Renoprotective Effects of Mineralocorticoid Receptor Antagonists Against Diabetic Kidney Disease.

Diabetic kidney disease (DKD) is a growing epidemic worldwide and a leading cause of end-stage kidney disease. Mineralocorticoid receptor (MR) blockade using Finerenone is a recently approved therapeutic approach to slow down the progression of DKD in patients with type 2 diabetes in addition to other therapies such as angiotensin-II converting enzyme inhibitors (ACEIs), angiotensin II receptor blockers (ARBs), sodium-glucose co-transporter 2 (SGLT2) inhibitors, and glucagon-like peptide 1 (GLP-1) analogs. This review elaborates on the pathophysiologic pathways activated by aldosterone (the human mineralocorticoid) in DKD, the pharmacology of three different generations of mineralocorticoid receptor antagonists (MRAs), specifically, spironolactone, eplerenone, and finerenone, and the mechanisms by which these MRAs elicit their protective effects on the kidney under diabetic settings.

Hypergraphs and centrality measures identifying key features in gene expression data.

Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing individual genes with hyperedges, and simultaneously testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a technique that reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which identifies salient features within a data set. For instance dominant or hub-like hyperedges, leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.

Anti-CD3 monoclonal antibodies for the prevention and treatment of type 1 diabetes: A literature review.

PURPOSE: Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of beta cells, resulting in a loss of insulin production. Patients with T1D carry a substantial disease burden as well as substantial short-term and long-term risks associated with inadequate glycemic control. Currently, treatment mainly consists of insulin, which only treats the symptoms of T1D and not the root cause. Thus, disease-modifying agents such as anti-CD3 monoclonal antibodies (mAbs) that target the autoimmune destruction of beta cells in T1D would provide significant relief and health benefits for patients with T1D. This review summarizes the clinical evidence regarding the safety and efficacy of anti-CD3 mAbs in the prevention and treatment of T1D. SUMMARY: A total of 27 studies reporting or evaluating data from clinical trials involving otelixizumab and teplizumab were included in the review. Anti-CD3 mAbs have shown significant benefits in both patients at high risk for T1D and those with recent-onset T1D. In high-risk populations, anti-CD3 mAbs delayed time to diagnosis, preserved C-peptide levels, and improved metabolic parameters. In recent-onset T1D, anti-CD3 mAbs preserved C-peptide levels and reduced insulin needs for extended periods. Anti-CD3 mAb therapy appears to be safe, with primarily transient and self-limiting adverse effects and no negative long-term effects. CONCLUSION: Anti-CD3 mAbs are promising disease-modifying treatments for T1D. Their role in T1D may introduce short-term and long-term benefits with the potential to mitigate the significant disease burden; however, more evidence is required for an accurate assessment.

Non-melanoma skin cancer segmentation for histopathology dataset.

Densely labelled segmentation data for digital pathology images is costly to produce but is invaluable to training effective machine learning models. We make available 290 hand-annotated histopathology tissue sections of the 3 most common skin cancers; basal cell carcinoma (BCC), squamous cell carcinoma (SCC) and intraepidermal carcinoma (IEC). These non-melanoma skin cancers constitute over 90% of all skin cancer diagnoses and hence this dataset gives an opportunity to the scientific community to benchmark analytic methodologies on a significant portion of the dermatopathology workflow. The data represents typical cases of the three cancer types (not requiring a differential diagnosis) across shave, punch and excision biopsy contexts. Each image is accompanied with a segmentation mask which characterizes the section into 12 tissue types, specifically: keratin, epidermis, papillary dermis, reticular dermis, hypodermis, inflammation, glands, hair follicles and background, as well as BCC, SCC and IEC. Included also are cancer margin measurements to work towards automated assessment of surgical margin clearance and tumour invasion. This leaves open many opportunities for researchers to utilize or extend the dataset, building upon recent work on image analysis problems in skin cancer (Thomas et al., 2021).

LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia.

