Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data.

Imaging-based spatial transcriptomics techniques generate data in the form of spatial points belonging to different mRNA classes. A crucial part of analyzing the data involves the identification of regions with similar composition of mRNA classes. These biologically interesting regions can manifest at different spatial scales. For example, the composition of mRNA classes on a cellular scale corresponds to cell types, whereas compositions on a millimeter scale correspond to tissue-level structures. Traditional techniques for identifying such regions often rely on complementary data, such as pre-segmented cells, or lengthy optimization. This limits their applicability to tasks on a particular scale, restricting their capabilities in exploratory analysis. This article introduces "Points2Regions," a computational tool for identifying regions with similar mRNA compositions. The tool's novelty lies in its rapid feature extraction by rasterizing points (representing mRNAs) onto a pyramidal grid and its efficient clustering using a combination of hierarchical and k $$ k $$ -means clustering. This enables fast and efficient region discovery across multiple scales without relying on additional data, making it a valuable resource for exploratory analysis. Points2Regions has demonstrated performance similar to state-of-the-art methods on two simulated datasets, without relying on segmented cells, while being several times faster. Experiments on real-world datasets show that regions identified by Points2Regions are similar to those identified in other studies, confirming that Points2Regions can be used to extract biologically relevant regions. The tool is shared as a Python package integrated into TissUUmaps and a Napari plugin, offering interactive clustering and visualization, significantly enhancing user experience in data exploration.

Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.

PURPOSE: We describe the fibrotic rim formed in the desmoplastic growth pattern (DHGP) of colorectal cancer liver metastasis (CLM) using in situ sequencing (ISS). The origin of the desmoplastic rim is still a matter of debate, and the detailed cellular organization has not yet been fully elucidated. Understanding the biology of the DHGP in CLM can explore targeted treatment to improve survival. EXPERIMENTAL DESIGN: We used ISS, targeting 150 genes, to characterize the desmoplastic rim by unsupervised clustering of gene co-expression patterns. The cohort comprised 10 chemo-naïve liver metastasis resection samples with a DHGP. RESULTS: Unsupervised clustering of spatially mapped genes revealed molecular and cellular diversity within the desmoplastic rim. We confirmed the presence of the ductular reaction and cancer-associated fibroblasts. Importantly, we discovered angiogenesis and outer and inner zonation in the rim, characterized by NGFR and POSTN expression. CONCLUSIONS: ISS enabled the analysis of the cellular organization of the fibrous rim surrounding CLM with a DHGP and suggests a transition from the outer part of the rim, with nonspecific liver injury response, into the inner part, with gene expression indicating collagen synthesis and extracellular matrix remodeling influenced by the interaction with cancer cells, creating a cancer cell supportive environment. Moreover, we found angiogenic processes in the rim. Our results provide a potential explanation of the origin of the rim in DHGP and lead to exploring novel targeted treatments for patients with CLM to improve survival.

Substantial decrease of PFAS with anion exchange resin treatment - A clinical cross-over trial.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are heat and stain resisting chemicals. They are persistent, bioaccumulating and spread ubiquitously. Many hotspots where humans are exposed to high levels of PFAS have been reported. A few small observational studies in humans suggest that treatment with an Anion Exchange Resin (AER) decreases serum PFAS. This first clinical controlled crossover study aimed to assess whether AER decreases perfluorooctanesulfonic acid (PFOS) in highly exposed adults. METHODS: An open label 1:1 randomized treatment sequence crossover study with allocation to oral AER (cholestyramine 4 g three times daily) or observation for 12 weeks was conducted among citizens from a PFAS hotspot. Main inclusion criteria was serum PFOS > 21 ng/mL. Primary endpoint was change in serum PFOS levels between treatment and observational period. RESULTS: In total, 45 participants were included with a mean age of 50 years (SD 13). Serum PFOS baseline median was 191 ng/mL (IQR: 129-229) and decreased with a mean of 115 ng/mL (95 % CI: 89-140) on treatment, and 4.3 ng/mL in observation period corresponding to a decrease of 60 % (95 % CI: 53-67; p < 0.0001). PFHxS, PFOA, PFNA and PFDA decreased during treatment between 15 and 44 %. No serious adverse events were reported. CONCLUSIONS: Oral treatment with AER significantly lowered serum PFOS concentrations suggesting a possible treatment for enhancing elimination of PFOS in highly exposed adults.

