The Novel, Clinical-Stage Soluble Guanylate Cyclase Activator BI 685509 Protects from Disease Progression in Models of Renal Injury and Disease.

Activation of soluble guanylate cyclase (sGC) to restore cyclic guanosine monophosphate (cGMP) and improve functionality of nitric oxide (NO) pathways impaired by oxidative stress is a potential treatment of diabetic and chronic kidney disease. We report the pharmacology of BI 685509, a novel, orally active small molecule sGC activator with disease-modifying potential. BI 685509 and human sGC α1/ß1 heterodimer containing a reduced heme group produced concentration-dependent increases in cGMP that were elevated modestly by NO, whereas heme-free sGC and BI 685509 greatly enhanced cGMP with no effect of NO. BI 685509 increased cGMP in human and rat platelet-rich plasma treated with the heme-oxidant ODQ; respective EC50 values were 467 nM and 304 nM. In conscious telemetry-instrumented rats, BI 685509 did not affect mean arterial pressure (MAP) or heart rate (HR) at 3 and 10 mg/kg (p.o.), whereas 30 mg/kg decreased MAP and increased HR. Ten days of BI 685509 at supratherapeutic doses (60 or 100 mg/kg p.o., daily) attenuated MAP and HR responses to a single 100 mg/kg challenge. In the ZSF1 rat model, BI 685509 (1, 3, 10, and 30 mg/kg per day, daily) coadministered with enalapril (3 mg/kg per day) dose-dependently reduced proteinuria and incidence of glomerular sclerosis; MAP was modestly reduced at the higher doses versus enalapril. In the 7-day rat unilateral ureteral obstruction model, BI 685509 dose-dependently reduced tubulointerstitial fibrosis (P < 0.05 at 30 mg/kg). In conclusion, BI 685509 is a potent, orally bioavailable sGC activator with clear renal protection and antifibrotic activity in preclinical models of kidney injury and disease. SIGNIFICANCE STATEMENT: BI 685509 is a novel small soluble guanylate cyclase (sGC) molecule activator that exhibits an in vitro profile consistent with that of an sGC activator. BI 685509 reduced proteinuria and glomerulosclerosis in the ZSF1 rat, a model of diabetic kidney disease (DKD), and reduced tubulointerstitial fibrosis in a rat 7-day unilateral ureteral obstruction model. Thus, BI 685509 is a promising new therapeutic agent and is currently in phase II clinical trials for chronic kidney disease and DKD.

Gene Teller: an extensible Alexa Skill for gene-relevant databases.

SUMMARY: Voice assistants have become increasingly embedded in consumer electronics, as the quality of their interaction improves and the cost of hardware continues to drop. Despite their ubiquity, these assistants remain underutilized as a means of accessing biological research data. Gene Teller is a voice assistant service based on the Alexa Skills Kit and Amazon Lambda functions that enables scientists to query for gene-centric information in an intuitive manner. It includes several features, such as synonym disambiguation and short-term memory, that enable a natural conversational interaction, and is extensible to include new resources. The underlying architecture, based on Simple Storage Service and Amazon Web Services Lambda, is cost efficient and scalable. AVAILABILITY AND IMPLEMENTATION: A publicly accessible version of Gene Teller is available as an Alexa Skill from the Amazon Marketplace at https://www.amazon.com/dp/B08BRD8SS8. The source code is freely available on GitHub at https://github.com/solinvicta/geneTeller.

Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease.