BACKGROUND: With recent advances in microscopy, recordings of cell behaviour can result in terabyte-size datasets. The lattice light sheet microscope (LLSM) images cells at high speed and high 3D resolution, accumulating data at 100 frames/second over hours, presenting a major challenge for interrogating these datasets. The surfaces of vertebrate cells can rapidly deform to create projections that interact with the microenvironment. Such surface projections include spike-like filopodia and wave-like ruffles on the surface of macrophages as they engage in immune surveillance. LLSM imaging has provided new insights into the complex surface behaviours of immune cells, including revealing new types of ruffles. However, full use of these data requires systematic and quantitative analysis of thousands of projections over hundreds of time steps, and an effective system for analysis of individual structures at this scale requires efficient and robust methods with minimal user intervention. RESULTS: We present LLAMA, a platform to enable systematic analysis of terabyte-scale 4D microscopy datasets. We use a machine learning method for semantic segmentation, followed by a robust and configurable object separation and tracking algorithm, generating detailed object level statistics. Our system is designed to run on high-performance computing to achieve high throughput, with outputs suitable for visualisation and statistical analysis. Advanced visualisation is a key element of LLAMA: we provide a specialised tool which supports interactive quality control, optimisation, and output visualisation processes to complement the processing pipeline. LLAMA is demonstrated in an analysis of macrophage surface projections, in which it is used to i) discriminate ruffles induced by lipopolysaccharide (LPS) and macrophage colony stimulating factor (CSF-1) and ii) determine the autonomy of ruffle morphologies. CONCLUSIONS: LLAMA provides an effective open source tool for running a cell microscopy analysis pipeline based on semantic segmentation, object analysis and tracking. Detailed numerical and visual outputs enable effective statistical analysis, identifying distinct patterns of increased activity under the two interventions considered in our example analysis. Our system provides the capacity to screen large datasets for specific structural configurations. LLAMA identified distinct features of LPS and CSF-1 induced ruffles and it identified a continuity of behaviour between tent pole ruffling, wave-like ruffling and filopodia deployment.

Interpretable deep learning systems for multi-class segmentation and classification of non-melanoma skin cancer.

We apply for the first-time interpretable deep learning methods simultaneously to the most common skin cancers (basal cell carcinoma, squamous cell carcinoma and intraepidermal carcinoma) in a histological setting. As these three cancer types constitute more than 90% of diagnoses, we demonstrate that the majority of dermatopathology work is amenable to automatic machine analysis. A major feature of this work is characterising the tissue by classifying it into 12 meaningful dermatological classes, including hair follicles, sweat glands as well as identifying the well-defined stratified layers of the skin. These provide highly interpretable outputs as the network is trained to represent the problem domain in the same way a pathologist would. While this enables a high accuracy of whole image classification (93.6-97.9%), by characterising the full context of the tissue we can also work towards performing routine pathologist tasks, for instance, orientating sections and automatically assessing and measuring surgical margins. This work seeks to inform ways in which future computer aided diagnosis systems could be applied usefully in a clinical setting with human interpretable outcomes.

Use of surrogate species to cost-effectively prioritize conservation actions.

Conservation efforts often focus on umbrella species whose distributions overlap with many other flora and fauna. However, because biodiversity is affected by different threats that are spatially variable, focusing only on the geographic range overlap of species may not be sufficient in allocating the necessary actions needed to efficiently abate threats. We developed a problem-based method for prioritizing conservation actions for umbrella species that maximizes the total number of flora and fauna benefiting from management while considering threats, actions, and costs. We tested our new method by assessing the performance of the Australian federal government's umbrella prioritization list, which identifies 73 umbrella species as priorities for conservation attention. Our results show that the federal government priority list benefits only 6% of all Australia's threatened terrestrial species. This could be increased to benefit nearly half (or 46%) of all threatened terrestrial species for the same budget of AU$550 million/year if more suitable umbrella species were chosen. This results in a 7-fold increase in management efficiency. We believe nations around the world can markedly improve the selection of prioritized umbrella species for conservation action with this transparent, quantitative, and objective prioritization approach.

Uso de Especies Sustitutas para Priorizar las Acciones de Conservación de Manera Rentable Resumen Los esfuerzos de conservación comúnmente se enfocan en las especies paraguas cuyas distribuciones se traslapan con la de muchos otros componentes de la flora y fauna. Sin embargo, como la biodiversidad se ve afectada por diferentes amenazas que presentan una variabilidad espacial, enfocarse solamente en el traslape de la extensión geográfica de las especies puede no ser suficiente para la asignación de las acciones necesarias para abatir eficientemente a las amenazas. Desarrollamos un método basado en problemas para la priorización de las acciones de conservación para las especies paraguas, el cual maximiza el total de flora y fauna beneficiado con el manejo a la vez que considera amenazas, acciones y costos. Probamos nuestro método al valorar el desempeño de la lista de priorización de especies paraguas del gobierno federal de Australia, la cual identifica a 73 especies paraguas como prioritarias para la atención de la conservación. Nuestros resultados muestran que la lista de prioridades del gobierno federal beneficia sólo al 6% de las especies terrestres amenazadas en Australia. Esto podría incrementarse para beneficiar a casi la mitad (o el 46%) de las especies terrestres amenazadas con el mismo presupuesto de AU$550 millones al año si se eligieran a especies paraguas más adecuadas. Esto resulta en un incremento siete veces mayor en la eficiencia del manejo. Creemos que en todo el mundo los países pueden mejorar de una manera muy marcada la selección de las especies paraguas para las acciones de conservación con una estrategia de priorización transparente, cuantitativa y objetiva.

