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Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.

PURPOSE: To investigate the modulation of circulating exosome-like extracellular vesicles (ELVs) after 6 weeks of sprint interval training (SIT) at sea-level, 2,000 m, 3,000 m and 4,000 m. METHODS: Thirty trained endurance male athletes (18-35y) participated in a six-week SIT program (30 s all-out sprint, 4 min 30 s recovery; 4-9 repetitions, 2 sessions/week) at sea-level (SL, n = 8), 2,000 m (FiO2 0.167, n = 8), 3,000 m (FiO2 0.145, n = 7) or 4,000 m (FiO2 0.13, n = 7). Venous blood samples were taken before and after the training period. Plasma ELVs were isolated by size exclusion chromatography, counted by nanoparticle tracking analysis (NTA), and characterized according to international standards. Candidate ELVs miRNAs were quantified by real-time PCR. RESULTS: When the 3 hypoxic groups were analyzed separately, only very minor differences could be detected in the levels of circulating particles, ELVs markers or miRNA. However, the levels of circulating particles increased (+262%) after training when the 3 hypoxic groups were pooled, and tended to increase at sea-level (+65%), with no difference between these two groups. A trend to an increase was observed for the two ELVs markers, TSG101 (+65%) and HSP60 (+441%), at sea-level, but not in hypoxia. Training also seemed to decrease the abundance of miR-23a-3p and to increase the abundance of miR-21-5p in hypoxia but not at sea-level. CONCLUSIONS: A 6-week SIT program tended to increase the basal levels of circulating ELVs when performed at sea-level, but not in hypoxia. In contrast, ELVs miRNA cargo seemed to be modulated in hypoxic conditions only. Further research should explore the potential differences in the origin of ELVs between normoxic and local and systemic hypoxic conditions.

Boreal forests are important global carbon (C) sinks and, therefore, considered as a key element in climate change mitigation policies. However, their actual C sink strength is uncertain and under debate, particularly for the actively managed forests in the boreal regions of Fennoscandia. In this study, we use an extensive set of biometric- and chamber-based C flux data collected in 50 forest stands (ranging from 5 to 211 years) over 3 years (2016-2018) with the aim to explore the variations of the annual net ecosystem production (NEP; i.e., the ecosystem C balance) across a 68 km(2) managed boreal forest landscape in northern Sweden. Our results demonstrate that net primary production rather than heterotrophic respiration regulated the spatio-temporal variations of NEP across the heterogeneous mosaic of the managed boreal forest landscape. We further find divergent successional patterns of NEP in our managed forests relative to naturally regenerating boreal forests, including (i) a fast recovery of the C sink function within the first decade after harvest due to the rapid establishment of a productive understory layer and (ii) a sustained C sink in old stands (131-211 years). We estimate that the rotation period for optimum C sequestration extends to 138 years, which over multiple rotations results in a long-term C sequestration rate of 86.5 t C ha(-1) per rotation. Our study highlights the potential of forest management to maximize C sequestration of boreal forest landscapes and associate climate change mitigation effects by developing strategies that optimize tree biomass production rather than heterotrophic soil C emissions.

Vegetation holds the key to many properties that make natural mires unique, such as surface microtopography, high biodiversity values, effective carbon sequestration and regulation of water and nutrient fluxes across the landscape. Despite this, landscape controls behind mire vegetation patterns have previously been poorly described at large spatial scales, which limits the understanding of basic drivers underpinning mire ecosystem services. We studied catchment controls on mire nutrient regimes and vegetation patterns using a geographically constrained natural mire chronosequence along the isostatically rising coastline in Northern Sweden. By comparing mires of different ages, we can partition vegetation patterns caused by long-term mire succession (<5000 years) and present-day vegetation responses to catchment eco-hydrological settings. We used the remote sensing based normalized difference vegetation index (NDVI) to describe mire vegetation and combined peat physicochemical measures with catchment properties to identify the most important factors that determine mire NDVI. We found strong evidence that mire NDVI depends on nutrient inputs from the catchment area or underlying mineral soil, especially concerning phosphorus and potassium concentrations. Steep mire and catchment slopes, dry conditions and large catchment areas relative to mire areas were associated with higher NDVI. We also found long-term successional patterns, with lower NDVI in older mires. Importantly, the NDVI should be used to describe mire vegetation patterns in open mires if the focus is on surface vegetation, since the canopy cover in tree-covered mires completely dominated the NDVI signal. With our study approach, we can quantitatively describe the connection between landscape properties and mire nutrient regime. Our results confirm that mire vegetation responds to the upslope catchment area, but importantly, also suggest that mire and catchment aging can override the role of catchment i