BACKGROUND: Patients with diabetic or hypertensive kidney disease rarely undergo kidney biopsy because nephrologists commonly believe that biopsy-related risk outweighs the potential benefits of obtaining histologic information to guide clinical decisions. Although kidney function is acutely regulated, histologic changes such as interstitial fibrosis, tubular atrophy, and glomerulosclerosis may represent chronic kidney damage, and thus might provide additional information about disease severity. However, whether histologic analysis provides information complementary to clinically used kidney function measurements, such as eGFR and proteinuria, is unclear. METHODS: We performed a standardized semiquantitative histologic analysis of 859 nephrectomies obtained from individuals with or without diabetes mellitus or hypertension and varying degrees of kidney dysfunction. Changes in glomeruli, tubules, interstitium, and the vasculature were scored using 17 descriptive parameters in a standardized manner. We used multivariable linear and logistic regression analyses and unbiased, hierarchical clustering to assess associations between histologic alterations and clinical variables. RESULTS: At CKD stages 3-5, eGFR correlates reasonably well with the degree of glomerulosclerosis and interstitial fibrosis and tubular atrophy (IFTA). In patients with CKD stages 1-2, the degree of histologic damage was highly variable and eGFR poorly estimated the degree of damage. Individuals with diabetes mellitus, hypertension, or Black race had significantly more glomerulosclerosis and IFTA, at the same eGFR level. Inclusion of glomerulosclerosis improved the kidney function decline estimation, even at early disease stages. CONCLUSIONS: Histologic analysis is an important complementary method for kidney disease evaluation, especially at early disease stages. Some individuals present with relatively severe structural damage despite preserved eGFR.

Changes in Albuminuria But Not GFR are Associated with Early Changes in Kidney Structure in Type 2 Diabetes.

BACKGROUND: In type 1 diabetes, changes in the GFR and urine albumin-to-creatinine ratio (ACR) are related to changes in kidney structure that reflect disease progression. However, such changes have not been studied in type 2 diabetes. METHODS: Participants were American Indians with type 2 diabetes enrolled in a clinical trial of losartan versus placebo. We followed a subset who underwent kidney biopsy at the end of the 6-year trial, with annual measurements of GFR (by urinary clearance of iothalamate) and ACR. Participants had a second kidney biopsy after a mean follow-up of 9.3 years. We used quantitative morphometric analyses to evaluate both biopsy specimens. RESULTS: Baseline measures for 48 participants (12 men and 36 women, mean age 45.6 years) who completed the study included diabetes duration (14.6 years), GFR (156 ml/min), and ACR (15 mg/g). During follow-up, glomerular basement membrane (GBM) width, mesangial fractional volume, and ACR increased, and surface density of peripheral GBM and GFR decreased. After adjustment for sex, age, ACR, and each morphometric variable at baseline, an increase in ACR during follow-up was significantly associated with increases in GBM width, mesangial fractional volume, and mean glomerular volume, and a decrease in surface density of peripheral GBM. Decline in GFR was not associated with changes in these morphometric variables after additionally adjusting for baseline GFR. CONCLUSIONS: In American Indians with type 2 diabetes and preserved GFR at baseline, increasing ACR reflects the progression of earlier structural glomerular lesions, whereas early GFR decline may not accurately reflect such lesions.

Sharing Ideas and Practice: Institutional Partnership Influences Change in Approaches to Teaching to Enhance Veterinary Education in Vietnam in Conjunction with an OIE Veterinary Education Twinning Project.

A World Organisation for Animal Health (OIE) Veterinary Education Twinning Project was established between the veterinary schools at Nong Lam University (NLU) in Ho Chi Minh City, Vietnam, and the University of Queensland, Gatton, Australia, as part of the scheme established to promote high-quality veterinary services through improved veterinary education. Included in the partnership's primary aims were building the capacity of veterinary teaching staff with respect to general teaching practice and also in response to identified deficiency areas, and to develop outcome assessment processes. One challenge facing the project was the different approaches and experiences of teaching and learning for the faculty and students between the two widely different historical and cultural contexts of Australia and Vietnam. The project enhanced the pedagogy capability in NLU faculty and introduced student-focused approaches to teaching. The NLU staff involved in the project strongly embraced a student-centered approach to learning and case-based teaching in particular, adopting these strategies in their own teaching. An analysis of students' approach to learning demonstrates that the majority preferred a deep approach to learning and that these students valued case studies, problem-solving exercises, and working in small groups during teaching sessions more than students who took a surface approach to learning. An improved recognition of the ways the Vietnamese students approach their learning in their home country will guide future teaching design, as well as give insight into the approaches to teaching for Southeast Asian students within the Australian veterinary science programs.

Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data.