Nephron progenitor commitment is a stochastic process influenced by cell migration.

Progenitor self-renewal and differentiation is often regulated by spatially restricted cues within a tissue microenvironment. Here, we examine how progenitor cell migration impacts regionally induced commitment within the nephrogenic niche in mice. We identify a subset of cells that express Wnt4, an early marker of nephron commitment, but migrate back into the progenitor population where they accumulate over time. Single cell RNA-seq and computational modelling of returning cells reveals that nephron progenitors can traverse the transcriptional hierarchy between self-renewal and commitment in either direction. This plasticity may enable robust regulation of nephrogenesis as niches remodel and grow during organogenesis.

Branching morphogenesis in the developing kidney is not impacted by nephron formation or integration.

Branching morphogenesis of the ureteric bud is integral to kidney development; establishing the collecting ducts of the adult organ and driving organ expansion via peripheral interactions with nephron progenitor cells. A recent study suggested that termination of tip branching within the developing kidney involved stochastic exhaustion in response to nephron formation, with such a termination event representing a unifying developmental process evident in many organs. To examine this possibility, we have profiled the impact of nephron formation and maturation on elaboration of the ureteric bud during mouse kidney development. We find a distinct absence of random branch termination events within the kidney or evidence that nephrogenesis impacts the branching program or cell proliferation in either tip or progenitor cell niches. Instead, organogenesis proceeds in a manner indifferent to the development of these structures. Hence, stochastic cessation of branching is not a unifying developmental feature in all branching organs.

Time to CT head in adult patients with suspected traumatic brain injury: Association with the 'Shorter Stays in Emergency Departments' health target in Aotearoa New Zealand.

A national health target for length of stay in emergency departments (ED) was introduced in 2009 to reduce crowding and improve quality of care. We aimed to determine whether the target was associated with changes in time to CT and appropriateness of CT imaging, as markers of care quality for suspected acute traumatic brain injury (TBI). We undertook a retrospective review of the case records of a random sample of people aged ≥15 years presenting to the ED with TBI from 2006 to 2013. General linear models were used to investigate changes in outcomes along with routine process times before and after the introduction of the target. Among 501 eligible cases the median (IQR) time to CT was 136 (76-247) pre target versus 119 (59-209) minutes post target, p = 0.014. The proportion of appropriate imaging was similar between periods: 77.9% (95% CI 71-83%) versus 76.6% (95%CI 72-81%), p = 0.825. Interactions suggested that the time to CT and appropriateness of imaging before and after the introduction of the target varied by ethnicity, although the changes were not clinically important. Time to assessment and length of stay did not change importantly. We found no evidence of a clinically important change in time to CT or appropriateness of imaging for suspected TBI in association with the introduction of the SSED time target. Additional research with larger cohorts of Maori and Pacific participants is recommended to understand our observed patterns by ethnicity.

Branching morphogenesis in the developing kidney is governed by rules that pattern the ureteric tree.

Metanephric kidney development is orchestrated by the iterative branching morphogenesis of the ureteric bud. We describe an underlying patterning associated with the ramification of this structure and show that this pattern is conserved between developing kidneys, in different parts of the organ and across developmental time. This regularity is associated with a highly reproducible branching asymmetry that is consistent with locally operative growth mechanisms. We then develop a class of tip state models to represent elaboration of the ureteric tree and describe rules for 'half-delay' branching morphogenesis that describe almost perfectly the patterning of this structure. Spatial analysis suggests that the observed asymmetry may arise from mutual suppression of bifurcation, but not extension, between the growing ureteric tips, and demonstrates that disruption of patterning occurs in mouse mutants in which the distribution of tips on the surface of the kidney is altered. These findings demonstrate that kidney development occurs by way of a highly conserved reiterative pattern of asymmetric bifurcation that is governed by intrinsic and locally operative mechanisms.

Self-organisation after embryonic kidney dissociation is driven via selective adhesion of ureteric epithelial cells.