High Exposure to Perfluoroalkyl Substances and Antibody Responses to SARS-CoV-2 mRNA Vaccine-an Observational Study in Adults from Ronneby, Sweden.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are widely used, environmentally ubiquitous, and stable chemicals that have been associated with lower vaccine-induced antibody responses in children; however, data on adults are limited. The drinking water from one of the two waterworks in Ronneby, Sweden, was heavily contaminated for decades with PFAS from firefighting foams, primarily perfluorohexane sulfonic acid and perfluorooctanesulfonic acid (PFOS). Vaccination against SARS-CoV-2 offered a unique opportunity to investigate antibody responses to primary vaccination in adults who had been exposed to PFAS. OBJECTIVES: Our objective was to evaluate associations between PFAS, across a wide range of exposure levels, and antibody responses in adults 5 wk and 6 months after a two-dose vaccination regime against SARS-CoV-2. METHODS: Adults age 20-60 y from Ronneby (n=309, median PFOS serum level 47 ng/mL, fifth to 95th percentile 4-213 ng/mL) and a group with background exposure (n=47, median PFOS serum level 4 ng/mL) received two doses of the Spikevax (Moderna) mRNA vaccine. The levels of seven PFAS were measured in serum before vaccination. Serum immunoglobulin G antibodies against the SARS-CoV-2 spike antigen (S-Abs) were measured before vaccination and at 5 wk (n=350) and 6 months (n=329) after the second vaccine dose. Linear regression analyses were fitted against current, historical, and prenatal exposure to PFAS, adjusting for sex, age, and smoking, excluding individuals with previous SARS-CoV-2-infection. RESULTS: PFAS exposure, regardless of how it was estimated, was not negatively associated with antibody levels 5 wk [current PFOS: -0.5% S-Abs/PFOS interquartile range (IQR); 95% confidence interval (CI): -8, 7] or 6 months (current PFOS: 3% S-Abs/PFOS IQR; 95% CI: -6, 12) after COVID-19 vaccination. DISCUSSION: Following a strict study protocol, rigorous study design, and few dropouts, we found no indication that PFAS exposure negatively affected antibody responses to COVID-19 mRNA vaccination for up to 6 months after vaccination. https://doi.org/10.1289/EHP11847.

TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data.

Background and objectives: Spatially resolved techniques for exploring the molecular landscape of tissue samples, such as spatial transcriptomics, often result in millions of data points and images too large to view on a regular desktop computer, limiting the possibilities in visual interactive data exploration. TissUUmaps is a free, open-source browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ data points overlaying tissue samples. Methods: Herein we describe how TissUUmaps 3 provides instant multiresolution image viewing and can be customized, shared, and also integrated into Jupyter Notebooks. We introduce new modules where users can visualize markers and regions, explore spatial statistics, perform quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. Results: We show that thanks to targeted optimizations the time and cost associated with interactive data exploration were reduced, enabling TissUUmaps 3 to handle the scale of today's spatial transcriptomics methods. Conclusion: TissUUmaps 3 provides significantly improved performance for large multiplex datasets as compared to previous versions. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of largescale spatial omics data.

The global historical climate database HCLIM.

There is a growing need for past weather and climate data to support science and decision-making. This paper describes the compilation and construction of a global multivariable (air temperature, pressure, precipitation sum, number of precipitation days) monthly instrumental climate database that encompasses a substantial body of the known early instrumental time series. The dataset contains series compiled from existing databases that start before 1890 (though continuing to the present) as well as a large amount of newly rescued data. All series underwent a quality control procedure and subdaily series were processed to monthly mean values. An inventory was compiled, and the collection was deduplicated based on coordinates and mutual correlations. The data are provided in a common format accompanied by the inventory. The collection totals 12452 meteorological records in 118 countries. The data can be used for climate reconstructions and analyses. It is the most comprehensive global monthly climate dataset for the preindustrial period so far.

Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3.

Large-scale multiplex tissue analysis aims to understand processes such as development and tumor formation by studying the occurrence and interaction of cells in local environments in, for example, tissue samples from patient cohorts. A typical procedure in the analysis is to delineate individual cells, classify them into cell types, and analyze their spatial relationships. All steps come with a number of challenges, and to address them and identify the bottlenecks of the analysis, it is necessary to include quality control tools in the analysis workflow. This makes it possible to optimize the steps and adjust settings in order to get better and more precise results. Additionally, the development of automated approaches for tissue analysis requires visual verification to reduce skepticism with regard to the accuracy of the results. Quality control tools could be used to build users' trust in automated approaches. In this paper, we present three plugins for visualization and quality control in large-scale multiplex tissue analysis of microscopy images. The first plugin focuses on the quality of cell staining, the second one was made for interactive evaluation and comparison of different cell classification results, and the third one serves for reviewing interactions of different cell types.