BACKGROUND: Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological expertise required to interpret the results in their biological context remains incompletely addressed by the currently available tools. RESULTS: Single Cell Explorer is a Python-based web server application we developed to enable computational and experimental scientists to iteratively and collaboratively annotate cell expression phenotypes within a user-friendly and visually appealing platform. These annotations can be modified and shared by multiple users to allow easy collaboration between computational scientists and experimental biologists. Data processing and analytic workflows can be integrated into the system using Jupyter notebooks. The application enables powerful yet accessible features such as the identification of differential gene expression patterns for user-defined cell populations and convenient annotation of cell types using marker genes or differential gene expression patterns. Users are able to produce plots without needing Python or R coding skills. As such, by making single cell RNA-seq data sharing and querying more user-friendly, the software promotes deeper understanding and innovation by research teams applying single cell transcriptomic approaches. CONCLUSIONS: Single cell explorer is a freely-available single cell transcriptomic analysis tool that enables computational and experimental biologists to collaboratively explore, annotate, and share results in a flexible software environment and a centralized database server that supports data portal functionality.

Pathogenesis of Renal Injury and Gene Expression Changes in the Male CD-1 Mouse Associated with Exposure to Empagliflozin.

An increased incidence of renal tubular adenomas and carcinomas was identified in the 2-year CD-1 mouse carcinogenicity study with empagliflozin (sodium-glucose transporter 2 inhibitor) in high dose (1,000 mg/kg/day) male mice. A 13-week mouse renal investigative pathogenesis study was conducted with empagliflozin to evaluate dose dependency and temporal onset of nonneoplastic degenerative/regenerative renal tubular and molecular (genes, pathways) changes which precede neoplasia. Male and female CD-1 mice were given daily oral doses of 0, 100, 300, or 1,000 mg/kg/day (corresponding carcinogenicity study dose levels) for 1, 2, 4, 8, or 13 weeks. The maximum expected pharmacology with secondary osmotic diuresis was observed by week 1 at ≥100 mg/kg/day in both genders. Histopathologic kidney changes were first detected after 4 weeks of dosing in the male 1,000 mg/kg/day dose group, with progressive increases in the incidence and/or number of findings in this dose group so that they were more readily detected during weeks 8 and 13. Changes detected starting on week 4 consisted of minimal single-cell necrosis and minimal increases in mitotic figures. These changes persisted at an increased incidence at weeks 8 and 13 and were accompanied by minimal to mild tubular epithelial karyomegaly, minimal proximal convoluted tubular epithelial cell hyperplasia, and a corresponding increase in Ki-67-positive nuclei in epithelial cells of the proximal convoluted tubules. There were no corresponding changes in serum chemistry or urinalysis parameters indicative of any physiologically meaningful effect on renal function and thus these findings were not considered to be adverse. Similar changes were not identified in lower-dose groups in males nor were they present in females of any dose group. RNA-sequencing analysis revealed male mouse-specific changes in kidney over 13 weeks of dosing at 1,000 mg/kg/day. Treatment-related changes included genes and pathways related to p53-regulated cell cycle and proliferation, transforming growth factor ß, oxidative stress, and renal injury and the number of genes with significant expression change dramatically increased at week 13. These treatment-related changes in genes and pathways were predominant in high-dose males and complemented the observed temporal renal tubular changes. Overall, these mouse investigative study results support the role of early empagliflozin-related degenerative/regenerative changes only observed in high-dose male CD-1 mice as a key contributing feature to a nongenotoxic mode of renal tumor pathogenesis.

Emerging therapeutics for the treatment of diabetic nephropathy.

Diabetic nephropathy (DN) is the most common pathology contributing to the development of chronic kidney disease (CKD). DN caused by hypertension and unmitigated inflammation in diabetics, renders the kidneys unable to perform normally, and leads to renal fibrosis and organ failure. The increasing global prevalence of DN has been directly attributed to rising incidences of Type II diabetes, and is now the largest non-communicable cause of death worldwide. Despite the high morbidity, successful new treatments for DN are lacking. This review seeks to provide new insight on emerging clinical candidates under investigation for the treatment of DN.

mARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes.