Background Mortality due to acute hypoxemic respiratory failure (AHRF) in patients with coronavirus disease-19 (COVID-19) differs across units, regions, and countries. These variations may be attributed to several factors, including comorbidities, acute physiological derangement, disease severity, treatment, ethnicity, healthcare system strain, and socioeconomic status. This study aimed to explore the features of patient characteristics, clinical management, and staffing that may be related to mortality among three intensive care units (ICUs) within the same hospital system in South Sweden.Methods We retrospectively analyzed ICU patients with COVID-19 and AHRF in Region Jonkoping County, Sweden. The primary outcome was the 90-day mortality rate. We used univariate and multivariable logistic regression analyses to investigate the relationship of predictors with outcomes.Results Between March 15, 2020, and May 31, 2021, 331 patients with AHRF and COVID-19 were admitted to the three ICUs. There were differences in disease severity, treatments, process-related factors, and socioeconomic factors between the units. These factors were related to 90-day mortality. After multivariable adjustment, age, severity of acute respiratory distress syndrome, and the number of nurses per ICU-bed independently predicted 90-day mortality.Conclusion Age, disease severity, and nurse staffing, but not treatment or socioeconomic status, were independently associated with 90-day mortality among critically ill patients with AHRF due to COVID-19. We also identified variations in care related processes, which may be a modifiable risk factor and warrants future investigation., Funding Agencies|Futurum-Akademin foer Haelsa och Vard, Region Joenkoepings laens; Futurum, Academy of Health and Care, Region Joenkoeping County, Joenkoeping, Sweden

The present article explores tourist attractions that include touch as a significant component of the tourist’splace-related experience. We have chosen to label this phenomenon “tactile tourism”. The tradition of touchingattractions is not new but has been a central part of the experience of specific place-related interests for a longtime. However, despite its frequent and often significant presence in tourist destinations, few studies in tourismresearch study the phenomenon. The article is based on a theoretical line of reasoning which starts from a fewconcrete examples of different places in Europe where we have identified tactile features relevant to tourism.The empirical material for our discussion has been collected partly through e-mail correspondence with touristorganizations in the places selected for the study and partly through articles in social media and other relevantsecondary data. This tactile experience contributes a substantial share of the primary enticement of the attractionand simultaneously invests the place with meaning, which in turn attracts tourists.

Boreal peatlands represent a biogeochemically unique and diverse environment in high-latitude landscape. They represent a long-term globally significant sink for carbon dioxide and a source of methane, hence playing an important role in regulating the global climate. There is an increasing interest in deciphering peatland biogeochemical processes to improve our understanding of how anthropogenic and climate change effects regulate the peatland biogeochemistry and greenhouse gas balances. At present, most studies investigating land-atmosphere exchanges of peatland ecosystems are commonly based on single-tower setups, which require the assumption of homogeneous conditions during upscaling to the landscape. However, the spatial organization of peatland complexes might feature large heterogeneity due to its varying underlying topography and vegetation composition. Little is known about how well single site studies represent the spatial variations of biogeochemical processes across entire peatland complexes. The recently established Kulbäcksliden Research Infrastructure (KRI) includes five peatland study sites located less than 3 km apart, thus providing a unique opportunity to explore the spatial variation in ecosystem-scale processes across a typical boreal peatland complex. All KRI sites are equipped with eddy covariance flux towers combined with installations for detailed monitoring of biotic and abiotic variables, as well as catchment-scale hydrology and hydrochemistry. Here, we review studies that were conducted in the Kulbäcksliden area and provide a description of the site characteristics as well as the instrumentation available at the KRI. We highlight the value of long-term infrastructures with ecosystem-scale and replicated experimental sites to advance our understanding of peatland biogeochemistry, hydrology, ecology, and its feedbacks on the environment and climate system.

This paper presents the first results of the ongoing development of new forest mapping methods for the Swedish national forest mapping case using Airborne Laser Scanning (ALS) data, utilizing the recent findings in machine learning (ML) and Artificial Intelligence (AI) techniques. We used Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) as ML models. In addition, Neural networks (NN) based approaches were utilized in this study. ALS derived features were used to estimate the stem volume (V), above-ground biomass (AGB), basal area (B), tree height (H), stem diameter (D), and forest stand age (A). XGBoost ML algorithm outperformed RF 1 % to 3 % in the R² metric. NN model performed similar to ML model, however it is superior in the estimation of V, AGB, and B parameters.

This paper presents the project ForestMap – a project aiming to develop and distribute new methods, which provide the benefits of accurate forest maps to a global audience. Using the recent developments in remote sensing, machine learning, and Artificial Intelligence (AI) the goal is to export the Scandinavian success stories to a wide range of stakeholders in the world.

Sountoulidis et al. provide a spatial gene expression atlas of human embryonic lung during the first trimester of gestation and identify 83 cell identities corresponding to stable cell types or transitional states. The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

Peatland vegetation takes up mercury (Hg) from the atmosphere, typically contributing to net production and export of neurotoxic methyl-Hg to downstream ecosystems. Chemical reduction processes can slow down methyl-Hg production by releasing Hg from peat back to the atmosphere. The extent of these processes remains, however, unclear. Here we present results from a comprehensive study covering concentrations and isotopic signatures of Hg in an open boreal peatland system to identify post-depositional Hg redox transformation processes. Isotope mass balances suggest photoreduction of HgII is the predominant process by which 30% of annually deposited Hg is emitted back to the atmosphere. Isotopic analyses indicate that above the water table, dark abiotic oxidation decreases peat soil gaseous Hg0 concentrations. Below the water table, supersaturation of gaseous Hg is likely created more by direct photoreduction of rainfall rather than by reduction and release of Hg from the peat soil. Identification and quantification of these light-driven and dark redox processes advance our understanding of the fate of Hg in peatlands, including the potential for mobilization and methylation of HgII.