In-hospital versus out-of-hospital cardiac arrest: Characteristics and outcomes in patients admitted to intensive care after return of spontaneous circulation.

INTRODUCTION: Cardiac arrest is characterized depending on location as in-hospital cardiac arrest (IHCA) or out-of-hospital cardiac arrest (OHCA). Strategies for Post Cardiac Arrest Care were developed based on evidence from OHCA. The aim of this study was to compare characteristics and outcomes in patients admitted to intensive care after IHCA and OHCA. METHODS: A retrospective multicenter observational study of adult survivors of cardiac arrest admitted to intensive care in southern Sweden between 2014-2018. Data was collected from registries and medical notes. The primary outcome was neurological outcome according to the Cerebral Performance Category (CPC) scale at 2-6 months. RESULTS: 799 patients were included, 245 IHCA and 554 OHCA. IHCA patients were older, less frequently male and less frequently without comorbidity. In IHCA the first recorded rhythm was more often non-shockable, all delay-times (ROSC, no-flow, low-flow, time to advanced life support) were shorter and a cardiac cause of the arrest was less common. Good long-term neurological outcome was more common after IHCA than OHCA. In multivariable analysis, witnessed arrest, age, shorter arrest duration (no-flow and low-flow times), low lactate, shockable rhythm, and a cardiac cause were all independent predictors of good long-term neurological outcome whereas location of arrest (IHCA vs OHCA) was not. CONCLUSION: In patients admitted to intensive care after cardiac arrest, patients who suffered IHCA vs OHCA differed in demographics, co-morbidities, cardiac arrest characteristics and outcomes. In multivariable analyses, cardiac arrest characteristics were independent predictors of outcome, whereas location of arrest (IHCA vs OHCA) was not.

Determinants of serum half-lives for linear and branched perfluoroalkyl substances after long-term high exposure-A study in Ronneby, Sweden.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are persistent substances with surfactant and repellent properties. Municipal drinking water contaminated with PFAS had been distributed for decades to one third of households in Ronneby, Sweden. The source was firefighting foam used in a nearby airfield since the mid-1980s. Clean water was provided from December 16, 2013. AIMS: The purpose was to estimate serum half-lives and their determinants in the study population for different PFAS. METHODS: Up to ten blood samples were collected between 2014 and 2018 from 114 participants (age 4-84 years at entry, 53% female). 19 PFAS were analysed. Linear mixed models were used to estimate the half-lives. RESULTS: Eight PFAS were increased in Ronneby: perfluorooctanoic acid (PFOA), perfluoropentane sulfonate (PFPeS), perfluorohexane sulfonate (PFHxS), perfluoroheptane sulfonate (PFHpS), linear perfluorooctane sulfonate (L-PFOS) and three branched perfluorooctane sulfonates (1 m-PFOS, 3/4/5m-PFOS and 2/6m-PFOS). The mean estimated half-lives (in years) were 0.94 (95 %CI 0.86-1.02) for PFPeS, 2.47 (2.27-2.7) for PFOA, 2.67 (2.51-2.85) for 2/6m-PFOS, 2.73 (2.55-2.92) for L-PFOS, 3.43 (3.19-3.71) for 3/4/5m-PFOS, 4.52 (4.14-4.99) for PFHxS, 4.55 (4.14-5.06) for PFHpS, and 5.01 (4.56-5.55) for 1 m-PFOS. The most important determinants of a shorter half-life were young age, and better kidney function measured by estimated glomerular filtration rate and ratio of paired urine and serum PFAS levels, followed by female sex during their fertile period aged 15-50. Markers of gut inflammation and reduced permeability i.e. zonulin and calprotectin were also possibly associated with shorter half-life. The results also suggested a time-dependent PFAS elimination process, with more rapid elimination in the first year after the end of exposure. CONCLUSION: The half-life estimates are in line with past estimates for some PFAS such as PFOA, and the novel results for different PFOS isomers. These results provide observational support for elimination routes - renal, fecal and maternal.

Large difference but high correlation between creatinine and cystatin C estimated glomerular filtration rate in Mesoamerican sugarcane cutters.