Human pluripotent stem cells, after directed differentiation in vitro, can spontaneously generate complex tissues via self-organisation of the component cells. Self-organisation can also reform embryonic organ structure after tissue disruption. It has previously been demonstrated that dissociated embryonic kidneys can recreate component epithelial and mesenchymal relationships sufficient to allow continued kidney morphogenesis. Here, we investigate the timing and underlying mechanisms driving self-organisation after dissociation of the embryonic kidney using time-lapse imaging, high-resolution confocal analyses and mathematical modelling. Organotypic self-organisation sufficient for nephron initiation was observed within a 24 h period. This involved cell movement, with structure emerging after the clustering of ureteric epithelial cells, a process consistent with models of random cell movement with preferential cell adhesion. Ureteric epithelialisation rapidly followed the formation of ureteric cell clusters with the reformation of nephron-forming niches representing a later event. Disruption of P-cadherin interactions was seen to impair this ureteric epithelial cell clustering without affecting epithelial maturation. This understanding could facilitate improved regulation of patterning within organoids and facilitate kidney engineering approaches guided by cell-cell self-organisation.

Analysed cap mesenchyme track data from live imaging of mouse kidney development.

This article provides detailed information on manually tracked cap mesenchyme cells from timelapse imaging of multiple ex vivo embryonic mouse kidneys. Cells were imaged for up to 18 h at 15 or 20 min intervals, and multiple cell divisions were tracked. Positional data is supplemented with a range of information including the relative location of the closest ureteric tip and a correction for drift due to bulk movement and tip growth. A subset of tracks were annotated to indicate the presence of processes attached to the ureteric epithelium. The calculations used for drift correction are described, as are the main methods used in the analysis of this data for the purpose of describing cap cell motility. The outcomes of this analysis are discussed in "Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip" (A.N. Combes, J.G. Lefevre, S. Wilson, N.A. Hamilton, M.H. Little, 2016) [1].

Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip.

Morphogenesis of the mammalian kidney requires reciprocal interactions between two cellular domains at the periphery of the developing organ: the tips of the epithelial ureteric tree and adjacent regions of cap mesenchyme. While the presence of the cap mesenchyme is essential for ureteric branching, how it is specifically maintained at the tips is unclear. Using ex vivo timelapse imaging we show that cells of the cap mesenchyme are highly motile. Individual cap mesenchyme cells move within and between cap domains. They also attach and detach from the ureteric tip across time. Timelapse tracks collected for >800 cells showed evidence that this movement was largely stochastic, with cell autonomous migration influenced by opposing attractive, repulsive and cell adhesion cues. The resulting swarming behaviour maintains a distinct cap mesenchyme domain while facilitating dynamic remodelling in response to underlying changes in the tip.

Is a national time target for emergency department stay associated with changes in the quality of care for acute asthma? A multicentre pre-intervention post-intervention study.

OBJECTIVE: There is debate whether targets for ED length of stay introduced to reduce ED overcrowding are helpful or harmful, as focus on a process target may divert attention from clinical care. Our objective was to investigate the effect of a national ED target in Aotearoa New Zealand on the recommended care for acute asthma as this is known to suffer in overcrowded departments. METHODS: We conducted a retrospective chart review study across four sites from 2006 to 2012 (target introduced mid 2009). The primary outcome was time to steroids in the ED. The secondary outcomes were other aspects of asthma care in ED. We used general linear models or logistic regression as appropriate to assess care before and after the target. RESULTS: Among the 570 (of 1270 randomly selected cases) eligible for analysis, no difference was demonstrated in time to steroids: least square mean (95% CI) = 58.1 (49-67.5) min before and 50.4 (42.9-55.8) min after the target (P = 0.15). More patients received steroids in ED after the target, OR (95% CI) = 2.1 (1.2-4.3). No differences were demonstrated in those receiving steroid prescriptions or re-presentations: OR (95% CI) = 1.3 (0.9-1.96) and 1.1 (0.5-2.3), respectively. Changes in pre-target and post-target ED and hospital length of stay varied between hospitals. CONCLUSION: Introduction of the target was not associated with a change in times to steroids in ED, although more patients received steroids in ED indicating closer adherence to recommended practice.

Comparing and distinguishing the structure of biological branching.

