiting Kidney Transplantation
ClinicalTrials.gov study NCT04294459. IPD Sharing: YES. Countries: 2. Publications: 2.
Vascular Endothelial Growth Factor-B (VEGF-B) Blockade With the Monoclonal Antibody CSL346 in Subjects With Diabetic Kidney Disease
ClinicalTrials.gov study NCT04419467. IPD Sharing: YES. Countries: 6. Publications: 1.
Clazakizumab for the Treatment of Chronic Active Antibody Mediated Rejection in Kidney Transplant Recipients
ClinicalTrials.gov study NCT03744910. IPD Sharing: YES. Countries: 15. Publications: 4.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.