OBJECTIVES: To explore the relationship between creatinine and cystatin C based estimated glomerular filtration rate (eGFR) in actively working sugarcane cutters. METHODS: This cohort study included 458 sugarcane cutters from Nicaragua and El Salvador. Serum samples were taken before and at end of harvest seasons and analysed for creatinine and cystatin C. Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) formulas were used to calculate eGFRs based on creatinine (eGFRcr), cystatin C (eGFRcys) and both creatinine and cystatin C (eGFRcrcys) at each time point. Bland-Altman plots and paired t-tests were used to compare the difference between eGFRcr and eGFRcys, and the difference in eGFRs between before and at end of the harvest seasons. RESULTS: The mean eGFRcr was higher than eGFRcys in both cohorts; absolute difference 22 mL/min/1.73 m2 (95% CI 21 to 23) in Nicaragua and 13 mL/min/1.73 m2 (95% CI 11 to 15) in El Salvador. Correlations between eGFRcr and eGFRcys were high, with r=0.69, 0.77 and 0.67 in Nicaragua at pre-harvest, end-harvest and cross-harvest, and r=0.89, 0.89 and 0.49 in El Salvador. CONCLUSIONS: Creatinine increases among heat-stressed workers reflect reduced glomerular filtration as estimated using eGFRcys, a marker independent of muscle mass and metabolism. The discrepancy between eGFRcr and eGFRcys may indicate reduced glomerular filtration of larger molecules and/or systemic bias in CKD-EPI performance in this population.

Transitioning from child to adult-oriented HIV clinical care for adolescents living with HIV in Ethiopia: results from a retrospective cohort study.

INTRODUCTION: Ethiopia has one of the largest number of adolescents living with HIV (ALHIV). As these adolescents reach adulthood they need to transfer from pediatric to adult-oriented clinics. Clear implementation guidelines for transition are lacking and factors associated with successful transition are inadequately investigated. Our objective was to describe the rate and age of transition from child- to adult-oriented care and the factors associated with transition success among ALHIV in selected health facilities in Ethiopia. METHODS: a retrospective cohort study of adolescents was conducted in eight health facilities in two regions of Ethiopia: Addis Ababa and the Southern Nations, Nationalities and Peoples´ Region (SNNPR). The study was embedded within a broader study originally aimed at studying clinical outcomes of adolescents. The proportion of adolescents who transitioned was calculated and the association between baseline characteristics and transition was assessed by bivariate and multivariate analysis. RESULTS: of 1072 adolescents, 8.7% transitioned to adult care. The most frequent age of transition was 15 (range: 10-22). Multivariate analysis generated two significant findings: adolescents from Addis Ababa were more to likely transitioned than adolescents from SNNPR (aOR: 2.18; 95% CI=1.17-4.06; p<0.01), as well as disclosed adolescents compared to those not disclosed of their HIV-status (aOR: 4.19; 95% CI=1.57-11.98; p<0.01). CONCLUSION: transition occurred in less than 10% of participants, in a wide range of age, indicating a lack of implementation policies regarding the transition process. Thereto, we found that adolescents from Addis Ababa and those disclosed of their disease, were more likely to transition. Further studies are needed to better understand factors associated with transition success.

Increased Intimal Hyperplasia After Vascular Injury in Male Androgen Receptor-Deficient Mice.

Intimal hyperplasia is a vascular pathological process involved in the pathogenesis of atherosclerosis. Data suggest that T, the most important sex steroid hormone in males, protects men from atherosclerotic cardiovascular disease. T mainly acts via the androgen receptor (AR), and in this study we evaluated formation of intimal hyperplasia in male AR knockout (ARKO) mice using a vascular injury model. Two weeks after ligation of the carotid artery, male ARKO mice showed increased intimal area and intimal thickness compared with controls. After endothelial denudation by an in vivo scraping injury, there was no difference in the reendothelialization in ARKO compared with control mice. Ex vivo, we observed increased outgrowth of vascular smooth muscle cells from ARKO compared with control aortic tissue explants; the number of outgrown cells was almost doubled in ARKO. In vitro, stimulation of human aortic vascular smooth muscle cells with a physiological T concentration inhibited both migration and proliferation of the cells. Analyzing the expression of central regulators of cell proliferation and migration, we found that mRNA and protein levels of p27 were lower in uninjured arteries from ARKO mice and that T replacement to castrated male mice increased p27 mRNA in an AR-dependent manner. In conclusion, AR deficiency in male mice increases intimal hyperplasia in response to vascular injury, potentially related to the effects of androgens/AR to inhibit proliferation and migration of smooth muscle cells.