Bifurcating developmental branching morphogenesis gives rise to complex organs such as the lung and the ureteric tree of the kidney. However, a few quantitative methods or tools exist to compare and distinguish, at a structural level, the critical features of these important biological systems. Here we develop novel graph alignment techniques to quantify the structural differences of rooted bifurcating trees and demonstrate their application in the analysis of developing kidneys from in normal and mutant mice. We have developed two graph based metrics: graph discordance, which measures how well the graphs representing the branching structures of distinct trees graphs can be aligned or overlayed; and graph inclusion, which measures the degree of containment of a tree graph within another. To demonstrate the application of these approaches we first benchmark the discordance metric on a data set of 32 normal and 28Tgfß(+/-) mutant mouse ureteric trees. We find that the discordance metric better distinguishes control and mutant mouse kidneys than alternative metrics based on graph size and fingerprints - the distribution of tip depths. Using this metric we then show that the structure of the mutant trees follows the same pattern as the normal kidneys, but undergo a major delay in elaboration at later stages. Analysis of both controls and mutants using the inclusion metric gives strong support to the hypothesis that ureteric tree growth is stereotypic. Additionally, we present a new generalised multi-tree alignment algorithm that minimises the sum of pairwise graph discordance and which can be used to generate maximum consensus trees that represent the archetype for fixed developmental stages. These tools represent an advance in the analysis and quantification of branching patterns and will be invaluable in gaining a deeper understanding of the mechanisms that drive development. All code is being made available with documentation and example data with this publication.

An integrated pipeline for the multidimensional analysis of branching morphogenesis.

Developmental branching morphogenesis establishes organ architecture, and it is driven by iterative interactions between epithelial and mesenchymal progenitor cell populations. We describe an approach for analyzing this interaction and how it contributes to organ development. After initial in vivo cell labeling with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU) and tissue-specific antibodies, optical projection tomography (OPT) and confocal microscopy are used to image the developing organ. These imaging data then inform a second analysis phase that quantifies (using Imaris and Tree Surveyor software), models and integrates these events at a cell and tissue level in 3D space and across developmental time. The protocol establishes a benchmark for assessing the impact of genetic change or fetal environment on organogenesis that does not rely on ex vivo organ culture or section-based reconstruction. By using this approach, examination of two developmental stages for an organ such as the kidney can be undertaken by a postdoctoral-level researcher in 6 weeks, with a full developmental analysis in mouse achievable in 5 months.

Global quantification of tissue dynamics in the developing mouse kidney.

Although kidneys of equal size can vary 10-fold in nephron number at birth, discovering what regulates such variation has been hampered by a lack of quantitative parameters defining kidney development. Here we report a comprehensive, quantitative, multiscale analysis of mammalian kidney development in which we measure changes in cell number, compartment volumes, and cellular dynamics across the entirety of organogenesis, focusing on two key nephrogenic progenitor populations: the ureteric epithelium and the cap mesenchyme. In doing so, we describe a discontinuous developmental program governed by dynamic changes in interactions between these key cellular populations occurring within a previously unappreciated structurally stereotypic organ architecture. We also illustrate the application of this approach to the detection of a subtle mutant phenotype. This baseline program of kidney morphogenesis provides a framework for assessing genetic and environmental developmental perturbation and will serve as a gold standard for the analysis of other organs.

Cortical F-actin stabilization generates apical-lateral patterns of junctional contractility that integrate cells into epithelia.

E-cadherin cell-cell junctions couple the contractile cortices of epithelial cells together, generating tension within junctions that influences tissue organization. Although junctional tension is commonly studied at the apical zonula adherens, we now report that E-cadherin adhesions induce the contractile actomyosin cortex throughout the apical-lateral axis of junctions. However, cells establish distinct regions of contractile activity even within individual contacts, producing high tension at the zonula adherens but substantially lower tension elsewhere. We demonstrate that N-WASP (also known as WASL) enhances apical junctional tension by stabilizing local F-actin networks, which otherwise undergo stress-induced turnover. Further, we find that cells are extruded from monolayers when this pattern of intra-junctional contractility is disturbed, either when N-WASP redistributes into lateral junctions in H-Ras(V12)-expressing cells or on mosaic redistribution of active N-WASP itself. We propose that local control of actin filament stability regulates the landscape of intra-junctional contractility to determine whether or not cells integrate into epithelial populations.

Independent contrasts and PGLS regression estimators are equivalent.

We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has several implications: 1. Understanding the structure of the linear model for GLS regression provides insight into when and why phylogeny is important in comparative studies. 2. The limitations of the PIC regression analysis are the same as the limitations of the GLS model. In particular, phylogenetic covariance applies only to the response variable in the regression and the explanatory variable should be regarded as fixed. Calculation of PICs for explanatory variables should be treated as a mathematical idiosyncrasy of the PIC regression algorithm. 3. Since the GLS estimator is the best linear unbiased estimator (BLUE), the slope parameter estimated using PICs is also BLUE. 4. If the slope is estimated using different branch lengths for the explanatory and response variables in the PIC algorithm, the estimator is no longer the BLUE, so this is not recommended. Finally, we discuss whether or not and how to accommodate phylogenetic covariance in regression analyses, particularly in relation to the problem of phylogenetic uncertainty. This discussion is from both frequentist and Bayesian perspectives.