BACKGROUND: Mutations in the gene MTARC1 (mitochondrial amidoxime-reducing component 1) protect carriers from metabolic dysfunction-associated steatohepatitis (MASH) and cirrhosis. MTARC1 encodes the mARC1 enzyme, which is localized to the mitochondria and has no known MASH-relevant molecular function. Our studies aimed to expand on the published human genetic mARC1 data and to observe the molecular effects of mARC1 modulation in preclinical MASH models. METHODS AND RESULTS: We identified a novel human structural variant deletion in MTARC1, which is associated with various biomarkers of liver health, including alanine aminotransferase levels. Phenome-wide Mendelian Randomization analyses additionally identified novel putatively causal associations between MTARC1 expression, and esophageal varices and cardiorespiratory traits. We observed that protective MTARC1 variants decreased protein accumulation in in vitro overexpression systems and used genetic tools to study mARC1 depletion in relevant human and mouse systems. Hepatocyte mARC1 knockdown in murine MASH models reduced body weight, liver steatosis, oxidative stress, cell death, and fibrogenesis markers. mARC1 siRNA treatment and overexpression modulated lipid accumulation and cell death consistently in primary human hepatocytes, hepatocyte cell lines, and primary human adipocytes. mARC1 depletion affected the accumulation of distinct lipid species and the expression of inflammatory and mitochondrial pathway genes/proteins in both in vitro and in vivo models. CONCLUSIONS: Depleting hepatocyte mARC1 improved metabolic dysfunction-associated steatotic liver disease-related outcomes. Given the functional role of mARC1 in human adipocyte lipid accumulation, systemic targeting of mARC1 should be considered when designing mARC1 therapies. Our data point to plasma lipid biomarkers predictive of mARC1 abundance, such as Ceramide 22:1. We propose future areas of study to describe the precise molecular function of mARC1, including lipid trafficking and subcellular location within or around the mitochondria and endoplasmic reticulum.

Applications of single-cell RNA sequencing in drug discovery and development.

Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery and development. New opportunities are emerging in target identification owing to improved disease understanding through cell subtyping, and highly multiplexed functional genomics screens incorporating scRNA-seq are enhancing target credentialling and prioritization. ScRNA-seq is also aiding the selection of relevant preclinical disease models and providing new insights into drug mechanisms of action. In clinical development, scRNA-seq can inform decision-making via improved biomarker identification for patient stratification and more precise monitoring of drug response and disease progression. Here, we illustrate how scRNA-seq methods are being applied in key steps in drug discovery and development, and discuss ongoing challenges for their implementation in the pharmaceutical industry.

Deep learning-based quantification of NAFLD/NASH progression in human liver biopsies.

Non-alcoholic fatty liver disease (NAFLD) affects about 24% of the world's population. Progression of early stages of NAFLD can lead to the more advanced form non-alcoholic steatohepatitis (NASH), and ultimately to cirrhosis or liver cancer. The current gold standard for diagnosis and assessment of NAFLD/NASH is liver biopsy followed by microscopic analysis by a pathologist. The Kleiner score is frequently used for a semi-quantitative assessment of disease progression. In this scoring system the features of active injury (steatosis, inflammation, and ballooning) and a separated fibrosis score are quantified. The procedure is time consuming for pathologists, scores have limited resolution and are subject to variation. We developed an automated deep learning method that provides full reproducibility and higher resolution. The system was established with 296 human liver biopsies and tested on 171 human liver biopsies with pathologist ground truth scores. The method is inspired by the way pathologist's analyze liver biopsies. First, the biopsies are analyzed microscopically for the relevant histopathological features. Subsequently, histopathological features are aggregated to a per-biopsy score. Scores are in the identical numeric range as the pathologist's ballooning, inflammation, steatosis, and fibrosis scores, but on a continuous scale. Resulting scores followed a pathologist's ground truth (quadratic weighted Cohen's κ on the test set: for steatosis 0.66, for inflammation 0.24, for ballooning 0.43, for fibrosis 0.62, and for the NAFLD activity score (NAS) 0.52. Mean absolute errors on a test set: for steatosis 0.29, for inflammation 0.53, for ballooning 0.61, for fibrosis 0.78, and for the NAS 0.77).

Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD.