Carbon dioxide (CO2) uptake by plant photosynthesis, referred to as gross primary production (GPP) at the ecosystem level, is sensitive to environmental factors, including pollutant exposure, pollutant uptake, and changes in the scattering of solar shortwave irradiance (SWin) − the energy source for photosynthesis. The 2020 spring lockdown due to COVID-19 resulted in improved air quality and atmospheric transparency, providing a unique opportunity to assess the impact of air pollutants on terrestrial ecosystem functioning. However, detecting these effects can be challenging as GPP is influenced by other meteorological drivers and management practices. Based on data collected from 44 European ecosystem-scale CO2 flux monitoring stations, we observed significant changes in spring GPP at 34 sites during 2020 compared to 2015–2019. Among these, 14 sites showed an increase in GPP associated with higher SWin, 10 sites had lower GPP linked to atmospheric and soil dryness, and seven sites were subjected to management practices. The remaining three sites exhibited varying dynamics, with one experiencing colder and rainier weather resulting in lower GPP, and two showing higher GPP associated with earlier spring melts. Analysis using the regional atmospheric chemical transport model (LOTOS-EUROS) indicated that the ozone (O3) concentration remained relatively unchanged at the research sites, making it unlikely that O3 exposure was the dominant factor driving the primary production anomaly. In contrast, SWin increased by 9.4 % at 36 sites, suggesting enhanced GPP possibly due to reduced aerosol optical depth and cloudiness. Our findings indicate that air pollution and cloudiness may weaken the terrestrial carbon sink by up to 16 %. Accurate and continuous ground-based observations are crucial for detecting and attributing subtle changes in terrestrial ecosystem functioning in response to environmental

Estimates of land-atmosphere exchanges of carbon, energy, water vapor, and other greenhouse gases based on the eddy covariance (EC) technique rely on the fundamental assumption that the flux footprint area is homo-geneous. We investigated the impact of source area heterogeneity on flux estimates in single-level EC mea-surements over a managed boreal forest landscape. For this purpose, we compared single-level measurements with those from a two-level approach consisting of concurrent EC measurements at 60 and 85 m above the ground. This two-level set-up provided a unique opportunity to obtain nearly congruent diel footprint areas by combining data from the higher and lower levels during day-and nighttime, respectively.We found that the variation in the averaged footprint area between day-and nighttime was reduced by up to 89% in the two-level approach compared to the single-level data at the higher level (85 m). Considering spring, summer, and fall months, the resulting relative potential bias in flux observations due to landscape heterogeneity was highest at short time steps (= daily) ranging between 35% and 325% for half-hourly data. During winter months, when stable atmospheric regimes prevailed during day and night, the footprints within the diel course nearly overlapped also at a given single level and hence no improvement of flux estimates was found. The ab-solute cumulated sums for the study period (excluding winter months) of gross primary production, ecosystem respiration, latent heat, and sensible heat flux were underestimated by about 28%, 52%, 5%, and 3%, respec-tively, whereas that of net ecosystem CO2 exchange was overestimated by about 109% in the single-level approach. Overall this study suggests that footprint heterogeneity may introduce considerable bias in single -level flux estimates - particularly at short time scales - with large implications for model-data fusion studies, site comparisons, and up-or downscaling of land-atmosphere exchange proce

Little is known about the long-term expansion of mire ecosystems, despite their importance in the global carbon and hydrogeochemical cycles. It has been firmly established that mires do not expand linearly over time. Despite this, mires are often assumed to have expanded at a constant rate after initiation simply for lack of a better understanding. There has not yet been a serious attempt to determine the rate and drivers of mire expansion at the regional, or larger spatial scales. Here we make use of a natural chronosequence, spanning the Holocene, which is provided by the retreating coastline of Northern Sweden. By studying an isostatic rebound area we can infer mire expansion dynamics by looking at the portion of the landscape where mires become progressively scarce as the land becomes younger. Our results confirms that mires expanded non-linearly across the landscape and that their expansion is related to the availability of suitably wet areas, which, in our case, depends primarily on the hydro-edaphic properties of the landscape. Importantly, we found that mires occupied the wettest locations in the landscape within only one to two thousand years, while it took mires three to four thousand years to expand into slightly drier areas. Our results imply that the lateral expansion of mires, and thus peat accumulation is a non-linear process, occurring at different rates depending, above all else, on the wetness of the landscape.

Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change

Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.

The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5–12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.