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease worldwide. In adults with NAFLD, fibrosis can develop and progress to liver cirrhosis and liver failure. However, the underlying molecular mechanisms of fibrosis progression are not fully understood. Using total RNA-Seq, we investigated the molecular mechanisms of NAFLD and fibrosis. We sequenced liver tissue from 143 adults across the full spectrum of fibrosis stage including those with stage 4 fibrosis (cirrhosis). We identified gene expression clusters that strongly correlate with fibrosis stage including four genes that have been found consistently across previously published transcriptomic studies on NASH i.e. COL1A2, EFEMP2, FBLN5 and THBS2. Using cell type deconvolution, we estimated the loss of hepatocytes versus gain of hepatic stellate cells, macrophages and cholangiocytes with advancing fibrosis stage. Hepatocyte-specific functional analysis indicated increase of pro-apoptotic pathways and markers of bipotent hepatocyte/cholangiocyte precursors. Regression modelling was used to derive predictors of fibrosis stage. This study elucidated molecular and cell composition changes associated with increasing fibrosis stage in NAFLD and defined informative gene signatures for the disease.

SPRINT: a new parallel framework for R.

BACKGROUND: Microarray analysis allows the simultaneous measurement of thousands to millions of genes or sequences across tens to thousands of different samples. The analysis of the resulting data tests the limits of existing bioinformatics computing infrastructure. A solution to this issue is to use High Performance Computing (HPC) systems, which contain many processors and more memory than desktop computer systems. Many biostatisticians use R to process the data gleaned from microarray analysis and there is even a dedicated group of packages, Bioconductor, for this purpose. However, to exploit HPC systems, R must be able to utilise the multiple processors available on these systems. There are existing modules that enable R to use multiple processors, but these are either difficult to use for the HPC novice or cannot be used to solve certain classes of problems. A method of exploiting HPC systems, using R, but without recourse to mastering parallel programming paradigms is therefore necessary to analyse genomic data to its fullest. RESULTS: We have designed and built a prototype framework that allows the addition of parallelised functions to R to enable the easy exploitation of HPC systems. The Simple Parallel R INTerface (SPRINT) is a wrapper around such parallelised functions. Their use requires very little modification to existing sequential R scripts and no expertise in parallel computing. As an example we created a function that carries out the computation of a pairwise calculated correlation matrix. This performs well with SPRINT. When executed using SPRINT on an HPC resource of eight processors this computation reduces by more than three times the time R takes to complete it on one processor. CONCLUSION: SPRINT allows the biostatistician to concentrate on the research problems rather than the computation, while still allowing exploitation of HPC systems. It is easy to use and with further development will become more useful as more functions are added to the framework.

Presentations of psychosis with violence: variations in different jurisdictions. A comparison of patients with psychosis in the high security hospitals of Scotland and England.

BACKGROUND: International literature is consistent on there being a significant relationship between psychosis and violence, less so on its extent and nature, but two main presentational types are increasingly recognized. In one, people are unremarkable before onset of illness and psychotic symptoms commonly drive violence; in the other, psychosis is preceded by childhood conduct problems, associated with personality disorder, and psychotic symptoms seem less relevant. AIMS: To explore the extent to which variations in aspects of social and service context in different jurisdictions affect presentational type among people admitted to high security hospitals. HYPOTHESES: There will be differences between jurisdictions in proportions of patients with pure psychosis or with psychosis and antecedent personality disorder, but symptom drive to violence will be more common in the pure psychosis group regardless of social, legal and service context. METHOD: Independently conducted record studies were used to compare high security hospital patients with psychosis in Scotland and England, all resident between 25 August 1992 and 13 August 1993. RESULTS: The cohorts were similar in offence histories, predominance of schizophrenia, age at first hospitalization for psychosis and first high security hospitalization. More Scottish patients had co-morbid substance misuse diagnoses and/or personality disorder than patients in England. Psychotic symptom drive to the index offence was, however, four times more likely in the pure psychosis groups, regardless of sex, ethnic group or country. Scottish patients spent less time in high security after the index act. CONCLUSIONS: Our hypotheses were sustained. Knowledge about lifestyle before onset of psychosis is important for interpreting literature on how psychotic symptoms relate to violence. This may also influence longer term outcome, although the shorter length of secure hospital stay in Scotland was perhaps affected more by greater availability of open 'step-down' beds.

Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease.

Chronic kidney disease (CKD), a condition in which the kidneys are unable to clear waste products, affects 700 million people globally. Genome-wide association studies (GWASs) have identified sequence variants for CKD; however, the biological basis of these GWAS results remains poorly understood. To address this issue, we created an expression quantitative trait loci (eQTL) atlas for the glomerular and tubular compartments of the human kidney. Through integrating the CKD GWAS with eQTL, single-cell RNA sequencing and regulatory region maps, we identified novel genes for CKD. Putative causal genes were enriched for proximal tubule expression and endolysosomal function, where DAB2, an adaptor protein in the TGF-ß pathway, formed a central node. Functional experiments confirmed that reducing Dab2 expression in renal tubules protected mice from CKD. In conclusion, compartment-specific eQTL analysis is an important avenue for the identification of novel genes and cellular pathways involved in CKD development and thus potential new opportunities for its treatment.

Tidal dynamics and mangrove carbon sequestration during the Oligo-Miocene in the South China Sea.

Modern mangroves are among the most carbon-rich biomes on Earth, but their long-term (≥106 years) impact on the global carbon cycle is unknown. The extent, productivity and preservation of mangroves are controlled by the interplay of tectonics, global sea level and sedimentation, including tide, wave and fluvial processes. The impact of these processes on mangrove-bearing successions in the Oligo-Miocene of the South China Sea (SCS) is evaluated herein. Palaeogeographic reconstructions, palaeotidal modelling and facies analysis suggest that elevated tidal range and bed shear stress optimized mangrove development along tide-influenced tropical coastlines. Preservation of mangrove organic carbon (OC) was promoted by high tectonic subsidence and fluvial sediment supply. Lithospheric storage of OC in peripheral SCS basins potentially exceeded 4,000 Gt (equivalent to 2,000 p.p.m. of atmospheric CO2). These results highlight the crucial impact of tectonic and oceanographic processes on mangrove OC sequestration within the global carbon cycle on geological timescales.

Global cooling as a driver of diversification in a major marine clade.

Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems.

BioAcoustica: a free and open repository and analysis platform for bioacoustics.

We describe an online open repository and analysis platform, BioAcoustica (http://bio.acousti.ca), for recordings of wildlife sounds. Recordings can be annotated using a crowdsourced approach, allowing voice introductions and sections with extraneous noise to be removed from analyses. This system is based on the Scratchpads virtual research environment, the BioVeL portal and the Taverna workflow management tool, which allows for analysis of recordings using a grid computing service. At present the analyses include spectrograms, oscillograms and dominant frequency analysis. Further analyses can be integrated to meet the needs of specific researchers or projects. Researchers can upload and annotate their recordings to supplement traditional publication.

Use of HFPV for adults with ARDS: the protocolized use of high-frequency percussive ventilation for adults with acute respiratory failure treated with extracorporeal membrane oxygenation.

Historically, patients on extracorporeal membrane oxygenation (ECMO) for acute respiratory distress syndrome have received ventilatory "lung rest" with conventional or high-frequency oscillating ventilators. We present a series of adults treated with high-frequency percussive ventilation (HFPV) to enhance recovery and recruitment during ECMO. Adult respiratory patients, treated between January 2009 and December 2012 were cared for with a combination of standard ECMO practices and a protocol of recruitment strategies, including HFPV. Data are reported as mean ± standard error of the mean, percentage, or median. Comparisons are made by χ for categorical variables and by t-test and Mann-Whitney test for continuous variables. Significance is noted at the 95% confidence level (p < 0.05). There were 39 HFPV patients. They were 39.9 ± 2.2 years of age and had 3.0 ± 0.37 days of mechanical ventilation before the initiation of ECMO. Their pre-ECMO PaO2 to FiO2 ratio (PF ratio) was 52.3 ± 3.0 and their pCO2 was 50.22 ± 2.4. HFPV patients required a mean of 143.1 ± 17.6 hours and a median of 106 hours (range 45.75-350.25) of ECMO support and had a 62% survival to discharge. The post-ECMO PF ratio in the HFPV cohort was 301.8 ± 16.7. A protocolized practice of active recruitment that includes HFPV is associated with reduced duration of ECMO support in adults with respiratory failure.

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.

Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.